[{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","title":"Identification of neural oscillations and epileptiform changes in human brain organoids","alternative_title":["Nature Neuroscience"],"pmid":1,"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.","day":"23","isi":1,"author":[{"full_name":"Samarasinghe, Ranmal A.","first_name":"Ranmal A.","last_name":"Samarasinghe"},{"full_name":"Miranda, Osvaldo","last_name":"Miranda","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","orcid":"0000-0001-6618-6889","first_name":"Osvaldo"},{"last_name":"Buth","first_name":"Jessie E.","full_name":"Buth, Jessie E."},{"full_name":"Mitchell, Simon","first_name":"Simon","last_name":"Mitchell"},{"last_name":"Ferando","first_name":"Isabella","full_name":"Ferando, Isabella"},{"first_name":"Momoko","last_name":"Watanabe","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"},{"first_name":"William E.","last_name":"Lowry","full_name":"Lowry, William E."},{"full_name":"Parent, Jack M.","first_name":"Jack M.","last_name":"Parent"},{"first_name":"Istvan","last_name":"Mody","full_name":"Mody, Istvan"},{"full_name":"Novitch, Bennett G.","first_name":"Bennett G.","last_name":"Novitch"}],"article_processing_charge":"Yes","volume":24,"external_id":{"isi":["000687516300001"],"pmid":["34426698 "]},"page":"32","date_created":"2019-11-10T11:23:58Z","type":"technical_report","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"language":[{"iso":"eng"}],"status":"public","oa":1,"publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]},"month":"08","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"}],"date_updated":"2023-08-04T10:49:44Z","year":"2021","_id":"6995","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41593-021-00906-5"}],"citation":{"chicago":"Samarasinghe, Ranmal A., Osvaldo Miranda, Jessie E. Buth, Simon Mitchell, Isabella Ferando, Momoko Watanabe, Arinnae Kurdian, et al. <i>Identification of Neural Oscillations and Epileptiform Changes in Human Brain Organoids</i>. Vol. 24. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41593-021-00906-5\">https://doi.org/10.1038/s41593-021-00906-5</a>.","apa":"Samarasinghe, R. A., Miranda, O., Buth, J. E., Mitchell, S., Ferando, I., Watanabe, M., … Novitch, B. G. (2021). <i>Identification of neural oscillations and epileptiform changes in human brain organoids</i> (Vol. 24). Springer Nature. <a href=\"https://doi.org/10.1038/s41593-021-00906-5\">https://doi.org/10.1038/s41593-021-00906-5</a>","mla":"Samarasinghe, Ranmal A., et al. <i>Identification of Neural Oscillations and Epileptiform Changes in Human Brain Organoids</i>. Vol. 24, Springer Nature, 2021, 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, Springer Nature, 32p.","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, Identification of Neural Oscillations and Epileptiform Changes in Human Brain Organoids, Springer Nature, 2021.","ama":"Samarasinghe RA, Miranda O, Buth JE, et al. <i>Identification of Neural Oscillations and Epileptiform Changes in Human Brain Organoids</i>. Vol 24. Springer Nature; 2021. 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>, <i>Identification of neural oscillations and epileptiform changes in human brain organoids</i>, vol. 24. Springer Nature, 2021."},"intvolume":"        24","doi":"10.1038/s41593-021-00906-5","publication_status":"published","oa_version":"Published Version","date_published":"2021-08-23T00:00:00Z"},{"doi":"10.1016/j.neucom.2020.05.126","publication_status":"published","date_published":"2021-05-13T00:00:00Z","oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1101/2020.02.03.930966","open_access":"1"}],"intvolume":"       461","citation":{"short":"F. Lombardi, O. Shriki, H.J. Herrmann, L. de Arcangelis, Neurocomputing 461 (2021) 657–666.","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>","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.","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>.","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>","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>."},"year":"2021","abstract":[{"lang":"eng","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."}],"date_updated":"2023-08-04T10:46:29Z","_id":"7463","publication_identifier":{"issn":["0925-2312"],"eissn":["1872-8286"]},"oa":1,"status":"public","ec_funded":1,"month":"05","publication":"Neurocomputing","page":"657-666","date_created":"2020-02-06T16:09:14Z","department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","article_type":"original","quality_controlled":"1","volume":461,"external_id":{"isi":["000704086300015"]},"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.","isi":1,"author":[{"full_name":"Lombardi, Fabrizio","last_name":"Lombardi","id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249","first_name":"Fabrizio"},{"last_name":"Shriki","first_name":"Oren","full_name":"Shriki, Oren"},{"full_name":"Herrmann, Hans J","last_name":"Herrmann","first_name":"Hans J"},{"first_name":"Lucilla","last_name":"de Arcangelis","full_name":"de Arcangelis, Lucilla"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"title":"Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier"},{"title":"Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"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.","file":[{"content_type":"application/pdf","relation":"main_file","file_size":4915964,"success":1,"date_updated":"2020-10-19T13:31:28Z","file_name":"2021_CurrentBiology_Fredes.pdf","date_created":"2020-10-19T13:31:28Z","file_id":"8678","checksum":"b7b9c8bc84a08befce365c675229a7d1","creator":"dernst","access_level":"open_access"}],"isi":1,"author":[{"full_name":"Fredes Tolorza, Felipe A","first_name":"Felipe A","last_name":"Fredes Tolorza","id":"384825DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Silva Sifuentes, Maria A","first_name":"Maria A","last_name":"Silva Sifuentes","id":"371B3D6E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter"},{"full_name":"Kobayashi, Kenta","last_name":"Kobayashi","first_name":"Kenta"},{"full_name":"Jösch, Maximilian A","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"}],"project":[{"call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539"}],"article_processing_charge":"No","article_type":"original","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/remembering-novelty/"}]},"volume":31,"quality_controlled":"1","external_id":{"isi":["000614361000020"]},"publication":"Current Biology","date_created":"2020-02-28T10:56:18Z","page":"P25-38.E5","has_accepted_license":"1","department":[{"_id":"MaJö"},{"_id":"RySh"}],"language":[{"iso":"eng"}],"type":"journal_article","oa":1,"status":"public","ec_funded":1,"month":"01","year":"2021","issue":"1","abstract":[{"lang":"eng","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."}],"date_updated":"2023-08-04T10:47:11Z","_id":"7551","ddc":["570"],"file_date_updated":"2020-10-19T13:31:28Z","intvolume":"        31","citation":{"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>.","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>","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.","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>.","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.","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>","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."},"doi":"10.1016/j.cub.2020.09.074","publication_status":"published","date_published":"2021-01-11T00:00:00Z","oa_version":"Published Version"},{"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>.","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.","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>.","short":"W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021) 1227–1241.e5.","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>","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."