[{"doi":"10.1038/s41467-023-40930-6","scopus_import":"1","intvolume":"        14","author":[{"full_name":"Vierra, Nicholas C.","last_name":"Vierra","first_name":"Nicholas C."},{"first_name":"Luisa","last_name":"Ribeiro-Silva","full_name":"Ribeiro-Silva, Luisa"},{"last_name":"Kirmiz","full_name":"Kirmiz, Michael","first_name":"Michael"},{"first_name":"Deborah","last_name":"Van Der List","full_name":"Van Der List, Deborah"},{"id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","first_name":"Pradeep","last_name":"Bhandari","full_name":"Bhandari, Pradeep","orcid":"0000-0003-0863-4481"},{"full_name":"Mack, Olivia A.","last_name":"Mack","first_name":"Olivia A."},{"last_name":"Carroll","full_name":"Carroll, James","first_name":"James"},{"full_name":"Le Monnier, Elodie","last_name":"Le Monnier","first_name":"Elodie","id":"3B59276A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Aicher","full_name":"Aicher, Sue A.","first_name":"Sue A."},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"James S.","last_name":"Trimmer","full_name":"Trimmer, James S."}],"volume":14,"date_created":"2023-09-03T22:01:14Z","oa":1,"month":"08","_id":"14253","ddc":["570"],"file_date_updated":"2023-09-06T06:50:07Z","status":"public","oa_version":"Published Version","article_number":"5231","year":"2023","language":[{"iso":"eng"}],"article_type":"original","publisher":"Springer Nature","day":"26","article_processing_charge":"Yes","has_accepted_license":"1","department":[{"_id":"RySh"}],"publication_status":"published","title":"Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling","date_updated":"2025-09-09T12:50:49Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"external_id":{"pmid":["37633939"],"isi":["001064563400013"]},"date_published":"2023-08-26T00:00:00Z","quality_controlled":"1","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"}],"publication_identifier":{"eissn":["2041-1723"]},"citation":{"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.","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.","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).","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>","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>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"publication":"Nature Communications","file":[{"file_name":"2023_NatureComm_Vierra.pdf","date_created":"2023-09-06T06:50:07Z","success":1,"date_updated":"2023-09-06T06:50:07Z","access_level":"open_access","creator":"dernst","file_id":"14270","file_size":9412549,"relation":"main_file","content_type":"application/pdf","checksum":"6ab8aab4e957f626a09a1c73db3388fb"}],"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.).","type":"journal_article"},{"publication":"Journal of Functional Analysis","citation":{"short":"R. Seiringer, J.P. Solovej, Journal of Functional Analysis 285 (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>","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>.","ista":"Seiringer R, Solovej JP. 2023. A simple approach to Lieb-Thirring type inequalities. Journal of Functional Analysis. 285(10), 110129.","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>.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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).","type":"journal_article","file":[{"file_id":"14915","file_size":232934,"checksum":"28e424ad91be6219e9d321054ce3a412","content_type":"application/pdf","relation":"main_file","date_created":"2024-01-30T14:15:16Z","file_name":"2023_JourFunctionalAnalysis_Seiringer.pdf","creator":"dernst","access_level":"open_access","success":1,"date_updated":"2024-01-30T14:15:16Z"}],"quality_controlled":"1","abstract":[{"lang":"eng","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."