[{"external_id":{"pmid":["31694962"],"isi":["000505167600016"]},"publication_status":"published","department":[{"_id":"GaTk"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"02","publication_identifier":{"eissn":["1529-2401"],"issn":["0270-6474"]},"has_accepted_license":"1","isi":1,"status":"public","file_date_updated":"2020-07-22T11:44:48Z","ec_funded":1,"date_created":"2020-07-05T15:24:51Z","author":[{"first_name":"Fabrizio","full_name":"Lombardi, Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","last_name":"Lombardi","orcid":"0000-0003-2623-5249"},{"full_name":"Gómez-Extremera, Manuel","first_name":"Manuel","last_name":"Gómez-Extremera"},{"last_name":"Bernaola-Galván","first_name":"Pedro","full_name":"Bernaola-Galván, Pedro"},{"full_name":"Vetrivelan, Ramalingam","first_name":"Ramalingam","last_name":"Vetrivelan"},{"last_name":"Saper","first_name":"Clifford B.","full_name":"Saper, Clifford B."},{"full_name":"Scammell, Thomas E.","first_name":"Thomas E.","last_name":"Scammell"},{"full_name":"Ivanov, Plamen Ch.","first_name":"Plamen Ch.","last_name":"Ivanov"}],"title":"Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake","file":[{"file_size":6646046,"date_created":"2020-07-22T11:44:48Z","creator":"dernst","file_name":"2020_JournNeuroscience_Lombardi.pdf","content_type":"application/pdf","file_id":"8150","access_level":"open_access","success":1,"relation":"main_file","date_updated":"2020-07-22T11:44:48Z"}],"issue":"1","date_published":"2020-01-02T00:00:00Z","article_type":"original","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"publication":"Journal of Neuroscience","year":"2020","scopus_import":"1","pmid":1,"volume":40,"ddc":["570"],"doi":"10.1523/jneurosci.1278-19.2019","intvolume":" 40","date_updated":"2025-04-14T07:44:04Z","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Society for Neuroscience","oa_version":"Published Version","oa":1,"page":"171-190","citation":{"short":"F. Lombardi, M. Gómez-Extremera, P. Bernaola-Galván, R. Vetrivelan, C.B. Saper, T.E. Scammell, P.C. Ivanov, Journal of Neuroscience 40 (2020) 171–190.","apa":"Lombardi, F., Gómez-Extremera, M., Bernaola-Galván, P., Vetrivelan, R., Saper, C. B., Scammell, T. E., & Ivanov, P. C. (2020). Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/jneurosci.1278-19.2019","ista":"Lombardi F, Gómez-Extremera M, Bernaola-Galván P, Vetrivelan R, Saper CB, Scammell TE, Ivanov PC. 2020. Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake. Journal of Neuroscience. 40(1), 171–190.","chicago":"Lombardi, Fabrizio, Manuel Gómez-Extremera, Pedro Bernaola-Galván, Ramalingam Vetrivelan, Clifford B. Saper, Thomas E. Scammell, and Plamen Ch. Ivanov. “Critical Dynamics and Coupling in Bursts of Cortical Rhythms Indicate Non-Homeostatic Mechanism for Sleep-Stage Transitions and Dual Role of VLPO Neurons in Both Sleep and Wake.” Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/jneurosci.1278-19.2019.","ama":"Lombardi F, Gómez-Extremera M, Bernaola-Galván P, et al. Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake. Journal of Neuroscience. 2020;40(1):171-190. doi:10.1523/jneurosci.1278-19.2019","ieee":"F. Lombardi et al., “Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake,” Journal of Neuroscience, vol. 40, no. 1. Society for Neuroscience, pp. 171–190, 2020.","mla":"Lombardi, Fabrizio, et al. “Critical Dynamics and Coupling in Bursts of Cortical Rhythms Indicate Non-Homeostatic Mechanism for Sleep-Stage Transitions and Dual Role of VLPO Neurons in Both Sleep and Wake.” Journal of Neuroscience, vol. 40, no. 1, Society for Neuroscience, 2020, pp. 171–90, doi:10.1523/jneurosci.1278-19.2019."},"month":"01","type":"journal_article","_id":"8084","abstract":[{"lang":"eng","text":"Origin and functions of intermittent transitions among sleep stages, including brief awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing sleep on scales of seconds and minutes results from intrinsic non-equilibrium critical dynamics. We investigate θ- and δ-wave dynamics in control rats and in rats where the sleep-promoting ventrolateral preoptic nucleus (VLPO) is lesioned (male Sprague-Dawley rats). We demonstrate that bursts in θ and δ cortical rhythms exhibit complex temporal organization, with long-range correlations and robust duality of power-law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, features typical of non-equilibrium systems self-organizing at criticality. We show that such non-equilibrium behavior relates to anti-correlated coupling between θ- and δ-bursts, persists across a range of time scales, and is independent of the dominant physiologic state; indications of a basic principle in sleep regulation. Further, we find that VLPO lesions lead to a modulation of cortical dynamics resulting in altered dynamical parameters of θ- and δ-bursts and significant reduction in θ–δ coupling. Our empirical findings and model simulations demonstrate that θ–δ coupling is essential for the emerging non-equilibrium critical dynamics observed across the sleep–wake cycle, and indicate that VLPO neurons may have dual role for both sleep and arousal/brief wake activation. The uncovered critical behavior in sleep- and wake-related cortical rhythms indicates a mechanism essential for the micro-architecture of spontaneous sleep-stage and arousal transitions within a novel, non-homeostatic paradigm of sleep regulation."}]},{"file_date_updated":"2020-11-25T15:05:04Z","has_accepted_license":"1","status":"public","isi":1,"publication_identifier":{"issn":["0022-4715"],"eissn":["1572-9613"]},"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"RoSe"}],"publication_status":"published","external_id":{"isi":["000543030000002"],"arxiv":["2001.07144"]},"intvolume":" 181","doi":"10.1007/s10955-020-02586-0","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).\r\nThe work of R.S. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No 694227). J.Y. gratefully acknowledges hospitality at the LPMMC Grenoble and valuable discussions with Alessandro Olgiati and Nicolas Rougerie. ","ddc":["530"],"volume":181,"scopus_import":"1","year":"2020","publication":"Journal of Statistical Physics","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"article_type":"original","date_published":"2020-10-01T00:00:00Z","file":[{"file_name":"2020_JourStatPhysics_Seiringer.pdf","date_updated":"2020-11-25T15:05:04Z","relation":"main_file","checksum":"5cbeef52caf18d0d952f17fed7b5545a","content_type":"application/pdf","access_level":"open_access","success":1,"file_id":"8812","file_size":404778,"creator":"dernst","date_created":"2020-11-25T15:05:04Z"}],"author":[{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","full_name":"Seiringer, Robert","first_name":"Robert"},{"last_name":"Yngvason","full_name":"Yngvason, Jakob","first_name":"Jakob"}],"date_created":"2020-07-05T22:00:46Z","title":"Emergence of Haldane pseudo-potentials in systems with short-range interactions","ec_funded":1,"oa_version":"Published Version","corr_author":"1","publisher":"Springer","quality_controlled":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_updated":"2025-07-10T11:55:04Z","language":[{"iso":"eng"}],"arxiv":1,"abstract":[{"lang":"eng","text":"In the setting of the fractional quantum Hall effect we study the effects of strong, repulsive two-body interaction potentials of short range. We prove that Haldane’s pseudo-potential operators, including their pre-factors, emerge as mathematically rigorous limits of such interactions when the range of the potential tends to zero while its strength tends to infinity. In a common approach the interaction potential is expanded in angular momentum eigenstates in the lowest Landau level, which amounts to taking the pre-factors to be the moments of the potential. Such a procedure is not appropriate for very strong interactions, however, in particular not in the case of hard spheres. We derive the formulas valid in the short-range case, which involve the scattering lengths of the interaction potential in different angular momentum channels rather than its moments. Our results hold for bosons and fermions alike and generalize previous results in [6], which apply to bosons in the lowest angular momentum channel. Our main theorem asserts the convergence in a norm-resolvent sense of the Hamiltonian on the whole Hilbert space, after appropriate energy scalings, to Hamiltonians with contact interactions in the lowest Landau level."}],"_id":"8091","month":"10","type":"journal_article","citation":{"ieee":"R. Seiringer and J. Yngvason, “Emergence of Haldane pseudo-potentials in systems with short-range interactions,” Journal of Statistical Physics, vol. 181. Springer, pp. 448–464, 2020.","mla":"Seiringer, Robert, and Jakob Yngvason. “Emergence of Haldane Pseudo-Potentials in Systems with Short-Range Interactions.” Journal of Statistical Physics, vol. 181, Springer, 2020, pp. 448–64, doi:10.1007/s10955-020-02586-0.","short":"R. Seiringer, J. Yngvason, Journal of Statistical Physics 181 (2020) 448–464.","apa":"Seiringer, R., & Yngvason, J. (2020). Emergence of Haldane pseudo-potentials in systems with short-range interactions. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-020-02586-0","chicago":"Seiringer, Robert, and Jakob Yngvason. “Emergence of Haldane Pseudo-Potentials in Systems with Short-Range Interactions.” Journal of Statistical Physics. Springer, 2020. https://doi.org/10.1007/s10955-020-02586-0.","ista":"Seiringer R, Yngvason J. 2020. Emergence of Haldane pseudo-potentials in systems with short-range interactions. Journal of Statistical Physics. 181, 448–464.","ama":"Seiringer R, Yngvason J. Emergence of Haldane pseudo-potentials in systems with short-range interactions. Journal of Statistical Physics. 2020;181:448-464. doi:10.1007/s10955-020-02586-0"},"page":"448-464","oa":1},{"file_date_updated":"2021-12-02T12:35:12Z","article_processing_charge":"No","department":[{"_id":"SiHi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","external_id":{"pmid":["32601464"],"isi":["000544152500001"]},"has_accepted_license":"1","status":"public","isi":1,"publication_identifier":{"issn":["0007-0920"],"eissn":["1532-1827"]},"day":"15","volume":123,"scopus_import":"1","pmid":1,"publication":"British Journal of Cancer","year":"2020","intvolume":" 123","acknowledgement":"The authors would like to thank A. van Lierop for technical assistance. In addition, we thank C. Dullin, J. Missbach-Güntner and S. Greco for advice and assistance with fpVCT imaging. Furthermore, the authors would like to thank H. K. Horst for advice on performing matrigel plug assays. This study has also been partially presented in A. Schorr’s doctoral thesis and the funding report of the SPP 1190 ‘The tumor-vessel interface’ of the ‘Deutsche Forschungsgemeinschaft’ (DFG).