},"intvolume":"       109","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1101/848374","open_access":"1"}],"oa_version":"Preprint","date_published":"2021-04-07T00:00:00Z","doi":"10.1016/j.neuron.2021.01.020","publication_status":"published","month":"04","ec_funded":1,"status":"public","oa":1,"_id":"7553","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"}],"issue":"7","date_updated":"2025-06-30T13:21:05Z","year":"2021","volume":109,"quality_controlled":"1","external_id":{"isi":["000637809600006"]},"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"15020"}],"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/can-evolution-be-predicted/"}]},"article_processing_charge":"No","type":"journal_article","department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"publication":"Neuron","page":"1227-1241.e5","date_created":"2020-02-28T11:00:12Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Cell Press","title":"Statistical analysis and optimality of neural systems","isi":1,"author":[{"first_name":"Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87","last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F"},{"full_name":"Hledik, Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87","first_name":"Michal"},{"id":"3E999752-F248-11E8-B48F-1D18A9856A87","last_name":"Sokolowski","orcid":"0000-0002-1287-3779","first_name":"Thomas R","full_name":"Sokolowski, Thomas R"},{"first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper"}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"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.","day":"07"},{"isi":1,"author":[{"first_name":"Chiara","id":"342E7E22-F248-11E8-B48F-1D18A9856A87","last_name":"Boccato","full_name":"Boccato, Chiara"}],"project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"day":"01","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"World Scientific","title":"The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime","type":"journal_article","department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"publication":"Reviews in Mathematical Physics","date_created":"2020-04-26T22:00:45Z","volume":33,"quality_controlled":"1","external_id":{"isi":["000613313200007"],"arxiv":["2001.00497"]},"article_processing_charge":"No","article_type":"original","article_number":"2060006","_id":"7685","arxiv":1,"abstract":[{"lang":"eng","text":"We consider a gas of interacting bosons trapped in a box of side length one in the Gross–Pitaevskii limit. We review the proof of the validity of Bogoliubov’s prediction for the ground state energy and the low-energy excitation spectrum. This note is based on joint work with C. Brennecke, S. Cenatiempo and B. Schlein."}],"issue":"1","date_updated":"2023-08-04T10:50:13Z","year":"2021","month":"01","ec_funded":1,"status":"public","publication_identifier":{"issn":["0129-055X"]},"oa":1,"oa_version":"Preprint","date_published":"2021-01-01T00:00:00Z","doi":"10.1142/S0129055X20600065","publication_status":"published","citation":{"mla":"Boccato, Chiara. “The Excitation Spectrum of the Bose Gas in the Gross-Pitaevskii Regime.” <i>Reviews in Mathematical Physics</i>, vol. 33, no. 1, 2060006, World Scientific, 2021, doi:<a href=\"https://doi.org/10.1142/S0129055X20600065\">10.1142/S0129055X20600065</a>.","ista":"Boccato C. 2021. The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime. Reviews in Mathematical Physics. 33(1), 2060006.","apa":"Boccato, C. (2021). The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime. <i>Reviews in Mathematical Physics</i>. World Scientific. <a href=\"https://doi.org/10.1142/S0129055X20600065\">https://doi.org/10.1142/S0129055X20600065</a>","chicago":"Boccato, Chiara. “The Excitation Spectrum of the Bose Gas in the Gross-Pitaevskii Regime.” <i>Reviews in Mathematical Physics</i>. World Scientific, 2021. <a href=\"https://doi.org/10.1142/S0129055X20600065\">https://doi.org/10.1142/S0129055X20600065</a>.","short":"C. Boccato, Reviews in Mathematical Physics 33 (2021).","ama":"Boccato C. The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime. <i>Reviews in Mathematical Physics</i>. 2021;33(1). doi:<a href=\"https://doi.org/10.1142/S0129055X20600065\">10.1142/S0129055X20600065</a>","ieee":"C. Boccato, “The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime,” <i>Reviews in Mathematical Physics</i>, vol. 33, no. 1. World Scientific, 2021."},"intvolume":"        33","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2001.00497","open_access":"1"}]},{"article_type":"review","article_processing_charge":"No","volume":37,"quality_controlled":"1","date_created":"2024-01-14T23:00:58Z","publication":"Acta Physico-Chimica Sinica","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"MaIb"}],"publisher":"Peking University","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Recent progress on two-dimensional materials","day":"13","author":[{"last_name":"Chang","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","first_name":"Cheng","orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng"},{"full_name":"Chen, Wei","first_name":"Wei","last_name":"Chen"},{"first_name":"Ye","last_name":"Chen","full_name":"Chen, Ye"},{"first_name":"Yonghua","last_name":"Chen","full_name":"Chen, Yonghua"},{"last_name":"Chen","first_name":"Yu","full_name":"Chen, Yu"},{"last_name":"Ding","first_name":"Feng","full_name":"Ding, Feng"},{"full_name":"Fan, Chunhai","first_name":"Chunhai","last_name":"Fan"},{"first_name":"Hong Jin","last_name":"Fan","full_name":"Fan, Hong Jin"},{"first_name":"Zhanxi","last_name":"Fan","full_name":"Fan, Zhanxi"},{"full_name":"Gong, Cheng","last_name":"Gong","first_name":"Cheng"},{"last_name":"Gong","first_name":"Yongji","full_name":"Gong, Yongji"},{"full_name":"He, Qiyuan","first_name":"Qiyuan","last_name":"He"},{"first_name":"Xun","last_name":"Hong","full_name":"Hong, Xun"},{"full_name":"Hu, Sheng","last_name":"Hu","first_name":"Sheng"},{"first_name":"Weida","last_name":"Hu","full_name":"Hu, Weida"},{"first_name":"Wei","last_name":"Huang","full_name":"Huang, Wei"},{"full_name":"Huang, Yuan","last_name":"Huang","first_name":"Yuan"},{"last_name":"Ji","first_name":"Wei","full_name":"Ji, Wei"},{"full_name":"Li, Dehui","last_name":"Li","first_name":"Dehui"},{"last_name":"Li","first_name":"Lain Jong","full_name":"Li, Lain Jong"},{"last_name":"Li","first_name":"Qiang","full_name":"Li, Qiang"},{"full_name":"Lin, Li","first_name":"Li","last_name":"Lin"},{"full_name":"Ling, Chongyi","first_name":"Chongyi","last_name":"Ling"},{"full_name":"Liu, Minghua","first_name":"Minghua","last_name":"Liu"},{"full_name":"Liu, Nan","first_name":"Nan","last_name":"Liu"},{"first_name":"Zhuang","last_name":"Liu","full_name":"Liu, Zhuang"},{"full_name":"Loh, Kian Ping","last_name":"Loh","first_name":"Kian Ping"},{"first_name":"Jianmin","last_name":"Ma","full_name":"Ma, Jianmin"},{"full_name":"Miao, Feng","last_name":"Miao","first_name":"Feng"},{"full_name":"Peng, Hailin","last_name":"Peng","first_name":"Hailin"},{"full_name":"Shao, Mingfei","last_name":"Shao","first_name":"Mingfei"},{"last_name":"Song","first_name":"Li","full_name":"Song, Li"},{"full_name":"Su, Shao","last_name":"Su","first_name":"Shao"},{"last_name":"Sun","first_name":"Shuo","full_name":"Sun, Shuo"},{"first_name":"Chaoliang","last_name":"Tan","full_name":"Tan, Chaoliang"},{"full_name":"Tang, Zhiyong","first_name":"Zhiyong","last_name":"Tang"},{"first_name":"Dingsheng","last_name":"Wang","full_name":"Wang, Dingsheng"},{"first_name":"Huan","last_name":"Wang","full_name":"Wang, Huan"},{"first_name":"Jinlan","last_name":"Wang","full_name":"Wang, Jinlan"},{"full_name":"Wang, Xin","last_name":"Wang","first_name":"Xin"},{"last_name":"Wang","first_name":"Xinran","full_name":"Wang, Xinran"},{"last_name":"Wee","first_name":"Andrew T.S.","full_name":"Wee, Andrew T.S."},{"first_name":"Zhongming","last_name":"Wei","full_name":"Wei, Zhongming"},{"last_name":"Wu","first_name":"Yuen","full_name":"Wu, Yuen"},{"first_name":"Zhong Shuai","last_name":"Wu","full_name":"Wu, Zhong Shuai"},{"first_name":"Jie","last_name":"Xiong","full_name":"Xiong, Jie"},{"first_name":"Qihua","last_name":"Xiong","full_name":"Xiong, Qihua"},{"full_name":"Xu, Weigao","first_name":"Weigao","last_name":"Xu"},{"last_name":"Yin","first_name":"Peng","full_name":"Yin, Peng"},{"last_name":"Zeng","first_name":"Haibo","full_name":"Zeng, Haibo"},{"full_name":"Zeng, Zhiyuan","first_name":"Zhiyuan","last_name":"Zeng"},{"first_name":"Tianyou","last_name":"Zhai","full_name":"Zhai, Tianyou"},{"full_name":"Zhang, Han","last_name":"Zhang","first_name":"Han"},{"first_name":"Hui","last_name":"Zhang","full_name":"Zhang, Hui"},{"full_name":"Zhang, Qichun","first_name":"Qichun","last_name":"Zhang"},{"last_name":"Zhang","first_name":"Tierui","full_name":"Zhang, Tierui"},{"first_name":"Xiang","last_name":"Zhang","full_name":"Zhang, Xiang"},{"full_name":"Zhao, Li Dong","last_name":"Zhao","first_name":"Li Dong"},{"full_name":"Zhao, Meiting","last_name":"Zhao","first_name":"Meiting"},{"first_name":"Weijie","last_name":"Zhao","full_name":"Zhao, Weijie"},{"full_name":"Zhao, Yunxuan","last_name":"Zhao","first_name":"Yunxuan"},{"first_name":"Kai Ge","last_name":"Zhou","full_name":"Zhou, Kai Ge"},{"full_name":"Zhou, Xing","first_name":"Xing","last_name":"Zhou"},{"first_name":"Yu","last_name":"Zhou","full_name":"Zhou, Yu"},{"first_name":"Hongwei","last_name":"Zhu","full_name":"Zhu, Hongwei"},{"first_name":"Hua","last_name":"Zhang","full_name":"Zhang, Hua"},{"full_name":"Liu, Zhongfan","first_name":"Zhongfan","last_name":"Liu"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.3866/PKU.WHXB202108017"}],"scopus_import":"1","intvolume":"        37","citation":{"chicago":"Chang, Cheng, Wei Chen, Ye Chen, Yonghua Chen, Yu Chen, Feng Ding, Chunhai Fan, et al. “Recent Progress on Two-Dimensional Materials.” <i>Acta Physico-Chimica Sinica</i>. Peking University, 2021. <a href=\"https://doi.org/10.3866/PKU.WHXB202108017\">https://doi.org/10.3866/PKU.WHXB202108017</a>.","mla":"Chang, Cheng, et al. “Recent Progress on Two-Dimensional Materials.” <i>Acta Physico-Chimica Sinica</i>, vol. 37, no. 12, 2108017, Peking University, 2021, doi:<a href=\"https://doi.org/10.3866/PKU.WHXB202108017\">10.3866/PKU.WHXB202108017</a>.","apa":"Chang, C., Chen, W., Chen, Y., Chen, Y., Chen, Y., Ding, F., … Liu, Z. (2021). Recent progress on two-dimensional materials. <i>Acta Physico-Chimica Sinica</i>. Peking University. <a href=\"https://doi.org/10.3866/PKU.WHXB202108017\">https://doi.org/10.3866/PKU.WHXB202108017</a>","ista":"Chang C, Chen W, Chen Y, Chen Y, Chen Y, Ding F, Fan C, Fan HJ, Fan Z, Gong C, Gong Y, He Q, Hong X, Hu S, Hu W, Huang W, Huang Y, Ji W, Li D, Li LJ, Li Q, Lin L, Ling C, Liu M, Liu N, Liu Z, Loh KP, Ma J, Miao F, Peng H, Shao M, Song L, Su S, Sun S, Tan C, Tang Z, Wang D, Wang H, Wang J, Wang X, Wang X, Wee ATS, Wei Z, Wu Y, Wu ZS, Xiong J, Xiong Q, Xu W, Yin P, Zeng H, Zeng Z, Zhai T, Zhang H, Zhang H, Zhang Q, Zhang T, Zhang X, Zhao LD, Zhao M, Zhao W, Zhao Y, Zhou KG, Zhou X, Zhou Y, Zhu H, Zhang H, Liu Z. 2021. Recent progress on two-dimensional materials. Acta Physico-Chimica Sinica. 