[{"project":[{"_id":"25E549F4-B435-11E9-9278-68D0E5697425","grant_number":"320593","call_identifier":"FP7","name":"Arithmetic and physics of Higgs moduli spaces"},{"_id":"25E6C798-B435-11E9-9278-68D0E5697425","grant_number":"153627","name":"Arithmetic quantization of character and quiver varities"}],"external_id":{"isi":["001049312700001"],"arxiv":["1807.04057"]},"title":"Arithmetic and metric aspects of open de Rham spaces","has_accepted_license":"1","issue":"4","citation":{"ama":"Hausel T, Wong ML, Wyss D. Arithmetic and metric aspects of open de Rham spaces. <i>Proceedings of the London Mathematical Society</i>. 2023;127(4):958-1027. doi:<a href=\"https://doi.org/10.1112/plms.12555\">10.1112/plms.12555</a>","apa":"Hausel, T., Wong, M. L., &#38; Wyss, D. (2023). Arithmetic and metric aspects of open de Rham spaces. <i>Proceedings of the London Mathematical Society</i>. Wiley. <a href=\"https://doi.org/10.1112/plms.12555\">https://doi.org/10.1112/plms.12555</a>","ieee":"T. Hausel, M. L. Wong, and D. Wyss, “Arithmetic and metric aspects of open de Rham spaces,” <i>Proceedings of the London Mathematical Society</i>, vol. 127, no. 4. Wiley, pp. 958–1027, 2023.","mla":"Hausel, Tamás, et al. “Arithmetic and Metric Aspects of Open de Rham Spaces.” <i>Proceedings of the London Mathematical Society</i>, vol. 127, no. 4, Wiley, 2023, pp. 958–1027, doi:<a href=\"https://doi.org/10.1112/plms.12555\">10.1112/plms.12555</a>.","ista":"Hausel T, Wong ML, Wyss D. 2023. Arithmetic and metric aspects of open de Rham spaces. Proceedings of the London Mathematical Society. 127(4), 958–1027.","chicago":"Hausel, Tamás, Michael Lennox Wong, and Dimitri Wyss. “Arithmetic and Metric Aspects of Open de Rham Spaces.” <i>Proceedings of the London Mathematical Society</i>. Wiley, 2023. <a href=\"https://doi.org/10.1112/plms.12555\">https://doi.org/10.1112/plms.12555</a>.","short":"T. Hausel, M.L. Wong, D. Wyss, Proceedings of the London Mathematical Society 127 (2023) 958–1027."},"date_updated":"2024-01-30T12:56:10Z","author":[{"first_name":"Tamás","last_name":"Hausel","full_name":"Hausel, Tamás","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael Lennox","last_name":"Wong","full_name":"Wong, Michael Lennox"},{"last_name":"Wyss","first_name":"Dimitri","full_name":"Wyss, Dimitri"}],"day":"01","publication":"Proceedings of the London Mathematical Society","publication_identifier":{"eissn":["1460-244X"],"issn":["0024-6115"]},"oa":1,"article_type":"original","publication_status":"published","file":[{"content_type":"application/pdf","file_size":651335,"checksum":"2af4d2d6a8ae42f7d3fba0188e79ae82","creator":"dernst","access_level":"open_access","success":1,"relation":"main_file","date_created":"2024-01-30T12:56:00Z","file_id":"14910","file_name":"2023_ProcLondonMathSoc_Hausel.pdf","date_updated":"2024-01-30T12:56:00Z"}],"abstract":[{"lang":"eng","text":"In this paper, we determine the motivic class — in particular, the weight polynomial and conjecturally the Poincaré polynomial — of the open de Rham space, defined and studied by Boalch, of certain moduli spaces of irregular meromorphic connections on the trivial rank \r\n bundle on P1. The computation is by motivic Fourier transform. We show that the result satisfies the purity conjecture, that is, it agrees with the pure part of the conjectured mixed Hodge polynomial of the corresponding wild character variety. We also identify the open de Rham spaces with quiver varieties with multiplicities of Yamakawa and Geiss–Leclerc–Schröer. We finish with constructing natural complete hyperkähler metrics on them, which in the four-dimensional cases are expected to be of type ALF."}],"quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","ec_funded":1,"date_created":"2023-08-27T22:01:18Z","year":"2023","_id":"14244","doi":"10.1112/plms.12555","date_published":"2023-10-01T00:00:00Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","ddc":["510"],"intvolume":"       127","type":"journal_article","volume":127,"file_date_updated":"2024-01-30T12:56:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","department":[{"_id":"TaHa"}],"month":"10","isi":1,"arxiv":1,"page":"958-1027","acknowledgement":"We would like to thank Gergely Bérczy, Roger Bielawski, Philip Boalch, Sergey Cherkis, Andrew Dancer, Brent Doran, Eloïse Hamilton, Frances Kirwan, Bernard Leclerc, Emmanuel Letellier, Alessia Mandini, Maxence Mayrand, András Némethi, Szilárd Szabó, and Daisuke Yamakawa for discussions related to the paper. We especially thank the referee for an extensive list of very careful comments. At various stages of this project, the authors were supported by the Advanced Grant “Arithmetic and physics of Higgs moduli spaces” no. 320593 of the European Research Council, by grant no. 153627 and NCCR SwissMAP, both funded by the Swiss National Science Foundation as well as by EPF Lausanne and IST Austria. In the final stages of this project, MLW was supported by SFB/TR 45 “Periods, moduli and arithmetic of algebraic varieties,” subproject M08-10 “Moduli of vector bundles on higher-dimensional varieties.” DW was also supported by the Fondation Sciences Mathématiques de Paris, as well as public grants overseen by the Agence national de la recherche (ANR) of France as part of the Investissements d'avenir program, under reference numbers ANR-10-LABX-0098 and ANR-15-CE40-0008 (Défigéo).","scopus_import":"1"},{"quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"Yes","article_type":"original","publication_status":"published","file":[{"file_name":"2023_PacificJourMaths_Horesh.pdf","file_id":"14267","success":1,"date_created":"2023-09-05T07:26:17Z","relation":"main_file","date_updated":"2023-09-05T07:26:17Z","checksum":"a675b53cfb31fa46be1e879b7e77fe8c","file_size":654895,"content_type":"application/pdf","access_level":"open_access","creator":"dernst"}],"abstract":[{"lang":"eng","text":"We establish effective counting results for lattice points in families of domains in real, complex and quaternionic hyperbolic spaces of any dimension. The domains we focus on are defined as product sets with respect to an Iwasawa decomposition. Several natural diophantine problems can be reduced to counting lattice points in such domains. These include equidistribution of the ratio of the length of the shortest solution (x,y) to the gcd equation bx−ay=1 relative to the length of (a,b), where (a,b) ranges over primitive vectors in a disc whose radius increases, the natural analog of this problem in imaginary quadratic number fields, as well as equidistribution of integral solutions to the diophantine equation defined by an integral Lorentz form in three or more variables. We establish an effective rate of convergence for these equidistribution problems, depending on the size of the spectral gap associated with a suitable lattice subgroup in the isometry group of the relevant hyperbolic space. The main result underlying our discussion amounts to establishing effective joint equidistribution for the horospherical component and the radial component in the Iwasawa decomposition of lattice elements."}],"date_created":"2023-08-27T22:01:18Z","year":"2023","_id":"14245","has_accepted_license":"1","issue":"2","external_id":{"arxiv":["1612.08215"],"isi":["001047690500001"]},"title":"Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution","day":"26","publication":"Pacific Journal of Mathematics","publication_identifier":{"eissn":["1945-5844"],"issn":["0030-8730"]},"oa":1,"date_updated":"2023-12-13T12:19:42Z","author":[{"id":"C8B7BF48-8D81-11E9-BCA9-F536E6697425","full_name":"Horesh, Tal","first_name":"Tal","last_name":"Horesh"},{"last_name":"Nevo","first_name":"Amos","full_name":"Nevo, Amos"}],"citation":{"mla":"Horesh, Tal, and Amos Nevo. “Horospherical Coordinates of Lattice Points in Hyperbolic Spaces: Effective Counting and Equidistribution.” <i>Pacific Journal of Mathematics</i>, vol. 324, no. 2, Mathematical Sciences Publishers, 2023, pp. 265–94, doi:<a href=\"https://doi.org/10.2140/pjm.2023.324.265\">10.2140/pjm.2023.324.265</a>.","apa":"Horesh, T., &#38; Nevo, A. (2023). Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution. <i>Pacific Journal of Mathematics</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/pjm.2023.324.265\">https://doi.org/10.2140/pjm.2023.324.265</a>","ama":"Horesh T, Nevo A. Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution. <i>Pacific Journal of Mathematics</i>. 2023;324(2):265-294. doi:<a href=\"https://doi.org/10.2140/pjm.2023.324.265\">10.2140/pjm.2023.324.265</a>","ieee":"T. Horesh and A. Nevo, “Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution,” <i>Pacific Journal of Mathematics</i>, vol. 324, no. 2. Mathematical Sciences Publishers, pp. 265–294, 2023.","chicago":"Horesh, Tal, and Amos Nevo. “Horospherical Coordinates of Lattice Points in Hyperbolic Spaces: Effective Counting and Equidistribution.” <i>Pacific Journal of Mathematics</i>. Mathematical Sciences Publishers, 2023. <a href=\"https://doi.org/10.2140/pjm.2023.324.265\">https://doi.org/10.2140/pjm.2023.324.265</a>.","ista":"Horesh T, Nevo A. 2023. Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution. Pacific Journal of Mathematics. 324(2), 265–294.","short":"T. Horesh, A. Nevo, Pacific Journal of Mathematics 324 (2023) 265–294."},"isi":1,"department":[{"_id":"TiBr"}],"publisher":"Mathematical Sciences Publishers","month":"07","acknowledgement":"The authors thank the referee for important comments which led to significant improvements is the presentation of several results in the paper. They also thank Ami Paz for preparing the figures for this paper. Horesh thanks Ami Paz and Yakov Karasik for helpful discussions. Nevo thanks John Parker and Rene Rühr for providing some very useful references. Nevo is supported by ISF Grant No. 2095/15.","scopus_import":"1","arxiv":1,"page":"265-294","intvolume":"       324","ddc":["510"],"doi":"10.2140/pjm.2023.324.265","date_published":"2023-07-26T00:00:00Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","file_date_updated":"2023-09-05T07:26:17Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":324},{"date_updated":"2023-12-13T12:21:09Z","citation":{"ista":"Brauneis F, Ghazaryan A, Hammer H-W, Volosniev A. 2023. Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux. Communications Physics. 6, 224.","chicago":"Brauneis, Fabian, Areg Ghazaryan, Hans-Werner Hammer, and Artem Volosniev. “Emergence of a Bose Polaron in a Small Ring Threaded by the Aharonov-Bohm Flux.” <i>Communications Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s42005-023-01281-2\">https://doi.org/10.1038/s42005-023-01281-2</a>.","ieee":"F. Brauneis, A. Ghazaryan, H.-W. Hammer, and A. Volosniev, “Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux,” <i>Communications Physics</i>, vol. 6. Springer Nature, 2023.","ama":"Brauneis F, Ghazaryan A, Hammer H-W, Volosniev A. Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux. <i>Communications Physics</i>. 2023;6. doi:<a href=\"https://doi.org/10.1038/s42005-023-01281-2\">10.1038/s42005-023-01281-2</a>","apa":"Brauneis, F., Ghazaryan, A., Hammer, H.-W., &#38; Volosniev, A. (2023). Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux. <i>Communications Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42005-023-01281-2\">https://doi.org/10.1038/s42005-023-01281-2</a>","mla":"Brauneis, Fabian, et al. “Emergence of a Bose Polaron in a Small Ring Threaded by the Aharonov-Bohm Flux.” <i>Communications Physics</i>, vol. 6, 224, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s42005-023-01281-2\">10.1038/s42005-023-01281-2</a>.","short":"F. Brauneis, A. Ghazaryan, H.-W. Hammer, A. Volosniev, Communications Physics 6 (2023)."