\r\nThis project was funded by the SPP 1190 “The tumor-vessel interface” and HO 2092/8-1 of the ‘Deutsche Forschungsgemeinschaft’ (DFG) to B. Homey. In addition, it was supported by grants from the Austrian Science Fund (FWF, W1212 to N. Amberg and J. Klufa and I4300-B to T. Bauer), the WWTF project LS16-025 and the European Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883) to M. Sibilia.","doi":"10.1038/s41416-020-0943-2","ddc":["610"],"file":[{"checksum":"05a8e65d49c3f5b8e37ac4afe68287e2","content_type":"application/pdf","success":1,"access_level":"open_access","file_id":"10398","relation":"main_file","date_updated":"2021-12-02T12:35:12Z","file_name":"2020_BrJournalCancer_Hippe.pdf","date_created":"2021-12-02T12:35:12Z","creator":"cchlebak","file_size":3620691}],"date_created":"2020-07-05T22:00:46Z","author":[{"last_name":"Hippe","first_name":"Andreas","full_name":"Hippe, Andreas"},{"full_name":"Braun, Stephan Alexander","first_name":"Stephan Alexander","last_name":"Braun"},{"last_name":"Oláh","first_name":"Péter","full_name":"Oláh, Péter"},{"last_name":"Gerber","first_name":"Peter Arne","full_name":"Gerber, Peter Arne"},{"last_name":"Schorr","full_name":"Schorr, Anne","first_name":"Anne"},{"last_name":"Seeliger","first_name":"Stephan","full_name":"Seeliger, Stephan"},{"first_name":"Stephanie","full_name":"Holtz, Stephanie","last_name":"Holtz"},{"full_name":"Jannasch, Katharina","first_name":"Katharina","last_name":"Jannasch"},{"first_name":"Andor","full_name":"Pivarcsi, Andor","last_name":"Pivarcsi"},{"last_name":"Buhren","first_name":"Bettina","full_name":"Buhren, Bettina"},{"last_name":"Schrumpf","first_name":"Holger","full_name":"Schrumpf, Holger"},{"full_name":"Kislat, Andreas","first_name":"Andreas","last_name":"Kislat"},{"first_name":"Erich","full_name":"Bünemann, Erich","last_name":"Bünemann"},{"last_name":"Steinhoff","first_name":"Martin","full_name":"Steinhoff, Martin"},{"full_name":"Fischer, Jens","first_name":"Jens","last_name":"Fischer"},{"last_name":"Lira","first_name":"Sérgio A.","full_name":"Lira, Sérgio A."},{"last_name":"Boukamp","full_name":"Boukamp, Petra","first_name":"Petra"},{"last_name":"Hevezi","full_name":"Hevezi, Peter","first_name":"Peter"},{"last_name":"Stoecklein","full_name":"Stoecklein, Nikolas Hendrik","first_name":"Nikolas Hendrik"},{"last_name":"Hoffmann","first_name":"Thomas","full_name":"Hoffmann, Thomas"},{"last_name":"Alves","first_name":"Frauke","full_name":"Alves, Frauke"},{"first_name":"Jonathan","full_name":"Sleeman, Jonathan","last_name":"Sleeman"},{"last_name":"Bauer","full_name":"Bauer, Thomas","first_name":"Thomas"},{"full_name":"Klufa, Jörg","first_name":"Jörg","last_name":"Klufa"},{"full_name":"Amberg, Nicole","first_name":"Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg"},{"first_name":"Maria","full_name":"Sibilia, Maria","last_name":"Sibilia"},{"last_name":"Zlotnik","full_name":"Zlotnik, Albert","first_name":"Albert"},{"last_name":"Müller-Homey","full_name":"Müller-Homey, Anja","first_name":"Anja"},{"last_name":"Homey","full_name":"Homey, Bernhard","first_name":"Bernhard"}],"title":"EGFR/Ras-induced CCL20 production modulates the tumour microenvironment","article_type":"original","date_published":"2020-09-15T00:00:00Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"date_updated":"2023-08-22T07:51:12Z","oa_version":"Published Version","publisher":"Springer Nature","quality_controlled":"1","type":"journal_article","citation":{"ieee":"A. Hippe et al., “EGFR/Ras-induced CCL20 production modulates the tumour microenvironment,” British Journal of Cancer, vol. 123. Springer Nature, pp. 942–954, 2020.","mla":"Hippe, Andreas, et al. “EGFR/Ras-Induced CCL20 Production Modulates the Tumour Microenvironment.” British Journal of Cancer, vol. 123, Springer Nature, 2020, pp. 942–54, doi:10.1038/s41416-020-0943-2.","short":"A. Hippe, S.A. Braun, P. Oláh, P.A. Gerber, A. Schorr, S. Seeliger, S. Holtz, K. Jannasch, A. Pivarcsi, B. Buhren, H. Schrumpf, A. Kislat, E. Bünemann, M. Steinhoff, J. Fischer, S.A. Lira, P. Boukamp, P. Hevezi, N.H. Stoecklein, T. Hoffmann, F. Alves, J. Sleeman, T. Bauer, J. Klufa, N. Amberg, M. Sibilia, A. Zlotnik, A. Müller-Homey, B. Homey, British Journal of Cancer 123 (2020) 942–954.","apa":"Hippe, A., Braun, S. A., Oláh, P., Gerber, P. A., Schorr, A., Seeliger, S., … Homey, B. (2020). EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. Springer Nature. https://doi.org/10.1038/s41416-020-0943-2","ama":"Hippe A, Braun SA, Oláh P, et al. EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. 2020;123:942-954. doi:10.1038/s41416-020-0943-2","ista":"Hippe A, Braun SA, Oláh P, Gerber PA, Schorr A, Seeliger S, Holtz S, Jannasch K, Pivarcsi A, Buhren B, Schrumpf H, Kislat A, Bünemann E, Steinhoff M, Fischer J, Lira SA, Boukamp P, Hevezi P, Stoecklein NH, Hoffmann T, Alves F, Sleeman J, Bauer T, Klufa J, Amberg N, Sibilia M, Zlotnik A, Müller-Homey A, Homey B. 2020. EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. 123, 942–954.","chicago":"Hippe, Andreas, Stephan Alexander Braun, Péter Oláh, Peter Arne Gerber, Anne Schorr, Stephan Seeliger, Stephanie Holtz, et al. “EGFR/Ras-Induced CCL20 Production Modulates the Tumour Microenvironment.” British Journal of Cancer. Springer Nature, 2020. https://doi.org/10.1038/s41416-020-0943-2."},"month":"09","related_material":{"link":[{"url":"https://doi.org/10.1038/s41416-021-01563-y","relation":"erratum"}],"record":[{"status":"deleted","id":"10170","relation":"later_version"}]},"page":"942-954","oa":1,"abstract":[{"text":"Background: The activation of the EGFR/Ras-signalling pathway in tumour cells induces a distinct chemokine repertoire, which in turn modulates the tumour microenvironment.\r\nMethods: The effects of EGFR/Ras on the expression and translation of CCL20 were analysed in a large set of epithelial cancer cell lines and tumour tissues by RT-qPCR and ELISA in vitro. CCL20 production was verified by immunohistochemistry in different tumour tissues and correlated with clinical data. The effects of CCL20 on endothelial cell migration and tumour-associated vascularisation were comprehensively analysed with chemotaxis assays in vitro and in CCR6-deficient mice in vivo.\r\nResults: Tumours facilitate progression by the EGFR/Ras-induced production of CCL20. Expression of the chemokine CCL20 in tumours correlates with advanced tumour stage, increased lymph node metastasis and decreased survival in patients. Microvascular endothelial cells abundantly express the specific CCL20 receptor CCR6. CCR6 signalling in endothelial cells induces angiogenesis. CCR6-deficient mice show significantly decreased tumour growth and tumour-associated vascularisation. The observed phenotype is dependent on CCR6 deficiency in stromal cells but not within the immune system.\r\nConclusion: We propose that the chemokine axis CCL20–CCR6 represents a novel and promising target to interfere with the tumour microenvironment, and opens an innovative multimodal strategy for cancer therapy.","lang":"eng"}],"_id":"8093"},{"year":"2020","doi":"10.15479/AT:ISTA:8097","date_created":"2020-07-06T20:40:19Z","author":[{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","orcid":"0000-0001-6041-254X","first_name":"Bor","full_name":"Kavcic, Bor"}],"title":"Analysis scripts and research data for the paper \"Mechanisms of drug interactions between translation-inhibiting antibiotics\"","oa":1,"type":"research_data","file":[{"file_name":"natComm_2020_scripts.zip","date_updated":"2020-07-14T12:48:09Z","relation":"main_file","checksum":"5c321dbbb6d4b3c85da786fd3ebbdc98","content_type":"application/zip","access_level":"open_access","file_id":"8098","file_size":255770756,"creator":"bkavcic","date_created":"2020-07-06T20:38:27Z"}],"citation":{"short":"B. Kavcic, (2020).","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8097","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8097.","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8097.","ama":"Kavcic B. Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” 2020. doi:10.15479/AT:ISTA:8097","mla":"Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8097.","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics.’” Institute of Science and Technology Austria, 2020."},"month":"07","_id":"8097","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"date_published":"2020-07-15T00:00:00Z","abstract":[{"lang":"eng","text":"Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by \"translation bottlenecks\": points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of \"continuous epistasis\" in bacterial physiology."}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_updated":"2024-02-21T12:40:51Z","file_date_updated":"2020-07-14T12:48:09Z","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GaTk"}],"article_processing_charge":"No","day":"15","contributor":[{"contributor_type":"research_group","first_name":"Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"research_group","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach"}],"status":"public","has_accepted_license":"1"},{"abstract":[{"lang":"eng","text":"Sewall Wright developed FST for describing population differentiation and it has since been extended to many novel applications, including the detection of homomorphic sex chromosomes. However, there has been confusion regarding the expected estimate of FST for a fixed difference between the X‐ and Y‐chromosome when comparing males and females. Here, we attempt to resolve this confusion by contrasting two common FST estimators and explain why they yield different estimates when applied to the case of sex chromosomes. We show that this difference is true for many allele frequencies, but the situation characterized by fixed differences between the X‐ and Y‐chromosome is among the most extreme. To avoid additional confusion, we recommend that all authors using FST clearly state which estimator of FST their work uses."}],"_id":"8099","citation":{"apa":"Gammerdinger, W. J., Toups, M. A., & Vicoso, B. (2020). Disagreement in FST estimators: A case study from sex chromosomes. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13210","short":"W.J. Gammerdinger, M.A. Toups, B. Vicoso, Molecular Ecology Resources 20 (2020) 1517–1525.","ista":"Gammerdinger WJ, Toups MA, Vicoso B. 2020. Disagreement in FST estimators: A case study from sex chromosomes. Molecular Ecology Resources. 20(6), 1517–1525.","chicago":"Gammerdinger, William J, Melissa A Toups, and Beatriz Vicoso. “Disagreement in FST Estimators: A Case Study from Sex Chromosomes.” Molecular Ecology Resources. Wiley, 2020. https://doi.org/10.1111/1755-0998.13210.","ama":"Gammerdinger WJ, Toups MA, Vicoso B. Disagreement in FST estimators: A case study from sex chromosomes. Molecular Ecology Resources. 2020;20(6):1517-1525. doi:10.1111/1755-0998.13210","ieee":"W. J. Gammerdinger, M. A. Toups, and B. Vicoso, “Disagreement in FST estimators: A case study from sex chromosomes,” Molecular Ecology Resources, vol. 20, no. 6. Wiley, pp. 1517–1525, 2020.","mla":"Gammerdinger, William J., et al. “Disagreement in FST Estimators: A Case Study from Sex Chromosomes.” Molecular Ecology Resources, vol. 20, no. 6, Wiley, 2020, pp. 1517–25, doi:10.1111/1755-0998.13210."},"type":"journal_article","month":"11","page":"1517-1525","oa":1,"oa_version":"Published Version","corr_author":"1","publisher":"Wiley","quality_controlled":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_updated":"2025-04-15T08:18:38Z","language":[{"iso":"eng"}],"intvolume":" 20","doi":"10.1111/1755-0998.13210","ddc":["570"],"volume":20,"pmid":1,"scopus_import":"1","publication":"Molecular Ecology Resources","year":"2020","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety"}],"article_type":"original","date_published":"2020-11-01T00:00:00Z","issue":"6","file":[{"file_name":"2020_MolecularEcologyRes_Gammerdinger.pdf","relation":"main_file","date_updated":"2020-11-26T11:46:43Z","checksum":"3d87ebb8757dcd504f20c618b72e6575","content_type":"application/pdf","access_level":"open_access","file_id":"8814","success":1,"file_size":820428,"creator":"dernst","date_created":"2020-11-26T11:46:43Z"}],"date_created":"2020-07-07T08:56:16Z","author":[{"first_name":"William J","full_name":"Gammerdinger, William J","last_name":"Gammerdinger","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9638-1220"},{"last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","first_name":"Melissa A","full_name":"Toups, Melissa A"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","full_name":"Vicoso, Beatriz"}],"title":"Disagreement in FST estimators: A case study from sex chromosomes","ec_funded":1,"file_date_updated":"2020-11-26T11:46:43Z","isi":1,"status":"public","has_accepted_license":"1","publication_identifier":{"eissn":["1755-0998"],"issn":["1755-098X"]},"day":"01","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"BeVi"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","external_id":{"isi":["000545451200001"],"pmid":["32543001"]}},{"language":[{"iso":"eng"}],"date_updated":"2025-04-23T08:51:12Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"corr_author":"1","oa_version":"Published Version","quality_controlled":"1","publisher":"American Physical Society","arxiv":1,"citation":{"ama":"Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. 