[{"file_date_updated":"2022-08-16T08:52:46Z","volume":22,"ddc":["510"],"date_created":"2022-08-16T08:39:43Z","type":"journal_article","month":"06","author":[{"orcid":"0000-0002-9573-2962","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","last_name":"Agresti","first_name":"Antonio","full_name":"Agresti, Antonio"},{"last_name":"Veraar","first_name":"Mark","full_name":"Veraar, Mark"}],"language":[{"iso":"eng"}],"publication":"Journal of Evolution Equations","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","abstract":[{"lang":"eng","text":"This paper is a continuation of Part I of this project, where we developed a new local well-posedness theory for nonlinear stochastic PDEs with Gaussian noise. In the current Part II we consider blow-up criteria and regularization phenomena. As in Part I we can allow nonlinearities with polynomial growth and rough initial values from critical spaces. In the first main result we obtain several new blow-up criteria for quasi- and semilinear stochastic evolution equations. In particular, for semilinear equations we obtain a Serrin type blow-up criterium, which extends a recent result of Prüss–Simonett–Wilke (J Differ Equ 264(3):2028–2074, 2018) to the stochastic setting. Blow-up criteria can be used to prove global well-posedness for SPDEs. As in Part I, maximal regularity techniques and weights in time play a central role in the proofs. Our second contribution is a new method to bootstrap Sobolev and Hölder regularity in time and space, which does not require smoothness of the initial data. The blow-up criteria are at the basis of these new methods. Moreover, in applications the bootstrap results can be combined with our blow-up criteria, to obtain efficient ways to prove global existence. This gives new results even in classical 𝐿2-settings, which we illustrate for a concrete SPDE. In future works in preparation we apply the results of the current paper to obtain global well-posedness results and regularity for several concrete SPDEs. These include stochastic Navier–Stokes equations, reaction– diffusion equations and the Allen–Cahn equation. Our setting allows to put these SPDEs into a more flexible framework, where less restrictions on the nonlinearities are needed, and we are able to treat rough initial values from critical spaces. Moreover, we will obtain higher-order regularity results."}],"acknowledgement":"The authors thank Emiel Lorist for helpful comments. The authors thank the anonymous referees for their helpful remarks to improve the presentation.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","_id":"11858","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","has_accepted_license":"1","title":"Nonlinear parabolic stochastic evolution equations in critical spaces part II","issue":"2","publication_identifier":{"issn":["1424-3199"],"eissn":["1424-3202"]},"day":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_number":"56","doi":"10.1007/s00028-022-00786-7","keyword":["Mathematics (miscellaneous)"],"isi":1,"year":"2022","oa":1,"external_id":{"isi":["000809108500001"]},"license":"https://creativecommons.org/licenses/by/4.0/","date_updated":"2023-08-03T12:53:51Z","intvolume":"        22","status":"public","publication_status":"published","citation":{"short":"A. Agresti, M. Veraar, Journal of Evolution Equations 22 (2022).","mla":"Agresti, Antonio, and Mark Veraar. “Nonlinear Parabolic Stochastic Evolution Equations in Critical Spaces Part II.” <i>Journal of Evolution Equations</i>, vol. 22, no. 2, 56, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s00028-022-00786-7\">10.1007/s00028-022-00786-7</a>.","ieee":"A. Agresti and M. Veraar, “Nonlinear parabolic stochastic evolution equations in critical spaces part II,” <i>Journal of Evolution Equations</i>, vol. 22, no. 2. Springer Nature, 2022.","ista":"Agresti A, Veraar M. 2022. Nonlinear parabolic stochastic evolution equations in critical spaces part II. Journal of Evolution Equations. 22(2), 56.","ama":"Agresti A, Veraar M. Nonlinear parabolic stochastic evolution equations in critical spaces part II. <i>Journal of Evolution Equations</i>. 2022;22(2). doi:<a href=\"https://doi.org/10.1007/s00028-022-00786-7\">10.1007/s00028-022-00786-7</a>","apa":"Agresti, A., &#38; Veraar, M. (2022). Nonlinear parabolic stochastic evolution equations in critical spaces part II. <i>Journal of Evolution Equations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00028-022-00786-7\">https://doi.org/10.1007/s00028-022-00786-7</a>","chicago":"Agresti, Antonio, and Mark Veraar. “Nonlinear Parabolic Stochastic Evolution Equations in Critical Spaces Part II.” <i>Journal of Evolution Equations</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00028-022-00786-7\">https://doi.org/10.1007/s00028-022-00786-7</a>."},"quality_controlled":"1","department":[{"_id":"JuFi"}],"file":[{"file_name":"2022_Journal of Evolution Equations_Agresti.pdf","file_size":1758371,"checksum":"59b99d1b48b6bd40983e7ce298524a21","access_level":"open_access","relation":"main_file","date_updated":"2022-08-16T08:52:46Z","creator":"kschuh","content_type":"application/pdf","file_id":"11862","date_created":"2022-08-16T08:52:46Z","success":1}],"oa_version":"Published Version","article_type":"original","date_published":"2022-06-01T00:00:00Z"},{"supervisor":[{"last_name":"Benková","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"}],"oa":1,"status":"public","date_updated":"2023-09-09T22:30:04Z","doi":"10.15479/at:ista:11879","keyword":["high ambient temperature","auxin","PINs","Zinc-Finger proteins","thermomorphogenesis","stress"],"day":"17","title":"Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature","has_accepted_license":"1","publication_identifier":{"isbn":["978-3-99078-022-0"],"issn":["2663-337X"]},"degree_awarded":"PhD","year":"2022","oa_version":"Published Version","file":[{"checksum":"a2c2fdc28002538840490bfa6a08b2cb","file_size":11113608,"relation":"main_file","access_level":"open_access","file_name":"ChristinaArtner_PhD_Thesis_2022.pdf","embargo":"2023-09-08","date_updated":"2023-09-09T22:30:03Z","creator":"cartner","date_created":"2022-08-17T12:08:49Z","content_type":"application/pdf","file_id":"11907"},{"date_updated":"2023-09-09T22:30:03Z","relation":"source_file","access_level":"closed","checksum":"66b461c074b815fbe63481b3f46a9f43","file_size":19097730,"embargo_to":"open_access","file_name":"ChristinaArtner_PhD_Thesis_2022.7z","date_created":"2022-08-17T12:08:59Z","file_id":"11908","content_type":"application/octet-stream","creator":"cartner"}],"department":[{"_id":"GradSch"},{"_id":"EvBe"}],"date_published":"2022-08-17T00:00:00Z","citation":{"chicago":"Artner, Christina. “Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11879\">https://doi.org/10.15479/at:ista:11879</a>.","ama":"Artner C. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11879\">10.15479/at:ista:11879</a>","apa":"Artner, C. (2022). <i>Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11879\">https://doi.org/10.15479/at:ista:11879</a>","ista":"Artner C. 2022. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. Institute of Science and Technology Austria.","ieee":"C. Artner, “Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature,” Institute of Science and Technology Austria, 2022.","mla":"Artner, Christina. <i>Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11879\">10.15479/at:ista:11879</a>.","short":"C. Artner, Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature, Institute of Science and Technology Austria, 2022."},"publication_status":"published","type":"dissertation","month":"08","language":[{"iso":"eng"}],"author":[{"id":"45DF286A-F248-11E8-B48F-1D18A9856A87","first_name":"Christina","full_name":"Artner, Christina","last_name":"Artner"}],"article_processing_charge":"No","file_date_updated":"2023-09-09T22:30:03Z","ddc":["580"],"date_created":"2022-08-17T07:58:53Z","page":"128","project":[{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"}],"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"SSU"}],"abstract":[{"text":"As the overall global mean surface temperature is increasing due to climate change, plant\r\nadaptation to those stressful conditions is of utmost importance for their survival. Plants are\r\nsessile organisms, thus to compensate for their lack of mobility, they evolved a variety of\r\nmechanisms enabling them to flexibly adjust their physiological, growth and developmental\r\nprocesses to fluctuating temperatures and to survive in harsh environments. While these unique\r\nadaptation abilities provide an important evolutionary advantage, overall modulation of plant\r\ngrowth and developmental program due to non-optimal temperature negatively affects biomass\r\nproduction, crop productivity or sensitivity to pathogens. Thus, understanding molecular\r\nprocesses underlying plant adaptation to increased temperature can provide important\r\nresources for breeding strategies to ensure sufficient agricultural food production.\r\nAn increase in ambient temperature by a few degrees leads to profound changes in organ growth\r\nincluding enhanced hypocotyl elongation, expansion of petioles, hyponastic growth of leaves and\r\ncotyledons, collectively named thermomorphogenesis (Casal & Balasubramanian, 2019). Auxin,\r\none of the best-studied growth hormones, plays an essential role in this process by direct\r\nactivation of transcriptional and non-transcriptional processes resulting in elongation growth\r\n(Majda & Robert, 2018).To modulate hypocotyl growth in response to high ambient temperature\r\n(hAT), auxin needs to be redistributed accordingly. PINs, auxin efflux transporters, are key\r\ncomponents of the polar auxin transport (PAT) machinery, which controls the amount and\r\ndirection of auxin translocated in the plant tissues and organs(Adamowski & Friml, 2015). Hence,\r\nPIN-mediated transport is tightly linked with thermo-morphogenesis, and interference with PAT\r\nthrough either chemical or genetic means dramatically affecting the adaptive responses to hAT.\r\nIntriguingly, despite the key role of PIN mediated transport in growth response to hAT, whether\r\nand how PINs at the level of expression adapt to fluctuation in temperature is scarcely\r\nunderstood.\r\nWith genetic, molecular and advanced bio-imaging approaches, we demonstrate the role of PIN\r\nauxin transporters in the regulation of hypocotyl growth in response to hAT. We show that via\r\nadjustment of PIN3, PIN4 and PIN7 expression in cotyledons and hypocotyls, auxin distribution is modulated thereby determining elongation pattern of epidermal cells at hAT. Furthermore, we\r\nidentified three Zinc-Finger (ZF) transcription factors as novel molecular components of the\r\nthermo-regulatory network, which through negative regulation of PIN transcription adjust the\r\ntransport of auxin at hAT. Our results suggest that the ZF-PIN module might be a part of the\r\nnegative feedback loop attenuating the activity of the thermo-sensing pathway to restrain\r\nexaggerated growth and developmental responses to hAT.","lang":"eng"}],"acknowledgement":"I would like to acknowledge ISTA and all the people from the Scientific Service Units and at ISTA, in particular Dorota Jaworska for excellent technical and scientific support as well as ÖAW for funding my research for over 3 years (DOC ÖAW Fellowship PR1022OEAW02).","alternative_title":["ISTA Thesis"],"_id":"11879"},{"scopus_import":"1","publication":"Advances in Operator Theory","article_processing_charge":"Yes (via OA deal)","type":"journal_article","month":"07","author":[{"full_name":"Wirth, Melchior","first_name":"Melchior","last_name":"Wirth","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","orcid":"0000-0002-0519-4241"}],"language":[{"iso":"eng"}],"date_created":"2022-08-18T07:22:24Z","file_date_updated":"2022-08-18T08:02:34Z","ddc":["510"],"volume":7,"publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The author was supported by the German Academic Scholarship Foundation (Studienstiftung des deutschen Volkes) and by the German Research Foundation (DFG) via RTG 1523/2. The author would like to thank Daniel Lenz for his support and encouragement during the author’s ongoing graduate studies and him as well as Marcel Schmidt for fruitful discussions on domination of quadratic forms. He wants to thank Batu Güneysu and Peter Stollmann for valuable comments on a preliminary version of this article. He would also like to thank the organizers of the conference Analysis and Geometry on Graphs and Manifolds in Potsdam, where the initial motivation of this article was conceived, and the organizers of the intense activity period Metric Measure Spaces and Ricci Curvature at MPIM in Bonn, where this work was finished.