},"author":[{"last_name":"Brauneis","first_name":"Fabian","full_name":"Brauneis, Fabian"},{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","first_name":"Areg","last_name":"Ghazaryan"},{"first_name":"Hans-Werner","last_name":"Hammer","full_name":"Hammer, Hans-Werner"},{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","last_name":"Volosniev","first_name":"Artem"}],"day":"22","publication_identifier":{"issn":["2399-3650"]},"publication":"Communications Physics","oa":1,"external_id":{"isi":["001052577500002"],"arxiv":["2301.10488"]},"title":"Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux","has_accepted_license":"1","article_number":"224","date_created":"2023-08-28T12:36:49Z","year":"2023","_id":"14246","article_type":"original","publication_status":"published","file":[{"access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":855960,"checksum":"6edfc59b0ee7dc406d0968b05236e83d","date_updated":"2023-09-05T08:45:49Z","file_id":"14268","date_created":"2023-09-05T08:45:49Z","success":1,"relation":"main_file","file_name":"2023_CommPhysics_Brauneis.pdf"}],"abstract":[{"text":"The model of a ring threaded by the Aharonov-Bohm flux underlies our understanding of a coupling between gauge potentials and matter. The typical formulation of the model is based upon a single particle picture, and should be extended when interactions with other particles become relevant. Here, we illustrate such an extension for a particle in an Aharonov-Bohm ring subject to interactions with a weakly interacting Bose gas. We show that the ground state of the system can be described using the Bose-polaron concept—a particle dressed by interactions with a bosonic environment. We connect the energy spectrum to the effective mass of the polaron, and demonstrate how to change currents in the system by tuning boson-particle interactions. Our results suggest the Aharonov-Bohm ring as a platform for studying coherence and few- to many-body crossover of quasi-particles that arise from an impurity immersed in a medium.","lang":"eng"}],"quality_controlled":"1","oa_version":"Published Version","keyword":["General Physics and Astronomy"],"article_processing_charge":"Yes (via OA deal)","type":"journal_article","volume":6,"file_date_updated":"2023-09-05T08:45:49Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1038/s42005-023-01281-2","date_published":"2023-08-22T00:00:00Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","ddc":["530"],"intvolume":"         6","arxiv":1,"acknowledgement":"Open Access funding enabled and organized by Projekt DEAL.\r\nWe would like to thank Jonas Jager for sharing his data with us in the early stages of this project. We thank Joachim Brand and Ray Yang for sharing with us data from Yang et al.46. This work has received funding from the DFG Project no. 413495248 [VO 2437/1-1] (F.B., H.-W.H., A.G.V.). We acknowledge support from the Deutsche Forschungsgemeinschaft (DFG - German Research Foundation) and the Open Access Publishing Fund of the Technical University of Darmstadt.","scopus_import":"1","publisher":"Springer Nature","department":[{"_id":"MiLe"}],"month":"08","isi":1},{"acknowledgement":"We thank Kayla Templeton and Peter Turcanu for technical assistance, Michelle Salemi for assistance with LC-MS data acquisition and analysis, Dr. Belvin Gong for advice on monoclonal antibody generation, Drs. Maria Casas Prat and Eamonn Dickson for assistance with super-resolution TIRF microscopy, Dr. Oscar Cerda for assistance with the design of TAT-FFAT peptides, Dr. Fernando Santana for helpful discussions, and Dr. Jodi Nunnari for a careful reading of our manuscript. We also thank Dr. Alan Howe, Dr. Sohum Mehta, and Dr. Jin Zhang for providing plasmids used in this study. This project was funded by NIH Grants R01NS114210 and R21NS101648 (J.S.T.), and F32NS108519 (N.C.V.).","scopus_import":"1","month":"08","publisher":"Springer Nature","department":[{"_id":"RySh"}],"type":"journal_article","volume":14,"file_date_updated":"2023-09-06T06:50:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-08-26T00:00:00Z","doi":"10.1038/s41467-023-40930-6","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","language":[{"iso":"eng"}],"intvolume":"        14","ddc":["570"],"pmid":1,"date_created":"2023-09-03T22:01:14Z","_id":"14253","year":"2023","publication_status":"published","article_type":"original","abstract":[{"text":"Junctions between the endoplasmic reticulum (ER) and the plasma membrane (PM) are specialized membrane contacts ubiquitous in eukaryotic cells. Concentration of intracellular signaling machinery near ER-PM junctions allows these domains to serve critical roles in lipid and Ca2+ signaling and homeostasis. Subcellular compartmentalization of protein kinase A (PKA) signaling also regulates essential cellular functions, however, no specific association between PKA and ER-PM junctional domains is known. Here, we show that in brain neurons type I PKA is directed to Kv2.1 channel-dependent ER-PM junctional domains via SPHKAP, a type I PKA-specific anchoring protein. SPHKAP association with type I PKA regulatory subunit RI and ER-resident VAP proteins results in the concentration of type I PKA between stacked ER cisternae associated with ER-PM junctions. This ER-associated PKA signalosome enables reciprocal regulation between PKA and Ca2+ signaling machinery to support Ca2+ influx and excitation-transcription coupling. These data reveal that neuronal ER-PM junctions support a receptor-independent form of PKA signaling driven by membrane depolarization and intracellular Ca2+, allowing conversion of information encoded in electrical signals into biochemical changes universally recognized throughout the cell.","lang":"eng"}],"file":[{"date_updated":"2023-09-06T06:50:07Z","date_created":"2023-09-06T06:50:07Z","relation":"main_file","success":1,"file_id":"14270","file_name":"2023_NatureComm_Vierra.pdf","creator":"dernst","access_level":"open_access","content_type":"application/pdf","file_size":9412549,"checksum":"6ab8aab4e957f626a09a1c73db3388fb"}],"quality_controlled":"1","article_processing_charge":"Yes","oa_version":"Published Version","date_updated":"2023-09-06T06:53:32Z","author":[{"full_name":"Vierra, Nicholas C.","first_name":"Nicholas C.","last_name":"Vierra"},{"last_name":"Ribeiro-Silva","first_name":"Luisa","full_name":"Ribeiro-Silva, Luisa"},{"full_name":"Kirmiz, Michael","last_name":"Kirmiz","first_name":"Michael"},{"last_name":"Van Der List","first_name":"Deborah","full_name":"Van Der List, Deborah"},{"full_name":"Bhandari, Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0863-4481","first_name":"Pradeep","last_name":"Bhandari"},{"full_name":"Mack, Olivia A.","last_name":"Mack","first_name":"Olivia A."},{"last_name":"Carroll","first_name":"James","full_name":"Carroll, James"},{"id":"3B59276A-F248-11E8-B48F-1D18A9856A87","full_name":"Le Monnier, Elodie","first_name":"Elodie","last_name":"Le Monnier"},{"full_name":"Aicher, Sue A.","last_name":"Aicher","first_name":"Sue A."},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Trimmer, James S.","first_name":"James S.","last_name":"Trimmer"}],"citation":{"ama":"Vierra NC, Ribeiro-Silva L, Kirmiz M, et al. Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-40930-6\">10.1038/s41467-023-40930-6</a>","ieee":"N. C. Vierra <i>et al.</i>, “Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","apa":"Vierra, N. C., Ribeiro-Silva, L., Kirmiz, M., Van Der List, D., Bhandari, P., Mack, O. A., … Trimmer, J. S. (2023). Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-40930-6\">https://doi.org/10.1038/s41467-023-40930-6</a>","mla":"Vierra, Nicholas C., et al. “Neuronal ER-Plasma Membrane Junctions Couple Excitation to Ca2+-Activated PKA Signaling.” <i>Nature Communications</i>, vol. 14, 5231, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-40930-6\">10.1038/s41467-023-40930-6</a>.","ista":"Vierra NC, Ribeiro-Silva L, Kirmiz M, Van Der List D, Bhandari P, Mack OA, Carroll J, Le Monnier E, Aicher SA, Shigemoto R, Trimmer JS. 2023. Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications. 14, 5231.","chicago":"Vierra, Nicholas C., Luisa Ribeiro-Silva, Michael Kirmiz, Deborah Van Der List, Pradeep Bhandari, Olivia A. Mack, James Carroll, et al. “Neuronal ER-Plasma Membrane Junctions Couple Excitation to Ca2+-Activated PKA Signaling.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-40930-6\">https://doi.org/10.1038/s41467-023-40930-6</a>.","short":"N.C. Vierra, L. Ribeiro-Silva, M. Kirmiz, D. Van Der List, P. Bhandari, O.A. Mack, J. Carroll, E. Le Monnier, S.A. Aicher, R. Shigemoto, J.S. Trimmer, Nature Communications 14 (2023)."},"day":"26","oa":1,"publication":"Nature Communications","publication_identifier":{"eissn":["2041-1723"]},"external_id":{"pmid":["37633939"]},"title":"Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling","has_accepted_license":"1","article_number":"5231"},{"article_number":"110129","issue":"10","has_accepted_license":"1","external_id":{"isi":["001071552300001"],"arxiv":["2303.04504"]},"title":"A simple approach to Lieb-Thirring type inequalities","publication":"Journal of Functional Analysis","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"oa":1,"day":"15","date_updated":"2024-01-30T14:17:23Z","citation":{"short":"R. Seiringer, J.P. Solovej, Journal of Functional Analysis 285 (2023).","ista":"Seiringer R, Solovej JP. 2023. A simple approach to Lieb-Thirring type inequalities. Journal of Functional Analysis. 285(10), 110129.","chicago":"Seiringer, Robert, and Jan Philip Solovej. “A Simple Approach to Lieb-Thirring Type Inequalities.” <i>Journal of Functional Analysis</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.jfa.2023.110129\">https://doi.org/10.1016/j.jfa.2023.110129</a>.","ama":"Seiringer R, Solovej JP. A simple approach to Lieb-Thirring type inequalities. <i>Journal of Functional Analysis</i>. 2023;285(10). doi:<a href=\"https://doi.org/10.1016/j.jfa.2023.110129\">10.1016/j.jfa.2023.110129</a>","ieee":"R. Seiringer and J. P. Solovej, “A simple approach to Lieb-Thirring type inequalities,” <i>Journal of Functional Analysis</i>, vol. 285, no. 10. Elsevier, 2023.","apa":"Seiringer, R., &#38; Solovej, J. P. (2023). A simple approach to Lieb-Thirring type inequalities. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2023.110129\">https://doi.org/10.1016/j.jfa.2023.110129</a>","mla":"Seiringer, Robert, and Jan Philip Solovej. “A Simple Approach to Lieb-Thirring Type Inequalities.” <i>Journal of Functional Analysis</i>, vol. 285, no. 10, 110129, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.jfa.2023.110129\">10.1016/j.jfa.2023.110129</a>."},"author":[{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer"},{"full_name":"Solovej, Jan Philip","first_name":"Jan Philip","last_name":"Solovej"}],"oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","file":[{"file_name":"2023_JourFunctionalAnalysis_Seiringer.pdf","success":1,"date_created":"2024-01-30T14:15:16Z","relation":"main_file","file_id":"14915","date_updated":"2024-01-30T14:15:16Z","checksum":"28e424ad91be6219e9d321054ce3a412","file_size":232934,"content_type":"application/pdf","creator":"dernst","access_level":"open_access"}],"abstract":[{"text":"In [10] Nam proved a Lieb–Thirring Inequality for the kinetic energy of a fermionic quantum system, with almost optimal (semi-classical) constant and a gradient correction term. We present a stronger version of this inequality, with a much simplified proof. As a corollary we obtain a simple proof of the original Lieb–Thirring inequality.","lang":"eng"}],"publication_status":"published","article_type":"original","year":"2023","_id":"14254","date_created":"2023-09-03T22:01:14Z","ddc":["510"],"intvolume":"       285","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","doi":"10.1016/j.jfa.2023.110129","date_published":"2023-11-15T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-01-30T14:15:16Z","volume":285,"type":"journal_article","isi":1,"publisher":"Elsevier","department":[{"_id":"RoSe"}],"month":"11","scopus_import":"1","acknowledgement":"J.P.S. thanks the Institute of Science and Technology Austria for the hospitality and support during a visit where this work was done. J.P.S. was also partially supported by the VILLUM Centre of Excellence for the Mathematics of Quantum Theory (QMATH) (grant No. 10059).","arxiv":1},{"intvolume":"        19","ddc":["570"],"doi":"10.1371/journal.ppat.1011562","date_published":"2023-08-14T00:00:00Z","language":[{"iso":"eng"}],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file_date_updated":"2023-09-06T06:41:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":19,"isi":1,"publisher":"Public Library of Science","department":[{"_id":"FlSc"}],"month":"08","acknowledgement":"We acknowledge Elodie Chatre and the Imaging Platform Platim, SFR Biosciences, Lyon, as well as Vibor Laketa and the Infectious Diseases Imaging Platform (IDIP) at the Center for Integrative Infectious Disease Research (CIID) Heidelberg. The sand fly cell lines were supplied by the Tick Cell Biobank at the University of Liverpool. F.K.M.S. acknowledges support from the Scientific Service Units (SSUs) of ISTA through resources provided by the Electron Microscopy Facility (EMF).