2020;4(8). doi:10.1103/PhysRevMaterials.4.082602","ista":"Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. 2020. Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. 4(8), 082602.","chicago":"Grosjean, Galien M, Sebastian Wald, Juan Carlos A Sobarzo Ponce, and Scott R Waitukaitis. “Quantitatively Consistent Scale-Spanning Model for Same-Material Tribocharging.” Physical Review Materials. American Physical Society, 2020. https://doi.org/10.1103/PhysRevMaterials.4.082602.","short":"G.M. Grosjean, S. Wald, J.C.A. Sobarzo Ponce, S.R. Waitukaitis, Physical Review Materials 4 (2020).","apa":"Grosjean, G. M., Wald, S., Sobarzo Ponce, J. C. A., & Waitukaitis, S. R. (2020). Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. American Physical Society. https://doi.org/10.1103/PhysRevMaterials.4.082602","ieee":"G. M. Grosjean, S. Wald, J. C. A. Sobarzo Ponce, and S. R. Waitukaitis, “Quantitatively consistent scale-spanning model for same-material tribocharging,” Physical Review Materials, vol. 4, no. 8. American Physical Society, 2020.","mla":"Grosjean, Galien M., et al. “Quantitatively Consistent Scale-Spanning Model for Same-Material Tribocharging.” Physical Review Materials, vol. 4, no. 8, 082602, American Physical Society, 2020, doi:10.1103/PhysRevMaterials.4.082602."},"type":"journal_article","month":"08","related_material":{"record":[{"status":"public","id":"12697","relation":"popular_science"}]},"oa":1,"abstract":[{"lang":"eng","text":"By rigorously accounting for mesoscale spatial correlations in donor/acceptor surface properties, we develop a scale-spanning model for same-material tribocharging. We find that mesoscale correlations affect not only the magnitude of charge transfer but also the fluctuations—suppressing otherwise overwhelming charge-transfer variability that is not observed experimentally. We furthermore propose a generic theoretical mechanism by which the mesoscale features might emerge, which is qualitatively consistent with other proposals in the literature."}],"keyword":["electric charge","tribocharging","soft matter","granular materials","polymers"],"_id":"8101","file_date_updated":"2020-08-17T15:54:20Z","article_processing_charge":"Yes","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"ScWa"}],"external_id":{"isi":["000561897000001"],"arxiv":["2006.07120"]},"publication_status":"published","status":"public","isi":1,"has_accepted_license":"1","publication_identifier":{"issn":["2475-9953"]},"day":"17","volume":4,"year":"2020","publication":"Physical Review Materials","scopus_import":"1","intvolume":" 4","ddc":["530"],"doi":"10.1103/PhysRevMaterials.4.082602","acknowledgement":"We would like to thank Philip Born, Bartosz Grzybowski, Tarik Baytekin, and Bilge Baytekin for helpful discussions.\r\nThis project has received funding from the European Unions Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","file":[{"file_name":"Grosjean2020.pdf","date_updated":"2020-08-17T15:54:20Z","relation":"main_file","checksum":"288fef1eeb6540c6344bb8f7c8159dc9","content_type":"application/pdf","access_level":"open_access","success":1,"file_id":"8277","file_size":853753,"creator":"ggrosjea","date_created":"2020-08-17T15:54:20Z"}],"issue":"8","ec_funded":1,"title":"Quantitatively consistent scale-spanning model for same-material tribocharging","article_number":"082602","date_created":"2020-07-07T11:33:54Z","author":[{"full_name":"Grosjean, Galien M","first_name":"Galien M","orcid":"0000-0001-5154-417X","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","last_name":"Grosjean"},{"first_name":"Sebastian","full_name":"Wald, Sebastian","id":"133F200A-B015-11E9-AD41-0EDAE5697425","last_name":"Wald","orcid":"0000-0002-5869-1604"},{"last_name":"Sobarzo Ponce","id":"4B807D68-AE37-11E9-AC72-31CAE5697425","first_name":"Juan Carlos A","full_name":"Sobarzo Ponce, Juan Carlos A"},{"first_name":"Scott R","full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","orcid":"0000-0002-2299-3176"}],"article_type":"original","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"date_published":"2020-08-17T00:00:00Z"},{"type":"journal_article","citation":{"mla":"Lombardi, Fabrizio, et al. “Power-Law Correlations and Coupling of Active and Quiet States Underlie a Class of Complex Systems with Self-Organization at Criticality.” EPJ Web of Conferences, vol. 230, 00005, EDP Sciences, 2020, doi:10.1051/epjconf/202023000005.","ieee":"F. Lombardi, J. W. J. L. Wang, X. Zhang, and P. C. Ivanov, “Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality,” EPJ Web of Conferences, vol. 230. EDP Sciences, 2020.","ama":"Lombardi F, Wang JWJL, Zhang X, Ivanov PC. Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality. EPJ Web of Conferences. 2020;230. doi:10.1051/epjconf/202023000005","chicago":"Lombardi, Fabrizio, Jilin W.J.L. Wang, Xiyun Zhang, and Plamen Ch Ivanov. “Power-Law Correlations and Coupling of Active and Quiet States Underlie a Class of Complex Systems with Self-Organization at Criticality.” EPJ Web of Conferences. EDP Sciences, 2020. https://doi.org/10.1051/epjconf/202023000005.","ista":"Lombardi F, Wang JWJL, Zhang X, Ivanov PC. 2020. Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality. EPJ Web of Conferences. 230, 00005.","apa":"Lombardi, F., Wang, J. W. J. L., Zhang, X., & Ivanov, P. C. (2020). Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality. EPJ Web of Conferences. EDP Sciences. https://doi.org/10.1051/epjconf/202023000005","short":"F. Lombardi, J.W.J.L. Wang, X. Zhang, P.C. Ivanov, EPJ Web of Conferences 230 (2020)."},"month":"03","oa":1,"abstract":[{"text":"Physical and biological systems often exhibit intermittent dynamics with bursts or avalanches (active states) characterized by power-law size and duration distributions. These emergent features are typical of systems at the critical point of continuous phase transitions, and have led to the hypothesis that such systems may self-organize at criticality, i.e. without any fine tuning of parameters. Since the introduction of the Bak-Tang-Wiesenfeld (BTW) model, the paradigm of self-organized criticality (SOC) has been very fruitful for the analysis of emergent collective behaviors in a number of systems, including the brain. Although considerable effort has been devoted in identifying and modeling scaling features of burst and avalanche statistics, dynamical aspects related to the temporal organization of bursts remain often poorly understood or controversial. Of crucial importance to understand the mechanisms responsible for emergent behaviors is the relationship between active and quiet periods, and the nature of the correlations. Here we investigate the dynamics of active (θ-bursts) and quiet states (δ-bursts) in brain activity during the sleep-wake cycle. We show the duality of power-law (θ, active phase) and exponential-like (δ, quiescent phase) duration distributions, typical of SOC, jointly emerge with power-law temporal correlations and anti-correlated coupling between active and quiet states. Importantly, we demonstrate that such temporal organization shares important similarities with earthquake dynamics, and propose that specific power-law correlations and coupling between active and quiet states are distinctive characteristics of a class of systems with self-organization at criticality.","lang":"eng"}],"_id":"8105","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_updated":"2025-06-12T07:19:19Z","language":[{"iso":"eng"}],"oa_version":"Published Version","corr_author":"1","publisher":"EDP Sciences","quality_controlled":"1","file":[{"date_created":"2020-07-22T06:17:11Z","creator":"dernst","file_size":2197543,"file_id":"8144","access_level":"open_access","success":1,"content_type":"application/pdf","date_updated":"2020-07-22T06:17:11Z","relation":"main_file","file_name":"2020_EPJWebConf_Lombardi.pdf"}],"author":[{"orcid":"0000-0003-2623-5249","id":"A057D288-3E88-11E9-986D-0CF4E5697425","last_name":"Lombardi","full_name":"Lombardi, Fabrizio","first_name":"Fabrizio"},{"last_name":"Wang","first_name":"Jilin W.J.L.","full_name":"Wang, Jilin W.J.L."},{"first_name":"Xiyun","full_name":"Zhang, Xiyun","last_name":"Zhang"},{"full_name":"Ivanov, Plamen Ch","first_name":"Plamen Ch","last_name":"Ivanov"}],"article_number":"00005","title":"Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality","date_created":"2020-07-12T16:20:33Z","article_type":"original","date_published":"2020-03-11T00:00:00Z","volume":230,"pmid":1,"publication":"EPJ Web of Conferences","year":"2020","intvolume":" 230","doi":"10.1051/epjconf/202023000005","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GaTk"}],"article_processing_charge":"No","publication_status":"published","external_id":{"pmid":["32655977"]},"status":"public","has_accepted_license":"1","publication_identifier":{"issn":["2100-014X"]},"day":"11","file_date_updated":"2020-07-22T06:17:11Z"},{"OA_place":"repository","_id":"8112","type":"journal_article","month":"07","citation":{"chicago":"Barton, Nicholas H. “On the Completion of Speciation.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0530.","ista":"Barton NH. 2020. On the completion of speciation. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190530.","ama":"Barton NH. On the completion of speciation. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0530","apa":"Barton, N. H. (2020). On the completion of speciation. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0530","short":"N.H. Barton, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","mla":"Barton, Nicholas H. “On the Completion of Speciation.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190530, The Royal Society, 2020, doi:10.1098/rstb.2019.0530.","ieee":"N. H. Barton, “On the completion of speciation,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020."},"oa":1,"oa_version":"Submitted Version","publisher":"The Royal Society","quality_controlled":"1","language":[{"iso":"eng"}],"date_updated":"2025-06-25T07:45:22Z","intvolume":" 375","doi":"10.1098/rstb.2019.0530","volume":375,"scopus_import":"1","pmid":1,"publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","year":"2020","article_type":"letter_note","date_published":"2020-07-12T00:00:00Z","issue":"1806","author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"title":"On the completion of speciation","article_number":"20190530","date_created":"2020-07-13T03:41:39Z","OA_type":"green","main_file_link":[{"open_access":"1","url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC7423282/"}],"isi":1,"status":"public","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"day":"12","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"publication_status":"published","external_id":{"isi":["000552662100002"],"pmid":["32654647"]}},{"doi":"10.1523/JNEUROSCI.0276-20.2020","ddc":["570"],"intvolume":" 40","scopus_import":"1","pmid":1,"year":"2020","publication":"The Journal of Neuroscience","volume":40,"date_published":"2020-12-09T00:00:00Z","article_type":"original","date_created":"2020-07-16T12:25:04Z","title":"Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields","author":[{"orcid":"0000-0001-7184-7311","last_name":"Agnes","full_name":"Agnes, Everton J.","first_name":"Everton J."