37(12), 2108017.","short":"C. Chang, W. Chen, Y. Chen, Y. Chen, Y. Chen, F. Ding, C. Fan, H.J. Fan, Z. Fan, C. Gong, Y. Gong, Q. He, X. Hong, S. Hu, W. Hu, W. Huang, Y. Huang, W. Ji, D. Li, L.J. Li, Q. Li, L. Lin, C. Ling, M. Liu, N. Liu, Z. Liu, K.P. Loh, J. Ma, F. Miao, H. Peng, M. Shao, L. Song, S. Su, S. Sun, C. Tan, Z. Tang, D. Wang, H. Wang, J. Wang, X. Wang, X. Wang, A.T.S. Wee, Z. Wei, Y. Wu, Z.S. Wu, J. Xiong, Q. Xiong, W. Xu, P. Yin, H. Zeng, Z. Zeng, T. Zhai, H. Zhang, H. Zhang, Q. Zhang, T. Zhang, X. Zhang, L.D. Zhao, M. Zhao, W. Zhao, Y. Zhao, K.G. Zhou, X. Zhou, Y. Zhou, H. Zhu, H. Zhang, Z. Liu, Acta Physico-Chimica Sinica 37 (2021).","ama":"Chang C, Chen W, Chen Y, et al. Recent progress on two-dimensional materials. <i>Acta Physico-Chimica Sinica</i>. 2021;37(12). doi:<a href=\"https://doi.org/10.3866/PKU.WHXB202108017\">10.3866/PKU.WHXB202108017</a>","ieee":"C. Chang <i>et al.</i>, “Recent progress on two-dimensional materials,” <i>Acta Physico-Chimica Sinica</i>, vol. 37, no. 12. Peking University, 2021."},"publication_status":"published","doi":"10.3866/PKU.WHXB202108017","oa_version":"Submitted Version","date_published":"2021-10-13T00:00:00Z","status":"public","oa":1,"publication_identifier":{"issn":["1001-4861"]},"month":"10","date_updated":"2024-01-17T11:29:33Z","issue":"12","abstract":[{"text":"Research on two-dimensional (2D) materials has been explosively increasing in last seventeen years in varying subjects including condensed matter physics, electronic engineering, materials science, and chemistry since the mechanical exfoliation of graphene in 2004. Starting from graphene, 2D materials now have become a big family with numerous members and diverse categories. The unique structural features and physicochemical properties of 2D materials make them one class of the most appealing candidates for a wide range of potential applications. In particular, we have seen some major breakthroughs made in the field of 2D materials in last five years not only in developing novel synthetic methods and exploring new structures/properties but also in identifying innovative applications and pushing forward commercialisation. In this review, we provide a critical summary on the recent progress made in the field of 2D materials with a particular focus on last five years. After a brief background introduction, we first discuss the major synthetic methods for 2D materials, including the mechanical exfoliation, liquid exfoliation, vapor phase deposition, and wet-chemical synthesis as well as phase engineering of 2D materials belonging to the field of phase engineering of nanomaterials (PEN). We then introduce the superconducting/optical/magnetic properties and chirality of 2D materials along with newly emerging magic angle 2D superlattices. Following that, the promising applications of 2D materials in electronics, optoelectronics, catalysis, energy storage, solar cells, biomedicine, sensors, environments, etc. are described sequentially. Thereafter, we present the theoretic calculations and simulations of 2D materials. Finally, after concluding the current progress, we provide some personal discussions on the existing challenges and future outlooks in this rapidly developing field. ","lang":"eng"}],"year":"2021","article_number":"2108017","_id":"14800"},{"article_type":"original","article_processing_charge":"No","external_id":{"arxiv":["2005.02098"]},"quality_controlled":"1","volume":3,"date_created":"2024-01-28T23:01:43Z","page":"653-676","publication":"Pure and Applied Analysis","language":[{"iso":"eng"}],"department":[{"_id":"RoSe"}],"type":"journal_article","title":"Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron","publisher":"Mathematical Sciences Publishers","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","acknowledgement":"Financial support by the European Union’s Horizon 2020 research and innovation programme\r\nunder the Marie Skłodowska-Curie grant agreement No. 754411 (S.R.) and the European\r\nResearch Council under grant agreement No. 694227 (N.L. and R.S.), as well as by the SNSF\r\nEccellenza project PCEFP2 181153 (N.L.), the NCCR SwissMAP (N.L. and B.S.) and by the\r\nDeutsche Forschungsgemeinschaft (DFG) through the Research Training Group 1838: Spectral\r\nTheory and Dynamics of Quantum Systems (D.M.) is gratefully acknowledged. B.S. gratefully\r\nacknowledges financial support from the Swiss National Science Foundation through the Grant\r\n“Dynamical and energetic properties of Bose-Einstein condensates” and from the European\r\nResearch Council through the ERC-AdG CLaQS (grant agreement No 834782). D.M. thanks\r\nMarcel Griesemer for helpful discussions.","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"author":[{"full_name":"Leopold, Nikolai K","orcid":"0000-0002-0495-6822","first_name":"Nikolai K","last_name":"Leopold","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mitrouskas","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","first_name":"David Johannes","full_name":"Mitrouskas, David Johannes"},{"full_name":"Rademacher, Simone Anna Elvira","last_name":"Rademacher","id":"856966FE-A408-11E9-977E-802DE6697425","first_name":"Simone Anna Elvira","orcid":"0000-0001-5059-4466"},{"full_name":"Schlein, Benjamin","first_name":"Benjamin","last_name":"Schlein"},{"first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2005.02098","open_access":"1"}],"scopus_import":"1","intvolume":"         3","citation":{"short":"N.K. Leopold, D.J. Mitrouskas, S.A.E. Rademacher, B. Schlein, R. Seiringer, Pure and Applied Analysis 3 (2021) 653–676.","ieee":"N. K. Leopold, D. J. Mitrouskas, S. A. E. Rademacher, B. Schlein, and R. Seiringer, “Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron,” <i>Pure and Applied Analysis</i>, vol. 3, no. 4. Mathematical Sciences Publishers, pp. 653–676, 2021.","ama":"Leopold NK, Mitrouskas DJ, Rademacher SAE, Schlein B, Seiringer R. Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron. <i>Pure and Applied Analysis</i>. 2021;3(4):653-676. doi:<a href=\"https://doi.org/10.2140/paa.2021.3.653\">10.2140/paa.2021.3.653</a>","chicago":"Leopold, Nikolai K, David Johannes Mitrouskas, Simone Anna Elvira Rademacher, Benjamin Schlein, and Robert Seiringer. “Landau–Pekar Equations and Quantum Fluctuations for the Dynamics of a Strongly Coupled Polaron.” <i>Pure and Applied Analysis</i>. Mathematical Sciences Publishers, 2021. <a href=\"https://doi.org/10.2140/paa.2021.3.653\">https://doi.org/10.2140/paa.2021.3.653</a>.","apa":"Leopold, N. K., Mitrouskas, D. J., Rademacher, S. A. E., Schlein, B., &#38; Seiringer, R. (2021). Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron. <i>Pure and Applied Analysis</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/paa.2021.3.653\">https://doi.org/10.2140/paa.2021.3.653</a>","mla":"Leopold, Nikolai K., et al. “Landau–Pekar Equations and Quantum Fluctuations for the Dynamics of a Strongly Coupled Polaron.” <i>Pure and Applied Analysis</i>, vol. 3, no. 4, Mathematical Sciences Publishers, 2021, pp. 653–76, doi:<a href=\"https://doi.org/10.2140/paa.2021.3.653\">10.2140/paa.2021.3.653</a>.","ista":"Leopold NK, Mitrouskas DJ, Rademacher SAE, Schlein B, Seiringer R. 2021. Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron. Pure and Applied Analysis. 3(4), 653–676."