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","_id":"11916","abstract":[{"lang":"eng","text":"A domain is called Kac regular for a quadratic form on L2 if every functions vanishing almost everywhere outside the domain can be approximated in form norm by functions with compact support in the domain. It is shown that this notion is stable under domination of quadratic forms. As applications measure perturbations of quasi-regular Dirichlet forms, Cheeger energies on metric measure spaces and Schrödinger operators on manifolds are studied. Along the way a characterization of the Sobolev space with Dirichlet boundary conditions on domains in infinitesimally Riemannian metric measure spaces is obtained."}],"intvolume":"         7","status":"public","date_updated":"2023-02-21T10:08:07Z","oa":1,"year":"2022","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_number":"38","day":"01","doi":"10.1007/s43036-022-00199-w","keyword":["Algebra and Number Theory","Analysis"],"title":"Kac regularity and domination of quadratic forms","has_accepted_license":"1","issue":"3","publication_identifier":{"eissn":["2538-225X"]},"article_type":"original","date_published":"2022-07-01T00:00:00Z","oa_version":"Published Version","file":[{"date_updated":"2022-08-18T08:02:34Z","file_name":"2022_AdvancesOperatorTheory_Wirth.pdf","relation":"main_file","access_level":"open_access","checksum":"913474844a1b38264fb710746d5e2e98","file_size":389060,"file_id":"11921","content_type":"application/pdf","success":1,"date_created":"2022-08-18T08:02:34Z","creator":"dernst"}],"department":[{"_id":"JaMa"}],"quality_controlled":"1","citation":{"ista":"Wirth M. 2022. Kac regularity and domination of quadratic forms. Advances in Operator Theory. 7(3), 38.","mla":"Wirth, Melchior. “Kac Regularity and Domination of Quadratic Forms.” <i>Advances in Operator Theory</i>, vol. 7, no. 3, 38, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s43036-022-00199-w\">10.1007/s43036-022-00199-w</a>.","short":"M. Wirth, Advances in Operator Theory 7 (2022).","ieee":"M. Wirth, “Kac regularity and domination of quadratic forms,” <i>Advances in Operator Theory</i>, vol. 7, no. 3. Springer Nature, 2022.","chicago":"Wirth, Melchior. “Kac Regularity and Domination of Quadratic Forms.” <i>Advances in Operator Theory</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s43036-022-00199-w\">https://doi.org/10.1007/s43036-022-00199-w</a>.","apa":"Wirth, M. (2022). Kac regularity and domination of quadratic forms. <i>Advances in Operator Theory</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s43036-022-00199-w\">https://doi.org/10.1007/s43036-022-00199-w</a>","ama":"Wirth M. Kac regularity and domination of quadratic forms. <i>Advances in Operator Theory</i>. 2022;7(3). doi:<a href=\"https://doi.org/10.1007/s43036-022-00199-w\">10.1007/s43036-022-00199-w</a>"},"publication_status":"published"},{"publication_identifier":{"issn":["0022-4715"],"eissn":["1572-9613"]},"has_accepted_license":"1","title":"Large deviation estimates for weakly interacting bosons","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"01","doi":"10.1007/s10955-022-02940-4","article_number":"9","isi":1,"year":"2022","oa":1,"external_id":{"isi":["000805175000001"]},"date_updated":"2023-08-03T12:55:58Z","intvolume":"       188","status":"public","publication_status":"published","citation":{"apa":"Rademacher, S. A. E., &#38; Seiringer, R. (2022). Large deviation estimates for weakly interacting bosons. <i>Journal of Statistical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10955-022-02940-4\">https://doi.org/10.1007/s10955-022-02940-4</a>","ama":"Rademacher SAE, Seiringer R. Large deviation estimates for weakly interacting bosons. <i>Journal of Statistical Physics</i>. 2022;188. doi:<a href=\"https://doi.org/10.1007/s10955-022-02940-4\">10.1007/s10955-022-02940-4</a>","chicago":"Rademacher, Simone Anna Elvira, and Robert Seiringer. “Large Deviation Estimates for Weakly Interacting Bosons.” <i>Journal of Statistical Physics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s10955-022-02940-4\">https://doi.org/10.1007/s10955-022-02940-4</a>.","mla":"Rademacher, Simone Anna Elvira, and Robert Seiringer. “Large Deviation Estimates for Weakly Interacting Bosons.” <i>Journal of Statistical Physics</i>, vol. 188, 9, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s10955-022-02940-4\">10.1007/s10955-022-02940-4</a>.","short":"S.A.E. Rademacher, R. Seiringer, Journal of Statistical Physics 188 (2022).","ieee":"S. A. E. Rademacher and R. Seiringer, “Large deviation estimates for weakly interacting bosons,” <i>Journal of Statistical Physics</i>, vol. 188. Springer Nature, 2022.","ista":"Rademacher SAE, Seiringer R. 2022. Large deviation estimates for weakly interacting bosons. Journal of Statistical Physics. 188, 9."},"quality_controlled":"1","department":[{"_id":"RoSe"}],"oa_version":"Published Version","file":[{"date_updated":"2022-08-18T08:09:00Z","relation":"main_file","access_level":"open_access","checksum":"44418cb44f07fa21ed3907f85abf7f39","file_size":483481,"file_name":"2022_JournalStatisticalPhysics_Rademacher.pdf","success":1,"date_created":"2022-08-18T08:09:00Z","file_id":"11922","content_type":"application/pdf","creator":"dernst"}],"article_type":"original","date_published":"2022-07-01T00:00:00Z","file_date_updated":"2022-08-18T08:09:00Z","volume":188,"ddc":["510"],"date_created":"2022-08-18T07:23:26Z","type":"journal_article","author":[{"orcid":"0000-0001-5059-4466","id":"856966FE-A408-11E9-977E-802DE6697425","last_name":"Rademacher","full_name":"Rademacher, Simone Anna Elvira","first_name":"Simone Anna Elvira"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","full_name":"Seiringer, Robert","first_name":"Robert"}],"language":[{"iso":"eng"}],"month":"07","publication":"Journal of Statistical Physics","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","abstract":[{"lang":"eng","text":"We study the many-body dynamics of an initially factorized bosonic wave function in the mean-field regime. We prove large deviation estimates for the fluctuations around the condensate. We derive an upper bound extending a recent result to more general interactions. Furthermore, we derive a new lower bound which agrees with the upper bound in leading order."}],"acknowledgement":"The authors thank Gérard Ben Arous for pointing out the question of a lower bound. Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC Grant Agreement No. 694227 (R.S.) and under the Marie Skłodowska-Curie Grant Agreement No. 754411 (S.R.) is gratefully acknowledged.\r\nOpen access funding provided by IST Austria.","_id":"11917","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227"},{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publisher":"Springer Nature","ec_funded":1},{"file":[{"content_type":"application/zip","file_id":"11935","date_created":"2022-08-19T16:31:34Z","creator":"mnardin","date_updated":"2023-06-20T22:30:04Z","file_name":"Michele Nardin, Ph.D. Thesis - ISTA (1).zip","embargo_to":"open_access","file_size":13515457,"checksum":"2dbb70c74aaa3b64c1f463e943baf09c","relation":"source_file","access_level":"closed"},{"creator":"mnardin","date_created":"2022-08-22T09:43:50Z","file_id":"11941","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"0ec94035ea35a47a9f589ed168e60b48","file_size":9906458,"embargo":"2023-06-19","file_name":"Michele_Nardin_Phd_Thesis_PDFA.pdf","date_updated":"2023-06-20T22:30:04Z"}],"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"date_published":"2022-08-19T00:00:00Z","citation":{"apa":"Nardin, M. (2022). <i>On the encoding, transfer, and consolidation of spatial memories</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11932\">https://doi.org/10.15479/at:ista:11932</a>","ama":"Nardin M. On the encoding, transfer, and consolidation of spatial memories. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11932\">10.15479/at:ista:11932</a>","chicago":"Nardin, Michele. “On the Encoding, Transfer, and Consolidation of Spatial Memories.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11932\">https://doi.org/10.15479/at:ista:11932</a>.","mla":"Nardin, Michele. <i>On the Encoding, Transfer, and Consolidation of Spatial Memories</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11932\">10.15479/at:ista:11932</a>.","short":"M. Nardin, On the Encoding, Transfer, and Consolidation of Spatial Memories, Institute of Science and Technology Austria, 2022.","ieee":"M. Nardin, “On the encoding, transfer, and consolidation of spatial memories,” Institute of Science and Technology Austria, 2022.","ista":"Nardin M. 2022. On the encoding, transfer, and consolidation of spatial memories. Institute of Science and Technology Austria."},"publication_status":"published","oa":1,"supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","last_name":"Csicsvari"}],"status":"public","date_updated":"2023-09-05T12:02:14Z","doi":"10.15479/at:ista:11932","day":"19","has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"title":"On the encoding, transfer, and consolidation of spatial memories","degree_awarded":"PhD","year":"2022","publisher":"Institute of Science and Technology Austria","project":[{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ec_funded":1,"abstract":[{"lang":"eng","text":"The ability to form and retrieve memories is central to survival. In mammals, the hippocampus\r\nis a brain region essential to the acquisition and consolidation of new memories. It is also\r\ninvolved in keeping track of one’s position in space and aids navigation. Although this\r\nspace-memory has been a source of contradiction, evidence supports the view that the role of\r\nthe hippocampus in navigation is memory, thanks to the formation of cognitive maps. First\r\nintroduced by Tolman in 1948, cognitive maps are generally used to organize experiences in\r\nmemory; however, the detailed mechanisms by which these maps are formed and stored are not\r\nyet agreed upon. Some influential theories describe this process as involving three fundamental\r\nsteps: initial encoding by the hippocampus, interactions between the hippocampus and other\r\ncortical areas, and long-term extra-hippocampal consolidation. In this thesis, I will show how\r\nthe investigation of cognitive maps of space helped to shed light on each of these three memory\r\nprocesses.\r\nThe first study included in this thesis deals with the initial encoding of spatial memories in\r\nthe hippocampus. Much is known about encoding at the level of single cells, but less about\r\ntheir co-activity or joint contribution to the encoding of novel spatial information. I will\r\ndescribe the structure of an interaction network that allows for efficient encoding of noisy\r\nspatial information during the first exploration of a novel environment.\r\nThe second study describes the interactions between the hippocampus and the prefrontal\r\ncortex (PFC), two areas directly and indirectly connected. It is known that the PFC, in concert\r\nwith the hippocampus, is involved in various processes, including memory storage and spatial\r\nnavigation. Nonetheless, the detailed mechanisms by which PFC receives information from the\r\nhippocampus are not clear. I will show how a transient improvement in theta phase locking of\r\nPFC cells enables interactions of cell pairs across the two regions.\r\nThe third study describes the learning of behaviorally-relevant spatial locations in the hippocampus and the medial entorhinal cortex. I will show how the accumulation of firing around\r\ngoal locations, a correlate of learning, can shed light on the transition from short- to long-term\r\nspatial memories and the speed of consolidation in different brain areas.\r\nThe studies included in this thesis represent the main scientific contributions of my Ph.D. They\r\ninvolve statistical analyses and models of neural responses of cells in different brain areas of\r\nrats executing spatial tasks. I will conclude the thesis by discussing the impact of the findings\r\non principles of memory formation and retention, including the mechanisms, the speed, and\r\nthe duration of these processes."