\r\nThis work was supported by CellNetworks Research Group funds and Deutsche Forschungsgemeinschaft (DFG) funding (LO-2338/3-1) and the Agence Nationale de la Recherche (ANR) funding (grant numbers ANR-21-CE11-0012 and ANR-22-CE15-0034), all awarded to P.-Y.L. This work was also supported by the LABEX ECOFECT (ANR-11-LABX-0048) of Université de Lyon (UDL), within the program “Investissements d’Avenir” (ANR-11-IDEX-0007) operated by the ANR and by the RESPOND program of the UDL (awarded to P.-Y.L) . C.A. was supported by the Chica and Heinz Schaller Research Group funds, NARSAD 2019 award, a Fritz Thyssen Research Grant, and the SFB1158-S02 grant. L.B-S. is supported by a United Kingdom Biotechnology and Biological Sciences Research Council grant (BB/P024270/1) and a Wellcome Trust grant (223743/Z/21/Z). F.K.M.S acknowledges support from the Austrian Science Fund (FWF, P31445). J.K. received a salary from the DFG (LO-2338/3-1) and then from the ANR (ANR-11-LABX-0048). The salary of Z.M.U. was partially covered by the DFG (LO-2338/3-1). S.K. received a salary from the DFG (SFB1129). We are grateful to the Chinese Scholarship Council (CSC; 201904910701), DAAD/ANID (57451854/62180003), the Rufus A. Kellogg fellowship program (Amherst College, Massachusetts, USA) for awarding fellowships to Q.X., J.C., and H.A.A., respectively.","scopus_import":"1","has_accepted_license":"1","issue":"8","article_number":"e1011562","project":[{"grant_number":"P31445","call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid"}],"external_id":{"pmid":["37578957"],"isi":["001050846300004"]},"title":"The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells","day":"14","publication":"PLoS Pathogens","publication_identifier":{"eissn":["1553-7374"],"issn":["1553-7366"]},"oa":1,"date_updated":"2023-12-13T12:22:22Z","author":[{"last_name":"Koch","first_name":"Jana","full_name":"Koch, Jana"},{"full_name":"Xin, Qilin","first_name":"Qilin","last_name":"Xin"},{"orcid":"0000-0003-1756-6564","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Obr, Martin","first_name":"Martin","last_name":"Obr"},{"full_name":"Schäfer, Alicia","first_name":"Alicia","last_name":"Schäfer"},{"first_name":"Nina","last_name":"Rolfs","full_name":"Rolfs, Nina"},{"last_name":"Anagho","first_name":"Holda A.","full_name":"Anagho, Holda A."},{"last_name":"Kudulyte","first_name":"Aiste","full_name":"Kudulyte, Aiste"},{"full_name":"Woltereck, Lea","last_name":"Woltereck","first_name":"Lea"},{"full_name":"Kummer, Susann","first_name":"Susann","last_name":"Kummer"},{"full_name":"Campos, Joaquin","first_name":"Joaquin","last_name":"Campos"},{"first_name":"Zina M.","last_name":"Uckeley","full_name":"Uckeley, Zina M."},{"full_name":"Bell-Sakyi, Lesley","last_name":"Bell-Sakyi","first_name":"Lesley"},{"full_name":"Kräusslich, Hans Georg","first_name":"Hans Georg","last_name":"Kräusslich"},{"full_name":"Schur, Florian Km","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian Km","last_name":"Schur"},{"last_name":"Acuna","first_name":"Claudio","full_name":"Acuna, Claudio"},{"first_name":"Pierre Yves","last_name":"Lozach","full_name":"Lozach, Pierre Yves"}],"citation":{"short":"J. Koch, Q. Xin, M. Obr, A. Schäfer, N. Rolfs, H.A. Anagho, A. Kudulyte, L. Woltereck, S. Kummer, J. Campos, Z.M. Uckeley, L. Bell-Sakyi, H.G. Kräusslich, F.K. Schur, C. Acuna, P.Y. Lozach, PLoS Pathogens 19 (2023).","chicago":"Koch, Jana, Qilin Xin, Martin Obr, Alicia Schäfer, Nina Rolfs, Holda A. Anagho, Aiste Kudulyte, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” <i>PLoS Pathogens</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.ppat.1011562\">https://doi.org/10.1371/journal.ppat.1011562</a>.","ista":"Koch J, Xin Q, Obr M, Schäfer A, Rolfs N, Anagho HA, Kudulyte A, Woltereck L, Kummer S, Campos J, Uckeley ZM, Bell-Sakyi L, Kräusslich HG, Schur FK, Acuna C, Lozach PY. 2023. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. PLoS Pathogens. 19(8), e1011562.","mla":"Koch, Jana, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” <i>PLoS Pathogens</i>, vol. 19, no. 8, e1011562, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.ppat.1011562\">10.1371/journal.ppat.1011562</a>.","ama":"Koch J, Xin Q, Obr M, et al. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. <i>PLoS Pathogens</i>. 2023;19(8). doi:<a href=\"https://doi.org/10.1371/journal.ppat.1011562\">10.1371/journal.ppat.1011562</a>","ieee":"J. Koch <i>et al.</i>, “The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells,” <i>PLoS Pathogens</i>, vol. 19, no. 8. Public Library of Science, 2023.","apa":"Koch, J., Xin, Q., Obr, M., Schäfer, A., Rolfs, N., Anagho, H. A., … Lozach, P. Y. (2023). The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. <i>PLoS Pathogens</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.ppat.1011562\">https://doi.org/10.1371/journal.ppat.1011562</a>"},"quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"Yes","publication_status":"published","article_type":"original","file":[{"access_level":"open_access","creator":"dernst","file_size":4458336,"content_type":"application/pdf","checksum":"47ca3bb54b27f28b05644be0ad064bc6","date_updated":"2023-09-06T06:41:52Z","file_id":"14269","date_created":"2023-09-06T06:41:52Z","success":1,"relation":"main_file","file_name":"2023_PloSPathogens_Koch.pdf"}],"abstract":[{"lang":"eng","text":"Toscana virus is a major cause of arboviral disease in humans in the Mediterranean basin during summer. However, early virus-host cell interactions and entry mechanisms remain poorly characterized. Investigating iPSC-derived human neurons and cell lines, we found that virus binding to the cell surface was specific, and 50% of bound virions were endocytosed within 10 min. Virions entered Rab5a+ early endosomes and, subsequently, Rab7a+ and LAMP-1+ late endosomal compartments. Penetration required intact late endosomes and occurred within 30 min following internalization. Virus entry relied on vacuolar acidification, with an optimal pH for viral membrane fusion at pH 5.5. The pH threshold increased to 5.8 with longer pre-exposure of virions to the slightly acidic pH in early endosomes. Strikingly, the particles remained infectious after entering late endosomes with a pH below the fusion threshold. Overall, our study establishes Toscana virus as a late-penetrating virus and reveals an atypical use of vacuolar acidity by this virus to enter host cells."}],"date_created":"2023-09-03T22:01:14Z","pmid":1,"year":"2023","_id":"14255","acknowledged_ssus":[{"_id":"EM-Fac"}]},{"title":"Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields","external_id":{"arxiv":["2306.11587"],"isi":["001046037700007"]},"has_accepted_license":"1","article_number":"L9","citation":{"chicago":"Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” <i>Astronomy and Astrophysics</i>. EDP Sciences, 2023. <a href=\"https://doi.org/10.1051/0004-6361/202346832\">https://doi.org/10.1051/0004-6361/202346832</a>.","ista":"Mathis S, Bugnet LA. 2023. Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. Astronomy and Astrophysics. 676, L9.","mla":"Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” <i>Astronomy and Astrophysics</i>, vol. 676, L9, EDP Sciences, 2023, doi:<a href=\"https://doi.org/10.1051/0004-6361/202346832\">10.1051/0004-6361/202346832</a>.","apa":"Mathis, S., &#38; Bugnet, L. A. (2023). Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. <i>Astronomy and Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202346832\">https://doi.org/10.1051/0004-6361/202346832</a>","ieee":"S. Mathis and L. A. Bugnet, “Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields,” <i>Astronomy and Astrophysics</i>, vol. 676. EDP Sciences, 2023.","ama":"Mathis S, Bugnet LA. Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. <i>Astronomy and Astrophysics</i>. 2023;676. doi:<a href=\"https://doi.org/10.1051/0004-6361/202346832\">10.1051/0004-6361/202346832</a>","short":"S. Mathis, L.A. Bugnet, Astronomy and Astrophysics 676 (2023)."},"author":[{"full_name":"Mathis, S.","first_name":"S.","last_name":"Mathis"},{"first_name":"Lisa Annabelle","last_name":"Bugnet","orcid":"0000-0003-0142-4000","full_name":"Bugnet, Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501"}],"date_updated":"2023-09-06T11:05:58Z","day":"01","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"publication":"Astronomy and Astrophysics","oa":1,"publication_status":"published","article_type":"letter_note","file":[{"content_type":"application/pdf","file_size":458120,"checksum":"7b30d26fb2b7bcb5b5be1414950615f9","creator":"dernst","access_level":"open_access","date_created":"2023-09-06T07:13:19Z","success":1,"relation":"main_file","file_id":"14271","file_name":"2023_AstronomyAstrophysics_Mathis.pdf","date_updated":"2023-09-06T07:13:19Z"}],"abstract":[{"text":"Context. Space asteroseismology is revolutionizing our knowledge of the internal structure and dynamics of stars. A breakthrough is ongoing with the recent discoveries of signatures of strong magnetic fields in the core of red giant stars. The key signature for such a detection is the asymmetry these fields induce in the frequency splittings of observed dipolar mixed gravito-acoustic modes.\r\nAims. We investigate the ability of the observed asymmetries of the frequency splittings of dipolar mixed modes to constrain the geometrical properties of deep magnetic fields.\r\nMethods. We used the powerful analytical Racah-Wigner algebra used in quantum mechanics to characterize the geometrical couplings of dipolar mixed oscillation modes with various realistically plausible topologies of fossil magnetic fields. We also computed the induced perturbation of their frequencies.\r\nResults. First, in the case of an oblique magnetic dipole, we provide the exact analytical expression of the asymmetry as a function of the angle between the rotation and magnetic axes. Its value provides a direct measure of this angle. Second, considering a combination of axisymmetric dipolar and quadrupolar fields, we show how the asymmetry is blind to the unraveling of the relative strength and sign of each component. Finally, in the case of a given multipole, we show that a negative asymmetry is a signature of non-axisymmetric topologies.