},"publication_status":"published","doi":"10.2140/paa.2021.3.653","date_published":"2021-10-01T00:00:00Z","oa_version":"Preprint","oa":1,"publication_identifier":{"eissn":["2578-5885"],"issn":["2578-5893"]},"status":"public","ec_funded":1,"month":"10","year":"2021","date_updated":"2024-02-05T10:02:45Z","arxiv":1,"abstract":[{"text":"We consider the Fröhlich Hamiltonian with large coupling constant α. For initial data of Pekar product form with coherent phonon field and with the electron minimizing the corresponding energy, we provide a norm approximation of the evolution, valid up to times of order α2. The approximation is given in terms of a Pekar product state, evolved through the Landau-Pekar equations, corrected by a Bogoliubov dynamics taking quantum fluctuations into account. This allows us to show that the Landau-Pekar equations approximately describe the evolution of the electron- and one-phonon reduced density matrices under the Fröhlich dynamics up to times of order α2.","lang":"eng"}],"issue":"4","_id":"14889"},{"article_type":"original","article_processing_charge":"No","volume":3,"quality_controlled":"1","external_id":{"arxiv":["1912.11004"]},"publication":"Pure and Applied Analysis","date_created":"2024-01-28T23:01:43Z","page":"677-726","type":"journal_article","department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Mathematical Sciences Publishers","title":"Beyond Bogoliubov dynamics","acknowledgement":"We are grateful for the hospitality of Central China Normal University (CCNU),\r\nwhere parts of this work were done, and thank Phan Th`anh Nam, Simone\r\nRademacher, Robert Seiringer and Stefan Teufel for helpful discussions. L.B. gratefully acknowledges the support by the German Research Foundation (DFG) within the Research\r\nTraining Group 1838 “Spectral Theory and Dynamics of Quantum Systems”, and the funding\r\nfrom the European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSk lodowska-Curie Grant Agreement No. 754411.","day":"01","author":[{"full_name":"Bossmann, Lea","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","last_name":"Bossmann","orcid":"0000-0002-6854-1343","first_name":"Lea"},{"full_name":"Petrat, Sören P","orcid":"0000-0002-9166-5889","first_name":"Sören P","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrat"},{"full_name":"Pickl, Peter","last_name":"Pickl","first_name":"Peter"},{"full_name":"Soffer, Avy","first_name":"Avy","last_name":"Soffer"}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1912.11004"}],"scopus_import":"1","intvolume":"         3","citation":{"short":"L. Bossmann, S.P. Petrat, P. Pickl, A. Soffer, Pure and Applied Analysis 3 (2021) 677–726.","ieee":"L. Bossmann, S. P. Petrat, P. Pickl, and A. Soffer, “Beyond Bogoliubov dynamics,” <i>Pure and Applied Analysis</i>, vol. 3, no. 4. Mathematical Sciences Publishers, pp. 677–726, 2021.","ama":"Bossmann L, Petrat SP, Pickl P, Soffer A. Beyond Bogoliubov dynamics. <i>Pure and Applied Analysis</i>. 2021;3(4):677-726. doi:<a href=\"https://doi.org/10.2140/paa.2021.3.677\">10.2140/paa.2021.3.677</a>","mla":"Bossmann, Lea, et al. “Beyond Bogoliubov Dynamics.” <i>Pure and Applied Analysis</i>, vol. 3, no. 4, Mathematical Sciences Publishers, 2021, pp. 677–726, doi:<a href=\"https://doi.org/10.2140/paa.2021.3.677\">10.2140/paa.2021.3.677</a>.","ista":"Bossmann L, Petrat SP, Pickl P, Soffer A. 2021. Beyond Bogoliubov dynamics. Pure and Applied Analysis. 3(4), 677–726.","apa":"Bossmann, L., Petrat, S. P., Pickl, P., &#38; Soffer, A. (2021). Beyond Bogoliubov dynamics. <i>Pure and Applied Analysis</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/paa.2021.3.677\">https://doi.org/10.2140/paa.2021.3.677</a>","chicago":"Bossmann, Lea, Sören P Petrat, Peter Pickl, and Avy Soffer. “Beyond Bogoliubov Dynamics.” <i>Pure and Applied Analysis</i>. Mathematical Sciences Publishers, 2021. <a href=\"https://doi.org/10.2140/paa.2021.3.677\">https://doi.org/10.2140/paa.2021.3.677</a>."},"doi":"10.2140/paa.2021.3.677","publication_status":"published","oa_version":"Preprint","date_published":"2021-10-01T00:00:00Z","status":"public","publication_identifier":{"eissn":["2578-5885"],"issn":["2578-5893"]},"oa":1,"month":"10","ec_funded":1,"abstract":[{"text":"We consider a system of N interacting bosons in the mean-field scaling regime and construct corrections to the Bogoliubov dynamics that approximate the true N-body dynamics in norm to arbitrary precision. The N-independent corrections are given in terms of the solutions of the Bogoliubov and Hartree equations and satisfy a generalized form of Wick's theorem. We determine the n-point correlation functions of the excitations around the condensate, as well as the reduced densities of the N-body system, to arbitrary accuracy, given only the knowledge of the two-point functions of a quasi-free state and the solution of the Hartree equation. In this way, the complex problem of computing all n-point correlation functions for an interacting N-body system is essentially reduced to the problem of solving the Hartree equation and the PDEs for the Bogoliubov two-point functions.","lang":"eng"}],"arxiv":1,"issue":"4","date_updated":"2024-02-05T09:26:31Z","year":"2021","_id":"14890"},{"ddc":["580"],"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5747100"}],"related_material":{"record":[{"id":"9887","status":"public","relation":"used_in_publication"}]},"citation":{"chicago":"Johnson, Alexander J. “Raw Data from Johnson et Al, PNAS, 2021.” Zenodo, 2021. <a href=\"https://doi.org/10.5281/ZENODO.5747100\">https://doi.org/10.5281/ZENODO.5747100</a>.","apa":"Johnson, A. J. (2021). Raw data from Johnson et al, PNAS, 2021. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.5747100\">https://doi.org/10.5281/ZENODO.5747100</a>","ista":"Johnson AJ. 2021. Raw data from Johnson et al, PNAS, 2021, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.5747100\">10.5281/ZENODO.5747100</a>.","mla":"Johnson, Alexander J. <i>Raw Data from Johnson et Al, PNAS, 2021</i>. Zenodo, 2021, doi:<a href=\"https://doi.org/10.5281/ZENODO.5747100\">10.5281/ZENODO.5747100</a>.","short":"A.J. Johnson, (2021).","ieee":"A. J. Johnson, “Raw data from Johnson et al, PNAS, 2021.” Zenodo, 2021.","ama":"Johnson AJ. Raw data from Johnson et al, PNAS, 2021. 2021. doi:<a href=\"https://doi.org/10.5281/ZENODO.5747100\">10.5281/ZENODO.5747100</a>"},"date_created":"2024-02-14T14:13:48Z","doi":"10.5281/ZENODO.5747100","has_accepted_license":"1","department":[{"_id":"JiFr"}],"date_published":"2021-12-01T00:00:00Z","oa_version":"Published Version","type":"research_data_reference","oa":1,"title":"Raw data from Johnson et al, PNAS, 2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Zenodo","month":"12","year":"2021","day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"lang":"eng","text":"Raw data generated from the publication - The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis by Johnson et al., 2021 In PNAS"}],"date_updated":"2024-02-19T11:06:09Z","_id":"14988","author":[{"full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"}]},{"day":"21","acknowledgement":"Partially supported by ERC Starting Grant RandMat No. 715539 and the SwissMap grant of Swiss National Science Foundation. Partially supported by ERC Advanced Grant RanMat No. 338804. Partially supported by the Hausdorff Center for Mathematics in Bonn.","author":[{"first_name":"Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","last_name":"Alt","full_name":"Alt, Johannes"},{"first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H"}],"project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"title":"Spectral radius of random matrices with independent entries","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Mathematical Sciences Publishers","publication":"Probability and Mathematical Physics","page":"221-280","date_created":"2024-02-18T23:01:03Z","department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","article_type":"original","quality_controlled":"1","volume":2,"external_id":{"arxiv":["1907.13631"]},"year":"2021","abstract":[{"text":"We consider random n×n matrices X with independent and centered entries and a general variance profile. We show that the spectral radius of X converges with very high probability to the square root of the spectral radius of the variance matrix of X when n tends to infinity. We also establish the optimal rate of convergence, that is a new result even for general i.i.d. matrices beyond the explicitly solvable Gaussian cases. The main ingredient is the proof of the local inhomogeneous circular law [arXiv:1612.07776] at the spectral edge.","lang":"eng"}],"issue":"2","arxiv":1,"date_updated":"2024-02-19T08:30:00Z","_id":"15013","oa":1,"publication_identifier":{"issn":["2690-0998"],"eissn":["2690-1005"]},"status":"public","ec_funded":1,"month":"05","doi":"10.2140/pmp.2021.2.221","publication_status":"published","date_published":"2021-05-21T00:00:00Z","oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1907.13631","open_access":"1"}],"citation":{"ama":"Alt J, Erdös L, Krüger TH. Spectral radius of random matrices with independent entries. <i>Probability and Mathematical Physics</i>. 2021;2(2):221-280. doi:<a href=\"https://doi.org/10.2140/pmp.2021.2.221\">10.2140/pmp.2021.2.221</a>","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “Spectral radius of random matrices with independent entries,” <i>Probability and Mathematical Physics</i>, vol. 2, no. 2. Mathematical Sciences Publishers, pp. 221–280, 2021.","short":"J. Alt, L. Erdös, T.H. Krüger, Probability and Mathematical Physics 2 (2021) 221–280.","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “Spectral Radius of Random Matrices with Independent Entries.” <i>Probability and Mathematical Physics</i>. Mathematical Sciences Publishers, 2021. <a href=\"https://doi.org/10.2140/pmp.2021.2.221\">https://doi.org/10.2140/pmp.2021.2.221</a>.","mla":"Alt, Johannes, et al. “Spectral Radius of Random Matrices with Independent Entries.” <i>Probability and Mathematical Physics</i>, vol. 2, no. 2, Mathematical Sciences Publishers, 2021, pp. 221–80, doi:<a href=\"https://doi.org/10.2140/pmp.2021.2.221\">10.2140/pmp.2021.2.221</a>.","ista":"Alt J, Erdös L, Krüger TH. 2021. Spectral radius of random matrices with independent entries. Probability and Mathematical Physics. 