}],"_id":"11932","acknowledgement":"I acknowledge the support from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","alternative_title":["ISTA Thesis"],"month":"08","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","full_name":"Nardin, Michele","first_name":"Michele","last_name":"Nardin"}],"type":"dissertation","article_processing_charge":"No","ddc":["573"],"file_date_updated":"2023-06-20T22:30:04Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10077"},{"status":"public","id":"6194","relation":"part_of_dissertation"}]},"date_created":"2022-08-19T08:52:30Z","page":"136"},{"year":"2022","publication_identifier":{"eissn":["2041-1723"]},"has_accepted_license":"1","title":"Thermodynamics of high-pressure ice phases explored with atomistic simulations","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_number":"4707","day":"10","doi":"10.1038/s41467-022-32374-1","date_updated":"2023-08-03T13:00:40Z","status":"public","intvolume":"        13","oa":1,"external_id":{"isi":["000838655300022"],"pmid":["35948550"]},"quality_controlled":"1","citation":{"ista":"Reinhardt A, Bethkenhagen M, Coppari F, Millot M, Hamel S, Cheng B. 2022. Thermodynamics of high-pressure ice phases explored with atomistic simulations. Nature Communications. 13, 4707.","ieee":"A. Reinhardt, M. Bethkenhagen, F. Coppari, M. Millot, S. Hamel, and B. Cheng, “Thermodynamics of high-pressure ice phases explored with atomistic simulations,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","mla":"Reinhardt, Aleks, et al. “Thermodynamics of High-Pressure Ice Phases Explored with Atomistic Simulations.” <i>Nature Communications</i>, vol. 13, 4707, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-32374-1\">10.1038/s41467-022-32374-1</a>.","short":"A. Reinhardt, M. Bethkenhagen, F. Coppari, M. Millot, S. Hamel, B. Cheng, Nature Communications 13 (2022).","chicago":"Reinhardt, Aleks, Mandy Bethkenhagen, Federica Coppari, Marius Millot, Sebastien Hamel, and Bingqing Cheng. “Thermodynamics of High-Pressure Ice Phases Explored with Atomistic Simulations.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-32374-1\">https://doi.org/10.1038/s41467-022-32374-1</a>.","ama":"Reinhardt A, Bethkenhagen M, Coppari F, Millot M, Hamel S, Cheng B. Thermodynamics of high-pressure ice phases explored with atomistic simulations. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-32374-1\">10.1038/s41467-022-32374-1</a>","apa":"Reinhardt, A., Bethkenhagen, M., Coppari, F., Millot, M., Hamel, S., &#38; Cheng, B. (2022). Thermodynamics of high-pressure ice phases explored with atomistic simulations. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-32374-1\">https://doi.org/10.1038/s41467-022-32374-1</a>"},"publication_status":"published","date_published":"2022-08-10T00:00:00Z","article_type":"original","department":[{"_id":"BiCh"}],"oa_version":"Published Version","file":[{"file_name":"2022_NatureCommunications_Reinhardt.pdf","checksum":"8ff9b689cde59fd3a9959a9f01929dea","file_size":1767206,"relation":"main_file","access_level":"open_access","date_updated":"2022-08-22T06:33:02Z","creator":"dernst","content_type":"application/pdf","file_id":"11939","date_created":"2022-08-22T06:33:02Z","success":1}],"date_created":"2022-08-21T22:01:55Z","ddc":["540"],"volume":13,"file_date_updated":"2022-08-22T06:33:02Z","article_processing_charge":"No","publication":"Nature Communications","scopus_import":"1","month":"08","author":[{"full_name":"Reinhardt, Aleks","first_name":"Aleks","last_name":"Reinhardt"},{"last_name":"Bethkenhagen","full_name":"Bethkenhagen, Mandy","first_name":"Mandy"},{"last_name":"Coppari","first_name":"Federica","full_name":"Coppari, Federica"},{"first_name":"Marius","full_name":"Millot, Marius","last_name":"Millot"},{"full_name":"Hamel, Sebastien","first_name":"Sebastien","last_name":"Hamel"},{"orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","full_name":"Cheng, Bingqing","last_name":"Cheng"}],"language":[{"iso":"eng"}],"type":"journal_article","pmid":1,"_id":"11937","acknowledgement":"We thank Chris Pickard for providing the initial structures of high-pressure ice phases and for useful advice. A.R. and B.C. acknowledge resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital grant EP/P020259/1. M.B. was supported by the European Union within the Marie Skłodowska-Curie actions (xICE grant 894725) and acknowledges computational resources at North-German Supercomputing Alliance (HLRN) facilities. S.H. and M.M. acknowledge support from LDRD 19-ERD-031 and computing support from the Lawrence Livermore National Laboratory (LLNL) Institutional Computing Grand Challenge programme. F.C. acknowledges support from the US DOE Office of Science, Office of Fusion Energy Sciences. Lawrence Livermore National Laboratory is operated by Lawrence Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear Security Administration under Contract DE-AC52-07NA27344.","abstract":[{"lang":"eng","text":"Most experimentally known high-pressure ice phases have a body-centred cubic (bcc) oxygen lattice. Our large-scale molecular-dynamics simulations with a machine-learning potential indicate that, amongst these bcc ice phases, ices VII, VII′ and X are the same thermodynamic phase under different conditions, whereas superionic ice VII″ has a first-order phase boundary with ice VII′. Moreover, at about 300 GPa, the transformation between ice X and the Pbcm phase has a sharp structural change but no apparent activation barrier, whilst at higher pressures the barrier gradually increases. Our study thus clarifies the phase behaviour of the high-pressure ices and reveals peculiar solid–solid transition mechanisms not known in other systems."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature"},{"oa":1,"external_id":{"arxiv":["2101.03928"]},"date_updated":"2023-02-23T13:54:21Z","status":"public","intvolume":"        26","title":"On compatible matchings","issue":"2","has_accepted_license":"1","publication_identifier":{"issn":["1526-1719"]},"doi":"10.7155/jgaa.00591","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"01","year":"2022","department":[{"_id":"UlWa"},{"_id":"HeEd"},{"_id":"KrCh"}],"file":[{"file_id":"11940","content_type":"application/pdf","date_created":"2022-08-22T06:42:42Z","success":1,"creator":"dernst","date_updated":"2022-08-22T06:42:42Z","file_name":"2022_JourGraphAlgorithmsApplic_Aichholzer.pdf","access_level":"open_access","relation":"main_file","checksum":"dc6e255e3558faff924fd9e370886c11","file_size":694538}],"oa_version":"Published Version","date_published":"2022-06-01T00:00:00Z","article_type":"original","citation":{"chicago":"Aichholzer, Oswin, Alan M Arroyo Guevara, Zuzana Masárová, Irene Parada, Daniel Perz, Alexander Pilz, Josef Tkadlec, and Birgit Vogtenhuber. “On Compatible Matchings.” <i>Journal of Graph Algorithms and Applications</i>. Brown University, 2022. <a href=\"https://doi.org/10.7155/jgaa.00591\">https://doi.org/10.7155/jgaa.00591</a>.","ama":"Aichholzer O, Arroyo Guevara AM, Masárová Z, et al. On compatible matchings. <i>Journal of Graph Algorithms and Applications</i>. 2022;26(2):225-240. doi:<a href=\"https://doi.org/10.7155/jgaa.00591\">10.7155/jgaa.00591</a>","apa":"Aichholzer, O., Arroyo Guevara, A. M., Masárová, Z., Parada, I., Perz, D., Pilz, A., … Vogtenhuber, B. (2022). On compatible matchings. <i>Journal of Graph Algorithms and Applications</i>. Brown University. <a href=\"https://doi.org/10.7155/jgaa.00591\">https://doi.org/10.7155/jgaa.00591</a>","ista":"Aichholzer O, Arroyo Guevara AM, Masárová Z, Parada I, Perz D, Pilz A, Tkadlec J, Vogtenhuber B. 2022. On compatible matchings. Journal of Graph Algorithms and Applications. 26(2), 225–240.","ieee":"O. Aichholzer <i>et al.</i>, “On compatible matchings,” <i>Journal of Graph Algorithms and Applications</i>, vol. 26, no. 2. Brown University, pp. 225–240, 2022.","mla":"Aichholzer, Oswin, et al. “On Compatible Matchings.” <i>Journal of Graph Algorithms and Applications</i>, vol. 26, no. 2, Brown University, 2022, pp. 225–40, doi:<a href=\"https://doi.org/10.7155/jgaa.00591\">10.7155/jgaa.00591</a>.","short":"O. Aichholzer, A.M. Arroyo Guevara, Z. Masárová, I. Parada, D. Perz, A. Pilz, J. Tkadlec, B. Vogtenhuber, Journal of Graph Algorithms and Applications 26 (2022) 225–240."},"publication_status":"published","arxiv":1,"quality_controlled":"1","language":[{"iso":"eng"}],"month":"06","author":[{"full_name":"Aichholzer, Oswin","first_name":"Oswin","last_name":"Aichholzer"},{"full_name":"Arroyo Guevara, Alan M","first_name":"Alan M","last_name":"Arroyo Guevara","orcid":"0000-0003-2401-8670","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Masárová, Zuzana","first_name":"Zuzana","last_name":"Masárová","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6660-1322"},{"last_name":"Parada","full_name":"Parada, Irene","first_name":"Irene"},{"last_name":"Perz","full_name":"Perz, Daniel","first_name":"Daniel"},{"full_name":"Pilz, Alexander","first_name":"Alexander","last_name":"Pilz"},{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","last_name":"Tkadlec","first_name":"Josef","full_name":"Tkadlec, Josef"},{"last_name":"Vogtenhuber","first_name":"Birgit","full_name":"Vogtenhuber, Birgit"}],"type":"journal_article","article_processing_charge":"No","publication":"Journal of Graph Algorithms and Applications","scopus_import":"1","volume":26,"ddc":["000"],"file_date_updated":"2022-08-22T06:42:42Z","related_material":{"record":[{"status":"public","id":"9296","relation":"earlier_version"}]},"page":"225-240","date_created":"2022-08-21T22:01:56Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Brown University","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"},{"name":"The Wittgenstein Prize","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00342"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"},{"call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"abstract":[{"lang":"eng","text":"A matching is compatible to two or more labeled point sets of size n with labels {1, . . . , n} if its straight-line drawing on each of these point sets is crossing-free. We study the maximum number of edges in a matching compatible to two or more labeled point sets in general position in the plane. We show that for any two labeled sets of n points in convex position there exists a compatible matching with ⌊√2n + 1 − 1⌋ edges. More generally, for any ℓ labeled point sets we construct compatible matchings of size Ω(n1/ℓ). As a corresponding upper bound, we use probabilistic arguments to show that for any ℓ given sets of n points there exists a labeling of each set such that the largest compatible matching has O(n2/(ℓ+1)) edges. Finally, we show that Θ(log n) copies of any set of n points are necessary and sufficient for the existence of labelings of these point sets such that any compatible matching consists only of a single edge."}],"_id":"11938","acknowledgement":"A.A. funded by the Marie Sklodowska-Curie grant agreement No 754411. Z.M. partially funded by Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31. I.P., D.P., and B.V. partially supported by FWF within the collaborative DACH project Arrangements and Drawings as FWF project I 3340-N35. A.P. supported by a Schrödinger fellowship of the FWF: J-3847-N35. J.T. partially supported by ERC Start grant no. (279307: Graph Games), FWF grant no. P23499-N23 and S11407-N23 (RiSE)."},{"_id":"11943","abstract":[{"lang":"eng","text":"Complex wiring between neurons underlies the information-processing network enabling all brain functions, including cognition and memory. For understanding how the network is structured, processes information, and changes over time, comprehensive visualization of the architecture of living brain tissue with its cellular and molecular components would open up major opportunities. However, electron microscopy (EM) provides nanometre-scale resolution required for full <jats:italic>in-silico</jats:italic> reconstruction<jats:sup>1–5</jats:sup>, yet is limited to fixed specimens and static representations. Light microscopy allows live observation, with super-resolution approaches<jats:sup>6–12</jats:sup> facilitating nanoscale visualization, but comprehensive 3D-reconstruction of living brain tissue has been hindered by tissue photo-burden, photobleaching, insufficient 3D-resolution, and inadequate signal-to-noise ratio (SNR). Here we demonstrate saturated reconstruction of living brain tissue. We developed an integrated imaging and analysis technology, adapting stimulated emission depletion (STED) microscopy<jats:sup>6,13</jats:sup> in extracellularly labelled tissue<jats:sup>14</jats:sup> for high SNR and near-isotropic resolution. Centrally, a two-stage deep-learning approach leveraged previously obtained information on sample structure to drastically reduce photo-burden and enable automated volumetric reconstruction down to single synapse level. Live reconstruction provides unbiased analysis of tissue architecture across time in relation to functional activity and targeted activation, and contextual understanding of molecular labelling. This adoptable technology will facilitate novel insights into the dynamic functional architecture of living brain tissue."