\r\nConclusions. Asymmetries of dipolar mixed modes provide a key bit of information on the geometrical topology of deep fossil magnetic fields, but this is insufficient on its own. Asteroseismic constraints should therefore be combined with spectropolarimetric observations and numerical simulations, which aim to predict the more probable stable large-scale geometries.","lang":"eng"}],"quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","date_created":"2023-09-03T22:01:15Z","year":"2023","_id":"14256","doi":"10.1051/0004-6361/202346832","date_published":"2023-08-01T00:00:00Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","intvolume":"       676","ddc":["520"],"type":"journal_article","volume":676,"file_date_updated":"2023-09-06T07:13:19Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"EDP Sciences","department":[{"_id":"LiBu"}],"month":"08","isi":1,"arxiv":1,"acknowledgement":"The authors are grateful to the referee for her/his detailed and constructive report, which has allowed us to improve our article. S. M. acknowledges support from the CNES GOLF-SOHO and PLATO grants at CEA/DAp and PNPS (CNRS/INSU). We thank R. A. Garcia for fruitful discussions and suggestions.","scopus_import":"1"},{"main_file_link":[{"url":"https://doi.org/10.1038/s41587-023-01911-8","open_access":"1"}],"isi":1,"month":"08","publisher":"Springer Nature","department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"},{"_id":"Bio"},{"_id":"RySh"}],"scopus_import":"1","acknowledgement":"We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I. Erber for technical assistance; and M. Tomschik for support with obtaining human samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata for computational support and hardware control. We are grateful to R. Shigemoto and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University) for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly provided by S. Grant (University of Edinburgh). We acknowledge expert support by Institute of Science and Technology Austria’s scientific computing, imaging and optics, preclinical and lab support facilities and by the Miba machine shop and library. We gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).","status":"public","language":[{"iso":"eng"}],"date_published":"2023-08-31T00:00:00Z","doi":"10.1038/s41587-023-01911-8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","quality_controlled":"1","abstract":[{"text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease.","lang":"eng"}],"article_type":"original","related_material":{"link":[{"relation":"software","url":"https://github.com/danzllab/CATS"}],"record":[{"relation":"research_data","id":"13126","status":"public"}]},"publication_status":"epub_ahead","_id":"14257","year":"2023","date_created":"2023-09-03T22:01:15Z","ec_funded":1,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"title":"Imaging brain tissue architecture across millimeter to nanometer scales","external_id":{"isi":["001065254200001"]},"project":[{"grant_number":"I03600","call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","name":"Optical control of synaptic function via adhesion molecules"},{"name":"Molecular Drug Targets","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"},{"call_identifier":"FWF","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"},{"name":"High content imaging to decode human immune cell interactions in health and allergic disease","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715508"},{"grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","grant_number":"101026635","call_identifier":"H2020","name":"Synaptic computations of the hippocampal CA3 circuitry"}],"oa":1,"publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"publication":"Nature Biotechnology","day":"31","date_updated":"2024-02-21T12:18:18Z","author":[{"orcid":"0000-0003-3862-1235","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","full_name":"Michalska, Julia M","first_name":"Julia M","last_name":"Michalska"},{"last_name":"Lyudchik","first_name":"Julia","full_name":"Lyudchik, Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Velicky","first_name":"Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431"},{"first_name":"Hana","last_name":"Korinkova","full_name":"Korinkova, Hana","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed"},{"full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","orcid":"0000-0002-8698-3823","last_name":"Watson","first_name":"Jake"},{"first_name":"Alban","last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886","full_name":"Cenameri, Alban"},{"orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M","last_name":"Sommer","first_name":"Christoph M"},{"orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole","last_name":"Amberg"},{"last_name":"Venturino","first_name":"Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403"},{"first_name":"Karl","last_name":"Roessler","full_name":"Roessler, Karl"},{"full_name":"Czech, Thomas","first_name":"Thomas","last_name":"Czech"},{"last_name":"Höftberger","first_name":"Romana","full_name":"Höftberger, Romana"},{"first_name":"Sandra","last_name":"Siegert","full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877"},{"last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"},{"last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"},{"first_name":"Johann G","last_name":"Danzl","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"}],"citation":{"ama":"Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. 2023. doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>","ieee":"J. M. Michalska <i>et al.</i>, “Imaging brain tissue architecture across millimeter to nanometer scales,” <i>Nature Biotechnology</i>. Springer Nature, 2023.","apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (2023). Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>","mla":"Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>.","ista":"Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino G, Jonas PM, Danzl JG. 2023. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology.","chicago":"Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>.","short":"J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology (2023)."}},{"acknowledgement":"This project was funded by an SNSF Eccellenza grant to M.R.R. (PCEGP3-181181) and by core funding from the Institute of Science and Technology Austria. K.L. and R.M. were supported by the Estonian Research Council grant 1911. Estonian Biobank computations were performed in the High-Performance Computing Center, University of Tartu. We thank Triin Laisk for her valuable insights and comments that helped greatly. We would like to acknowledge the participants and investigators of UK Biobank and Estonian Biobank studies. This project uses UK Biobank data under project number 35520.","scopus_import":"1","page":"1549-1563","department":[{"_id":"MaRo"}],"publisher":"Elsevier","month":"09","file_date_updated":"2024-01-30T13:20:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":110,"intvolume":"       110","ddc":["570"],"doi":"10.1016/j.ajhg.2023.07.006","date_published":"2023-09-07T00:00:00Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","date_created":"2023-09-03T22:01:15Z","pmid":1,"year":"2023","_id":"14258","quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","article_type":"original","publication_status":"published","file":[{"checksum":"4108b031dc726ae6b4a5ae7e021ba188","file_size":2551276,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_AJHG_Ojavee.pdf","relation":"main_file","success":1,"date_created":"2024-01-30T13:20:35Z","file_id":"14912","date_updated":"2024-01-30T13:20:35Z"}],"abstract":[{"lang":"eng","text":"There is currently little evidence that the genetic basis of human phenotype varies significantly across the lifespan. However, time-to-event phenotypes are understudied and can be thought of as reflecting an underlying hazard, which is unlikely to be constant through life when values take a broad range. Here, we find that 74% of 245 genome-wide significant genetic associations with age at natural menopause (ANM) in the UK Biobank show a form of age-specific effect. Nineteen of these replicated discoveries are identified only by our modeling framework, which determines the time dependency of DNA-variant age-at-onset associations without a significant multiple-testing burden. Across the range of early to late menopause, we find evidence for significantly different underlying biological pathways, changes in the signs of genetic correlations of ANM to health indicators and outcomes, and differences in inferred causal relationships. We find that DNA damage response processes only act to shape ovarian reserve and depletion for women of early ANM. Genetically mediated delays in ANM were associated with increased relative risk of breast cancer and leiomyoma at all ages and with high cholesterol and heart failure for late-ANM women. These findings suggest that a better understanding of the age dependency of genetic risk factor relationships among health indicators and outcomes is achievable through appropriate statistical modeling of large-scale biobank data."}],"day":"07","publication":"American Journal of Human Genetics","publication_identifier":{"issn":["0002-9297"],"eissn":["1537-6605"]},"oa":1,"author":[{"full_name":"Ojavee, Sven E.","first_name":"Sven E.","last_name":"Ojavee"},{"full_name":"Darrous, Liza","last_name":"Darrous","first_name":"Liza"},{"last_name":"Patxot","first_name":"Marion","full_name":"Patxot, Marion"},{"last_name":"Läll","first_name":"Kristi","full_name":"Läll, Kristi"},{"full_name":"Fischer, Krista","last_name":"Fischer","first_name":"Krista"},{"last_name":"Mägi","first_name":"Reedik","full_name":"Mägi, Reedik"},{"full_name":"Kutalik, Zoltan","last_name":"Kutalik","first_name":"Zoltan"},{"last_name":"Robinson","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813"}],"date_updated":"2024-01-30T13:21:05Z","citation":{"short":"S.E. Ojavee, L. Darrous, M. Patxot, K. Läll, K. Fischer, R. Mägi, Z. Kutalik, M.R. Robinson, American Journal of Human Genetics 110 (2023) 1549–1563.","mla":"Ojavee, Sven E., et al. “Genetic Insights into the Age-Specific Biological Mechanisms Governing Human Ovarian Aging.” <i>American Journal of Human Genetics</i>, vol. 110, no. 9, Elsevier, 2023, pp. 1549–63, doi:<a href=\"https://doi.org/10.1016/j.ajhg.2023.07.006\">10.1016/j.ajhg.2023.07.006</a>.","ieee":"S. E. Ojavee <i>et al.</i>, “Genetic insights into the age-specific biological mechanisms governing human ovarian aging,” <i>American Journal of Human Genetics</i>, vol. 110, no. 9. Elsevier, pp. 1549–1563, 2023.","apa":"Ojavee, S. E., Darrous, L., Patxot, M., Läll, K., Fischer, K., Mägi, R., … Robinson, M. R. (2023). Genetic insights into the age-specific biological mechanisms governing human ovarian aging. <i>American Journal of Human Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ajhg.2023.07.006\">https://doi.org/10.1016/j.ajhg.2023.07.006</a>","ama":"Ojavee SE, Darrous L, Patxot M, et al. Genetic insights into the age-specific biological mechanisms governing human ovarian aging. <i>American Journal of Human Genetics</i>. 2023;110(9):1549-1563. doi:<a href=\"https://doi.org/10.1016/j.ajhg.2023.07.006\">10.1016/j.ajhg.2023.07.006</a>","chicago":"Ojavee, Sven E., Liza Darrous, Marion Patxot, Kristi Läll, Krista Fischer, Reedik Mägi, Zoltan Kutalik, and Matthew Richard Robinson. “Genetic Insights into the Age-Specific Biological Mechanisms Governing Human Ovarian Aging.” <i>American Journal of Human Genetics</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.ajhg.2023.07.006\">https://doi.org/10.1016/j.ajhg.2023.07.006</a>.","ista":"Ojavee SE, Darrous L, Patxot M, Läll K, Fischer K, Mägi R, Kutalik Z, Robinson MR. 2023. Genetic insights into the age-specific biological mechanisms governing human ovarian aging. American Journal of Human Genetics. 110(9), 1549–1563."},"has_accepted_license":"1","issue":"9","external_id":{"pmid":["37543033"]},"title":"Genetic insights into the age-specific biological mechanisms governing human ovarian aging"},{"date_published":"2023-07-17T00:00:00Z","doi":"10.1007/978-3-031-37706-8_20","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"alternative_title":["LNCS"],"ddc":["000"],"intvolume":"     13964","type":"conference","volume":13964,"file_date_updated":"2023-09-06T08:25:50Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"conference":{"location":"Paris, France","start_date":"2023-07-17","name":"CAV: Computer Aided Verification","end_date":"2023-07-22"},"page":"390-414","acknowledgement":"This research was funded in part by the German Research Foundation (DFG) project 427755713 Group-By Objectives in Probabilistic Verification (GOPro).","scopus_import":"1","title":"Guessing winning policies in LTL synthesis by semantic learning","has_accepted_license":"1","date_updated":"2023-09-06T08:27:33Z","author":[{"full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","last_name":"Kretinsky","first_name":"Jan"},{"full_name":"Meggendorfer, Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","last_name":"Meggendorfer","first_name":"Tobias"},{"first_name":"Maximilian","last_name":"Prokop","full_name":"Prokop, Maximilian"},{"full_name":"Rieder, Sabine","first_name":"Sabine","last_name":"Rieder"}],"citation":{"mla":"Kretinsky, Jan, et al. “Guessing Winning Policies in LTL Synthesis by Semantic Learning.” <i>35th International Conference on Computer Aided Verification </i>, vol. 13964, Springer Nature, 2023, pp. 390–414, doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_20\">10.1007/978-3-031-37706-8_20</a>.","apa":"Kretinsky, J., Meggendorfer, T., Prokop, M., &#38; Rieder, S. (2023). Guessing winning policies in LTL synthesis by semantic learning. In <i>35th International Conference on Computer Aided Verification </i> (Vol. 13964, pp. 390–414). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_20\">https://doi.org/10.1007/978-3-031-37706-8_20</a>","ieee":"J. Kretinsky, T. Meggendorfer, M. Prokop, and S. Rieder, “Guessing winning policies in LTL synthesis by semantic learning,” in <i>35th International Conference on Computer Aided Verification </i>, Paris, France, 2023, vol. 13964, pp. 390–414.","ama":"Kretinsky J, Meggendorfer T, Prokop M, Rieder S. Guessing winning policies in LTL synthesis by semantic learning. In: <i>35th International Conference on Computer Aided Verification </i>. Vol 13964. Springer Nature; 2023:390-414. doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_20\">10.1007/978-3-031-37706-8_20</a>","chicago":"Kretinsky, Jan, Tobias Meggendorfer, Maximilian Prokop, and Sabine Rieder. “Guessing Winning Policies in LTL Synthesis by Semantic Learning.” In <i>35th International Conference on Computer Aided Verification </i>, 13964:390–414. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_20\">https://doi.org/10.1007/978-3-031-37706-8_20</a>.","ista":"Kretinsky J, Meggendorfer T, Prokop M, Rieder S. 2023. Guessing winning policies in LTL synthesis by semantic learning. 35th International Conference on Computer Aided Verification . CAV: Computer Aided Verification, LNCS, vol. 13964, 390–414.","short":"J. Kretinsky, T. Meggendorfer, M. Prokop, S. Rieder, in:, 35th International Conference on Computer Aided Verification , Springer Nature, 2023, pp. 390–414."},"day":"17","oa":1,"publication":"35th International Conference on Computer Aided Verification ","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031377051"],"issn":["0302-9743"]},"publication_status":"published","abstract":[{"lang":"eng","text":"We provide a learning-based technique for guessing a winning strategy in a parity game originating from an LTL synthesis problem. A cheaply obtained guess can be useful in several applications. Not only can the guessed strategy be applied as best-effort in cases where the game’s huge size prohibits rigorous approaches, but it can also increase the scalability of rigorous LTL synthesis in several ways. Firstly, checking whether a guessed strategy is winning is easier than constructing one. Secondly, even if the guess is wrong in some places, it can be fixed by strategy iteration faster than constructing one from scratch. Thirdly, the guess can be used in on-the-fly approaches to prioritize exploration in the most fruitful directions.\r\nIn contrast to previous works, we (i) reflect the highly structured logical information in game’s states, the so-called semantic labelling, coming from the recent LTL-to-automata translations, and (ii) learn to reflect it properly by learning from previously solved games, bringing the solving process closer to human-like reasoning."}],"file":[{"date_updated":"2023-09-06T08:25:50Z","date_created":"2023-09-06T08:25:50Z","relation":"main_file","success":1,"file_id":"14276","file_name":"2023_LNCS_CAV_Kretinsky.pdf","creator":"dernst","access_level":"open_access","file_size":428354,"content_type":"application/pdf","checksum":"ed66278b61bb869e1baba3d9b9081271"}],"quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","date_created":"2023-09-03T22:01:16Z","_id":"14259","year":"2023"},{"intvolume":"     13964","alternative_title":["LNCS"],"ddc":["000"],"date_published":"2023-07-17T00:00:00Z","doi":"10.1007/978-3-031-37706-8_8","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"file_date_updated":"2023-09-06T08:16:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","volume":13964,"month":"07","publisher":"Springer Nature","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"scopus_import":"1","conference":{"end_date":"2023-07-22","start_date":"2023-07-17","name":"CAV: Computer Aided Verification","location":"Paris, France"},"page":"156-169","has_accepted_license":"1","title":"Lincheck: A practical framework for testing concurrent data structures on JVM","day":"17","oa":1,"publication_identifier":{"issn":["0302-9743"],"isbn":["9783031377051"],"eissn":["1611-3349"]},"publication":"35th International Conference on Computer Aided Verification ","citation":{"ista":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck: A practical framework for testing concurrent data structures on JVM. 35th International Conference on Computer Aided Verification . CAV: Computer Aided Verification, LNCS, vol. 13964, 156–169.","chicago":"Koval, Nikita, Alexander Fedorov, Maria Sokolova, Dmitry Tsitelov, and Dan-Adrian Alistarh. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” In <i>35th International Conference on Computer Aided Verification </i>, 13964:156–69. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">https://doi.org/10.1007/978-3-031-37706-8_8</a>.","ama":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical framework for testing concurrent data structures on JVM. In: <i>35th International Conference on Computer Aided Verification </i>. Vol 13964. Springer Nature; 2023:156-169. doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">10.1007/978-3-031-37706-8_8</a>","apa":"Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., &#38; Alistarh, D.-A. (2023). Lincheck: A practical framework for testing concurrent data structures on JVM. In <i>35th International Conference on Computer Aided Verification </i> (Vol. 13964, pp. 156–169). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">https://doi.org/10.1007/978-3-031-37706-8_8</a>","ieee":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, and D.-A. Alistarh, “Lincheck: A practical framework for testing concurrent data structures on JVM,” in <i>35th International Conference on Computer Aided Verification </i>, Paris, France, 2023, vol. 13964, pp. 156–169.","mla":"Koval, Nikita, et al. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” <i>35th International Conference on Computer Aided Verification </i>, vol. 13964, Springer Nature, 2023, pp. 156–69, doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">10.1007/978-3-031-37706-8_8</a>.","short":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, in:, 35th International Conference on Computer Aided Verification , Springer Nature, 2023, pp. 156–169."},"date_updated":"2024-02-27T07:46:52Z","author":[{"id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita","first_name":"Nikita","last_name":"Koval"},{"full_name":"Fedorov, Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","first_name":"Alexander","last_name":"Fedorov"},{"full_name":"Sokolova, Maria","first_name":"Maria","last_name":"Sokolova"},{"full_name":"Tsitelov, Dmitry","first_name":"Dmitry","last_name":"Tsitelov"},{"first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"14995","relation":"research_data"}]},"publication_status":"published","abstract":[{"text":"This paper presents Lincheck, a new practical and user-friendly framework for testing concurrent algorithms on the Java Virtual Machine (JVM). Lincheck provides a simple and declarative way to write concurrent tests: instead of describing how to perform the test, users specify what to test by declaring all the operations to examine; the framework automatically handles the rest. As a result, tests written with Lincheck are concise and easy to understand. The framework automatically generates a set of concurrent scenarios, examines them using stress-testing or bounded model checking, and verifies that the results of each invocation are correct. Notably, if an error is detected via model checking, Lincheck provides an easy-to-follow trace to reproduce it, significantly simplifying the bug investigation.\r\n\r\nTo the best of our knowledge, Lincheck is the first production-ready tool on the JVM that offers such a simple way of writing concurrent tests, without requiring special skills or expertise. We successfully integrated Lincheck in the development process of several large projects, such as Kotlin Coroutines, and identified new bugs in popular concurrency libraries, such as a race in Java’s standard ConcurrentLinkedDeque and a liveliness bug in Java’s AbstractQueuedSynchronizer framework, which is used in most of the synchronization primitives. We believe that Lincheck can significantly improve the quality and productivity of concurrent algorithms research and development and become the state-of-the-art tool for checking their correctness.","lang":"eng"}],"file":[{"date_updated":"2023-09-06T08:16:25Z","file_name":"2023_LNCS_Koval.pdf","file_id":"14275","success":1,"date_created":"2023-09-06T08:16:25Z","relation":"main_file","access_level":"open_access","creator":"dernst","checksum":"c346016393123a0a2338ad4d976f61bc","file_size":421408,"content_type":"application/pdf"}],"date_created":"2023-09-03T22:01:16Z","_id":"14260","year":"2023"},{"date_created":"2023-09-03T22:01:16Z","pmid":1,"year":"2023","_id":"14261","quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","article_type":"original","publication_status":"published","file":[{"file_id":"14272","success":1,"relation":"main_file","date_created":"2023-09-06T07:32:39Z","file_name":"2023_JourPhysChemistry_Gamper.pdf","date_updated":"2023-09-06T07:32:39Z","file_size":4986859,"content_type":"application/pdf","checksum":"637454e2b3a357498d8d622d241c4bf6","access_level":"open_access","creator":"dernst"}],"abstract":[{"lang":"eng","text":"In this work, a generalized, adapted Numerov implementation capable of determining band structures of periodic quantum systems is outlined. Based on the input potential, the presented approach numerically solves the Schrödinger equation in position space at each momentum space point. Thus, in addition to the band structure, the method inherently provides information about the state functions and probability densities in position space at each momentum space point considered. The generalized, adapted Numerov framework provided reliable estimates for a variety of increasingly complex test suites in one, two, and three dimensions. The accuracy of the proposed methodology was benchmarked against results obtained for the analytically solvable Kronig-Penney model. Furthermore, the presented numerical solver was applied to a model potential representing a 2D optical lattice being a challenging application relevant, for example, in the field of quantum computing."}],"day":"11","publication":"Journal of Physical Chemistry Letters","publication_identifier":{"eissn":["1948-7185"]},"oa":1,"citation":{"short":"J. Gamper, F. Kluibenschedl, A.K.H. Weiss, T.S. Hofer, Journal of Physical Chemistry Letters 14 (2023) 7395–7403.","ista":"Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. 2023. Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. Journal of Physical Chemistry Letters. 14(33), 7395–7403.","chicago":"Gamper, Jakob, Florian Kluibenschedl, Alexander K.H. Weiss, and Thomas S. Hofer. “Accessing Position Space Wave Functions in Band Structure Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-, Two-, and Three-Dimensional Quantum Problems.” <i>Journal of Physical Chemistry Letters</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">https://doi.org/10.1021/acs.jpclett.3c01707</a>.","ama":"Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. <i>Journal of Physical Chemistry Letters</i>. 2023;14(33):7395-7403. doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">10.1021/acs.jpclett.3c01707</a>","ieee":"J. Gamper, F. Kluibenschedl, A. K. H. Weiss, and T. S. Hofer, “Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems,” <i>Journal of Physical Chemistry Letters</i>, vol. 14, no. 33. American Chemical Society, pp. 7395–7403, 2023.","apa":"Gamper, J., Kluibenschedl, F., Weiss, A. K. H., &#38; Hofer, T. S. (2023). Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. <i>Journal of Physical Chemistry Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">https://doi.org/10.1021/acs.jpclett.3c01707</a>","mla":"Gamper, Jakob, et al. “Accessing Position Space Wave Functions in Band Structure Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-, Two-, and Three-Dimensional Quantum Problems.” <i>Journal of Physical Chemistry Letters</i>, vol. 14, no. 33, American Chemical Society, 2023, pp. 7395–403, doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">10.1021/acs.jpclett.3c01707</a>."