2(2), 221–280.","apa":"Alt, J., Erdös, L., &#38; Krüger, T. H. (2021). Spectral radius of random matrices with independent entries. <i>Probability and Mathematical Physics</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/pmp.2021.2.221\">https://doi.org/10.2140/pmp.2021.2.221</a>"},"intvolume":"         2"},{"month":"10","title":"Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction","oa":1,"status":"public","publisher":"Zenodo","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13057","author":[{"orcid":"0000-0002-3415-4628","first_name":"Matilda","last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","full_name":"Peruzzo, Matilda"},{"first_name":"Farid","orcid":"0000-0001-6937-5773","last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","full_name":"Hassani, Farid"},{"first_name":"Grisha","last_name":"Szep","full_name":"Szep, Grisha"},{"full_name":"Trioni, Andrea","first_name":"Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","last_name":"Trioni"},{"first_name":"Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","last_name":"Zemlicka","first_name":"Martin","full_name":"Zemlicka, Martin"},{"last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"day":"22","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2021","date_updated":"2023-08-11T10:44:21Z","abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the figures of the submitted article \"Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction\". Additional raw data are available from the corresponding author on reasonable request."}],"related_material":{"record":[{"id":"9928","status":"public","relation":"used_in_publication"}]},"citation":{"short":"M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M. Fink, (2021).","ieee":"M. Peruzzo <i>et al.</i>, “Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction.” Zenodo, 2021.","ama":"Peruzzo M, Hassani F, Szep G, et al. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. 2021. doi:<a href=\"https://doi.org/10.5281/ZENODO.5592103\">10.5281/ZENODO.5592103</a>","mla":"Peruzzo, Matilda, et al. <i>Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction</i>. Zenodo, 2021, doi:<a href=\"https://doi.org/10.5281/ZENODO.5592103\">10.5281/ZENODO.5592103</a>.","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. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.5592103\">https://doi.org/10.5281/ZENODO.5592103</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, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.5592103\">10.5281/ZENODO.5592103</a>.","chicago":"Peruzzo, Matilda, Farid Hassani, Grisha Szep, Andrea Trioni, Elena Redchenko, Martin Zemlicka, and Johannes M Fink. “Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction.” Zenodo, 2021. <a href=\"https://doi.org/10.5281/ZENODO.5592103\">https://doi.org/10.5281/ZENODO.5592103</a>."},"ddc":["530"],"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.5592104","open_access":"1"}],"article_processing_charge":"No","date_published":"2021-10-22T00:00:00Z","department":[{"_id":"JoFi"}],"type":"research_data_reference","oa_version":"Published Version","date_created":"2023-05-23T13:42:27Z","doi":"10.5281/ZENODO.5592103"},{"article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.5257161","open_access":"1"}],"ddc":["570"],"citation":{"ama":"Ucar MC. Source data for the manuscript “Theory of branching morphogenesis by local interactions and global guidance.” 2021. doi:<a href=\"https://doi.org/10.5281/ZENODO.5257160\">10.5281/ZENODO.5257160</a>","ieee":"M. C. Ucar, “Source data for the manuscript ‘Theory of branching morphogenesis by local interactions and global guidance.’” Zenodo, 2021.","short":"M.C. Ucar, (2021).","chicago":"Ucar, Mehmet C. “Source Data for the Manuscript ‘Theory of Branching Morphogenesis by Local Interactions and Global Guidance.’” Zenodo, 2021. <a href=\"https://doi.org/10.5281/ZENODO.5257160\">https://doi.org/10.5281/ZENODO.5257160</a>.","ista":"Ucar MC. 2021. Source data for the manuscript ‘Theory of branching morphogenesis by local interactions and global guidance’, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.5257160\">10.5281/ZENODO.5257160</a>.","mla":"Ucar, Mehmet C. <i>Source Data for the Manuscript “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.”</i> Zenodo, 2021, doi:<a href=\"https://doi.org/10.5281/ZENODO.5257160\">10.5281/ZENODO.5257160</a>.","apa":"Ucar, M. C. (2021). Source data for the manuscript “Theory of branching morphogenesis by local interactions and global guidance.” Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.5257160\">https://doi.org/10.5281/ZENODO.5257160</a>"},"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"10402"}]},"doi":"10.5281/ZENODO.5257160","date_created":"2023-05-23T13:46:34Z","type":"research_data_reference","oa_version":"Published Version","date_published":"2021-08-25T00:00:00Z","department":[{"_id":"EdHa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Zenodo","oa":1,"title":"Source data for the manuscript \"Theory of branching morphogenesis by local interactions and global guidance\"","month":"08","abstract":[{"lang":"eng","text":"The zip file includes source data used in the main text of the manuscript \"Theory of branching morphogenesis by local interactions and global guidance\", as well as a representative Jupyter notebook to reproduce the main figures. A sample script for the simulations of branching and annihilating random walks is also included (Sample_script_for_simulations_of_BARWs.ipynb) to generate exemplary branched networks under external guidance. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt."}],"date_updated":"2023-08-14T13:18:46Z","year":"2021","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"25","author":[{"first_name":"Mehmet C","orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","last_name":"Ucar","full_name":"Ucar, Mehmet C"}],"_id":"13058"},{"department":[{"_id":"SyCr"}],"date_published":"2021-10-29T00:00:00Z","oa_version":"Published Version","type":"research_data_reference","date_created":"2023-05-23T16:14:35Z","doi":"10.5061/DRYAD.7PVMCVDTJ","related_material":{"record":[{"id":"10284","status":"public","relation":"used_in_publication"}]},"citation":{"mla":"Casillas Perez, Barbara E., et al. <i>Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies</i>. Dryad, 2021, doi:<a href=\"https://doi.org/10.5061/DRYAD.7PVMCVDTJ\">10.5061/DRYAD.7PVMCVDTJ</a>.","apa":"Casillas Perez, B. E., Pull, C., Naiser, F., Naderlinger, E., Matas, J., &#38; Cremer, S. (2021). Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.7PVMCVDTJ\">https://doi.org/10.5061/DRYAD.7PVMCVDTJ</a>","ista":"Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. 2021. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.7PVMCVDTJ\">10.5061/DRYAD.7PVMCVDTJ</a>.","chicago":"Casillas Perez, Barbara E, Christopher Pull, Filip Naiser, Elisabeth Naderlinger, Jiri Matas, and Sylvia Cremer. “Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.” Dryad, 2021. <a href=\"https://doi.org/10.5061/DRYAD.7PVMCVDTJ\">https://doi.org/10.5061/DRYAD.7PVMCVDTJ</a>.","ama":"Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. 2021. doi:<a href=\"https://doi.org/10.5061/DRYAD.7PVMCVDTJ\">10.5061/DRYAD.7PVMCVDTJ</a>","ieee":"B. E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, and S. Cremer, “Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies.” Dryad, 2021.","short":"B.E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, S. Cremer, (2021)."