}],"citation":{"ieee":"P. Velicky <i>et al.</i>, “Saturated reconstruction of living brain tissue,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","short":"P. Velicky, E. Miguel Villalba, J.M. Michalska, D. Wei, Z. Lin, J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri, J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel, J.G. Danzl, BioRxiv (n.d.).","mla":"Velicky, Philipp, et al. “Saturated Reconstruction of Living Brain Tissue.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2022.03.16.484431\">10.1101/2022.03.16.484431</a>.","ista":"Velicky P, Miguel Villalba E, Michalska JM, Wei D, Lin Z, Watson J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. Saturated reconstruction of living brain tissue. bioRxiv, <a href=\"https://doi.org/10.1101/2022.03.16.484431\">10.1101/2022.03.16.484431</a>.","apa":"Velicky, P., Miguel Villalba, E., Michalska, J. M., Wei, D., Lin, Z., Watson, J., … Danzl, J. G. (n.d.). Saturated reconstruction of living brain tissue. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2022.03.16.484431\">https://doi.org/10.1101/2022.03.16.484431</a>","ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Saturated reconstruction of living brain tissue. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2022.03.16.484431\">10.1101/2022.03.16.484431</a>","chicago":"Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Donglai Wei, Zudi Lin, Jake Watson, Jakob Troidl, et al. “Saturated Reconstruction of Living Brain Tissue.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2022.03.16.484431\">https://doi.org/10.1101/2022.03.16.484431</a>."},"publication_status":"submitted","date_published":"2022-05-09T00:00:00Z","department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1101/2022.03.16.484431","open_access":"1"}],"publisher":"Cold Spring Harbor Laboratory","oa_version":"Preprint","date_created":"2022-08-23T11:07:59Z","year":"2022","title":"Saturated reconstruction of living brain tissue","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12470"}]},"day":"09","doi":"10.1101/2022.03.16.484431","publication":"bioRxiv","date_updated":"2024-03-25T23:30:11Z","article_processing_charge":"No","status":"public","type":"preprint","oa":1,"author":[{"orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","last_name":"Velicky","first_name":"Philipp","full_name":"Velicky, Philipp"},{"last_name":"Miguel Villalba","full_name":"Miguel Villalba, Eder","first_name":"Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5665-0430"},{"last_name":"Michalska","full_name":"Michalska, Julia M","first_name":"Julia M","orcid":"0000-0003-3862-1235","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wei, Donglai","first_name":"Donglai","last_name":"Wei"},{"last_name":"Lin","first_name":"Zudi","full_name":"Lin, Zudi"},{"id":"63836096-4690-11EA-BD4E-32803DDC885E","orcid":"0000-0002-8698-3823","last_name":"Watson","full_name":"Watson, Jake","first_name":"Jake"},{"last_name":"Troidl","first_name":"Jakob","full_name":"Troidl, Jakob"},{"first_name":"Johanna","full_name":"Beyer, Johanna","last_name":"Beyer"},{"id":"43DF3136-F248-11E8-B48F-1D18A9856A87","first_name":"Yoav","full_name":"Ben Simon, Yoav","last_name":"Ben Simon"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","last_name":"Sommer","full_name":"Sommer, Christoph M","first_name":"Christoph M"},{"full_name":"Jahr, Wiebke","first_name":"Wiebke","last_name":"Jahr","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87"},{"id":"9ac8f577-2357-11eb-997a-e566c5550886","last_name":"Cenameri","first_name":"Alban","full_name":"Cenameri, Alban"},{"full_name":"Broichhagen, Johannes","first_name":"Johannes","last_name":"Broichhagen"},{"last_name":"Grant","full_name":"Grant, Seth G. N.","first_name":"Seth G. N."},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","full_name":"Jonas, Peter M","last_name":"Jonas"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","full_name":"Novarino, Gaia","last_name":"Novarino"},{"first_name":"Hanspeter","full_name":"Pfister, Hanspeter","last_name":"Pfister"},{"last_name":"Bickel","full_name":"Bickel, Bernd","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"},{"orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl"}],"language":[{"iso":"eng"}],"month":"05"},{"alternative_title":["ISTA Thesis"],"_id":"11945","abstract":[{"text":"G protein-coupled receptors (GPCRs) respond to specific ligands and regulate multiple processes ranging from cell growth and immune responses to neuronal signal transmission. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additional challenges exist to dissect cell-type specific responses when the same GPCR is expressed on several cell types within the body. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that selectively bind their agonist clozapine-N-oxide (CNO) and mimic a GPCR-of-interest in a desired cell type.\r\nWe validated our approach with β2-adrenergic receptor (β2AR/ADRB2) and show that our chimeric DREADD-β2AR triggers comparable responses on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Since β2AR is also enriched in microglia, which can drive inflammation in the central nervous system, we expressed chimeric DREADD-β2AR in primary microglia and successfully recapitulate β2AR-mediated filopodia formation through CNO stimulation. To dissect the role of selected GPCRs during microglial inflammation, we additionally generated DREADD-based chimeras for microglia-enriched GPR65 and GPR109A/HCAR2. In a microglia cell line, DREADD-β2AR and DREADD-GPR65 both modulated the inflammatory response with a similar profile as endogenously expressed β2AR, while DREADD-GPR109A showed no impact.\r\nOur DREADD-based approach provides the means to obtain mechanistic and functional insights into GPCR signaling on a cell-type specific level.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"name":"Modulating microglia through G protein-coupled receptor (GPCR) signaling","_id":"267F75D8-B435-11E9-9278-68D0E5697425"}],"publisher":"Institute of Science and Technology Austria","page":"133","date_created":"2022-08-23T11:33:11Z","file_date_updated":"2022-08-25T09:33:31Z","related_material":{"record":[{"id":"11995","relation":"dissertation_contains","status":"public"}]},"ddc":["570"],"article_processing_charge":"No","type":"dissertation","month":"08","language":[{"iso":"eng"}],"author":[{"last_name":"Schulz","full_name":"Schulz, Rouven","first_name":"Rouven","orcid":"0000-0001-5297-733X","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ama":"Schulz R. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11945\">10.15479/at:ista:11945</a>","apa":"Schulz, R. (2022). <i>Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11945\">https://doi.org/10.15479/at:ista:11945</a>","chicago":"Schulz, Rouven. “Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11945\">https://doi.org/10.15479/at:ista:11945</a>.","ieee":"R. Schulz, “Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function,” Institute of Science and Technology Austria, 2022.","mla":"Schulz, Rouven. <i>Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11945\">10.15479/at:ista:11945</a>.","short":"R. Schulz, Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function, Institute of Science and Technology Austria, 2022.","ista":"Schulz R. 2022. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. Institute of Science and Technology Austria."},"publication_status":"published","date_published":"2022-08-23T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"file":[{"success":1,"date_created":"2022-08-25T08:59:57Z","file_id":"11970","content_type":"application/pdf","creator":"rschulz","date_updated":"2022-08-25T08:59:57Z","relation":"main_file","access_level":"open_access","checksum":"61b1b666a210ff7cdd0e95ea75207a13","file_size":28079331,"file_name":"Thesis_Rouven_Schulz_2022_final.pdf"},{"date_updated":"2022-08-25T09:33:31Z","file_name":"Thesis_Rouven_Schulz_2022_final.docx","checksum":"2b8f95ea1c134dbdb927b41b1dbeeeb5","file_size":27226963,"access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"11971","date_created":"2022-08-25T09:00:11Z","creator":"rschulz"}],"oa_version":"Published Version","degree_awarded":"PhD","year":"2022","publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","title":"Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function","doi":"10.15479/at:ista:11945","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"23","date_updated":"2023-08-03T13:02:26Z","status":"public","supervisor":[{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","last_name":"Siegert","first_name":"Sandra","full_name":"Siegert, Sandra"}],"oa":1},{"_id":"11950","abstract":[{"lang":"eng","text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanoscopic synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS leverages fixation-compatible extracellular labeling and advanced optical readout, in particular stimulated-emission depletion and expansion microscopy, to comprehensively delineate cellular structures. It enables 3D-reconstructing single synapses and mapping synaptic connectivity by identification and tailored analysis of putative synaptic cleft regions. Applying CATS to the hippocampal mossy fiber circuitry, we demonstrate its power to reveal the system’s molecularly informed ultrastructure across spatial scales and assess local connectivity by reconstructing and quantifying the synaptic input and output structure of identified neurons."}],"publication_status":"submitted","citation":{"ista":"Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Venturino A, Roessler K, Czech T, Siegert S, Novarino G, Jonas PM, Danzl JG. Uncovering brain tissue architecture across scales with super-resolution light microscopy. bioRxiv, <a href=\"https://doi.org/10.1101/2022.08.17.504272\">10.1101/2022.08.17.504272</a>.","mla":"Michalska, Julia M., et al. “Uncovering Brain Tissue Architecture across Scales with Super-Resolution Light Microscopy.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2022.08.17.504272\">10.1101/2022.08.17.504272</a>.","short":"J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, A. Venturino, K. Roessler, T. Czech, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, BioRxiv (n.d.).","ieee":"J. M. Michalska <i>et al.</i>, “Uncovering brain tissue architecture across scales with super-resolution light microscopy,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","chicago":"Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Uncovering Brain Tissue Architecture across Scales with Super-Resolution Light Microscopy.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2022.08.17.504272\">https://doi.org/10.1101/2022.08.17.504272</a>.","apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (n.d.). Uncovering brain tissue architecture across scales with super-resolution light microscopy. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2022.08.17.504272\">https://doi.org/10.1101/2022.08.17.504272</a>","ama":"Michalska JM, Lyudchik J, Velicky P, et al. Uncovering brain tissue architecture across scales with super-resolution light microscopy. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2022.08.17.504272\">10.1101/2022.08.17.504272</a>"},"date_published":"2022-08-18T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1101/2022.08.17.504272","open_access":"1"}],"oa_version":"Preprint","publisher":"Cold Spring Harbor Laboratory","department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-08-24T08:24:52Z","year":"2022","doi":"10.1101/2022.08.17.504272","day":"18","title":"Uncovering brain tissue architecture across scales with super-resolution light microscopy","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12470"}]},"status":"public","publication":"bioRxiv","date_updated":"2024-03-25T23:30:11Z","article_processing_charge":"No","type":"preprint","author":[{"last_name":"Michalska","full_name":"Michalska, Julia M","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3862-1235"},{"full_name":"Lyudchik, Julia","first_name":"Julia","last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","last_name":"Velicky","full_name":"Velicky, Philipp","first_name":"Philipp"},{"full_name":"Korinkova, Hana","first_name":"Hana","last_name":"Korinkova","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed"},{"last_name":"Watson","first_name":"Jake","full_name":"Watson, Jake","orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"id":"9ac8f577-2357-11eb-997a-e566c5550886","last_name":"Cenameri","first_name":"Alban","full_name":"Cenameri, Alban"},{"last_name":"Sommer","full_name":"Sommer, Christoph M","first_name":"Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Venturino","first_name":"Alessandro","full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Roessler, Karl","first_name":"Karl","last_name":"Roessler"},{"first_name":"Thomas","full_name":"Czech, Thomas","last_name":"Czech"},{"orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra","first_name":"Sandra","last_name":"Siegert"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","full_name":"Novarino, Gaia","last_name":"Novarino"},{"last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"},{"last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"}],"language":[{"iso":"eng"}],"month":"08","oa":1},{"external_id":{"isi":["000841396400008"]},"oa":1,"intvolume":"        13","status":"public","date_updated":"2023-08-03T13:01:19Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"16","doi":"10.1038/s41467-022-32559-8","article_number":"4826","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"isi":1,"publication_identifier":{"issn":["2041-1723"]},"title":"A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory","has_accepted_license":"1","year":"2022","file":[{"checksum":"405936d9e4d33625d80c093c9713a91f","file_size":5910357,"access_level":"open_access","relation":"main_file","file_name":"2022_NatureCommunications_BenSimon.pdf","date_updated":"2022-08-26T11:51:40Z","creator":"dernst","date_created":"2022-08-26T11:51:40Z","success":1,"content_type":"application/pdf","file_id":"11990"}],"oa_version":"Published Version","department":[{"_id":"JoCs"},{"_id":"PeJo"},{"_id":"JoDa"}],"article_type":"original","date_published":"2022-08-16T00:00:00Z","citation":{"ista":"Ben Simon Y, Käfer K, Velicky P, Csicsvari JL, Danzl JG, Jonas PM. 2022. A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory. Nature Communications. 13, 4826.","ieee":"Y. Ben Simon, K. Käfer, P. Velicky, J. L. Csicsvari, J. G. Danzl, and P. M. Jonas, “A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","short":"Y. Ben Simon, K. Käfer, P. Velicky, J.L. Csicsvari, J.G. Danzl, P.M. Jonas, Nature Communications 13 (2022).","mla":"Ben Simon, Yoav, et al. “A Direct Excitatory Projection from Entorhinal Layer 6b Neurons to the Hippocampus Contributes to Spatial Coding and Memory.” <i>Nature Communications</i>, vol. 13, 4826, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-32559-8\">10.1038/s41467-022-32559-8</a>.","chicago":"Ben Simon, Yoav, Karola Käfer, Philipp Velicky, Jozsef L Csicsvari, Johann G Danzl, and Peter M Jonas. “A Direct Excitatory Projection from Entorhinal Layer 6b Neurons to the Hippocampus Contributes to Spatial Coding and Memory.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-32559-8\">https://doi.org/10.1038/s41467-022-32559-8</a>.","apa":"Ben Simon, Y., Käfer, K., Velicky, P., Csicsvari, J. L., Danzl, J. G., &#38; Jonas, P. M. (2022). A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-32559-8\">https://doi.org/10.1038/s41467-022-32559-8</a>","ama":"Ben Simon Y, Käfer K, Velicky P, Csicsvari JL, Danzl JG, Jonas PM. A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-32559-8\">10.1038/s41467-022-32559-8</a>"},"publication_status":"published","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"month":"08","author":[{"id":"43DF3136-F248-11E8-B48F-1D18A9856A87","full_name":"Ben Simon, Yoav","first_name":"Yoav","last_name":"Ben Simon"},{"id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","last_name":"Käfer","first_name":"Karola","full_name":"Käfer, Karola"},{"last_name":"Velicky","first_name":"Philipp","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L"},{"first_name":"Johann G","full_name":"Danzl, Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","last_name":"Jonas","full_name":"Jonas, Peter M","first_name":"Peter M"}],"publication":"Nature Communications","article_processing_charge":"No","file_date_updated":"2022-08-26T11:51:40Z","volume":13,"ddc":["570"],"date_created":"2022-08-24T08:25:50Z","project":[{"call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","call_identifier":"FWF"},{"grant_number":"Z00312","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"}],"publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledged_ssus":[{"_id":"Bio"},{"_id":"SSU"}],"ec_funded":1,"abstract":[{"text":"The mammalian hippocampal formation (HF) plays a key role in several higher brain functions, such as spatial coding, learning and memory. Its simple circuit architecture is often viewed as a trisynaptic loop, processing input originating from the superficial layers of the entorhinal cortex (EC) and sending it back to its deeper layers. Here, we show that excitatory neurons in layer 6b of the mouse EC project to all sub-regions comprising the HF and receive input from the CA1, thalamus and claustrum. Furthermore, their output is characterized by unique slow-decaying excitatory postsynaptic currents capable of driving plateau-like potentials in their postsynaptic targets. Optogenetic inhibition of the EC-6b pathway affects spatial coding in CA1 pyramidal neurons, while cell ablation impairs not only acquisition of new spatial memories, but also degradation of previously acquired ones. Our results provide evidence of a functional role for cortical layer 6b neurons in the adult brain.","lang":"eng"}],"acknowledgement":"We thank F. Marr and A. Schlögl for technical assistance, E. Kralli-Beller for manuscript editing, as well as C. Sommer and the Imaging and Optics Facility of the Institute of Science and Technology Austria (ISTA) for image analysis scripts and microscopy support. We extend our gratitude to J. Wallenschus and D. Rangel Guerrero for technical assistance acquiring single-unit data and I. Gridchyn for help with single-unit clustering. Finally, we also thank B. Suter for discussions, A. Saunders, M. Jösch, and H. Monyer for critically reading earlier versions of the manuscript, C. Petersen for sharing clearing protocols, and the Scientific Service Units of ISTA for efficient support. This project was funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (ERC advanced grant No 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award for P.J. and I3600-B27 for J.G.D. and P.V.).","_id":"11951"},{"department":[{"_id":"UlWa"}],"oa_version":"Preprint","article_type":"original","date_published":"2022-07-01T00:00:00Z","citation":{"chicago":"Krokhin, Andrei, and Jakub Opršal. “An Invitation to the Promise Constraint Satisfaction Problem.” <i>ACM SIGLOG News</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3559736.3559740\">https://doi.org/10.1145/3559736.3559740</a>.","ama":"Krokhin A, Opršal J. An invitation to the promise constraint satisfaction problem. <i>ACM SIGLOG News</i>. 2022;9(3):30-59. doi:<a href=\"https://doi.org/10.1145/3559736.3559740\">10.1145/3559736.3559740</a>","apa":"Krokhin, A., &#38; Opršal, J. (2022). An invitation to the promise constraint satisfaction problem. <i>ACM SIGLOG News</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3559736.3559740\">https://doi.org/10.1145/3559736.3559740</a>","ista":"Krokhin A, Opršal J. 2022. An invitation to the promise constraint satisfaction problem. ACM SIGLOG News. 9(3), 30–59.","mla":"Krokhin, Andrei, and Jakub Opršal. “An Invitation to the Promise Constraint Satisfaction Problem.” <i>ACM SIGLOG News</i>, vol. 9, no. 3, Association for Computing Machinery, 2022, pp. 30–59, doi:<a href=\"https://doi.org/10.1145/3559736.3559740\">10.1145/3559736.3559740</a>.","short":"A. Krokhin, J. Opršal, ACM SIGLOG News 9 (2022) 30–59.","ieee":"A. Krokhin and J. Opršal, “An invitation to the promise constraint satisfaction problem,” <i>ACM SIGLOG News</i>, vol. 9, no. 3. Association for Computing Machinery, pp. 30–59, 2022."},"publication_status":"published","quality_controlled":"1","arxiv":1,"oa":1,"external_id":{"arxiv":["2208.13538"]},"date_updated":"2022-09-05T08:19:38Z","intvolume":"         9","status":"public","publication_identifier":{"issn":["2372-3491"]},"title":"An invitation to the promise constraint satisfaction problem","issue":"3","doi":"10.1145/3559736.3559740","day":"01","year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"http://arxiv.org/abs/2208.13538","open_access":"1"}],"publisher":"Association for Computing Machinery","abstract":[{"text":"The study of the complexity of the constraint satisfaction problem (CSP), centred around the Feder-Vardi Dichotomy Conjecture, has been very prominent in the last two decades. After a long concerted effort and many partial results, the Dichotomy Conjecture has been proved in 2017 independently by Bulatov and Zhuk. At about the same time, a vast generalisation of CSP, called promise CSP, has started to gain prominence. In this survey, we explain the importance of promise CSP and highlight many new very interesting features that the study of promise CSP has brought to light. The complexity classification quest for the promise CSP is wide open, and we argue that, despite the promise CSP being more general, this quest is rather more accessible to a wide range of researchers than the dichotomy-led study of the CSP has been.","lang":"eng"}],"_id":"11991","type":"journal_article","month":"07","language":[{"iso":"eng"}],"author":[{"first_name":"Andrei","full_name":"Krokhin, Andrei","last_name":"Krokhin"},{"orcid":"0000-0003-1245-3456","id":"ec596741-c539-11ec-b829-c79322a91242","full_name":"Opršal, Jakub","first_name":"Jakub","last_name":"Opršal"}],"publication":"ACM SIGLOG News","article_processing_charge":"No","volume":9,"page":"30-59","date_created":"2022-08-27T11:23:37Z"},{"publication":"Computer Graphics Forum","article_processing_charge":"No","scopus_import":"1","type":"journal_article","author":[{"last_name":"Alderighi","full_name":"Alderighi, Thomas","first_name":"Thomas"},{"full_name":"Malomo, Luigi","first_name":"Luigi","last_name":"Malomo"},{"first_name":"Thomas","full_name":"Auzinger, Thomas","last_name":"Auzinger","id":"4718F954-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1546-3265"},{"last_name":"Bickel","full_name":"Bickel, Bernd","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"},{"first_name":"Paulo","full_name":"Cignoni, Paulo","last_name":"Cignoni"},{"last_name":"Pietroni","full_name":"Pietroni, Nico","first_name":"Nico"}],"language":[{"iso":"eng"}],"month":"09","page":"435-452","date_created":"2022-08-28T18:17:01Z","file_date_updated":"2022-08-28T18:18:08Z","volume":41,"ddc":["000"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Wiley","_id":"11993","abstract":[{"text":"Moulding refers to a set of manufacturing techniques in which a mould, usually a cavity or a solid frame, is used to shape a liquid or pliable material into an object of the desired shape. The popularity of moulding comes from its effectiveness, scalability and versatility in terms of employed materials. Its relevance as a fabrication process is demonstrated by the extensive literature covering different aspects related to mould design, from material flow simulation to the automation of mould geometry design. In this state-of-the-art report, we provide an extensive review of the automatic methods for the design of moulds, focusing on contributions from a geometric perspective. We classify existing mould design methods based on their computational approach and the nature of their target moulding process. We summarize the relationships between computational approaches and moulding techniques, highlighting their strengths and limitations. Finally, we discuss potential future research directions.","lang":"eng"}],"date_updated":"2023-08-03T13:21:55Z","intvolume":"        41","status":"public","oa":1,"external_id":{"isi":["000842638900001"]},"year":"2022","title":"State of the art in computational mould design","publication_identifier":{"issn":["0167-7055"],"eissn":["1467-8659"]},"issue":"6","has_accepted_license":"1","keyword":["Computer Graphics and Computer-Aided Design"],"day":"01","doi":"10.1111/cgf.14581","isi":1,"article_type":"original","date_published":"2022-09-01T00:00:00Z","department":[{"_id":"BeBi"}],"oa_version":"Submitted Version","file":[{"date_updated":"2022-08-28T18:18:08Z","checksum":"c40cc8ceb7b7f0512172b883d712198e","file_size":32480850,"access_level":"open_access","relation":"main_file","file_name":"star_molding_preprint.pdf","date_created":"2022-08-28T18:18:08Z","description":"This is the pre-peer reviewed version of the following article: Alderighi, T., Malomo, L., Auzinger, T., Bickel, B., Cignoni, P. and Pietroni, N. (2022), State of the Art in Computational Mould Design. Computer Graphics Forum, which has been published in final form at https://doi.org/10.1111/cgf.14581. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.","content_type":"application/pdf","file_id":"11994","creator":"bbickel","title":"pre-peer reviewed version"}],"quality_controlled":"1","publication_status":"published","citation":{"ista":"Alderighi T, Malomo L, Auzinger T, Bickel B, Cignoni P, Pietroni N. 2022. State of the art in computational mould design. Computer Graphics Forum. 41(6), 435–452.","short":"T. Alderighi, L. Malomo, T. Auzinger, B. Bickel, P. Cignoni, N. Pietroni, Computer Graphics Forum 41 (2022) 435–452.","mla":"Alderighi, Thomas, et al. “State of the Art in Computational Mould Design.” <i>Computer Graphics Forum</i>, vol. 41, no. 6, Wiley, 2022, pp. 435–52, doi:<a href=\"https://doi.org/10.1111/cgf.14581\">10.1111/cgf.14581</a>.","ieee":"T. Alderighi, L. Malomo, T. Auzinger, B. Bickel, P. Cignoni, and N. Pietroni, “State of the art in computational mould design,” <i>Computer Graphics Forum</i>, vol. 41, no. 6. Wiley, pp. 435–452, 2022.","chicago":"Alderighi, Thomas, Luigi Malomo, Thomas Auzinger, Bernd Bickel, Paulo Cignoni, and Nico Pietroni. “State of the Art in Computational Mould Design.” <i>Computer Graphics Forum</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/cgf.14581\">https://doi.org/10.1111/cgf.14581</a>.","apa":"Alderighi, T., Malomo, L., Auzinger, T., Bickel, B., Cignoni, P., &#38; Pietroni, N. (2022). State of the art in computational mould design. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.14581\">https://doi.org/10.1111/cgf.14581</a>","ama":"Alderighi T, Malomo L, Auzinger T, Bickel B, Cignoni P, Pietroni N. State of the art in computational mould design. <i>Computer Graphics Forum</i>. 2022;41(6):435-452. doi:<a href=\"https://doi.org/10.1111/cgf.14581\">10.1111/cgf.14581</a>"}},{"pmid":1,"_id":"11995","acknowledgement":"The authors thank the Scientific Service Units at ISTA, in particular the Molecular Biology Service of the Lab Support Facility, Imaging & Optics Facility, and the Preclinical Facility, and the Novarino group, Harald Janoviak, and Marco Benevento for sharing reagents and expertise. This research was supported by a DOC Fellowship (24979) awarded to R.S. by the Austrian Academy of Sciences.","abstract":[{"text":"G protein-coupled receptors (GPCRs) regulate processes ranging from immune responses to neuronal signaling. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additionally, dissecting cell type-specific responses is challenging when the same GPCR is expressed on different cells within a tissue. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that bind clozapine-N-oxide and mimic a GPCR-of-interest. We show that chimeric DREADD-β2AR triggers responses comparable to β2AR on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Moreover, we successfully recapitulate β2AR-mediated filopodia formation in microglia, an immune cell capable of driving central nervous system inflammation. When dissecting microglial inflammation, we included two additional DREADD-based chimeras mimicking microglia-enriched GPR65 and GPR109A. DREADD-β2AR and DREADD-GPR65 modulate the inflammatory response with high similarity to endogenous β2AR, while DREADD-GPR109A shows no impact. Our DREADD-based approach allows investigation of cell type-dependent pathways without known endogenous ligands.","lang":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","project":[{"_id":"267F75D8-B435-11E9-9278-68D0E5697425","name":"Modulating microglia through G protein-coupled receptor (GPCR) signaling"}],"date_created":"2022-08-28T22:01:59Z","ddc":["570"],"volume":13,"file_date_updated":"2022-08-29T06:44:30Z","related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/dreaddful-mimicry/"}],"record":[{"status":"public","id":"11945","relation":"part_of_dissertation"},{"relation":"research_data","id":"11542","status":"public"}]},"article_processing_charge":"No","publication":"Nature Communications","scopus_import":"1","month":"08","language":[{"iso":"eng"}],"author":[{"full_name":"Schulz, Rouven","first_name":"Rouven","last_name":"Schulz","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5297-733X"},{"first_name":"Medina","full_name":"Korkut, Medina","last_name":"Korkut","id":"4B51CE74-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4309-2251"},{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2356-9403","last_name":"Venturino","full_name":"Venturino, Alessandro","first_name":"Alessandro"},{"orcid":"0000-0001-9434-8902","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","full_name":"Colombo, Gloria","first_name":"Gloria","last_name":"Colombo"},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","last_name":"Siegert","full_name":"Siegert, Sandra","first_name":"Sandra"}],"type":"journal_article","quality_controlled":"1","publication_status":"published","citation":{"mla":"Schulz, Rouven, et al. “Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses.” <i>Nature Communications</i>, vol. 13, 4728, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-32390-1\">10.1038/s41467-022-32390-1</a>.","short":"R. Schulz, M. Korkut, A. Venturino, G. Colombo, S. Siegert, Nature Communications 13 (2022).","ieee":"R. Schulz, M. Korkut, A. Venturino, G. Colombo, and S. Siegert, “Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","ista":"Schulz R, Korkut M, Venturino A, Colombo G, Siegert S. 2022. Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses. Nature Communications. 13, 4728.","ama":"Schulz R, Korkut M, Venturino A, Colombo G, Siegert S. Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-32390-1\">10.1038/s41467-022-32390-1</a>","apa":"Schulz, R., Korkut, M., Venturino, A., Colombo, G., &#38; Siegert, S. (2022). Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-32390-1\">https://doi.org/10.1038/s41467-022-32390-1</a>","chicago":"Schulz, Rouven, Medina Korkut, Alessandro Venturino, Gloria Colombo, and Sandra Siegert. “Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-32390-1\">https://doi.org/10.1038/s41467-022-32390-1</a>."},"date_published":"2022-08-15T00:00:00Z","article_type":"original","department":[{"_id":"SaSi"}],"file":[{"file_id":"12002","content_type":"application/pdf","date_created":"2022-08-29T06:44:30Z","success":1,"creator":"cchlebak","date_updated":"2022-08-29T06:44:30Z","file_name":"2022_NatComm_Schulz.pdf","relation":"main_file","access_level":"open_access","file_size":7317396,"checksum":"191d9db0266e14a28d3a56dc7f65da84"}],"oa_version":"Published Version","year":"2022","title":"Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses","has_accepted_license":"1","publication_identifier":{"eissn":["2041-1723"]},"isi":1,"article_number":"4728","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"15","doi":"10.1038/s41467-022-32390-1","date_updated":"2024-02-21T12:34:51Z","status":"public","intvolume":"        13","oa":1,"external_id":{"isi":["000840984400032"],"pmid":["35970889"]}},{"external_id":{"pmid":["35951689 "]},"date_updated":"2022-09-05T07:37:37Z","intvolume":"       377","status":"public","title":"A soft active matter that can climb walls","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"issue":"6607","doi":"10.1126/science.adc9202","day":"12","year":"2022","department":[{"_id":"JePa"}],"oa_version":"None","article_type":"letter_note","date_published":"2022-08-12T00:00:00Z","citation":{"chicago":"Palacci, Jérémie A. “A Soft Active Matter That Can Climb Walls.” <i>Science</i>. American Association for the Advancement of Science, 2022. <a href=\"https://doi.org/10.1126/science.adc9202\">https://doi.org/10.1126/science.adc9202</a>.","ama":"Palacci JA. A soft active matter that can climb walls. <i>Science</i>. 2022;377(6607):710-711. doi:<a href=\"https://doi.org/10.1126/science.adc9202\">10.1126/science.adc9202</a>","apa":"Palacci, J. A. (2022). A soft active matter that can climb walls. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adc9202\">https://doi.org/10.1126/science.adc9202</a>","ista":"Palacci JA. 2022. A soft active matter that can climb walls. Science. 377(6607), 710–711.","ieee":"J. A. Palacci, “A soft active matter that can climb walls,” <i>Science</i>, vol. 377, no. 6607. American Association for the Advancement of Science, pp. 710–711, 2022.","short":"J.A. Palacci, Science 377 (2022) 710–711.","mla":"Palacci, Jérémie A. “A Soft Active Matter That Can Climb Walls.” <i>Science</i>, vol. 377, no. 6607, American Association for the Advancement of Science, 2022, pp. 710–11, doi:<a href=\"https://doi.org/10.1126/science.adc9202\">10.1126/science.adc9202</a>."},"publication_status":"published","quality_controlled":"1","type":"journal_article","month":"08","author":[{"last_name":"Palacci","full_name":"Palacci, Jérémie A","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"}],"language":[{"iso":"eng"}],"publication":"Science","article_processing_charge":"No","scopus_import":"1","volume":377,"page":"710-711","date_created":"2022-08-28T22:02:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Association for the Advancement of Science","abstract":[{"lang":"eng","text":"If you mix fruit syrups with alcohol to make a schnapps, the two liquids will remain perfectly blended forever. But if you mix oil with vinegar to make a vinaigrette, the oil and vinegar will soon separate back into their previous selves. Such liquid-liquid phase separation is a thermodynamically driven phenomenon and plays an important role in many biological processes (1). Although energy injection at the macroscale can reverse the phase separation—a strong shake is the normal response to a separated vinaigrette—little is known about the effect of energy added at the microscopic level on phase separation. This fundamental question has deep ramifications, notably in biology, because active processes also make the interior of a living cell different from a dead one. On page 768 of this issue, Adkins et al. (2) examine how mechanical activity at the microscopic scale affects liquid-liquid phase separation and allows liquids to climb surfaces."}],"pmid":1,"_id":"11996"},{"scopus_import":"1","publication":"Physical Review A","article_processing_charge":"No","type":"journal_article","month":"08","language":[{"iso":"eng"}],"author":[{"last_name":"Bighin","full_name":"Bighin, Giacomo","first_name":"Giacomo","orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Burchianti","first_name":"A.","full_name":"Burchianti, A."},{"last_name":"Minardi","full_name":"Minardi, F.","first_name":"F."},{"first_name":"T.","full_name":"Macrì, T.","last_name":"Macrì"}],"date_created":"2022-08-28T22:02:00Z","volume":106,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2109.07451"}],"project":[{"name":"A path-integral approach to composite impurities","_id":"26986C82-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02641"}],"publisher":"American Physical Society","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We thank A. Simoni for providing the calculations of the intercomponent scattering lengths. We gratefully acknowledge stimulating discussions with L. A. Peña Ardila, R. Schmidt, H. Silva, V. Zampronio, and M. Prevedelli for careful reading. G.B. acknowledges support from the Austrian Science Fund (FWF) under Project No. M2641-N27. T.M. acknowledges CNPq for support through Bolsa de produtividade em Pesquisa No. 311079/2015-6. This work is supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy No. EXC2181/1-390900948 (the Heidelberg STRUCTURES Excellence Cluster). This work was supported by the Serrapilheira Institute (Grant No. Serra-1812-27802). We thank the High-Performance Computing Center (NPAD) at UFRN for providing computational resources.","_id":"11997","abstract":[{"lang":"eng","text":"We study the fate of an impurity in an ultracold heteronuclear Bose mixture, focusing on the experimentally relevant case of a ⁴¹K - ⁸⁷Rb mixture, with the impurity in a ⁴¹K hyperfine state. Our paper provides a comprehensive description of an impurity in a BEC mixture with contact interactions across its phase diagram. We present results for the miscible and immiscible regimes, as well as for the impurity in a self-bound quantum droplet. Here, varying the interactions, we find exotic states where the impurity localizes either at the center or\r\nat the surface of the droplet. "}],"intvolume":"       106","status":"public","date_updated":"2024-08-07T07:16:52Z","external_id":{"arxiv":["2109.07451"],"isi":["000837953600006"]},"oa":1,"year":"2022","doi":"10.1103/PhysRevA.106.023301","day":"04","article_number":"023301","isi":1,"title":"Impurity in a heteronuclear two-component Bose mixture","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"issue":"2","article_type":"original","date_published":"2022-08-04T00:00:00Z","oa_version":"Preprint","department":[{"_id":"MiLe"}],"quality_controlled":"1","arxiv":1,"publication_status":"published","citation":{"chicago":"Bighin, Giacomo, A. Burchianti, F. Minardi, and T. Macrì. “Impurity in a Heteronuclear Two-Component Bose Mixture.” <i>Physical Review A</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevA.106.023301\">https://doi.org/10.1103/PhysRevA.106.023301</a>.","ama":"Bighin G, Burchianti A, Minardi F, Macrì T. Impurity in a heteronuclear two-component Bose mixture. <i>Physical Review A</i>. 