},"author":[{"last_name":"Gamper","first_name":"Jakob","full_name":"Gamper, Jakob"},{"full_name":"Kluibenschedl, Florian","id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","last_name":"Kluibenschedl","first_name":"Florian"},{"full_name":"Weiss, Alexander K.H.","first_name":"Alexander K.H.","last_name":"Weiss"},{"full_name":"Hofer, Thomas S.","last_name":"Hofer","first_name":"Thomas S."}],"date_updated":"2023-09-06T11:04:31Z","has_accepted_license":"1","issue":"33","title":"Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems","external_id":{"pmid":["37566743"],"isi":["001048165800001"]},"acknowledgement":"Financial supports for this work via a PhD scholarship for J. Gamper issued by the Leopold-Franzens-University of Innsbruck (Vicerector Prof. Dr Ulrike Tanzer) are gratefully acknowledged. The computational results presented have been achieved (in part) using the HPC infrastructure of the University of Innsbruck.","scopus_import":"1","page":"7395-7403","isi":1,"publisher":"American Chemical Society","department":[{"_id":"GradSch"}],"month":"08","file_date_updated":"2023-09-06T07:32:39Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","volume":14,"intvolume":"        14","ddc":["530","540"],"doi":"10.1021/acs.jpclett.3c01707","date_published":"2023-08-11T00:00:00Z","language":[{"iso":"eng"}],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"type":"journal_article","volume":8,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-09-01T00:00:00Z","doi":"10.1126/sciimmunol.adc9584","status":"public","language":[{"iso":"eng"}],"intvolume":"         8","acknowledgement":"We thank I. de Vries and the Scientific Service Units (Life Sciences, Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute of Science and Technology Austria for excellent support, as well as all the rotation students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis work was supported by grants from the European Research Council under the European Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20) to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U. was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411.","scopus_import":"1","month":"09","publisher":"American Association for the Advancement of Science","department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/sciimmunol.adc9584"}],"isi":1,"citation":{"short":"J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B. Hannezo, M.K. Sixt, Science Immunology 8 (2023).","mla":"Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” <i>Science Immunology</i>, vol. 8, no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">10.1126/sciimmunol.adc9584</a>.","ieee":"J. H. Alanko <i>et al.</i>, “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration,” <i>Science Immunology</i>, vol. 8, no. 87. American Association for the Advancement of Science, 2023.","ama":"Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. <i>Science Immunology</i>. 2023;8(87). doi:<a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">10.1126/sciimmunol.adc9584</a>","apa":"Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin, J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. <i>Science Immunology</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">https://doi.org/10.1126/sciimmunol.adc9584</a>","chicago":"Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz, Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” <i>Science Immunology</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">https://doi.org/10.1126/sciimmunol.adc9584</a>.","ista":"Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB, Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 8(87), adc9584."},"date_updated":"2023-12-21T14:30:01Z","author":[{"orcid":"0000-0002-7698-3061","full_name":"Alanko, Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","first_name":"Jonna H","last_name":"Alanko"},{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217","last_name":"Ucar","first_name":"Mehmet C"},{"id":"3795523E-F248-11E8-B48F-1D18A9856A87","full_name":"Canigova, Nikola","orcid":"0000-0002-8518-5926","last_name":"Canigova","first_name":"Nikola"},{"last_name":"Stopp","first_name":"Julian A","full_name":"Stopp, Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87"},{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Jan","last_name":"Schwarz","first_name":"Jan"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin"},{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}],"day":"01","oa":1,"publication":"Science Immunology","publication_identifier":{"issn":["2470-9468"]},"external_id":{"isi":["001062110600003"],"pmid":["37656776"]},"title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","call_identifier":"H2020","name":"Cellular navigation along spatial gradients"},{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis"},{"name":"Nano-Analytics of Cellular Systems","call_identifier":"FWF","grant_number":"W01250-B20","_id":"265E2996-B435-11E9-9278-68D0E5697425"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"}],"issue":"87","article_number":"adc9584","pmid":1,"ec_funded":1,"date_created":"2023-09-06T08:07:51Z","_id":"14274","year":"2023","article_type":"original","related_material":{"record":[{"id":"14279","status":"public","relation":"research_data"},{"relation":"dissertation_contains","id":"14697","status":"public"}]},"publication_status":"published","abstract":[{"lang":"eng","text":"Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization."}],"quality_controlled":"1","article_processing_charge":"No","keyword":["General Medicine","Immunology"],"oa_version":"Published Version"},{"doi":"10.1103/prxlife.1.013001","date_published":"2023-07-20T00:00:00Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","intvolume":"         1","ddc":["570"],"type":"journal_article","volume":1,"file_date_updated":"2023-09-15T06:30:50Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"EdHa"}],"publisher":"American Physical Society","month":"07","acknowledgement":"We thank all members of the Hannezo group for discussions and suggestions, as well as Sound Wai Phow for technical assistance. This work received funding from the European Research Council under the EU Horizon 2020 research and innovation program Grant Agreement No. 851288 (E.H.), JSPS KAKENHI Grant No. 21H05290, and the Ministry of Education under the Research Centres of Excellence program through the MBI at NUS.","project":[{"grant_number":"851288","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis"}],"title":"Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers","has_accepted_license":"1","article_number":"013001","issue":"1","citation":{"short":"D.R. Boocock, T. Hirashima, E.B. Hannezo, PRX Life 1 (2023).","mla":"Boocock, Daniel R., et al. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” <i>PRX Life</i>, vol. 1, no. 1, 013001, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/prxlife.1.013001\">10.1103/prxlife.1.013001</a>.","ieee":"D. R. Boocock, T. Hirashima, and E. B. Hannezo, “Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers,” <i>PRX Life</i>, vol. 1, no. 1. American Physical Society, 2023.","ama":"Boocock DR, Hirashima T, Hannezo EB. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. <i>PRX Life</i>. 2023;1(1). doi:<a href=\"https://doi.org/10.1103/prxlife.1.013001\">10.1103/prxlife.1.013001</a>","apa":"Boocock, D. R., Hirashima, T., &#38; Hannezo, E. B. (2023). Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. <i>PRX Life</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxlife.1.013001\">https://doi.org/10.1103/prxlife.1.013001</a>","chicago":"Boocock, Daniel R, Tsuyoshi Hirashima, and Edouard B Hannezo. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” <i>PRX Life</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/prxlife.1.013001\">https://doi.org/10.1103/prxlife.1.013001</a>.","ista":"Boocock DR, Hirashima T, Hannezo EB. 2023. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 1(1), 013001."},"author":[{"last_name":"Boocock","first_name":"Daniel R","orcid":"0000-0002-1585-2631","full_name":"Boocock, Daniel R","id":"453AF628-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hirashima","first_name":"Tsuyoshi","full_name":"Hirashima, Tsuyoshi"},{"first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"}],"date_updated":"2023-09-15T06:39:17Z","day":"20","publication_identifier":{"issn":["2835-8279"]},"publication":"PRX Life","oa":1,"publication_status":"published","article_type":"original","file":[{"date_updated":"2023-09-15T06:30:50Z","file_id":"14335","date_created":"2023-09-15T06:30:50Z","success":1,"relation":"main_file","file_name":"2023_PRXLife_Boocock.pdf","access_level":"open_access","creator":"dernst","file_size":2559520,"content_type":"application/pdf","checksum":"f881d98c89eb9f1aa136d7b781511553"}],"abstract":[{"text":"Living tissues are characterized by an intrinsically mechanochemical interplay of active physical forces and complex biochemical signaling pathways. Either feature alone can give rise to complex emergent phenomena, for example, mechanically driven glassy dynamics and rigidity transitions, or chemically driven reaction-diffusion instabilities. An important question is how to quantitatively assess the contribution of these different cues to the large-scale dynamics of biological materials. We address this in Madin-Darby canine kidney (MDCK) monolayers, considering both mechanochemical feedback between extracellular signal-regulated kinase (ERK) signaling activity and cellular density as well as a mechanically active tissue rheology via a self-propelled vertex model. We show that the relative strength of active migration forces to mechanochemical couplings controls a transition from a uniform active glass to periodic spatiotemporal waves. We parametrize the model from published experimental data sets on MDCK monolayers and use it to make new predictions on the correlation functions of cellular dynamics and the dynamics of topological defects associated with the oscillatory phase of cells. Interestingly, MDCK monolayers are best described by an intermediary parameter region in which both mechanochemical couplings and noisy active propulsion have a strong influence on the dynamics. Finally, we study how tissue rheology and ERK waves produce feedback on one another and uncover a mechanism via which tissue fluidity can be controlled by mechanochemical waves at both the local and global levels.","lang":"eng"}],"quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"Yes","ec_funded":1,"date_created":"2023-09-06T08:30:59Z","year":"2023","_id":"14277"},{"day":"11","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-10-03T11:42:58Z","citation":{"short":"M.C. Ucar, (2023).","ista":"Ucar MC. 2023. Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration’, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8133960\">10.5281/ZENODO.8133960</a>.","chicago":"Ucar, Mehmet C. “Source Data for the Manuscript ‘CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.’” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8133960\">https://doi.org/10.5281/ZENODO.8133960</a>.","ama":"Ucar MC. Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8133960\">10.5281/ZENODO.8133960</a>","ieee":"M. C. Ucar, “Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.’” Zenodo, 2023.","apa":"Ucar, M. C. (2023). Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8133960\">https://doi.org/10.5281/ZENODO.8133960</a>","mla":"Ucar, Mehmet C. <i>Source Data for the Manuscript “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.”</i> Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8133960\">10.5281/ZENODO.8133960</a>."