},{"full_name":"Luppi, Andrea I.","first_name":"Andrea I.","last_name":"Luppi"},{"first_name":"Tim P","full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","orcid":"0000-0003-3295-6181"}],"issue":"50","file":[{"date_updated":"2020-12-28T08:31:47Z","relation":"main_file","access_level":"open_access","success":1,"file_id":"8977","content_type":"application/pdf","checksum":"7977e4dd6b89357d1a5cc88babac56da","file_name":"2020_JourNeuroscience_Agnes.pdf","creator":"dernst","date_created":"2020-12-28T08:31:47Z","file_size":2750920}],"file_date_updated":"2020-12-28T08:31:47Z","publication_identifier":{"eissn":["1529-2401"]},"day":"09","has_accepted_license":"1","isi":1,"status":"public","publication_status":"published","external_id":{"pmid":["33168622"],"isi":["000606706400009"]},"department":[{"_id":"TiVo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","_id":"8126","abstract":[{"text":"Cortical areas comprise multiple types of inhibitory interneurons with stereotypical connectivity motifs, but their combined effect on postsynaptic dynamics has been largely unexplored. Here, we analyse the response of a single postsynaptic model neuron receiving tuned excitatory connections alongside inhibition from two plastic populations. Depending on the inhibitory plasticity rule, synapses remain unspecific (flat), become anti-correlated to, or mirror excitatory synapses. Crucially, the neuron’s receptive field, i.e., its response to presynaptic stimuli, depends on the modulatory state of inhibition. When both inhibitory populations are active, inhibition balances excitation, resulting in uncorrelated postsynaptic responses regardless of the inhibitory tuning profiles. Modulating the activity of a given inhibitory population produces strong correlations to either preferred or non-preferred inputs, in line with recent experimental findings showing dramatic context-dependent changes of neurons’ receptive fields. We thus confirm that a neuron’s receptive field doesn’t follow directly from the weight profiles of its presynaptic afferents.","lang":"eng"}],"page":"9634-9649","oa":1,"citation":{"ieee":"E. J. Agnes, A. I. Luppi, and T. P. Vogels, “Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields,” The Journal of Neuroscience, vol. 40, no. 50. Society for Neuroscience, pp. 9634–9649, 2020.","mla":"Agnes, Everton J., et al. “Complementary Inhibitory Weight Profiles Emerge from Plasticity and Allow Attentional Switching of Receptive Fields.” The Journal of Neuroscience, vol. 40, no. 50, Society for Neuroscience, 2020, pp. 9634–49, doi:10.1523/JNEUROSCI.0276-20.2020.","short":"E.J. Agnes, A.I. Luppi, T.P. Vogels, The Journal of Neuroscience 40 (2020) 9634–9649.","apa":"Agnes, E. J., Luppi, A. I., & Vogels, T. P. (2020). Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0276-20.2020","chicago":"Agnes, Everton J., Andrea I. Luppi, and Tim P Vogels. “Complementary Inhibitory Weight Profiles Emerge from Plasticity and Allow Attentional Switching of Receptive Fields.” The Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/JNEUROSCI.0276-20.2020.","ista":"Agnes EJ, Luppi AI, Vogels TP. 2020. Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. 40(50), 9634–9649.","ama":"Agnes EJ, Luppi AI, Vogels TP. Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. 2020;40(50):9634-9649. doi:10.1523/JNEUROSCI.0276-20.2020"},"type":"journal_article","month":"12","publisher":"Society for Neuroscience","quality_controlled":"1","oa_version":"Published Version","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_updated":"2023-08-22T07:54:26Z","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"date_updated":"2025-04-14T07:54:31Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","publisher":"eLife Sciences Publications","oa_version":"Published Version","oa":1,"citation":{"ama":"Gonçalves PJ, Lueckmann J-M, Deistler M, et al. Training deep neural density estimators to identify mechanistic models of neural dynamics. eLife. 2020;9. doi:10.7554/eLife.56261","ista":"Gonçalves PJ, Lueckmann J-M, Deistler M, Nonnenmacher M, Öcal K, Bassetto G, Chintaluri C, Podlaski WF, Haddad SA, Vogels TP, Greenberg DS, Macke JH. 2020. Training deep neural density estimators to identify mechanistic models of neural dynamics. eLife. 9, e56261.","chicago":"Gonçalves, Pedro J., Jan-Matthis Lueckmann, Michael Deistler, Marcel Nonnenmacher, Kaan Öcal, Giacomo Bassetto, Chaitanya Chintaluri, et al. “Training Deep Neural Density Estimators to Identify Mechanistic Models of Neural Dynamics.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.56261.","apa":"Gonçalves, P. J., Lueckmann, J.-M., Deistler, M., Nonnenmacher, M., Öcal, K., Bassetto, G., … Macke, J. H. (2020). Training deep neural density estimators to identify mechanistic models of neural dynamics. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.56261","short":"P.J. Gonçalves, J.-M. Lueckmann, M. Deistler, M. Nonnenmacher, K. Öcal, G. Bassetto, C. Chintaluri, W.F. Podlaski, S.A. Haddad, T.P. Vogels, D.S. Greenberg, J.H. Macke, ELife 9 (2020).","ieee":"P. J. Gonçalves et al., “Training deep neural density estimators to identify mechanistic models of neural dynamics,” eLife, vol. 9. eLife Sciences Publications, 2020.","mla":"Gonçalves, Pedro J., et al. “Training Deep Neural Density Estimators to Identify Mechanistic Models of Neural Dynamics.” ELife, vol. 9, e56261, eLife Sciences Publications, 2020, doi:10.7554/eLife.56261."},"type":"journal_article","month":"09","_id":"8127","abstract":[{"lang":"eng","text":"Mechanistic modeling in neuroscience aims to explain observed phenomena in terms of underlying causes. However, determining which model parameters agree with complex and stochastic neural data presents a significant challenge. We address this challenge with a machine learning tool which uses deep neural density estimators—trained using model simulations—to carry out Bayesian inference and retrieve the full space of parameters compatible with raw data or selected data features. Our method is scalable in parameters and data features and can rapidly analyze new data after initial training. We demonstrate the power and flexibility of our approach on receptive fields, ion channels, and Hodgkin–Huxley models. We also characterize the space of circuit configurations giving rise to rhythmic activity in the crustacean stomatogastric ganglion, and use these results to derive hypotheses for underlying compensation mechanisms. Our approach will help close the gap between data-driven and theory-driven models of neural dynamics."}],"external_id":{"pmid":["32940606"],"isi":["000584989400001"]},"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"TiVo"}],"article_processing_charge":"No","day":"17","publication_identifier":{"eissn":["2050-084X"]},"status":"public","has_accepted_license":"1","isi":1,"file_date_updated":"2020-10-27T11:37:32Z","ec_funded":1,"title":"Training deep neural density estimators to identify mechanistic models of neural dynamics","author":[{"orcid":"0000-0002-6987-4836","last_name":"Gonçalves","full_name":"Gonçalves, Pedro J.","first_name":"Pedro J."},{"last_name":"Lueckmann","orcid":"0000-0003-4320-4663","first_name":"Jan-Matthis","full_name":"Lueckmann, Jan-Matthis"},{"full_name":"Deistler, Michael","first_name":"Michael","orcid":"0000-0002-3573-0404","last_name":"Deistler"},{"full_name":"Nonnenmacher, Marcel","first_name":"Marcel","orcid":"0000-0001-6044-6627","last_name":"Nonnenmacher"},{"orcid":"0000-0002-8528-6858","last_name":"Öcal","full_name":"Öcal, Kaan","first_name":"Kaan"},{"last_name":"Bassetto","full_name":"Bassetto, Giacomo","first_name":"Giacomo"},{"first_name":"Chaitanya","full_name":"Chintaluri, Chaitanya","last_name":"Chintaluri","id":"BA06AFEE-A4BA-11EA-AE5C-14673DDC885E","orcid":"0000-0003-4252-1608"},{"full_name":"Podlaski, William F.","first_name":"William F.","orcid":"0000-0001-6619-7502","last_name":"Podlaski"},{"full_name":"Haddad, Sara A.","first_name":"Sara A.","orcid":"0000-0003-0807-0823","last_name":"Haddad"},{"last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","first_name":"Tim P","full_name":"Vogels, Tim P"},{"first_name":"David S.","full_name":"Greenberg, David S.","last_name":"Greenberg"},{"first_name":"Jakob H.","full_name":"Macke, Jakob H.","last_name":"Macke","orcid":"0000-0001-5154-8912"}],"article_number":"e56261","date_created":"2020-07-16T12:26:04Z","file":[{"date_updated":"2020-10-27T11:37:32Z","relation":"main_file","file_id":"8709","success":1,"access_level":"open_access","content_type":"application/pdf","checksum":"c4300ddcd93ed03fc9c6cdf1f77890be","file_name":"2020_eLife_Gonçalves.pdf","creator":"cziletti","date_created":"2020-10-27T11:37:32Z","file_size":17355867}],"date_published":"2020-09-17T00:00:00Z","article_type":"original","project":[{"call_identifier":"H2020","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","grant_number":"819603","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234"}],"year":"2020","publication":"eLife","scopus_import":"1","pmid":1,"volume":9,"ddc":["570"],"doi":"10.7554/eLife.56261","acknowledgement":"We thank Mahmood S Hoseini and Michael Stryker for sharing their data for Figure 2, and Philipp Berens, Sean Bittner, Jan Boelts, John Cunningham, Richard Gao, Scott Linderman, Eve Marder, Iain Murray, George Papamakarios, Astrid Prinz, Auguste Schulz and Srinivas Turaga for discussions and/or comments on the manuscript. This work was supported by the German Research Foundation (DFG) through SFB 1233 ‘Robust Vision’, (276693517), SFB 1089 ‘Synaptic Microcircuits’, SPP 2041 ‘Computational Connectomics’ and Germany's Excellence Strategy – EXC-Number 2064/1 – Project number 390727645 and the German Federal Ministry of Education and Research (BMBF, project ‘ADIMEM’, FKZ 01IS18052 A-D) to JHM, a Sir Henry Dale Fellowship by the Wellcome Trust and the Royal Society (WT100000; WFP and TPV), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z; TPV), a ERC Consolidator Grant (SYNAPSEEK; WPF and CC), and a UK Research and Innovation, Biotechnology and Biological Sciences Research Council (CC, UKRI-BBSRC BB/N019512/1). We gratefully acknowledge the Leibniz Supercomputing Centre for funding this project by providing computing time on its Linux-Cluster.","intvolume":" 9"},{"arxiv":1,"type":"journal_article","citation":{"ista":"Bossmann L. 2020. Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons. Archive for Rational Mechanics and Analysis. 238(11), 541–606.","chicago":"Bossmann, Lea. “Derivation of the 2d Gross–Pitaevskii Equation for Strongly Confined 3d Bosons.” Archive for Rational Mechanics and Analysis. Springer Nature, 2020. https://doi.org/10.1007/s00205-020-01548-w.","ama":"Bossmann L. Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons. Archive for Rational Mechanics and Analysis. 2020;238(11):541-606. doi:10.1007/s00205-020-01548-w","apa":"Bossmann, L. (2020). Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-020-01548-w","short":"L. Bossmann, Archive for Rational Mechanics and Analysis 238 (2020) 541–606.","mla":"Bossmann, Lea. “Derivation of the 2d Gross–Pitaevskii Equation for Strongly Confined 3d Bosons.” Archive for Rational Mechanics and Analysis, vol. 238, no. 11, Springer Nature, 2020, pp. 541–606, doi:10.1007/s00205-020-01548-w.","ieee":"L. Bossmann, “Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons,” Archive for Rational Mechanics and Analysis, vol. 238, no. 11. Springer Nature, pp. 541–606, 2020."},"month":"11","page":"541-606","oa":1,"abstract":[{"lang":"eng","text":"We study the dynamics of a system of N interacting bosons in a disc-shaped trap, which is realised by an external potential that confines the bosons in one spatial dimension to an interval of length of order ε. The interaction is non-negative and scaled in such a way that its scattering length is of order ε/N, while its range is proportional to (ε/N)β with scaling parameter β∈(0,1]. We consider the simultaneous limit (N,ε)→(∞,0) and assume that the system initially exhibits Bose–Einstein condensation. We prove that condensation is preserved by the N-body dynamics, where the time-evolved condensate wave function is the solution of a two-dimensional non-linear equation. The strength of the non-linearity depends on the scaling parameter β. For β∈(0,1), we obtain a cubic defocusing non-linear Schrödinger equation, while the choice β=1 yields a Gross–Pitaevskii equation featuring the scattering length of the interaction. In both cases, the coupling parameter depends on the confining potential."}],"_id":"8130","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_updated":"2025-04-14T07:44:05Z","language":[{"iso":"eng"}],"oa_version":"Published Version","corr_author":"1","publisher":"Springer Nature","quality_controlled":"1","volume":238,"scopus_import":"1","publication":"Archive for Rational Mechanics and Analysis","year":"2020","intvolume":" 238","doi":"10.1007/s00205-020-01548-w","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). I thank Stefan Teufel for helpful remarks and for his involvement in the closely related joint project [10]. Helpful discussions with Serena Cenatiempo and Nikolai Leopold are gratefully acknowledged. This work was supported by the German Research Foundation within the Research Training Group 1838 “Spectral Theory and Dynamics of Quantum Systems” and has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","ddc":["510"],"issue":"11","file":[{"relation":"main_file","date_updated":"2020-12-02T08:50:38Z","content_type":"application/pdf","checksum":"cc67a79a67bef441625fcb1cd031db3d","success":1,"access_level":"open_access","file_id":"8826","file_name":"2020_ArchiveRatMech_Bossmann.pdf","creator":"dernst","date_created":"2020-12-02T08:50:38Z","file_size":942343}],"author":[{"full_name":"Bossmann, Lea","first_name":"Lea","orcid":"0000-0002-6854-1343","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","last_name":"Bossmann"}],"title":"Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons","date_created":"2020-07-18T15:06:35Z","ec_funded":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"article_type":"original","date_published":"2020-11-01T00:00:00Z","file_date_updated":"2020-12-02T08:50:38Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"RoSe"}],"article_processing_charge":"Yes (via OA deal)","publication_status":"published","external_id":{"arxiv":["1907.04547"],"isi":["000550164400001"]},"isi":1,"status":"public","has_accepted_license":"1","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"day":"01"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.08281"}],"isi":1,"status":"public","publication_identifier":{"issn":["0022-2488"]},"day":"22","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RoSe"}],"publication_status":"published","external_id":{"arxiv":["2002.08281"],"isi":["000544595100001"]},"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"article_type":"original","date_published":"2020-06-22T00:00:00Z","issue":"6","article_number":"061901","title":"The free energy of the two-dimensional dilute Bose gas. II. Upper bound","author":[{"last_name":"Mayer","id":"30C4630A-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Mayer, Simon"},{"first_name":"Robert","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","orcid":"0000-0002-6781-0521"}],"date_created":"2020-07-19T22:00:59Z","ec_funded":1,"intvolume":" 61","doi":"10.1063/5.0005950","volume":61,"scopus_import":"1","publication":"Journal of Mathematical Physics","year":"2020","oa_version":"Preprint","corr_author":"1","publisher":"AIP Publishing","quality_controlled":"1","date_updated":"2025-07-10T11:55:05Z","language":[{"iso":"eng"}],"abstract":[{"text":"We prove an upper bound on the free energy of a two-dimensional homogeneous Bose gas in the thermodynamic limit. We show that for a2ρ ≪ 1 and βρ ≳ 1, the free energy per unit volume differs from the one of the non-interacting system by at most 4πρ2|lna2ρ|−1(2−[1−βc/β]2+) to leading order, where a is the scattering length of the two-body interaction potential, ρ is the density, β is the inverse temperature, and βc is the inverse Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity. In combination with the corresponding matching lower bound proved by Deuchert et al. [Forum Math. Sigma 8, e20 (2020)], this shows equality in the asymptotic expansion.","lang":"eng"}],"_id":"8134","type":"journal_article","month":"06","citation":{"ieee":"S. Mayer and R. Seiringer, “The free energy of the two-dimensional dilute Bose gas. II. Upper bound,” Journal of Mathematical Physics, vol. 61, no. 6. AIP Publishing, 2020.","mla":"Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics, vol. 61, no. 6, 061901, AIP Publishing, 2020, doi:10.1063/5.0005950.","short":"S. Mayer, R. Seiringer, Journal of Mathematical Physics 61 (2020).","apa":"Mayer, S., & Seiringer, R. (2020). The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0005950","ama":"Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. 2020;61(6). doi:10.1063/5.0005950","chicago":"Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0005950.","ista":"Mayer S, Seiringer R. 2020. The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. 61(6), 061901."},"oa":1,"arxiv":1},{"abstract":[{"lang":"eng","text":"Cell production and differentiation for the acquisition of specific functions are key features of living systems. The dynamic network of cellular microtubules provides the necessary platform to accommodate processes associated with the transition of cells through the individual phases of cytogenesis. Here, we show that the plant hormone cytokinin fine‐tunes the activity of the microtubular cytoskeleton during cell differentiation and counteracts microtubular rearrangements driven by the hormone auxin. The endogenous upward gradient of cytokinin activity along the longitudinal growth axis in Arabidopsis thaliana roots correlates with robust rearrangements of the microtubule cytoskeleton in epidermal cells progressing from the proliferative to the differentiation stage. Controlled increases in cytokinin activity result in premature re‐organization of the microtubule network from transversal to an oblique disposition in cells prior to their differentiation, whereas attenuated hormone perception delays cytoskeleton conversion into a configuration typical for differentiated cells. Intriguingly, cytokinin can interfere with microtubules also in animal cells, such as leukocytes, suggesting that a cytokinin‐sensitive control pathway for the microtubular cytoskeleton may be at least partially conserved between plant and animal cells."}],"_id":"8142","month":"09","type":"journal_article","citation":{"mla":"Montesinos López, Juan C., et al. “Phytohormone Cytokinin Guides Microtubule Dynamics during Cell Progression from Proliferative to Differentiated Stage.” The Embo Journal, vol. 39, no. 17, e104238, Embo Press, 2020, doi:10.15252/embj.2019104238.","ieee":"J. C. Montesinos López et al., “Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage,” The Embo Journal, vol. 39, no. 17. Embo Press, 2020.","apa":"Montesinos López, J. C., Abuzeineh, A., Kopf, A., Juanes Garcia, A., Ötvös, K., Petrášek, J., … Benková, E. (2020). Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. The Embo Journal. Embo Press. https://doi.org/10.15252/embj.2019104238","short":"J.C. Montesinos López, A. Abuzeineh, A. Kopf, A. Juanes Garcia, K. Ötvös, J. Petrášek, M.K. Sixt, E. Benková, The Embo Journal 39 (2020).","ista":"Montesinos López JC, Abuzeineh A, Kopf A, Juanes Garcia A, Ötvös K, Petrášek J, Sixt MK, Benková E. 2020. Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. The Embo Journal. 39(17), e104238.","chicago":"Montesinos López, Juan C, A Abuzeineh, Aglaja Kopf, Alba Juanes Garcia, Krisztina Ötvös, J Petrášek, Michael K Sixt, and Eva Benková. “Phytohormone Cytokinin Guides Microtubule Dynamics during Cell Progression from Proliferative to Differentiated Stage.” The Embo Journal. Embo Press, 2020. https://doi.org/10.15252/embj.2019104238.","ama":"Montesinos López JC, Abuzeineh A, Kopf A, et al. Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. The Embo Journal. 2020;39(17). doi:10.15252/embj.2019104238"},"oa":1,"oa_version":"Published Version","corr_author":"1","publisher":"Embo Press","quality_controlled":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"date_updated":"2025-04-15T06:37:27Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"intvolume":" 39","acknowledgement":"We thank Takashi Aoyama, David Alabadi, and Bert De Rybel for sharing material, Jiří Friml, Maciek Adamowski, and Katerina Schwarzerová for inspiring discussions, and Martine De Cock for help in preparing the manuscript. This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by the Bioimaging Facility (BIF), especially to Robert Hauschild; and the Life Science Facility (LSF). J.C.M. is the recipient of a EMBO Long‐Term Fellowship (ALTF number 710‐2016). This work was supported with MEYS CR, project no.CZ.02.1.01/0.0/0.0/16_019/0000738 to J.P., and by the Austrian Science Fund (FWF01_I1774S) to E.B.","doi":"10.15252/embj.2019104238","ddc":["580"],"volume":39,"pmid":1,"scopus_import":"1","year":"2020","publication":"The Embo Journal","project":[{"name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants","_id":"253E54C8-B435-11E9-9278-68D0E5697425","grant_number":"ALTF710-2016"},{"call_identifier":"FWF","name":"Hormone cross-talk drives nutrient dependent plant development","grant_number":"I 1774-B16","_id":"2542D156-B435-11E9-9278-68D0E5697425"}],"article_type":"original","date_published":"2020-09-01T00:00:00Z","issue":"17","file":[{"date_created":"2020-12-02T09:13:23Z","creator":"dernst","file_size":3497156,"checksum":"43d2b36598708e6ab05c69074e191d57","content_type":"application/pdf","file_id":"8827","success":1,"access_level":"open_access","relation":"main_file","date_updated":"2020-12-02T09:13:23Z","file_name":"2020_EMBO_Montesinos.pdf"}],"date_created":"2020-07-21T09:08:38Z","title":"Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage","article_number":"e104238","author":[{"first_name":"Juan C","full_name":"Montesinos López, Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","last_name":"Montesinos López","orcid":"0000-0001-9179-6099"},{"full_name":"Abuzeineh, A","first_name":"A","last_name":"Abuzeineh"},{"orcid":"0000-0002-2187-6656","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","last_name":"Kopf","full_name":"Kopf, Aglaja","first_name":"Aglaja"},{"orcid":"0000-0002-1009-9652","last_name":"Juanes Garcia","id":"40F05888-F248-11E8-B48F-1D18A9856A87","full_name":"Juanes Garcia, Alba","first_name":"Alba"},{"first_name":"Krisztina","full_name":"Ötvös, Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","last_name":"Ötvös","orcid":"0000-0002-5503-4983"},{"full_name":"Petrášek, J","first_name":"J","last_name":"Petrášek"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739","first_name":"Eva","full_name":"Benková, Eva"}],"file_date_updated":"2020-12-02T09:13:23Z","isi":1,"has_accepted_license":"1","status":"public","day":"01","publication_identifier":{"eissn":["1460-2075"],"issn":["0261-4189"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"MiSi"},{"_id":"EvBe"}],"publication_status":"published","external_id":{"isi":["000548311800001"],"pmid":["32667089"]}},{"file_date_updated":"2020-12-02T09:26:46Z","department":[{"_id":"SiHi"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","external_id":{"isi":["000579698700006"],"pmid":["32707083"]},"has_accepted_license":"1","isi":1,"status":"public","day":"23","publication_identifier":{"issn":["0896-6273"]},"volume":107,"pmid":1,"scopus_import":"1","year":"2020","publication":"Neuron","intvolume":" 107","doi":"10.1016/j.neuron.2020.06.031","acknowledgement":"We thank A. Heger (IST Austria Preclinical Facility), A. Sommer and C. Czepe (VBCF GmbH, NGS Unit), and A. Seitz and P. Moll (Lexogen GmbH) for technical support; G. Arque, S. Resch, C. Igler, C. Dotter, C. Yahya, Q. Hudson, and D. Andergassen for initial experiments and/or assistance; D. Barlow, O. Bell, and all members of the Hippenmeyer lab for discussion; and N. Barton, B. Vicoso, M. Sixt, and L. Luo for comments on earlier versions of the manuscript. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facilities (BIF), Life Science Facilities (LSF), and Preclinical Facilities (PCF). A.H.H. is a recipient of a DOC fellowship (24812) of the Austrian Academy of Sciences. N.A. received support from the FWF Firnberg-Programm (T 1031). R.B. received support from the FWF Meitner-Programm (M 2416). This work was also supported by IST Austria institutional funds; a NÖ Forschung und Bildung n[f+b] life science call grant (C13-002) to S.H.; a program grant from the Human Frontiers Science Program (RGP0053/2014) to S.H.; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 618444 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 725780 LinPro) to S.H.","ddc":["570"],"issue":"6","file":[{"file_name":"2020_Neuron_Laukoter.pdf","access_level":"open_access","success":1,"file_id":"8828","content_type":"application/pdf","checksum":"7becdc16a6317304304631087ae7dd7f","date_updated":"2020-12-02T09:26:46Z","relation":"main_file","file_size":8911830,"date_created":"2020-12-02T09:26:46Z","creator":"dernst"}],"title":"Cell-type specificity of genomic imprinting in cerebral cortex","author":[{"orcid":"0000-0002-7903-3010","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","last_name":"Laukoter","full_name":"Laukoter, Susanne","first_name":"Susanne"},{"first_name":"Florian","full_name":"Pauler, Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048"},{"first_name":"Robert J","full_name":"Beattie, Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","last_name":"Beattie","orcid":"0000-0002-8483-8753"},{"first_name":"Nicole","full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","orcid":"0000-0002-3183-8207"},{"last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H","first_name":"Andi H"},{"last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen","first_name":"Carmen"},{"last_name":"Penz","first_name":"Thomas","full_name":"Penz, Thomas"},{"orcid":"0000-0001-6091-3088","last_name":"Bock","full_name":"Bock, Christoph","first_name":"Christoph"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","first_name":"Simon"}],"date_created":"2020-07-23T16:03:12Z","ec_funded":1,"project":[{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812","name":"Molecular mechanisms of radial neuronal migration"},{"call_identifier":"FWF","name":"Role of Eed in neural stem cell lineage progression","grant_number":"T01031","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"_id":"264E56E2-B435-11E9-9278-68D0E5697425","grant_number":"M02416","name":"Molecular Mechanisms Regulating Gliogenesis in the Neocortex","call_identifier":"FWF"},{"grant_number":"LS13-002","_id":"25D92700-B435-11E9-9278-68D0E5697425","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain"},{"grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level"},{"name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"article_type":"original","date_published":"2020-09-23T00:00:00Z","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"date_updated":"2025-06-12T07:19:46Z","language":[{"iso":"eng"}],"oa_version":"Published Version","corr_author":"1","publisher":"Elsevier","quality_controlled":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"related_material":{"link":[{"description":"News on IST Website","relation":"press_release","url":"https://ist.ac.at/en/news/cells-react-differently-to-genomic-imprinting/"}]},"citation":{"mla":"Laukoter, Susanne, et al. “Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex.” Neuron, vol. 107, no. 6, Elsevier, 2020, p. 1160–1179.e9, doi:10.1016/j.neuron.2020.06.031.","ieee":"S. Laukoter et al., “Cell-type specificity of genomic imprinting in cerebral cortex,” Neuron, vol. 107, no. 6. Elsevier, p. 1160–1179.e9, 2020.","ista":"Laukoter S, Pauler F, Beattie RJ, Amberg N, Hansen AH, Streicher C, Penz T, Bock C, Hippenmeyer S. 2020. Cell-type specificity of genomic imprinting in cerebral cortex. Neuron. 107(6), 1160–1179.e9.","chicago":"Laukoter, Susanne, Florian Pauler, Robert J Beattie, Nicole Amberg, Andi H Hansen, Carmen Streicher, Thomas Penz, Christoph Bock, and Simon Hippenmeyer. “Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.06.031.","ama":"Laukoter S, Pauler F, Beattie RJ, et al. Cell-type specificity of genomic imprinting in cerebral cortex. Neuron. 2020;107(6):1160-1179.e9. doi:10.1016/j.neuron.2020.06.031","short":"S. Laukoter, F. Pauler, R.J. Beattie, N. Amberg, A.H. Hansen, C. Streicher, T. Penz, C. Bock, S. Hippenmeyer, Neuron 107 (2020) 1160–1179.e9.","apa":"Laukoter, S., Pauler, F., Beattie, R. J., Amberg, N., Hansen, A. H., Streicher, C., … Hippenmeyer, S. (2020). Cell-type specificity of genomic imprinting in cerebral cortex. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.06.031"},"month":"09","type":"journal_article","page":"1160-1179.e9","oa":1,"abstract":[{"text":"In mammalian genomes, a subset of genes is regulated by genomic imprinting, resulting in silencing of one parental allele. Imprinting is essential for cerebral cortex development, but prevalence and functional impact in individual cells is unclear. Here, we determined allelic expression in cortical cell types and established a quantitative platform to interrogate imprinting in single cells. We created cells with uniparental chromosome disomy (UPD) containing two copies of either the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold overexpressed or not expressed. By genetic labeling of UPD, we determined cellular phenotypes and transcriptional responses to deregulated imprinted gene expression at unprecedented single-cell resolution. We discovered an unexpected degree of cell-type specificity and a novel function of imprinting in the regulation of cortical astrocyte survival. More generally, our results suggest functional relevance of imprinted gene expression in glial astrocyte lineage and thus for generating cortical cell-type diversity.","lang":"eng"}],"_id":"8162"},{"file":[{"file_name":"57-2-05_4214-1454Vegter-Wintraecken_OpenAccess_CC-BY-NC.pdf","date_updated":"2020-07-24T07:09:06Z","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"8164","file_size":1476072,"creator":"mwintrae","date_created":"2020-07-24T07:09:06Z"}],"issue":"2","ec_funded":1,"date_created":"2020-07-24T07:09:18Z","author":[{"last_name":"Vegter","first_name":"Gert","full_name":"Vegter, Gert"},{"id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken","orcid":"0000-0002-7472-2220","first_name":"Mathijs","full_name":"Wintraecken, Mathijs"}],"title":"Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes","article_type":"original","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","call_identifier":"FWF","name":"Mathematics, Computer Science"}],"date_published":"2020-07-24T00:00:00Z","volume":57,"year":"2020","publication":"Studia Scientiarum Mathematicarum Hungarica","scopus_import":"1","intvolume":" 57","ddc":["510"],"acknowledgement":"The authors are greatly indebted to Dror Atariah, Günther Rote and John Sullivan for discussion and suggestions. The authors also thank Jean-Daniel Boissonnat, Ramsay Dyer, David de Laat and Rien van de Weijgaert for discussion. This work has been supported in part by the European Union’s Seventh Framework Programme for Research of the\r\nEuropean Commission, under FET-Open grant number 255827 (CGL Computational Geometry Learning) and ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions), the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement number 754411,and the Austrian Science Fund (FWF): Z00342 N31.","doi":"10.1556/012.2020.57.2.1454","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"article_processing_charge":"No","external_id":{"isi":["000570978400005"]},"publication_status":"published","status":"public","has_accepted_license":"1","isi":1,"day":"24","publication_identifier":{"issn":["0081-6906"],"eissn":["1588-2896"]},"file_date_updated":"2020-07-24T07:09:06Z","citation":{"short":"G. Vegter, M. Wintraecken, Studia Scientiarum Mathematicarum Hungarica 57 (2020) 193–199.","apa":"Vegter, G., & Wintraecken, M. (2020). Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. Akadémiai Kiadó. https://doi.org/10.1556/012.2020.57.2.1454","chicago":"Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” Studia Scientiarum Mathematicarum Hungarica. Akadémiai Kiadó, 2020. https://doi.org/10.1556/012.2020.57.2.1454.","ista":"Vegter G, Wintraecken M. 2020. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 57(2), 193–199.","ama":"Vegter G, Wintraecken M. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 2020;57(2):193-199. doi:10.1556/012.2020.57.2.1454","mla":"Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” Studia Scientiarum Mathematicarum Hungarica, vol. 57, no. 2, Akadémiai Kiadó, 2020, pp. 193–99, doi:10.1556/012.2020.57.2.1454.","ieee":"G. Vegter and M. Wintraecken, “Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes,” Studia Scientiarum Mathematicarum Hungarica, vol. 57, no. 2. Akadémiai Kiadó, pp. 193–199, 2020."