},"ddc":["570"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.7pvmcvdtj"}],"article_processing_charge":"No","_id":"13061","project":[{"name":"Epidemics in ant societies on a chip","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","grant_number":"771402"}],"author":[{"last_name":"Casillas Perez","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara E","full_name":"Casillas Perez, Barbara E"},{"id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","last_name":"Pull","orcid":"0000-0003-1122-3982","first_name":"Christopher","full_name":"Pull, Christopher"},{"first_name":"Filip","last_name":"Naiser","full_name":"Naiser, Filip"},{"first_name":"Elisabeth","last_name":"Naderlinger","full_name":"Naderlinger, Elisabeth"},{"full_name":"Matas, Jiri","last_name":"Matas","first_name":"Jiri"},{"last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","image":"/images/cc_0.png"},"day":"29","year":"2021","date_updated":"2023-08-14T11:45:28Z","abstract":[{"text":"Infections early in life can have enduring effects on an organism’s development and immunity. In this study, we show that this equally applies to developing “superorganisms” – incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen’s immune system to suppress pathogen proliferation. Early-life queen pathogen-exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen’s pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism.","lang":"eng"}],"ec_funded":1,"license":"https://creativecommons.org/publicdomain/zero/1.0/","month":"10","title":"Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies","oa":1,"publisher":"Dryad","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"month":"03","publisher":"Dryad","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model","oa":1,"author":[{"full_name":"Szep, Eniko","last_name":"Szep","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","first_name":"Eniko"},{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","first_name":"Himani","full_name":"Sachdeva, Himani"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"_id":"13062","date_updated":"2023-09-05T15:44:05Z","abstract":[{"text":"This paper analyzes the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat-dependent directional selection. Our analysis is based on the diffusion approximation and  accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which  exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.","lang":"eng"}],"day":"02","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","image":"/images/cc_0.png"},"year":"2021","citation":{"short":"E. Szep, H. Sachdeva, N.H. Barton, (2021).","ama":"Szep E, Sachdeva H, Barton NH. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. 2021. doi:<a href=\"https://doi.org/10.5061/DRYAD.8GTHT76P1\">10.5061/DRYAD.8GTHT76P1</a>","ieee":"E. Szep, H. Sachdeva, and N. H. Barton, “Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model.” Dryad, 2021.","chicago":"Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model.” Dryad, 2021. <a href=\"https://doi.org/10.5061/DRYAD.8GTHT76P1\">https://doi.org/10.5061/DRYAD.8GTHT76P1</a>.","apa":"Szep, E., Sachdeva, H., &#38; Barton, N. H. (2021). Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.8GTHT76P1\">https://doi.org/10.5061/DRYAD.8GTHT76P1</a>","mla":"Szep, Eniko, et al. <i>Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model</i>. Dryad, 2021, doi:<a href=\"https://doi.org/10.5061/DRYAD.8GTHT76P1\">10.5061/DRYAD.8GTHT76P1</a>.","ista":"Szep E, Sachdeva H, Barton NH. 2021. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.8GTHT76P1\">10.5061/DRYAD.8GTHT76P1</a>."},"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"9252"}]},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.8gtht76p1","open_access":"1"}],"article_processing_charge":"No","ddc":["570"],"oa_version":"Published Version","type":"research_data_reference","department":[{"_id":"NiBa"}],"date_published":"2021-03-02T00:00:00Z","doi":"10.5061/DRYAD.8GTHT76P1","date_created":"2023-05-23T16:17:02Z"},{"doi":"10.5061/dryad.sqv9s4n51","date_created":"2023-05-23T16:20:16Z","type":"research_data_reference","oa_version":"Published Version","date_published":"2021-11-04T00:00:00Z","department":[{"_id":"MaRo"}],"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.sqv9s4n51"}],"ddc":["570"],"citation":{"ieee":"M. R. Robinson, “Probabilistic inference of the genetic architecture of functional enrichment of complex traits.” Dryad, 2021.","ama":"Robinson MR. Probabilistic inference of the genetic architecture of functional enrichment of complex traits. 2021. doi:<a href=\"https://doi.org/10.5061/dryad.sqv9s4n51\">10.5061/dryad.sqv9s4n51</a>","short":"M.R. Robinson, (2021).","chicago":"Robinson, Matthew Richard. “Probabilistic Inference of the Genetic Architecture of Functional Enrichment of Complex Traits.” Dryad, 2021. <a href=\"https://doi.org/10.5061/dryad.sqv9s4n51\">https://doi.org/10.5061/dryad.sqv9s4n51</a>.","apa":"Robinson, M. R. (2021). Probabilistic inference of the genetic architecture of functional enrichment of complex traits. Dryad. <a href=\"https://doi.org/10.5061/dryad.sqv9s4n51\">https://doi.org/10.5061/dryad.sqv9s4n51</a>","mla":"Robinson, Matthew Richard. <i>Probabilistic Inference of the Genetic Architecture of Functional Enrichment of Complex Traits</i>. Dryad, 2021, doi:<a href=\"https://doi.org/10.5061/dryad.sqv9s4n51\">10.5061/dryad.sqv9s4n51</a>.","ista":"Robinson MR. 2021. Probabilistic inference of the genetic architecture of functional enrichment of complex traits, Dryad, <a href=\"https://doi.org/10.5061/dryad.sqv9s4n51\">10.5061/dryad.sqv9s4n51</a>."},"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8429"}],"link":[{"relation":"software","url":"https://github.com/medical-genomics-group/gmrm"}]},"abstract":[{"text":"We develop a Bayesian model (BayesRR-RC) that provides robust SNP-heritability estimation, an alternative to marker discovery, and accurate genomic prediction, taking 22 seconds per iteration to estimate 8.4 million SNP-effects and 78 SNP-heritability parameters in the UK Biobank. We find that only $\\leq$ 10\\% of the genetic variation captured for height, body mass index, cardiovascular disease, and type 2 diabetes is attributable to proximal regulatory regions within 10kb upstream of genes, while 12-25% is attributed to coding regions, 32-44% to introns, and 22-28% to distal 10-500kb upstream regions. Up to 24% of all cis and coding regions of each chromosome are associated with each trait, with over 3,100 independent exonic and intronic regions and over 5,400 independent regulatory regions having &gt;95% probability of contributing &gt;0.001% to the genetic variance of these four traits. Our open-source software (GMRM) provides a scalable alternative to current approaches for biobank data.","lang":"eng"}],"date_updated":"2023-09-26T10:36:15Z","year":"2021","day":"04","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","image":"/images/cc_0.png"},"author":[{"last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard"}],"_id":"13063","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Dryad","oa":1,"title":"Probabilistic inference of the genetic architecture of functional enrichment of complex traits","month":"11"},{"abstract":[{"lang":"eng","text":"Source data and source code for the graphs in \"Spatiotemporal dynamics of self-organized branching pancreatic cancer-derived organoids\"."}],"date_updated":"2023-08-04T09:25:23Z","year":"2021","day":"30","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Randriamanantsoa, Samuel","last_name":"Randriamanantsoa","first_name":"Samuel"},{"last_name":"Papargyriou","first_name":"Aristeidis","full_name":"Papargyriou, Aristeidis"},{"full_name":"Maurer, Carlo","last_name":"Maurer","first_name":"Carlo"},{"last_name":"Peschke","first_name":"Katja","full_name":"Peschke, Katja"},{"first_name":"Maximilian","last_name":"Schuster","full_name":"Schuster, Maximilian"},{"full_name":"Zecchin, Giulia","last_name":"Zecchin","first_name":"Giulia"},{"first_name":"Katja","last_name":"Steiger","full_name":"Steiger, Katja"},{"full_name":"Öllinger, Rupert","last_name":"Öllinger","first_name":"Rupert"},{"full_name":"Saur, Dieter","last_name":"Saur","first_name":"Dieter"},{"first_name":"Christina","last_name":"Scheel","full_name":"Scheel, Christina"},{"full_name":"Rad, Roland","last_name":"Rad","first_name":"Roland"},{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"full_name":"Reichert, Maximilian","last_name":"Reichert","first_name":"Maximilian"},{"full_name":"Bausch, Andreas R.","last_name":"Bausch","first_name":"Andreas R."}],"_id":"13068","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Zenodo","oa":1,"title":"Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids","month":"07","doi":"10.5281/ZENODO.5148117","date_created":"2023-05-23T16:39:24Z","oa_version":"Published Version","type":"research_data_reference","date_published":"2021-07-30T00:00:00Z","department":[{"_id":"EdHa"}],"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.6577226"}],"ddc":["570"],"citation":{"short":"S. Randriamanantsoa, A. Papargyriou, C. Maurer, K. Peschke, M. Schuster, G. Zecchin, K. Steiger, R. Öllinger, D. Saur, C. Scheel, R. Rad, E.B. Hannezo, M. Reichert, A.R. Bausch, (2021).","ama":"Randriamanantsoa S, Papargyriou A, Maurer C, et al. Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. 2021. doi:<a href=\"https://doi.org/10.5281/ZENODO.5148117\">10.5281/ZENODO.5148117</a>","ieee":"S. Randriamanantsoa <i>et al.</i>, “Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids.” Zenodo, 2021.","apa":"Randriamanantsoa, S., Papargyriou, A., Maurer, C., Peschke, K., Schuster, M., Zecchin, G., … Bausch, A. R. (2021). Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.5148117\">https://doi.org/10.5281/ZENODO.5148117</a>","ista":"Randriamanantsoa S, Papargyriou A, Maurer C, Peschke K, Schuster M, Zecchin G, Steiger K, Öllinger R, Saur D, Scheel C, Rad R, Hannezo EB, Reichert M, Bausch AR. 2021. Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.5148117\">10.5281/ZENODO.5148117</a>.","mla":"Randriamanantsoa, Samuel, et al. <i>Spatiotemporal Dynamics of Self-Organized Branching in Pancreas-Derived Organoids</i>. Zenodo, 2021, doi:<a href=\"https://doi.org/10.5281/ZENODO.5148117\">10.5281/ZENODO.5148117</a>.","chicago":"Randriamanantsoa, Samuel, Aristeidis Papargyriou, Carlo Maurer, Katja Peschke, Maximilian Schuster, Giulia Zecchin, Katja Steiger, et al. “Spatiotemporal Dynamics of Self-Organized Branching in Pancreas-Derived Organoids.” Zenodo, 2021. <a href=\"https://doi.org/10.5281/ZENODO.5148117\">https://doi.org/10.5281/ZENODO.5148117</a>."},"related_material":{"record":[{"id":"12217","relation":"used_in_publication","status":"public"}]}},{"date_created":"2023-05-23T16:40:56Z","doi":"10.5281/ZENODO.5519410","department":[{"_id":"MaDe"}],"date_published":"2021-12-25T00:00:00Z","oa_version":"Published Version","type":"research_data_reference","ddc":["570"],"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.5547464","open_access":"1"}],"article_processing_charge":"No","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"10322"}]},"citation":{"short":"L. Chauve, F. Hodge, S. Murdoch, F. Masoudzadeh, H.-J. Mann, A. Lopez-Clavijo, H. Okkenhaug, G. West, B.C. Sousa, A. Segonds-Pichon, C. Li, S. Wingett, H. Kienberger, K. Kleigrewe, M. de Bono, M. Wakelam, O. Casanueva, (2021).","ieee":"L. Chauve <i>et al.</i>, “Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans.” Zenodo, 2021.","ama":"Chauve L, Hodge F, Murdoch S, et al. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. 2021. doi:<a href=\"https://doi.org/10.5281/ZENODO.5519410\">10.5281/ZENODO.5519410</a>","chicago":"Chauve, Laetitia, Francesca Hodge, Sharlene Murdoch, Fatemah Masoudzadeh, Harry-Jack Mann, Andrea Lopez-Clavijo, Hanneke Okkenhaug, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” Zenodo, 2021. <a href=\"https://doi.org/10.5281/ZENODO.5519410\">https://doi.org/10.5281/ZENODO.5519410</a>.","apa":"Chauve, L., Hodge, F., Murdoch, S., Masoudzadeh, F., Mann, H.-J., Lopez-Clavijo, A., … Casanueva, O. (2021). Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.5519410\">https://doi.org/10.5281/ZENODO.5519410</a>","ista":"Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann H-J, Lopez-Clavijo A, Okkenhaug H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett S, Kienberger H, Kleigrewe K, de Bono M, Wakelam M, Casanueva O. 2021. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.5519410\">10.5281/ZENODO.5519410</a>.","mla":"Chauve, Laetitia, et al. <i>Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans</i>. Zenodo, 2021, doi:<a href=\"https://doi.org/10.5281/ZENODO.5519410\">10.5281/ZENODO.5519410</a>."},"day":"25","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2021","date_updated":"2023-08-14T11:53:26Z","abstract":[{"text":"To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell-autonomous. We have discovered that, in Caenorhabditis elegans, neuronal Heat shock Factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR)- causes extensive fat remodelling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine, and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodelling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least six TAX-2/TAX-4 cGMP gated channel expressing sensory neurons and TGF-β/BMP are required for signalling across tissues to modulate fat desaturation. We also find neuronal hsf-1  is not only sufficient but also partially necessary to control the fat remodelling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell non-autonomously coordinate membrane saturation and composition across tissues in a multicellular animal.","lang":"eng"}],"_id":"13069","author":[{"full_name":"Chauve, Laetitia","first_name":"Laetitia","last_name":"Chauve"},{"full_name":"Hodge, Francesca","last_name":"Hodge","first_name":"Francesca"},{"first_name":"Sharlene","last_name":"Murdoch","full_name":"Murdoch, Sharlene"},{"full_name":"Masoudzadeh, Fatemah","first_name":"Fatemah","last_name":"Masoudzadeh"},{"full_name":"Mann, Harry-Jack","last_name":"Mann","first_name":"Harry-Jack"},{"first_name":"Andrea","last_name":"Lopez-Clavijo","full_name":"Lopez-Clavijo, Andrea"},{"full_name":"Okkenhaug, Hanneke","last_name":"Okkenhaug","first_name":"Hanneke"},{"full_name":"West, Greg","last_name":"West","first_name":"Greg"},{"full_name":"Sousa, Bebiana C.","first_name":"Bebiana C.","last_name":"Sousa"},{"full_name":"Segonds-Pichon, Anne","first_name":"Anne","last_name":"Segonds-Pichon"},{"full_name":"Li, Cheryl","last_name":"Li","first_name":"Cheryl"},{"first_name":"Steven","last_name":"Wingett","full_name":"Wingett, Steven"},{"last_name":"Kienberger","first_name":"Hermine","full_name":"Kienberger, Hermine"},{"first_name":"Karin","last_name":"Kleigrewe","full_name":"Kleigrewe, Karin"},{"full_name":"de Bono, Mario","first_name":"Mario","orcid":"0000-0001-8347-0443","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wakelam, Michael","last_name":"Wakelam","first_name":"Michael"},{"full_name":"Casanueva, Olivia","last_name":"Casanueva","first_name":"Olivia"}],"title":"Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans","oa":1,"publisher":"Zenodo","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12"},{"ddc":["570"],"article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.5794029","open_access":"1"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"10702"}]},"citation":{"ista":"McCartney DL, Hillary RF, Conole EL, Trejo Banos D, Gadd DA, Walker RM, Nangle C, Flaig R, Campbell A, Murray AD, Munoz Maniega S, del C Valdes-Hernandez M, Harris MA, Bastin ME, Wardlaw JM, Harris SE, Porteous DJ, Tucker-Drob EM, McIntosh AM, Evans KL, Deary IJ, Cox SR, Robinson MR, Marioni RE. 2021. Blood-based epigenome-wide analyses of cognitive abilities, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.5794028\">10.5281/ZENODO.5794028</a>.","apa":"McCartney, D. L., Hillary, R. F., Conole, E. L., Trejo Banos, D., Gadd, D. A., Walker, R. M., … Marioni, R. E. (2021). Blood-based epigenome-wide analyses of cognitive abilities. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.5794028\">https://doi.org/10.5281/ZENODO.5794028</a>","mla":"McCartney, Daniel L., et al. <i>Blood-Based Epigenome-Wide Analyses of Cognitive Abilities</i>. Zenodo, 2021, doi:<a href=\"https://doi.org/10.5281/ZENODO.5794028\">10.5281/ZENODO.5794028</a>.","chicago":"McCartney, Daniel L, Robert F Hillary, Eleanor LS Conole, Daniel Trejo Banos, Danni A Gadd, Rosie M Walker, Cliff Nangle, et al. “Blood-Based Epigenome-Wide Analyses of Cognitive Abilities.” Zenodo, 2021. <a href=\"https://doi.org/10.5281/ZENODO.5794028\">https://doi.org/10.5281/ZENODO.5794028</a>.","ama":"McCartney DL, Hillary RF, Conole EL, et al. Blood-based epigenome-wide analyses of cognitive abilities. 2021. doi:<a href=\"https://doi.org/10.5281/ZENODO.5794028\">10.5281/ZENODO.5794028</a>","ieee":"D. L. McCartney <i>et al.</i>, “Blood-based epigenome-wide analyses of cognitive abilities.” Zenodo, 2021.","short":"D.L. McCartney, R.F. Hillary, E.L. Conole, D. Trejo Banos, D.A. Gadd, R.M. Walker, C. Nangle, R. Flaig, A. Campbell, A.D. Murray, S. Munoz Maniega, M. del C Valdes-Hernandez, M.A. Harris, M.E. Bastin, J.M. Wardlaw, S.E. Harris, D.J. Porteous, E.M. Tucker-Drob, A.M. McIntosh, K.L. Evans, I.J. Deary, S.R. Cox, M.R. Robinson, R.E. Marioni, (2021)."},"date_created":"2023-05-23T16:46:20Z","doi":"10.5281/ZENODO.5794028","department":[{"_id":"MaRo"}],"date_published":"2021-12-20T00:00:00Z","oa_version":"Published Version","type":"research_data_reference","oa":1,"title":"Blood-based epigenome-wide analyses of cognitive abilities","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Zenodo","month":"12","year":"2021","day":"20","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"text":"CpGs and corresponding mean weights for DNAm-based prediction of cognitive abilities (6 traits)","lang":"eng"}],"date_updated":"2023-08-02T14:05:12Z","_id":"13072","author":[{"full_name":"McCartney, Daniel L","last_name":"McCartney","first_name":"Daniel L"},{"full_name":"Hillary, Robert F","last_name":"Hillary","first_name":"Robert F"},{"full_name":"Conole, Eleanor LS","last_name":"Conole","first_name":"Eleanor LS"},{"first_name":"Daniel","last_name":"Trejo Banos","full_name":"Trejo Banos, Daniel"},{"last_name":"Gadd","first_name":"Danni A","full_name":"Gadd, Danni A"},{"full_name":"Walker, Rosie M","last_name":"Walker","first_name":"Rosie M"},{"full_name":"Nangle, Cliff","last_name":"Nangle","first_name":"Cliff"},{"full_name":"Flaig, Robin","last_name":"Flaig","first_name":"Robin"},{"first_name":"Archie","last_name":"Campbell","full_name":"Campbell, Archie"},{"full_name":"Murray, Alison D","first_name":"Alison D","last_name":"Murray"},{"last_name":"Munoz Maniega","first_name":"Susana","full_name":"Munoz Maniega, Susana"},{"first_name":"Maria","last_name":"del C Valdes-Hernandez","full_name":"del C Valdes-Hernandez, Maria"},{"last_name":"Harris","first_name":"Mathew A","full_name":"Harris, Mathew A"},{"last_name":"Bastin","first_name":"Mark E","full_name":"Bastin, Mark E"},{"last_name":"Wardlaw","first_name":"Joanna