},"author":[{"first_name":"Mehmet C","last_name":"Ucar","full_name":"Ucar, Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217"}],"type":"research_data_reference","has_accepted_license":"1","ddc":["570"],"date_published":"2023-07-11T00:00:00Z","doi":"10.5281/ZENODO.8133960","title":"Source data for the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\"","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","date_created":"2023-09-06T08:39:25Z","_id":"14279","year":"2023","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133960","open_access":"1"}],"article_processing_charge":"No","oa_version":"Published Version","month":"07","related_material":{"record":[{"status":"public","id":"14274","relation":"used_in_publication"}]},"publisher":"Zenodo","department":[{"_id":"EdHa"}],"abstract":[{"lang":"eng","text":"The zip file includes source data used in the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\", as well as a representative Jupyter notebook to reproduce the main figures. Please see the preprint on bioRxiv and the DOI link there to access the final published version. Note the title change between the preprint and the published manuscript.\r\nA sample script for particle-based simulations of collective chemotaxis by self-generated gradients is also included (see Self-generated_chemotaxis_sample_script.ipynb) to generate exemplary cell trajectories. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt."}]},{"language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","doi":"10.15479/at:ista:14280","date_published":"2023-09-25T00:00:00Z","ddc":["572"],"alternative_title":["ISTA Thesis"],"type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file_date_updated":"2023-10-04T10:28:35Z","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"publisher":"Institute of Science and Technology Austria","month":"09","degree_awarded":"PhD","page":"156","project":[{"name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239"},{"grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"Understanding bacterial cell division by in vitro\r\nreconstitution"},{"grant_number":"ALTF 2015-1163","_id":"2596EAB6-B435-11E9-9278-68D0E5697425","name":"Synthesis of bacterial cell wall"},{"name":"Reconstitution of bacterial cell wall sythesis","grant_number":"LT000824/2016","_id":"259B655A-B435-11E9-9278-68D0E5697425"}],"title":"Spatiotemporal signaling during assembly of the bacterial divisome","has_accepted_license":"1","supervisor":[{"orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","last_name":"Loose","first_name":"Martin"}],"citation":{"ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria.","chicago":"Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14280\">https://doi.org/10.15479/at:ista:14280</a>.","ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14280\">10.15479/at:ista:14280</a>","ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023.","apa":"Radler, P. (2023). <i>Spatiotemporal signaling during assembly of the bacterial divisome</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14280\">https://doi.org/10.15479/at:ista:14280</a>","mla":"Radler, Philipp. <i>Spatiotemporal Signaling during Assembly of the Bacterial Divisome</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14280\">10.15479/at:ista:14280</a>.","short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023."},"date_updated":"2024-02-21T12:35:18Z","author":[{"last_name":"Radler","first_name":"Philipp","full_name":"Radler, Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 "}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-033-6"]},"day":"25","file":[{"file_id":"14390","relation":"source_file","date_created":"2023-10-04T10:11:53Z","file_name":"PhD Thesis_Philipp Radler_20231004.docx","date_updated":"2023-10-04T10:28:35Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":114932847,"checksum":"87eef11fbc5c7df0826f12a3a629b444","access_level":"closed","creator":"pradler"},{"access_level":"closed","creator":"pradler","checksum":"3253e099b7126469d941fd9419d68b4f","content_type":"application/pdf","file_size":37838778,"date_updated":"2023-10-04T10:28:35Z","embargo":"2024-10-04","file_name":"PhD Thesis_Philipp Radler_20231004.pdf","embargo_to":"open_access","file_id":"14391","date_created":"2023-10-04T10:11:21Z","relation":"main_file"}],"abstract":[{"lang":"eng","text":"Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome. \r\nA previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation."}],"publication_status":"published","related_material":{"record":[{"id":"11373","status":"public","relation":"part_of_dissertation"},{"id":"7387","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"10934","relation":"research_data"}]},"oa_version":"Published Version","article_processing_charge":"No","keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"year":"2023","_id":"14280","date_created":"2023-09-06T10:58:25Z","ec_funded":1},{"day":"17","publication":"Science","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"citation":{"short":"F.M. Praetorius, P.J.Y. Leung, M.H. Tessmer, A. Broerman, C. Demakis, A.F. Dishman, A. Pillai, A. Idris, D. Juergens, J. Dauparas, X. Li, P.M. Levine, M. Lamb, R.K. Ballard, S.R. Gerben, H. Nguyen, A. Kang, B. Sankaran, A.K. Bera, B.F. Volkman, J. Nivala, S. Stoll, D. Baker, Science 381 (2023) 754–760.","apa":"Praetorius, F. M., Leung, P. J. Y., Tessmer, M. H., Broerman, A., Demakis, C., Dishman, A. F., … Baker, D. (2023). Design of stimulus-responsive two-state hinge proteins. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adg7731\">https://doi.org/10.1126/science.adg7731</a>","ama":"Praetorius FM, Leung PJY, Tessmer MH, et al. Design of stimulus-responsive two-state hinge proteins. <i>Science</i>. 2023;381(6659):754-760. doi:<a href=\"https://doi.org/10.1126/science.adg7731\">10.1126/science.adg7731</a>","ieee":"F. M. Praetorius <i>et al.</i>, “Design of stimulus-responsive two-state hinge proteins,” <i>Science</i>, vol. 381, no. 6659. American Association for the Advancement of Science, pp. 754–760, 2023.","mla":"Praetorius, Florian M., et al. “Design of Stimulus-Responsive Two-State Hinge Proteins.” <i>Science</i>, vol. 381, no. 6659, American Association for the Advancement of Science, 2023, pp. 754–60, doi:<a href=\"https://doi.org/10.1126/science.adg7731\">10.1126/science.adg7731</a>.","ista":"Praetorius FM, Leung PJY, Tessmer MH, Broerman A, Demakis C, Dishman AF, Pillai A, Idris A, Juergens D, Dauparas J, Li X, Levine PM, Lamb M, Ballard RK, Gerben SR, Nguyen H, Kang A, Sankaran B, Bera AK, Volkman BF, Nivala J, Stoll S, Baker D. 2023. Design of stimulus-responsive two-state hinge proteins. Science. 381(6659), 754–760.","chicago":"Praetorius, Florian M, Philip J. Y. Leung, Maxx H. Tessmer, Adam Broerman, Cullen Demakis, Acacia F. Dishman, Arvind Pillai, et al. “Design of Stimulus-Responsive Two-State Hinge Proteins.” <i>Science</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/science.adg7731\">https://doi.org/10.1126/science.adg7731</a>."},"author":[{"full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius","first_name":"Florian M"},{"first_name":"Philip J. Y.","last_name":"Leung","full_name":"Leung, Philip J. Y."},{"first_name":"Maxx H.","last_name":"Tessmer","full_name":"Tessmer, Maxx H."},{"full_name":"Broerman, Adam","first_name":"Adam","last_name":"Broerman"},{"full_name":"Demakis, Cullen","last_name":"Demakis","first_name":"Cullen"},{"full_name":"Dishman, Acacia F.","last_name":"Dishman","first_name":"Acacia F."},{"last_name":"Pillai","first_name":"Arvind","full_name":"Pillai, Arvind"},{"first_name":"Abbas","last_name":"Idris","full_name":"Idris, Abbas"},{"full_name":"Juergens, David","last_name":"Juergens","first_name":"David"},{"full_name":"Dauparas, Justas","last_name":"Dauparas","first_name":"Justas"},{"last_name":"Li","first_name":"Xinting","full_name":"Li, Xinting"},{"first_name":"Paul M.","last_name":"Levine","full_name":"Levine, Paul M."},{"first_name":"Mila","last_name":"Lamb","full_name":"Lamb, Mila"},{"full_name":"Ballard, Ryanne K.","last_name":"Ballard","first_name":"Ryanne K."},{"last_name":"Gerben","first_name":"Stacey R.","full_name":"Gerben, Stacey R."},{"full_name":"Nguyen, Hannah","first_name":"Hannah","last_name":"Nguyen"},{"full_name":"Kang, Alex","last_name":"Kang","first_name":"Alex"},{"first_name":"Banumathi","last_name":"Sankaran","full_name":"Sankaran, Banumathi"},{"last_name":"Bera","first_name":"Asim K.","full_name":"Bera, Asim K."},{"full_name":"Volkman, Brian F.","first_name":"Brian F.","last_name":"Volkman"},{"full_name":"Nivala, Jeff","first_name":"Jeff","last_name":"Nivala"},{"full_name":"Stoll, Stefan","first_name":"Stefan","last_name":"Stoll"},{"full_name":"Baker, David","first_name":"David","last_name":"Baker"}],"date_updated":"2023-11-07T12:42:09Z","issue":"6659","title":"Design of stimulus-responsive two-state hinge proteins","external_id":{"pmid":["37590357"]},"pmid":1,"date_created":"2023-09-06T12:04:23Z","year":"2023","_id":"14281","quality_controlled":"1","oa_version":"None","article_processing_charge":"No","article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"In nature, proteins that switch between two conformations in response to environmental stimuli structurally transduce biochemical information in a manner analogous to how transistors control information flow in computing devices. Designing proteins with two distinct but fully structured conformations is a challenge for protein design as it requires sculpting an energy landscape with two distinct minima. Here we describe the design of “hinge” proteins that populate one designed state in the absence of ligand and a second designed state in the presence of ligand. X-ray crystallography, electron microscopy, double electron-electron resonance spectroscopy, and binding measurements demonstrate that despite the significant structural differences the two states are designed with atomic level accuracy and that the conformational and binding equilibria are closely coupled."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":381,"intvolume":"       381","extern":"1","doi":"10.1126/science.adg7731","date_published":"2023-08-17T00:00:00Z","language":[{"iso":"eng"}],"status":"public","scopus_import":"1","page":"754-760","publisher":"American Association for the Advancement of Science","month":"08"},{"type":"preprint","citation":{"ieee":"N. I. Edman <i>et al.</i>, “Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies,” <i>bioRxiv</i>. .","apa":"Edman, N. I., Redler, R. L., Phal, A., Schlichthaerle, T., Srivatsan, S. R., Etemadi, A., … Baker, D. (n.d.). Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2023.03.14.532666\">https://doi.org/10.1101/2023.03.14.532666</a>","ama":"Edman NI, Redler RL, Phal A, et al. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2023.03.14.532666\">10.1101/2023.03.14.532666</a>","mla":"Edman, Natasha I., et al. “Modulation of FGF Pathway Signaling and Vascular Differentiation Using Designed Oligomeric Assemblies.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2023.03.14.532666\">10.1101/2023.03.14.532666</a>.","ista":"Edman NI, Redler RL, Phal A, Schlichthaerle T, Srivatsan SR, Etemadi A, An S, Favor A, Ehnes D, Li Z, Praetorius FM, Gordon M, Yang W, Coventry B, Hicks DR, Cao L, Bethel N, Heine P, Murray AN, Gerben S, Carter L, Miranda M, Negahdari B, Lee S, Trapnell C, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha G, Ruohola-Baker H, Baker D. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. bioRxiv, <a href=\"https://doi.org/10.1101/2023.03.14.532666\">10.1101/2023.03.14.532666</a>.","chicago":"Edman, Natasha I, Rachel L Redler, Ashish Phal, Thomas Schlichthaerle, Sanjay R Srivatsan, Ali Etemadi, Seong An, et al. “Modulation of FGF Pathway Signaling and Vascular Differentiation Using Designed Oligomeric Assemblies.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2023.03.14.532666\">https://doi.org/10.1101/2023.03.14.532666</a>.","short":"N.I. Edman, R.L. Redler, A. Phal, T. Schlichthaerle, S.R. Srivatsan, A. Etemadi, S. An, A. Favor, D. Ehnes, Z. Li, F.M. Praetorius, M. Gordon, W. Yang, B. Coventry, D.R. Hicks, L. Cao, N. Bethel, P. Heine, A.N. Murray, S. Gerben, L. Carter, M. Miranda, B. Negahdari, S. Lee, C. Trapnell, L. Stewart, D.C. Ekiert, J. Schlessinger, J. Shendure, G. Bhabha, H. Ruohola-Baker, D. Baker, BioRxiv (n.d.)."