},"month":"07","type":"journal_article","oa":1,"page":"193-199","abstract":[{"text":"Fejes Tóth [3] studied approximations of smooth surfaces in three-space by piecewise flat triangular meshes with a given number of vertices on the surface that are optimal with respect to Hausdorff distance. He proves that this Hausdorff distance decreases inversely proportional with the number of vertices of the approximating mesh if the surface is convex. He also claims that this Hausdorff distance is inversely proportional to the square of the number of vertices for a specific non-convex surface, namely a one-sheeted hyperboloid of revolution bounded by two congruent circles. We refute this claim, and show that the asymptotic behavior of the Hausdorff distance is linear, that is the same as for convex surfaces.","lang":"eng"}],"_id":"8163","license":"https://creativecommons.org/licenses/by-nc/4.0/","date_updated":"2025-04-15T07:16:57Z","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"corr_author":"1","oa_version":"Published Version","quality_controlled":"1","publisher":"Akadémiai Kiadó"},{"file_date_updated":"2020-07-31T16:57:12Z","publication_status":"published","external_id":{"arxiv":["2004.04180"]},"article_processing_charge":"No","department":[{"_id":"ChLa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eisbn":["9781728171685"],"eissn":["2575-7075"]},"day":"01","has_accepted_license":"1","status":"public","main_file_link":[{"open_access":"1","url":"https://openaccess.thecvf.com/content_CVPR_2020/papers/Henderson_Leveraging_2D_Data_to_Learn_Textured_3D_Mesh_Generation_CVPR_2020_paper.pdf"}],"scopus_import":"1","year":"2020","publication":"Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition","doi":"10.1109/CVPR42600.2020.00752","ddc":["004"],"date_created":"2020-07-31T16:53:49Z","title":"Leveraging 2D data to learn textured 3D mesh generation","author":[{"full_name":"Henderson, Paul M","first_name":"Paul M","orcid":"0000-0002-5198-7445","id":"13C09E74-18D9-11E9-8878-32CFE5697425","last_name":"Henderson"},{"last_name":"Tsiminaki","first_name":"Vagia","full_name":"Tsiminaki, Vagia"},{"full_name":"Lampert, Christoph","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert"}],"file":[{"file_size":10262773,"creator":"phenders","date_created":"2020-07-31T16:57:12Z","file_name":"paper.pdf","date_updated":"2020-07-31T16:57:12Z","relation":"main_file","content_type":"application/pdf","file_id":"8187","success":1,"access_level":"open_access"}],"date_published":"2020-07-01T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2023-10-17T07:37:11Z","publisher":"IEEE","quality_controlled":"1","oa_version":"Submitted Version","arxiv":1,"page":"7498-7507","conference":{"start_date":"2020-06-14","name":"CVPR: Conference on Computer Vision and Pattern Recognition","end_date":"2020-06-19","location":"Virtual"},"oa":1,"month":"07","type":"conference","citation":{"apa":"Henderson, P. M., Tsiminaki, V., & Lampert, C. (2020). Leveraging 2D data to learn textured 3D mesh generation. In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 7498–7507). Virtual: IEEE. https://doi.org/10.1109/CVPR42600.2020.00752","short":"P.M. Henderson, V. Tsiminaki, C. Lampert, in:, Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2020, pp. 7498–7507.","ama":"Henderson PM, Tsiminaki V, Lampert C. Leveraging 2D data to learn textured 3D mesh generation. In: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2020:7498-7507. doi:10.1109/CVPR42600.2020.00752","chicago":"Henderson, Paul M, Vagia Tsiminaki, and Christoph Lampert. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 7498–7507. IEEE, 2020. https://doi.org/10.1109/CVPR42600.2020.00752.","ista":"Henderson PM, Tsiminaki V, Lampert C. 2020. Leveraging 2D data to learn textured 3D mesh generation. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 7498–7507.","mla":"Henderson, Paul M., et al. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2020, pp. 7498–507, doi:10.1109/CVPR42600.2020.00752.","ieee":"P. M. Henderson, V. Tsiminaki, and C. Lampert, “Leveraging 2D data to learn textured 3D mesh generation,” in Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, Virtual, 2020, pp. 7498–7507."},"_id":"8186","abstract":[{"text":"Numerous methods have been proposed for probabilistic generative modelling of\r\n3D objects. However, none of these is able to produce textured objects, which\r\nrenders them of limited use for practical tasks. In this work, we present the\r\nfirst generative model of textured 3D meshes. Training such a model would\r\ntraditionally require a large dataset of textured meshes, but unfortunately,\r\nexisting datasets of meshes lack detailed textures. We instead propose a new\r\ntraining methodology that allows learning from collections of 2D images without\r\nany 3D information. To do so, we train our model to explain a distribution of\r\nimages by modelling each image as a 3D foreground object placed in front of a\r\n2D background. Thus, it learns to generate meshes that when rendered, produce\r\nimages similar to those in its training set.\r\n A well-known problem when generating meshes with deep networks is the\r\nemergence of self-intersections, which are problematic for many use-cases. As a\r\nsecond contribution we therefore introduce a new generation process for 3D\r\nmeshes that guarantees no self-intersections arise, based on the physical\r\nintuition that faces should push one another out of the way as they move.\r\n We conduct extensive experiments on our approach, reporting quantitative and\r\nqualitative results on both synthetic data and natural images. These show our\r\nmethod successfully learns to generate plausible and diverse textured 3D\r\nsamples for five challenging object classes.","lang":"eng"}]},{"article_processing_charge":"No","department":[{"_id":"ChLa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","external_id":{"arxiv":["2007.06705"]},"alternative_title":["Advances in Neural Information Processing Systems"],"status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.06705"}],"day":"07","publication_identifier":{"isbn":["9781713829546"]},"volume":33,"publication":"34th Conference on Neural Information Processing Systems","year":"2020","intvolume":" 33","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources\r\nprovided by Scientific Computing (SciComp). PH is employed part-time by Blackford Analysis, but\r\nthey did not support this project in any way.","date_created":"2020-07-31T16:59:19Z","author":[{"full_name":"Henderson, Paul M","first_name":"Paul M","orcid":"0000-0002-5198-7445","last_name":"Henderson","id":"13C09E74-18D9-11E9-8878-32CFE5697425"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","orcid":"0000-0001-8622-7887","first_name":"Christoph","full_name":"Lampert, Christoph"}],"title":"Unsupervised object-centric video generation and decomposition in 3D","date_published":"2020-07-07T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2025-05-14T11:26:57Z","oa_version":"Preprint","corr_author":"1","publisher":"Neural Information Processing Systems Foundation","quality_controlled":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"arxiv":1,"month":"07","type":"conference","citation":{"short":"P.M. Henderson, C. Lampert, in:, 34th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2020, pp. 3106–3117.","apa":"Henderson, P. M., & Lampert, C. (2020). Unsupervised object-centric video generation and decomposition in 3D. In 34th Conference on Neural Information Processing Systems (Vol. 33, pp. 3106–3117). Vancouver, Canada: Neural Information Processing Systems Foundation.","chicago":"Henderson, Paul M, and Christoph Lampert. “Unsupervised Object-Centric Video Generation and Decomposition in 3D.” In 34th Conference on Neural Information Processing Systems, 33:3106–3117. Neural Information Processing Systems Foundation, 2020.","ista":"Henderson PM, Lampert C. 2020. Unsupervised object-centric video generation and decomposition in 3D. 34th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 33, 3106–3117.","ama":"Henderson PM, Lampert C. Unsupervised object-centric video generation and decomposition in 3D. In: 34th Conference on Neural Information Processing Systems. Vol 33. Neural Information Processing Systems Foundation; 2020:3106–3117.","mla":"Henderson, Paul M., and Christoph Lampert. “Unsupervised Object-Centric Video Generation and Decomposition in 3D.” 34th Conference on Neural Information Processing Systems, vol. 33, Neural Information Processing Systems Foundation, 2020, pp. 3106–3117.","ieee":"P. M. Henderson and C. Lampert, “Unsupervised object-centric video generation and decomposition in 3D,” in 34th Conference on Neural Information Processing Systems, Vancouver, Canada, 2020, vol. 33, pp. 3106–3117."},"page":"3106–3117","conference":{"end_date":"2020-12-12","name":"NeurIPS: Neural Information Processing Systems","start_date":"2020-12-06","location":"Vancouver, Canada"},"oa":1,"abstract":[{"lang":"eng","text":"A natural approach to generative modeling of videos is to represent them as a composition of moving objects. Recent works model a set of 2D sprites over a slowly-varying background, but without considering the underlying 3D scene that\r\ngives rise to them. We instead propose to model a video as the view seen while moving through a scene with multiple 3D objects and a 3D background. Our model is trained from monocular videos without any supervision, yet learns to\r\ngenerate coherent 3D scenes containing several moving objects. We conduct detailed experiments on two datasets, going beyond the visual complexity supported by state-of-the-art generative approaches. We evaluate our method on\r\ndepth-prediction and 3D object detection---tasks which cannot be addressed by those earlier works---and show it out-performs them even on 2D instance segmentation and tracking."}],"_id":"8188"},{"scopus_import":"1","publication":"Nano Energy","year":"2020","volume":77,"doi":"10.1016/j.nanoen.2020.105116","acknowledgement":"This work was supported by the European Regional Development Funds and by the Spanish Ministerio de Economía y Competitividad through the project SEHTOP, ENE2016- 77798-C4-3-R, and ENE2017-85087-C3. X. Y. thanks the China Scholarship Council for the scholarship support. J. Liu acknowledges support from the Jiangsu University Foundation (4111510011). J. Li obtained International Postdoctoral Exchange Fellowship Program (Talent-Introduction program) in 2019 and is grateful for the project (2019M663468) funded by the China Postdoctoral Science Foundation. Authors acknowledge funding from Generalitat de Catalunya 2017 SGR 327 and 2017 SGR 1246, and from IST Austria. ICN2 acknowledges the support from the Severo Ochoa Programme (MINECO, grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. J. Llorca is a Serra Húnter Fellow and is grateful to MICINN/FEDER RTI2018-093996-B-C31, GC 2017 SGR 128 and to ICREA Academia program.","intvolume":" 77","article_number":"105116","date_created":"2020-08-02T22:00:57Z","title":"Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation","author":[{"full_name":"Yu, Xiaoting","first_name":"Xiaoting","last_name":"Yu"},{"full_name":"Liu, Junfeng","first_name":"Junfeng","last_name":"Liu"},{"full_name":"Li, Junshan","first_name":"Junshan","last_name":"Li"},{"full_name":"Luo, Zhishan","first_name":"Zhishan","last_name":"Luo"},{"last_name":"Zuo","full_name":"Zuo, Yong","first_name":"Yong"},{"last_name":"Xing","first_name":"Congcong","full_name":"Xing, Congcong"},{"first_name":"Jordi","full_name":"Llorca, Jordi","last_name":"Llorca"},{"last_name":"Nasiou","first_name":"Déspina","full_name":"Nasiou, Déspina"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"full_name":"Pan, Kai","first_name":"Kai","last_name":"Pan"},{"last_name":"Kleinhanns","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias","full_name":"Kleinhanns, Tobias"},{"first_name":"Ying","full_name":"Xie, Ying","last_name":"Xie"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"}],"issue":"11","date_published":"2020-11-01T00:00:00Z","article_type":"original","OA_type":"green","publication_status":"published","external_id":{"isi":["000581738300030"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","department":[{"_id":"MaIb"}],"publication_identifier":{"issn":["2211-2855"]},"day":"01","isi":1,"status":"public","main_file_link":[{"open_access":"1","url":"http://hdl.handle.net/2117/335346"}],"OA_place":"repository","oa":1,"citation":{"short":"X. Yu, J. Liu, J. Li, Z. Luo, Y. Zuo, C. Xing, J. Llorca, D. Nasiou, J. Arbiol, K. Pan, T. Kleinhanns, Y. Xie, A. Cabot, Nano Energy 77 (2020).","apa":"Yu, X., Liu, J., Li, J., Luo, Z., Zuo, Y., Xing, C., … Cabot, A. (2020). Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. Nano Energy. Elsevier. https://doi.org/10.1016/j.nanoen.2020.105116","ama":"Yu X, Liu J, Li J, et al. Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. Nano Energy. 2020;77(11). doi:10.1016/j.nanoen.2020.105116","ista":"Yu X, Liu J, Li J, Luo Z, Zuo Y, Xing C, Llorca J, Nasiou D, Arbiol J, Pan K, Kleinhanns T, Xie Y, Cabot A. 2020. Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. Nano Energy. 77(11), 105116.","chicago":"Yu, Xiaoting, Junfeng Liu, Junshan Li, Zhishan Luo, Yong Zuo, Congcong Xing, Jordi Llorca, et al. “Phosphorous Incorporation in Pd2Sn Alloys for Electrocatalytic Ethanol Oxidation.” Nano Energy. Elsevier, 2020. https://doi.org/10.1016/j.nanoen.2020.105116.","ieee":"X. Yu et al., “Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation,” Nano Energy, vol. 77, no. 11. Elsevier, 2020.","mla":"Yu, Xiaoting, et al. “Phosphorous Incorporation in Pd2Sn Alloys for Electrocatalytic Ethanol Oxidation.” Nano Energy, vol. 77, no. 11, 105116, Elsevier, 2020, doi:10.1016/j.nanoen.2020.105116."},"type":"journal_article","month":"11","_id":"8189","abstract":[{"text":"Direct ethanol fuel cells (DEFCs) show a huge potential to power future electric vehicles and portable electronics, but their deployment is currently limited by the unavailability of proper electrocatalysis for the ethanol oxidation reaction (EOR). In this work, we engineer a new electrocatalyst by incorporating phosphorous into a palladium-tin alloy and demonstrate a significant performance improvement toward EOR. We first detail a synthetic method to produce Pd2Sn:P nanocrystals that incorporate 35% of phosphorus. These nanoparticles are supported on carbon black and tested for EOR. Pd2Sn:P/C catalysts exhibit mass current densities up to 5.03 A mgPd−1, well above those of Pd2Sn/C, PdP2/C and Pd/C reference catalysts. Furthermore, a twofold lower Tafel slope and a much longer durability are revealed for the Pd2Sn:P/C catalyst compared with Pd/C. The performance improvement is rationalized with the aid of density functional theory (DFT) calculations considering different phosphorous chemical environments. Depending on its oxidation state, surface phosphorus introduces sites with low energy OH− adsorption and/or strongly influences the electronic structure of palladium and tin to facilitate the oxidation of the acetyl to acetic acid, which is considered the EOR rate limiting step. DFT calculations also points out that the durability improvement of Pd2Sn:P/C catalyst is associated to the promotion of OH adsorption that accelerates the oxidation of intermediate poisoning COads, reactivating the catalyst surface.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2025-04-24T11:53:45Z","publisher":"Elsevier","quality_controlled":"1","oa_version":"Submitted Version"},{"page":"37-49","title":"Memory tagging: Minimalist synchronization for scalable concurrent data structures","date_created":"2020-08-02T22:00:58Z","conference":{"end_date":"2020-07-17","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","start_date":"2020-07-15","location":"Virtual Event, United States"},"author":[{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian"},{"first_name":"Trevor A","full_name":"Brown, Trevor A","last_name":"Brown","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Singhal, Nandini","first_name":"Nandini","last_name":"Singhal"}],"month":"07","citation":{"apa":"Alistarh, D.-A., Brown, T. A., & Singhal, N. (2020). Memory tagging: Minimalist synchronization for scalable concurrent data structures. In Annual ACM Symposium on Parallelism in Algorithms and Architectures (pp. 37–49). Virtual Event, United States: Association for Computing Machinery. https://doi.org/10.1145/3350755.3400213","short":"D.-A. Alistarh, T.A. Brown, N. Singhal, in:, Annual ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2020, pp. 37–49.","ama":"Alistarh D-A, Brown TA, Singhal N. Memory tagging: Minimalist synchronization for scalable concurrent data structures. In: Annual ACM Symposium on Parallelism in Algorithms and Architectures. Association for Computing Machinery; 2020:37-49. doi:10.1145/3350755.3400213","ista":"Alistarh D-A, Brown TA, Singhal N. 2020. Memory tagging: Minimalist synchronization for scalable concurrent data structures. Annual ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 37–49.","chicago":"Alistarh, Dan-Adrian, Trevor A Brown, and Nandini Singhal. “Memory Tagging: Minimalist Synchronization for Scalable Concurrent Data Structures.” In Annual ACM Symposium on Parallelism in Algorithms and Architectures, 37–49. Association for Computing Machinery, 2020. https://doi.org/10.1145/3350755.3400213.","mla":"Alistarh, Dan-Adrian, et al. “Memory Tagging: Minimalist Synchronization for Scalable Concurrent Data Structures.” Annual ACM Symposium on Parallelism in Algorithms and Architectures, no. 7, Association for Computing Machinery, 2020, pp. 37–49, doi:10.1145/3350755.3400213.","ieee":"D.-A. Alistarh, T. A. Brown, and N. Singhal, “Memory tagging: Minimalist synchronization for scalable concurrent data structures,” in Annual ACM Symposium on Parallelism in Algorithms and Architectures, Virtual Event, United States, 2020, no. 7, pp. 37–49."},"type":"conference","issue":"7","date_published":"2020-07-06T00:00:00Z","_id":"8191","abstract":[{"lang":"eng","text":"There has been a significant amount of research on hardware and software support for efficient concurrent data structures; yet, the question of how to build correct, simple, and scalable data structures has not yet been definitively settled. In this paper, we revisit this question from a minimalist perspective, and ask: what is the smallest amount of synchronization required for correct and efficient concurrent search data structures, and how could this minimal synchronization support be provided in hardware?\r\n\r\nTo address these questions, we introduce memory tagging, a simple hardware mechanism which enables the programmer to \"tag\" a dynamic set of memory locations, at cache-line granularity, and later validate whether the memory has been concurrently modified, with the possibility of updating one of the underlying locations atomically if validation succeeds. We provide several examples showing that this mechanism can enable fast and arguably simple concurrent data structure designs, such as lists, binary search trees, balanced search trees, range queries, and Software Transactional Memory (STM) implementations. We provide an implementation of memory tags in the Graphite multi-core simulator, showing that the mechanism can be implemented entirely at the level of L1 cache, and that it can enable non-trivial speedups versus existing implementations of the above data structures."}],"year":"2020","publication":"Annual ACM Symposium on Parallelism in Algorithms and Architectures","scopus_import":"1","doi":"10.1145/3350755.3400213","external_id":{"isi":["000744436200004"]},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","department":[{"_id":"DaAl"}],"publication_identifier":{"isbn":["9781450369350"]},"day":"06","status":"public","isi":1,"language":[{"iso":"eng"}],"date_updated":"2024-02-28T12:56:32Z","quality_controlled":"1","publisher":"Association for Computing Machinery","oa_version":"None"},{"date_published":"2020-07-29T00:00:00Z","article_type":"original","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"ec_funded":1,"title":"Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps","author":[{"orcid":"0000-0001-6814-7541","last_name":"Gulden","id":"1083E038-9F73-11E9-A4B5-532AE6697425","full_name":"Gulden, Tobias","first_name":"Tobias"},{"last_name":"Berg","full_name":"Berg, Erez","first_name":"Erez"},{"last_name":"Rudner","first_name":"Mark Spencer","full_name":"Rudner, Mark Spencer"},{"last_name":"Lindner","full_name":"Lindner, Netanel","first_name":"Netanel"}],"article_number":"015","date_created":"2020-08-04T13:04:15Z","file":[{"date_created":"2020-08-06T08:56:06Z","creator":"dernst","file_size":531137,"content_type":"application/pdf","success":1,"file_id":"8202","access_level":"open_access","date_updated":"2020-08-06T08:56:06Z","relation":"main_file","file_name":"2020_SciPostPhys_Gulden.pdf"}],"ddc":["530"],"doi":"10.21468/scipostphys.9.1.015","acknowledgement":"N.L., T.G. and E.B. acknowledge support from the European Research Council (ERC) under\r\nthe European Union Horizon 2020 Research and Innovation Programme (Grant Agreement\r\nNo. 639172). T.G. was in part supported by an Aly Kaufman Fellowship at the Technion. T.G.\r\nacknowledges funding from the Institute of Science and Technology (IST) Austria, and from\r\nthe European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411. N.L. acknowledges support from the People Programme (Marie Curie Actions) of the European Unions Seventh Framework 546 Programme (FP7/20072013), under REA Grant Agreement No. 631696, and by the Israeli Center\r\nof Research Excellence (I-CORE) Circle of Light funded by the Israel Science Foundation (Grant\r\nNo. 1802/12). M.R. gratefully acknowledges the support of the European Research Council\r\n(ERC) under the European Union Horizon 2020 Research and Innovation Programme (Grant\r\nAgreement No. 678862). M.R. acknowledges the support of the Villum Foundation. M.R. and\r\nE.B. acknowledge support from CRC 183 of the Deutsche Forschungsgemeinschaft","intvolume":" 9","year":"2020","publication":"SciPost Physics","scopus_import":"1","volume":9,"publication_identifier":{"issn":["2542-4653"]},"day":"29","isi":1,"has_accepted_license":"1","status":"public","external_id":{"isi":["000557362300008"]},"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","department":[{"_id":"MaSe"}],"file_date_updated":"2020-08-06T08:56:06Z","_id":"8199","abstract":[{"lang":"eng","text":"We investigate a mechanism to transiently stabilize topological phenomena in long-lived quasi-steady states of isolated quantum many-body systems driven at low frequencies. We obtain an analytical bound for the lifetime of the quasi-steady states which is exponentially large in the inverse driving frequency. Within this lifetime, the quasi-steady state is characterized by maximum entropy subject to the constraint of fixed number of particles in the system's Floquet-Bloch bands. In such a state, all the non-universal properties of these bands are washed out, hence only the topological properties persist."}],"oa":1,"type":"journal_article","citation":{"short":"T. Gulden, E. Berg, M.S. Rudner, N. Lindner, SciPost Physics 9 (2020).","apa":"Gulden, T., Berg, E., Rudner, M. S., & Lindner, N. (2020). Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.9.1.015","chicago":"Gulden, Tobias, Erez Berg, Mark Spencer Rudner, and Netanel Lindner. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” SciPost Physics. SciPost Foundation, 2020. https://doi.org/10.21468/scipostphys.9.1.015.","ista":"Gulden T, Berg E, Rudner MS, Lindner N. 2020. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. 9, 015.","ama":"Gulden T, Berg E, Rudner MS, Lindner N. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. 2020;9. doi:10.21468/scipostphys.9.1.015","mla":"Gulden, Tobias, et al. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” SciPost Physics, vol. 9, 015, SciPost Foundation, 2020, doi:10.21468/scipostphys.9.1.015.","ieee":"T. Gulden, E. Berg, M. S. Rudner, and N. Lindner, “Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps,” SciPost Physics, vol. 9. SciPost Foundation, 2020."},"month":"07","quality_controlled":"1","publisher":"SciPost Foundation","corr_author":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"date_updated":"2025-04-14T07:44:05Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"}}]