M","full_name":"Wardlaw, Joanna M"},{"full_name":"Harris, Sarah E","last_name":"Harris","first_name":"Sarah E"},{"full_name":"Porteous, David J","last_name":"Porteous","first_name":"David J"},{"full_name":"Tucker-Drob, Elliot M","first_name":"Elliot M","last_name":"Tucker-Drob"},{"first_name":"Andrew M","last_name":"McIntosh","full_name":"McIntosh, Andrew M"},{"first_name":"Kathryn L","last_name":"Evans","full_name":"Evans, Kathryn L"},{"full_name":"Deary, Ian J","last_name":"Deary","first_name":"Ian J"},{"last_name":"Cox","first_name":"Simon R","full_name":"Cox, Simon R"},{"first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard"},{"full_name":"Marioni, Riccardo E","last_name":"Marioni","first_name":"Riccardo E"}]},{"date_created":"2023-05-23T17:11:28Z","doi":"10.5281/ZENODO.4592435","date_published":"2021-03-09T00:00:00Z","department":[{"_id":"AnHi"}],"oa_version":"Published Version","type":"research_data_reference","ddc":["530"],"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.4592460","open_access":"1"}],"article_processing_charge":"No","related_material":{"link":[{"relation":"software","url":"https://github.com/caslu85/Induced-Gap-Closing-Shared/tree/1.1.3"}],"record":[{"id":"9570","status":"public","relation":"used_in_publication"}]},"citation":{"apa":"Puglia, D., Martinez, E., Menard, G., Pöschl, A., Gronin, S., Gardner, G., … Casparis, L. (2021). Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.4592435\">https://doi.org/10.5281/ZENODO.4592435</a>","ista":"Puglia D, Martinez E, Menard G, Pöschl A, Gronin S, Gardner G, Kallaher R, Manfra M, Marcus C, Higginbotham AP, Casparis L. 2021. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.4592435\">10.5281/ZENODO.4592435</a>.","mla":"Puglia, Denise, et al. <i>Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire</i>. Zenodo, 2021, doi:<a href=\"https://doi.org/10.5281/ZENODO.4592435\">10.5281/ZENODO.4592435</a>.","chicago":"Puglia, Denise, Esteban Martinez, Gerbold Menard, Andreas Pöschl, Sergei Gronin, Geoffrey Gardner, Ray Kallaher, et al. “Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Zenodo, 2021. <a href=\"https://doi.org/10.5281/ZENODO.4592435\">https://doi.org/10.5281/ZENODO.4592435</a>.","short":"D. Puglia, E. Martinez, G. Menard, A. Pöschl, S. Gronin, G. Gardner, R. Kallaher, M. Manfra, C. Marcus, A.P. Higginbotham, L. Casparis, (2021).","ama":"Puglia D, Martinez E, Menard G, et al. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. 2021. doi:<a href=\"https://doi.org/10.5281/ZENODO.4592435\">10.5281/ZENODO.4592435</a>","ieee":"D. Puglia <i>et al.</i>, “Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Zenodo, 2021."},"day":"09","year":"2021","date_updated":"2023-08-08T14:08:07Z","abstract":[{"lang":"eng","text":"Data for the manuscript 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire' ([2006.01275] Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire (arxiv.org))\r\n\r\nWe upload a pdf with extended data sets, and the raw data for these extended datasets as well."}],"_id":"13080","author":[{"first_name":"Denise","last_name":"Puglia","id":"4D495994-AE37-11E9-AC72-31CAE5697425","full_name":"Puglia, Denise"},{"first_name":"Esteban","last_name":"Martinez","full_name":"Martinez, Esteban"},{"full_name":"Menard, Gerbold","first_name":"Gerbold","last_name":"Menard"},{"full_name":"Pöschl, Andreas","first_name":"Andreas","last_name":"Pöschl"},{"first_name":"Sergei","last_name":"Gronin","full_name":"Gronin, Sergei"},{"full_name":"Gardner, Geoffrey","last_name":"Gardner","first_name":"Geoffrey"},{"first_name":"Ray","last_name":"Kallaher","full_name":"Kallaher, Ray"},{"last_name":"Manfra","first_name":"Michael","full_name":"Manfra, Michael"},{"full_name":"Marcus, Charles","first_name":"Charles","last_name":"Marcus"},{"last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P"},{"full_name":"Casparis, Lucas","first_name":"Lucas","last_name":"Casparis"}],"title":"Data for 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire","oa":1,"status":"public","publisher":"Zenodo","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03"},{"month":"07","oa":1,"publication_identifier":{"eissn":["2640-3498"],"isbn":["9781713845065"]},"status":"public","_id":"13146","year":"2021","arxiv":1,"abstract":[{"lang":"eng","text":"A recent line of work has analyzed the theoretical properties of deep neural networks via the Neural Tangent Kernel (NTK). In particular, the smallest eigenvalue of the NTK has been related to the memorization capacity, the global convergence of gradient descent algorithms and the generalization of deep nets. However, existing results either provide bounds in the two-layer setting or assume that the spectrum of the NTK matrices is bounded away from 0 for multi-layer networks. In this paper, we provide tight bounds on the smallest eigenvalue of NTK matrices for deep ReLU nets, both in the limiting case of infinite widths and for finite widths. In the finite-width setting, the network architectures we consider are fairly general: we require the existence of a wide layer with roughly order of N neurons, N being the number of data samples; and the scaling of the remaining layer widths is arbitrary (up to logarithmic factors). To obtain our results, we analyze various quantities of independent interest: we give lower bounds on the smallest singular value of hidden feature matrices, and upper bounds on the Lipschitz constant of input-output feature maps."}],"date_updated":"2024-09-10T13:03:17Z","intvolume":"       139","citation":{"mla":"Nguyen, Quynh, et al. “Tight Bounds on the Smallest Eigenvalue of the Neural Tangent Kernel for Deep ReLU Networks.” <i>Proceedings of the 38th International Conference on Machine Learning</i>, vol. 139, ML Research Press, 2021, pp. 8119–29.","ista":"Nguyen Q, Mondelli M, Montufar G. 2021. Tight bounds on the smallest Eigenvalue of the neural tangent kernel for deep ReLU networks. Proceedings of the 38th International Conference on Machine Learning. International Conference on Machine Learning vol. 139, 8119–8129.","apa":"Nguyen, Q., Mondelli, M., &#38; Montufar, G. (2021). Tight bounds on the smallest Eigenvalue of the neural tangent kernel for deep ReLU networks. In <i>Proceedings of the 38th International Conference on Machine Learning</i> (Vol. 139, pp. 8119–8129). Virtual: ML Research Press.","chicago":"Nguyen, Quynh, Marco Mondelli, and Guido Montufar. “Tight Bounds on the Smallest Eigenvalue of the Neural Tangent Kernel for Deep ReLU Networks.” In <i>Proceedings of the 38th International Conference on Machine Learning</i>, 139:8119–29. ML Research Press, 2021.","short":"Q. Nguyen, M. Mondelli, G. Montufar, in:, Proceedings of the 38th International Conference on Machine Learning, ML Research Press, 2021, pp. 8119–8129.","ama":"Nguyen Q, Mondelli M, Montufar G. Tight bounds on the smallest Eigenvalue of the neural tangent kernel for deep ReLU networks. In: <i>Proceedings of the 38th International Conference on Machine Learning</i>. Vol 139. ML Research Press; 2021:8119-8129.","ieee":"Q. Nguyen, M. Mondelli, and G. Montufar, “Tight bounds on the smallest Eigenvalue of the neural tangent kernel for deep ReLU networks,” in <i>Proceedings of the 38th International Conference on Machine Learning</i>, Virtual, 2021, vol. 139, pp. 8119–8129."},"ddc":["000"],"scopus_import":"1","file_date_updated":"2023-06-19T10:49:12Z","date_published":"2021-07-01T00:00:00Z","oa_version":"Published Version","conference":{"location":"Virtual","end_date":"2021-07-24","name":"International Conference on Machine Learning","start_date":"2021-07-18"},"publication_status":"published","title":"Tight bounds on the smallest Eigenvalue of the neural tangent kernel for deep ReLU networks","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ML Research Press","file":[{"content_type":"application/pdf","relation":"main_file","success":1,"file_size":591332,"date_updated":"2023-06-19T10:49:12Z","file_name":"2021_PMLR_Nguyen.pdf","date_created":"2023-06-19T10:49:12Z","file_id":"13155","checksum":"19489cf5e16a0596b1f92e317d97c9b0","creator":"dernst","access_level":"open_access"}],"author":[{"full_name":"Nguyen, Quynh","last_name":"Nguyen","first_name":"Quynh"},{"orcid":"0000-0002-3242-7020","first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco"},{"last_name":"Montufar","first_name":"Guido","full_name":"Montufar, Guido"}],"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","acknowledgement":"The authors would like to thank the anonymous reviewers for their helpful comments. MM was partially supported by the 2019 Lopez-Loreta Prize. QN and GM acknowledge support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no 757983).","quality_controlled":"1","volume":139,"external_id":{"arxiv":["2012.11654"]},"article_processing_charge":"No","department":[{"_id":"MaMo"}],"language":[{"iso":"eng"}],"type":"conference","publication":"Proceedings of the 38th International Conference on Machine Learning","date_created":"2023-06-18T22:00:48Z","page":"8119-8129","has_accepted_license":"1"}]