},"author":[{"full_name":"Edman, Natasha I","last_name":"Edman","first_name":"Natasha I"},{"full_name":"Redler, Rachel L","last_name":"Redler","first_name":"Rachel L"},{"full_name":"Phal, Ashish","last_name":"Phal","first_name":"Ashish"},{"full_name":"Schlichthaerle, Thomas","first_name":"Thomas","last_name":"Schlichthaerle"},{"last_name":"Srivatsan","first_name":"Sanjay R","full_name":"Srivatsan, Sanjay R"},{"first_name":"Ali","last_name":"Etemadi","full_name":"Etemadi, Ali"},{"full_name":"An, Seong","last_name":"An","first_name":"Seong"},{"full_name":"Favor, Andrew","first_name":"Andrew","last_name":"Favor"},{"last_name":"Ehnes","first_name":"Devon","full_name":"Ehnes, Devon"},{"first_name":"Zhe","last_name":"Li","full_name":"Li, Zhe"},{"full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","first_name":"Florian M","last_name":"Praetorius"},{"first_name":"Max","last_name":"Gordon","full_name":"Gordon, Max"},{"full_name":"Yang, Wei","last_name":"Yang","first_name":"Wei"},{"last_name":"Coventry","first_name":"Brian","full_name":"Coventry, Brian"},{"full_name":"Hicks, Derrick R","last_name":"Hicks","first_name":"Derrick R"},{"full_name":"Cao, Longxing","last_name":"Cao","first_name":"Longxing"},{"first_name":"Neville","last_name":"Bethel","full_name":"Bethel, Neville"},{"full_name":"Heine, Piper","last_name":"Heine","first_name":"Piper"},{"full_name":"Murray, Analisa N","last_name":"Murray","first_name":"Analisa N"},{"full_name":"Gerben, Stacey","first_name":"Stacey","last_name":"Gerben"},{"full_name":"Carter, Lauren","last_name":"Carter","first_name":"Lauren"},{"full_name":"Miranda, Marcos","last_name":"Miranda","first_name":"Marcos"},{"full_name":"Negahdari, Babak","last_name":"Negahdari","first_name":"Babak"},{"last_name":"Lee","first_name":"Sangwon","full_name":"Lee, Sangwon"},{"full_name":"Trapnell, Cole","last_name":"Trapnell","first_name":"Cole"},{"last_name":"Stewart","first_name":"Lance","full_name":"Stewart, Lance"},{"last_name":"Ekiert","first_name":"Damian C","full_name":"Ekiert, Damian C"},{"first_name":"Joseph","last_name":"Schlessinger","full_name":"Schlessinger, Joseph"},{"full_name":"Shendure, Jay","last_name":"Shendure","first_name":"Jay"},{"full_name":"Bhabha, Gira","first_name":"Gira","last_name":"Bhabha"},{"last_name":"Ruohola-Baker","first_name":"Hannele","full_name":"Ruohola-Baker, Hannele"},{"last_name":"Baker","first_name":"David","full_name":"Baker, David"}],"date_updated":"2023-11-07T12:21:58Z","day":"15","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"bioRxiv","date_published":"2023-03-15T00:00:00Z","doi":"10.1101/2023.03.14.532666","title":"Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies","status":"public","language":[{"iso":"eng"}],"extern":"1","date_created":"2023-09-06T12:31:49Z","_id":"14294","year":"2023","month":"03","publication_status":"submitted","abstract":[{"text":"Growth factors and cytokines signal by binding to the extracellular domains of their receptors and drive association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cascades. To enable systematic exploration of how receptor valency and geometry affects signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using repeat protein building blocks that can be modularly extended. By incorporating a de novo designed fibroblast growth-factor receptor (FGFR) binding module into these scaffolds, we generated a series of synthetic signaling ligands that exhibit potent valency- and geometry-dependent Ca2+ release and MAPK pathway activation. The high specificity of the designed agonists reveal distinct roles for two FGFR splice variants in driving endothelial and mesenchymal cell fates during early vascular development. The ability to incorporate receptor binding domains and repeat extensions in a modular fashion makes our designed scaffolds broadly useful for probing and manipulating cellular signaling pathways.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1101/2023.03.14.532666","open_access":"1"}],"article_processing_charge":"No","oa_version":"Preprint"},{"publisher":"Elsevier","department":[{"_id":"JiFr"}],"month":"10","acknowledgement":"The opening quote is not intended to reflect any political views of the authors. The authors by no means endorse the rhetoric of Donald Rumsfeld or the 2003 invasion of Iraq by the United States. Nevertheless, Rumsfeld's quote led to both public and academic debates on the concept of known and unknown unknowns, which can be applied to the recent unexpected developments in the auxin signaling field. We thank Linlin Qi and Huihuang Chen for their suggestions on figure presentation and inspiring discussions of TIR1/AFB signaling. Finally, we thank Aroosa Hussain for discussion of Greek mythology.","scopus_import":"1","doi":"10.1016/j.pbi.2023.102443","date_published":"2023-10-01T00:00:00Z","language":[{"iso":"eng"}],"status":"public","intvolume":"        75","ddc":["580"],"type":"journal_article","volume":75,"file_date_updated":"2023-11-02T17:03:20Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","article_type":"review","file":[{"file_id":"14482","success":1,"relation":"main_file","date_created":"2023-11-02T17:03:20Z","file_name":"Fiedler CurrOpinOlantBiol 2023_revised.pdf","date_updated":"2023-11-02T17:03:20Z","content_type":"application/pdf","file_size":737872,"checksum":"1c476c3414d2dfb0c85db0cb6cfd8a28","access_level":"open_access","creator":"amally"}],"abstract":[{"lang":"eng","text":"To respond to auxin, the chief orchestrator of their multicellularity, plants evolved multiple receptor systems and signal transduction cascades. Despite decades of research, however, we are still lacking a satisfactory synthesis of various auxin signaling mechanisms. The chief discrepancy and historical controversy of the field is that of rapid and slow auxin effects on plant physiology and development. How is it possible that ions begin to trickle across the plasma membrane as soon as auxin enters the cell, even though the best-characterized transcriptional auxin pathway can take effect only after tens of minutes? Recently, unexpected progress has been made in understanding this and other unknowns of auxin signaling. We provide a perspective on these exciting developments and concepts whose general applicability might have ramifications beyond auxin signaling."}],"quality_controlled":"1","oa_version":"Submitted Version","article_processing_charge":"No","date_created":"2023-09-10T22:01:11Z","pmid":1,"year":"2023","_id":"14313","title":"Rapid auxin signaling: Unknowns old and new","external_id":{"pmid":["37666097"]},"has_accepted_license":"1","issue":"10","article_number":"102443","author":[{"first_name":"Lukas","last_name":"Fiedler","id":"7c417475-8972-11ed-ae7b-8b674ca26986","full_name":"Fiedler, Lukas"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"citation":{"short":"L. Fiedler, J. Friml, Current Opinion in Plant Biology 75 (2023).","mla":"Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.” <i>Current Opinion in Plant Biology</i>, vol. 75, no. 10, 102443, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">10.1016/j.pbi.2023.102443</a>.","ama":"Fiedler L, Friml J. Rapid auxin signaling: Unknowns old and new. <i>Current Opinion in Plant Biology</i>. 2023;75(10). doi:<a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">10.1016/j.pbi.2023.102443</a>","apa":"Fiedler, L., &#38; Friml, J. (2023). Rapid auxin signaling: Unknowns old and new. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">https://doi.org/10.1016/j.pbi.2023.102443</a>","ieee":"L. Fiedler and J. Friml, “Rapid auxin signaling: Unknowns old and new,” <i>Current Opinion in Plant Biology</i>, vol. 75, no. 10. Elsevier, 2023.","chicago":"Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">https://doi.org/10.1016/j.pbi.2023.102443</a>.","ista":"Fiedler L, Friml J. 2023. Rapid auxin signaling: Unknowns old and new. Current Opinion in Plant Biology. 75(10), 102443."},"date_updated":"2023-11-07T08:17:13Z","day":"01","publication_identifier":{"issn":["1369-5266"]},"publication":"Current Opinion in Plant Biology","oa":1},{"file_date_updated":"2023-09-15T07:12:46Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":42,"intvolume":"        42","ddc":["570"],"date_published":"2023-09-26T00:00:00Z","doi":"10.1016/j.celrep.2023.113015","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","language":[{"iso":"eng"}],"acknowledgement":"We thank A. Cumpelik, H. Chiossi, and L. Bollman for comments on an earlier version of this manuscript. This work was funded by EU-FP7 MC-ITN IN-SENS (grant 607616).","scopus_import":"1","month":"09","publisher":"Elsevier","department":[{"_id":"JoCs"}],"day":"26","oa":1,"publication_identifier":{"eissn":["2211-1247"]},"publication":"Cell Reports","author":[{"orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","last_name":"Nardin","first_name":"Michele"},{"first_name":"Karola","last_name":"Käfer","full_name":"Käfer, Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Stella","first_name":"Federico","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","full_name":"Stella, Federico","orcid":"0000-0001-9439-3148"},{"full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari"}],"date_updated":"2023-09-15T07:14:12Z","citation":{"ista":"Nardin M, Käfer K, Stella F, Csicsvari JL. 2023. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. Cell Reports. 42(9), 113015.","chicago":"Nardin, Michele, Karola Käfer, Federico Stella, and Jozsef L Csicsvari. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” <i>Cell Reports</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">https://doi.org/10.1016/j.celrep.2023.113015</a>.","ama":"Nardin M, Käfer K, Stella F, Csicsvari JL. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. <i>Cell Reports</i>. 2023;42(9). doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">10.1016/j.celrep.2023.113015</a>","ieee":"M. Nardin, K. Käfer, F. Stella, and J. L. Csicsvari, “Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions,” <i>Cell Reports</i>, vol. 42, no. 9. Elsevier, 2023.","apa":"Nardin, M., Käfer, K., Stella, F., &#38; Csicsvari, J. L. (2023). Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">https://doi.org/10.1016/j.celrep.2023.113015</a>","mla":"Nardin, Michele, et al. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” <i>Cell Reports</i>, vol. 42, no. 9, 113015, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">10.1016/j.celrep.2023.113015</a>.","short":"M. Nardin, K. Käfer, F. Stella, J.L. Csicsvari, Cell Reports 42 (2023)."},"has_accepted_license":"1","article_number":"113015","issue":"9","title":"Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions","external_id":{"pmid":["37632747"]},"project":[{"name":"Inter-and intracellular signalling in schizophrenia","_id":"257BBB4C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"607616"}],"date_created":"2023-09-10T22:01:11Z","pmid":1,"ec_funded":1,"_id":"14314","year":"2023","quality_controlled":"1","article_processing_charge":"Yes","oa_version":"Published Version","publication_status":"published","article_type":"original","abstract":[{"text":"The execution of cognitive functions requires coordinated circuit activity across different brain areas that involves the associated firing of neuronal assemblies. Here, we tested the circuit mechanism behind assembly interactions between the hippocampus and the medial prefrontal cortex (mPFC) of adult rats by recording neuronal populations during a rule-switching task. We identified functionally coupled CA1-mPFC cells that synchronized their activity beyond that expected from common spatial coding or oscillatory firing. When such cell pairs fired together, the mPFC cell strongly phase locked to CA1 theta oscillations and maintained consistent theta firing phases, independent of the theta timing of their CA1 counterpart. These functionally connected CA1-mPFC cells formed interconnected assemblies. While firing together with their CA1 assembly partners, mPFC cells fired along specific theta sequences. Our results suggest that upregulated theta oscillatory firing of mPFC cells can signal transient interactions with specific CA1 assemblies, thus enabling distributed computations.","lang":"eng"}],"file":[{"access_level":"open_access","creator":"dernst","file_size":4879455,"content_type":"application/pdf","checksum":"ca77a304fb813c292550b8604b0fb41d","date_updated":"2023-09-15T07:12:46Z","file_id":"14337","relation":"main_file","success":1,"date_created":"2023-09-15T07:12:46Z","file_name":"2023_CellPress_Nardin.pdf"}]}]