2022;106(2). doi:<a href=\"https://doi.org/10.1103/PhysRevA.106.023301\">10.1103/PhysRevA.106.023301</a>","apa":"Bighin, G., Burchianti, A., Minardi, F., &#38; Macrì, T. (2022). Impurity in a heteronuclear two-component Bose mixture. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.106.023301\">https://doi.org/10.1103/PhysRevA.106.023301</a>","ista":"Bighin G, Burchianti A, Minardi F, Macrì T. 2022. Impurity in a heteronuclear two-component Bose mixture. Physical Review A. 106(2), 023301.","ieee":"G. Bighin, A. Burchianti, F. Minardi, and T. Macrì, “Impurity in a heteronuclear two-component Bose mixture,” <i>Physical Review A</i>, vol. 106, no. 2. American Physical Society, 2022.","short":"G. Bighin, A. Burchianti, F. Minardi, T. Macrì, Physical Review A 106 (2022).","mla":"Bighin, Giacomo, et al. “Impurity in a Heteronuclear Two-Component Bose Mixture.” <i>Physical Review A</i>, vol. 106, no. 2, 023301, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevA.106.023301\">10.1103/PhysRevA.106.023301</a>."}},{"file":[{"creator":"alisjak","file_id":"12005","content_type":"application/pdf","date_created":"2022-08-29T09:57:40Z","success":1,"file_name":"2022_NewJournalofPhysics_Cherepanov.pdf","relation":"main_file","access_level":"open_access","file_size":1912882,"checksum":"10116a08d3489befc13dba2cc44490f1","date_updated":"2022-08-29T09:57:40Z"}],"oa_version":"Published Version","department":[{"_id":"MiLe"}],"article_type":"original","date_published":"2022-08-11T00:00:00Z","publication_status":"published","citation":{"ista":"Cherepanov I, Bighin G, Schouder CA, Chatterley AS, Stapelfeldt H, Lemeshko M. 2022. A simple model for high rotational excitations of molecules in a superfluid. New Journal of Physics. 24(7), 075004.","ieee":"I. Cherepanov, G. Bighin, C. A. Schouder, A. S. Chatterley, H. Stapelfeldt, and M. Lemeshko, “A simple model for high rotational excitations of molecules in a superfluid,” <i>New Journal of Physics</i>, vol. 24, no. 7. IOP, 2022.","short":"I. Cherepanov, G. Bighin, C.A. Schouder, A.S. Chatterley, H. Stapelfeldt, M. Lemeshko, New Journal of Physics 24 (2022).","mla":"Cherepanov, Igor, et al. “A Simple Model for High Rotational Excitations of Molecules in a Superfluid.” <i>New Journal of Physics</i>, vol. 24, no. 7, 075004, IOP, 2022, doi:<a href=\"https://doi.org/10.1088/1367-2630/ac8113\">10.1088/1367-2630/ac8113</a>.","chicago":"Cherepanov, Igor, Giacomo Bighin, Constant A. Schouder, Adam S. Chatterley, Henrik Stapelfeldt, and Mikhail Lemeshko. “A Simple Model for High Rotational Excitations of Molecules in a Superfluid.” <i>New Journal of Physics</i>. IOP, 2022. <a href=\"https://doi.org/10.1088/1367-2630/ac8113\">https://doi.org/10.1088/1367-2630/ac8113</a>.","apa":"Cherepanov, I., Bighin, G., Schouder, C. A., Chatterley, A. S., Stapelfeldt, H., &#38; Lemeshko, M. (2022). A simple model for high rotational excitations of molecules in a superfluid. <i>New Journal of Physics</i>. IOP. <a href=\"https://doi.org/10.1088/1367-2630/ac8113\">https://doi.org/10.1088/1367-2630/ac8113</a>","ama":"Cherepanov I, Bighin G, Schouder CA, Chatterley AS, Stapelfeldt H, Lemeshko M. A simple model for high rotational excitations of molecules in a superfluid. <i>New Journal of Physics</i>. 2022;24(7). doi:<a href=\"https://doi.org/10.1088/1367-2630/ac8113\">10.1088/1367-2630/ac8113</a>"},"quality_controlled":"1","external_id":{"isi":["000839216900001"]},"oa":1,"intvolume":"        24","status":"public","date_updated":"2024-08-07T07:16:52Z","day":"11","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_number":"075004","doi":"10.1088/1367-2630/ac8113","isi":1,"issue":"7","title":"A simple model for high rotational excitations of molecules in a superfluid","publication_identifier":{"issn":["1367-2630"]},"has_accepted_license":"1","year":"2022","project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle"},{"call_identifier":"FWF","grant_number":"M02641","name":"A path-integral approach to composite impurities","_id":"26986C82-B435-11E9-9278-68D0E5697425"}],"publisher":"IOP","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ec_funded":1,"abstract":[{"lang":"eng","text":"Recently it became possible to study highly excited rotational states of molecules in superfluid helium through nonadiabatic alignment experiments (Cherepanov et al 2021 Phys. Rev. A 104 L061303). This calls for theoretical approaches that go beyond explaining renormalized values of molecular spectroscopic constants, which suffices when only the lowest few rotational states are involved. As the first step in this direction, here we present a basic quantum mechanical model describing highly excited rotational states of molecules in superfluid helium nanodroplets. We show that a linear molecule immersed in a superfluid can be seen as an effective symmetric top, similar to the rotational structure of radicals, such as OH or NO, but with the angular momentum of the superfluid playing the role of the electronic angular momentum in free molecules. The simple theory sheds light onto what happens when the rotational angular momentum of the molecule increases beyond the lowest excited states accessible by infrared spectroscopy. In addition, the model allows to estimate the effective rotational and centrifugal distortion constants for a broad range of species and to explain the crossover between light and heavy molecules in superfluid 4He in terms of the many-body wavefunction structure. Some of the above mentioned insights can be acquired by analyzing a simple 2 × 2 matrix."}],"acknowledgement":"IC acknowledges the support by the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. GB acknowledges support from the Austrian Science Fund (FWF), under Project No. M2461-N27 and from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy EXC2181/1-390900948 (the Heidelberg STRUCTURES Excellence Cluster). ML acknowledges support by the Austrian Science Fund (FWF), under Project No. P29902-N27, and by the European Research Council (ERC) starting Grant No. 801770 (ANGULON). HS acknowledges support from the Independent Research Fund Denmark (Project No. 8021-00232B) and from the Villum Fonden through a Villum Investigator Grant No. 25886.","_id":"11998","type":"journal_article","month":"08","language":[{"iso":"eng"}],"author":[{"id":"339C7E5A-F248-11E8-B48F-1D18A9856A87","last_name":"Cherepanov","first_name":"Igor","full_name":"Cherepanov, Igor"},{"last_name":"Bighin","first_name":"Giacomo","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Constant A.","full_name":"Schouder, Constant A.","last_name":"Schouder"},{"full_name":"Chatterley, Adam S.","first_name":"Adam S.","last_name":"Chatterley"},{"first_name":"Henrik","full_name":"Stapelfeldt, Henrik","last_name":"Stapelfeldt"},{"full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"}],"scopus_import":"1","publication":"New Journal of Physics","article_processing_charge":"Yes","file_date_updated":"2022-08-29T09:57:40Z","ddc":["530"],"volume":24,"date_created":"2022-08-28T22:02:01Z"},{"publication":"Proceedings of the 34th International Conference on Computer Aided Verification","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","type":"conference","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","last_name":"Goharshady","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-1712-2165","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","full_name":"Meggendorfer, Tobias","first_name":"Tobias","last_name":"Meggendorfer"},{"full_name":"Zikelic, Dorde","first_name":"Dorde","last_name":"Zikelic","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"conference":{"start_date":"2022-08-07","end_date":"2022-08-10","location":"Haifa, Israel","name":"CAV: Computer Aided Verification"},"month":"08","page":"55-78","date_created":"2022-08-28T22:02:02Z","related_material":{"record":[{"status":"public","id":"14539","relation":"dissertation_contains"}]},"file_date_updated":"2022-08-29T09:17:01Z","volume":13371,"ddc":["000"],"ec_funded":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"publisher":"Springer","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt), the HKUST-Kaisa Joint Research Institute Project Grant HKJRI3A-055, the HKUST Startup Grant R9272 and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","alternative_title":["LNCS"],"_id":"12000","abstract":[{"lang":"eng","text":"We consider the quantitative problem of obtaining lower-bounds on the probability of termination of a given non-deterministic probabilistic program. Specifically, given a non-termination threshold p∈[0,1], we aim for certificates proving that the program terminates with probability at least 1−p. The basic idea of our approach is to find a terminating stochastic invariant, i.e. a subset SI of program states such that (i) the probability of the program ever leaving SI is no more than p, and (ii) almost-surely, the program either leaves SI or terminates.\r\n\r\nWhile stochastic invariants are already well-known, we provide the first proof that the idea above is not only sound, but also complete for quantitative termination analysis. We then introduce a novel sound and complete characterization of stochastic invariants that enables template-based approaches for easy synthesis of quantitative termination certificates, especially in affine or polynomial forms. Finally, by combining this idea with the existing martingale-based methods that are relatively complete for qualitative termination analysis, we obtain the first automated, sound, and relatively complete algorithm for quantitative termination analysis. Notably, our completeness guarantees for quantitative termination analysis are as strong as the best-known methods for the qualitative variant.\r\n\r\nOur prototype implementation demonstrates the effectiveness of our approach on various probabilistic programs. We also demonstrate that our algorithm certifies lower bounds on termination probability for probabilistic programs that are beyond the reach of previous methods."}],"date_updated":"2025-07-14T09:09:58Z","intvolume":"     13371","status":"public","oa":1,"external_id":{"isi":["000870304500004"]},"year":"2022","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031131844"],"eissn":["1611-3349"]},"has_accepted_license":"1","title":"Sound and complete certificates for auantitative termination analysis of probabilistic programs","day":"07","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi":"10.1007/978-3-031-13185-1_4","isi":1,"date_published":"2022-08-07T00:00:00Z","department":[{"_id":"KrCh"}],"file":[{"file_id":"12003","content_type":"application/pdf","date_created":"2022-08-29T09:17:01Z","success":1,"creator":"alisjak","date_updated":"2022-08-29T09:17:01Z","file_name":"2022_LNCS_Chatterjee.pdf","relation":"main_file","access_level":"open_access","file_size":505094,"checksum":"24e0f810ec52735a90ade95198bc641d"}],"oa_version":"Published Version","quality_controlled":"1","publication_status":"published","citation":{"chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Tobias Meggendorfer, and Dorde Zikelic. “Sound and Complete Certificates for Auantitative Termination Analysis of Probabilistic Programs.” In <i>Proceedings of the 34th International Conference on Computer Aided Verification</i>, 13371:55–78. Springer, 2022. <a href=\"https://doi.org/10.1007/978-3-031-13185-1_4\">https://doi.org/10.1007/978-3-031-13185-1_4</a>.","apa":"Chatterjee, K., Goharshady, A. K., Meggendorfer, T., &#38; Zikelic, D. (2022). Sound and complete certificates for auantitative termination analysis of probabilistic programs. In <i>Proceedings of the 34th International Conference on Computer Aided Verification</i> (Vol. 13371, pp. 55–78). Haifa, Israel: Springer. <a href=\"https://doi.org/10.1007/978-3-031-13185-1_4\">https://doi.org/10.1007/978-3-031-13185-1_4</a>","ama":"Chatterjee K, Goharshady AK, Meggendorfer T, Zikelic D. Sound and complete certificates for auantitative termination analysis of probabilistic programs. In: <i>Proceedings of the 34th International Conference on Computer Aided Verification</i>. Vol 13371. Springer; 2022:55-78. doi:<a href=\"https://doi.org/10.1007/978-3-031-13185-1_4\">10.1007/978-3-031-13185-1_4</a>","ista":"Chatterjee K, Goharshady AK, Meggendorfer T, Zikelic D. 2022. Sound and complete certificates for auantitative termination analysis of probabilistic programs. Proceedings of the 34th International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13371, 55–78.","mla":"Chatterjee, Krishnendu, et al. “Sound and Complete Certificates for Auantitative Termination Analysis of Probabilistic Programs.” <i>Proceedings of the 34th International Conference on Computer Aided Verification</i>, vol. 13371, Springer, 2022, pp. 55–78, doi:<a href=\"https://doi.org/10.1007/978-3-031-13185-1_4\">10.1007/978-3-031-13185-1_4</a>.","short":"K. Chatterjee, A.K. Goharshady, T. Meggendorfer, D. Zikelic, in:, Proceedings of the 34th International Conference on Computer Aided Verification, Springer, 2022, pp. 55–78.","ieee":"K. Chatterjee, A. K. Goharshady, T. Meggendorfer, and D. Zikelic, “Sound and complete certificates for auantitative termination analysis of probabilistic programs,” in <i>Proceedings of the 34th International Conference on Computer Aided Verification</i>, Haifa, Israel, 2022, vol. 13371, pp. 55–78."}},{"volume":6,"ddc":["570"],"file_date_updated":"2023-02-27T07:17:42Z","page":"358-374","date_created":"2022-08-28T22:02:02Z","month":"10","author":[{"last_name":"Hearn","full_name":"Hearn, Katherine E.","first_name":"Katherine E."},{"first_name":"Eva L.","full_name":"Koch, Eva L.","last_name":"Koch"},{"first_name":"Sean","full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"Yes","publication":"Evolution Letters","scopus_import":"1","abstract":[{"lang":"eng","text":"Sexual antagonism is a common hypothesis for driving the evolution of sex chromosomes, whereby recombination suppression is favored between sexually antagonistic loci and the sex-determining locus to maintain beneficial combinations of alleles. This results in the formation of a sex-determining region. Chromosomal inversions may contribute to recombination suppression but their precise role in sex chromosome evolution remains unclear. Because local adaptation is frequently facilitated through the suppression of recombination between adaptive loci by chromosomal inversions, there is potential for inversions that cover sex-determining regions to be involved in local adaptation as well, particularly if habitat variation creates environment-dependent sexual antagonism. With these processes in mind, we investigated sex determination in a well-studied example of local adaptation within a species: the intertidal snail, Littorina saxatilis. Using SNP data from a Swedish hybrid zone, we find novel evidence for a female-heterogametic sex determination system that is restricted to one ecotype. Our results suggest that four putative chromosomal inversions, two previously described and two newly discovered, span the putative sex chromosome pair. We determine their differing associations with sex, which suggest distinct strata of differing ages. The same inversions are found in the second ecotype but do not show any sex association. The striking disparity in inversion-sex associations between ecotypes that are connected by gene flow across a habitat transition that is just a few meters wide indicates a difference in selective regime that has produced a distinct barrier to the spread of the newly discovered sex-determining region between ecotypes. Such sex chromosome-environment interactions have not previously been uncovered in L. saxatilis and are known in few other organisms. A combination of both sex-specific selection and divergent natural selection is required to explain these highly unusual patterns."}],"_id":"12001","acknowledgement":"We thank A. Wright and four anonymous reviewers for valuable comments on an earlier draft of this manuscript and all members of the Littorina group for helpful discussions. This work was supported by a European Research Council grant to RKB and by a Natural Environment Research Council studentship to KEH through the ACCE doctoral training program. KJ acknowledges support from the Swedish Science Research Council VR (Vetenskaprådet) (2017-03798). RF was supported by an FCT CEEC (Fundação para a Ciênca e a Tecnologia, Concurso Estímulo ao Emprego Científico) contract (2020.00275.CEECIND).","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Oxford Academic","issue":"5","has_accepted_license":"1","title":"Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis","publication_identifier":{"eissn":["2056-3744"]},"isi":1,"day":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi":"10.1002/evl3.295","year":"2022","oa":1,"external_id":{"isi":["000839621100001"]},"date_updated":"2023-08-03T13:18:17Z","status":"public","intvolume":"         6","publication_status":"published","citation":{"mla":"Hearn, Katherine E., et al. “Differing Associations between Sex Determination and Sex-Linked Inversions in Two Ecotypes of Littorina Saxatilis.” <i>Evolution Letters</i>, vol. 6, no. 5, Oxford Academic, 2022, pp. 358–74, doi:<a href=\"https://doi.org/10.1002/evl3.295\">10.1002/evl3.295</a>.","short":"K.E. Hearn, E.L. Koch, S. Stankowski, R.K. Butlin, R. Faria, K. Johannesson, A.M. Westram, Evolution Letters 6 (2022) 358–374.","ieee":"K. E. Hearn <i>et al.</i>, “Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis,” <i>Evolution Letters</i>, vol. 6, no. 5. Oxford Academic, pp. 358–374, 2022.","ista":"Hearn KE, Koch EL, Stankowski S, Butlin RK, Faria R, Johannesson K, Westram AM. 2022. Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. Evolution Letters. 6(5), 358–374.","ama":"Hearn KE, Koch EL, Stankowski S, et al. Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. <i>Evolution Letters</i>. 2022;6(5):358-374. doi:<a href=\"https://doi.org/10.1002/evl3.295\">10.1002/evl3.295</a>","apa":"Hearn, K. E., Koch, E. L., Stankowski, S., Butlin, R. K., Faria, R., Johannesson, K., &#38; Westram, A. M. (2022). Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. <i>Evolution Letters</i>. Oxford Academic. <a href=\"https://doi.org/10.1002/evl3.295\">https://doi.org/10.1002/evl3.295</a>","chicago":"Hearn, Katherine E., Eva L. Koch, Sean Stankowski, Roger K. Butlin, Rui Faria, Kerstin Johannesson, and Anja M Westram. “Differing Associations between Sex Determination and Sex-Linked Inversions in Two Ecotypes of Littorina Saxatilis.” <i>Evolution Letters</i>. Oxford Academic, 2022. <a href=\"https://doi.org/10.1002/evl3.295\">https://doi.org/10.1002/evl3.295</a>."},"quality_controlled":"1","department":[{"_id":"NiBa"}],"file":[{"success":1,"date_created":"2023-02-27T07:17:42Z","content_type":"application/pdf","file_id":"12686","creator":"dernst","date_updated":"2023-02-27T07:17:42Z","checksum":"2dcd06186a11b7d1be4cddc6b189f8fb","file_size":2368965,"access_level":"open_access","relation":"main_file","file_name":"2022_EvolutionLetters_Hearn.pdf"}],"oa_version":"Published Version","date_published":"2022-10-01T00:00:00Z","article_type":"original"},{"citation":{"ista":"Jia DW, Vogels TP, Costa RP. 2022. Developmental depression-to-facilitation shift controls excitation-inhibition balance. Communications biology. 5, 873.","ieee":"D. W. Jia, T. P. Vogels, and R. P. Costa, “Developmental depression-to-facilitation shift controls excitation-inhibition balance,” <i>Communications biology</i>, vol. 5. Springer Nature, 2022.","mla":"Jia, David W., et al. “Developmental Depression-to-Facilitation Shift Controls Excitation-Inhibition Balance.” <i>Communications Biology</i>, vol. 5, 873, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s42003-022-03801-2\">10.1038/s42003-022-03801-2</a>.","short":"D.W. Jia, T.P. Vogels, R.P. Costa, Communications Biology 5 (2022).","chicago":"Jia, David W., Tim P Vogels, and Rui Ponte Costa. “Developmental Depression-to-Facilitation Shift Controls Excitation-Inhibition Balance.” <i>Communications Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s42003-022-03801-2\">https://doi.org/10.1038/s42003-022-03801-2</a>.","ama":"Jia DW, Vogels TP, Costa RP. Developmental depression-to-facilitation shift controls excitation-inhibition balance. <i>Communications biology</i>. 2022;5. doi:<a href=\"https://doi.org/10.1038/s42003-022-03801-2\">10.1038/s42003-022-03801-2</a>","apa":"Jia, D. W., Vogels, T. P., &#38; Costa, R. P. (2022). Developmental depression-to-facilitation shift controls excitation-inhibition balance. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-022-03801-2\">https://doi.org/10.1038/s42003-022-03801-2</a>"},"publication_status":"published","quality_controlled":"1","department":[{"_id":"TiVo"}],"file":[{"date_updated":"2022-09-05T08:55:11Z","file_name":"2022_CommBiology_Jia.pdf","access_level":"open_access","relation":"main_file","checksum":"3ec724c4f6d3440028c217305e32915f","file_size":2491191,"file_id":"12022","content_type":"application/pdf","success":1,"date_created":"2022-09-05T08:55:11Z","creator":"dernst"}],"oa_version":"Published Version","date_published":"2022-08-25T00:00:00Z","article_type":"original","title":"Developmental depression-to-facilitation shift controls excitation-inhibition balance","publication_identifier":{"eissn":["2399-3642"]},"has_accepted_license":"1","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi":"10.1038/s42003-022-03801-2","article_number":"873","day":"25","year":"2022","oa":1,"external_id":{"isi":["000844814800007"]},"date_updated":"2023-08-03T13:22:42Z","status":"public","intvolume":"         5","abstract":[{"text":"Changes in the short-term dynamics of excitatory synapses over development have been observed throughout cortex, but their purpose and consequences remain unclear. Here, we propose that developmental changes in synaptic dynamics buffer the effect of slow inhibitory long-term plasticity, allowing for continuously stable neural activity. Using computational modeling we demonstrate that early in development excitatory short-term depression quickly stabilises neural activity, even in the face of strong, unbalanced excitation. We introduce a model of the commonly observed developmental shift from depression to facilitation and show that neural activity remains stable throughout development, while inhibitory synaptic plasticity slowly balances excitation, consistent with experimental observations. Our model predicts changes in the input responses from phasic to phasic-and-tonic and more precise spike timings. We also observe a gradual emergence of short-lasting memory traces governed by short-term plasticity development. We conclude that the developmental depression-to-facilitation shift may control excitation-inhibition balance throughout development with important functional consequences.","lang":"eng"}],"_id":"12009","acknowledgement":"We would like to thank the Vogels Lab for feedback on an earlier version of this manuscript. D.W.J. was supported by a Marshall Scholarship and a Clarendon Scholarship. R.P.C. and T.P.V. were supported by a Wellcome Trust and Royal Society Sir Henry Dale Fellowship (WT 100000), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z), and an ERC Consolidator Grant (SYNAPSEEK).","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","project":[{"_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks.","grant_number":"214316/Z/18/Z"},{"grant_number":"819603","call_identifier":"H2020","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning."}],"ec_funded":1,"ddc":["570"],"volume":5,"file_date_updated":"2022-09-05T08:55:11Z","date_created":"2022-09-04T22:02:02Z","language":[{"iso":"eng"}],"author":[{"last_name":"Jia","first_name":"David W.","full_name":"Jia, David W."},{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","last_name":"Vogels","full_name":"Vogels, Tim P","first_name":"Tim P"},{"last_name":"Costa","full_name":"Costa, Rui Ponte","first_name":"Rui Ponte"}],"month":"08","type":"journal_article","article_processing_charge":"No","publication":"Communications biology","scopus_import":"1"}]