}],"title":"A simple approach to Lieb-Thirring type inequalities","publication_status":"published","date_updated":"2024-10-09T21:06:47Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2303.04504"],"isi":["001071552300001"]},"isi":1,"date_published":"2023-11-15T00:00:00Z","arxiv":1,"corr_author":"1","publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"year":"2023","language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","department":[{"_id":"RoSe"}],"publisher":"Elsevier","article_type":"original","day":"15","issue":"10","author":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521"},{"full_name":"Solovej, Jan Philip","last_name":"Solovej","first_name":"Jan Philip"}],"volume":285,"date_created":"2023-09-03T22:01:14Z","doi":"10.1016/j.jfa.2023.110129","scopus_import":"1","intvolume":"       285","ddc":["510"],"_id":"14254","file_date_updated":"2024-01-30T14:15:16Z","oa_version":"Published Version","status":"public","article_number":"110129","oa":1,"month":"11"},{"publication":"PLoS Pathogens","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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>.","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>","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).","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.","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>."},"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.","type":"journal_article","file":[{"checksum":"47ca3bb54b27f28b05644be0ad064bc6","relation":"main_file","content_type":"application/pdf","file_size":4458336,"file_id":"14269","access_level":"open_access","creator":"dernst","success":1,"date_updated":"2023-09-06T06:41:52Z","file_name":"2023_PloSPathogens_Koch.pdf","date_created":"2023-09-06T06:41:52Z"}],"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."}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"external_id":{"pmid":["37578957"],"isi":["001050846300004"]},"date_published":"2023-08-14T00:00:00Z","date_updated":"2025-04-15T08:24:50Z","publication_status":"published","title":"The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells","project":[{"name":"Structural conservation and diversity in retroviral capsid","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P31445"}],"publication_identifier":{"issn":["1553-7366"],"eissn":["1553-7374"]},"language":[{"iso":"eng"}],"year":"2023","department":[{"_id":"FlSc"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"has_accepted_license":"1","article_processing_charge":"Yes","issue":"8","day":"14","publisher":"Public Library of Science","article_type":"original","date_created":"2023-09-03T22:01:14Z","volume":19,"author":[{"full_name":"Koch, Jana","last_name":"Koch","first_name":"Jana"},{"last_name":"Xin","full_name":"Xin, Qilin","first_name":"Qilin"},{"id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Obr, Martin","last_name":"Obr","orcid":"0000-0003-1756-6564"},{"first_name":"Alicia","full_name":"Schäfer, Alicia","last_name":"Schäfer"},{"full_name":"Rolfs, Nina","last_name":"Rolfs","first_name":"Nina"},{"first_name":"Holda A.","full_name":"Anagho, Holda A.","last_name":"Anagho"},{"last_name":"Kudulyte","full_name":"Kudulyte, Aiste","first_name":"Aiste"},{"first_name":"Lea","last_name":"Woltereck","full_name":"Woltereck, Lea"},{"first_name":"Susann","last_name":"Kummer","full_name":"Kummer, Susann"},{"last_name":"Campos","full_name":"Campos, Joaquin","first_name":"Joaquin"},{"last_name":"Uckeley","full_name":"Uckeley, Zina M.","first_name":"Zina M."},{"last_name":"Bell-Sakyi","full_name":"Bell-Sakyi, Lesley","first_name":"Lesley"},{"last_name":"Kräusslich","full_name":"Kräusslich, Hans Georg","first_name":"Hans Georg"},{"orcid":"0000-0003-4790-8078","last_name":"Schur","full_name":"Schur, Florian Km","first_name":"Florian Km","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Claudio","full_name":"Acuna, Claudio","last_name":"Acuna"},{"first_name":"Pierre Yves","full_name":"Lozach, Pierre Yves","last_name":"Lozach"}],"intvolume":"        19","scopus_import":"1","doi":"10.1371/journal.ppat.1011562","article_number":"e1011562","status":"public","oa_version":"Published Version","ddc":["570"],"_id":"14255","file_date_updated":"2023-09-06T06:41:52Z","month":"08","oa":1},{"publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"arxiv":1,"date_published":"2023-08-01T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"external_id":{"isi":["001046037700007"],"arxiv":["2306.11587"]},"date_updated":"2023-09-06T11:05:58Z","title":"Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields","publication_status":"published","quality_controlled":"1","abstract":[{"lang":"eng","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."}],"file":[{"file_id":"14271","file_size":458120,"content_type":"application/pdf","relation":"main_file","checksum":"7b30d26fb2b7bcb5b5be1414950615f9","date_created":"2023-09-06T07:13:19Z","file_name":"2023_AstronomyAstrophysics_Mathis.pdf","success":1,"date_updated":"2023-09-06T07:13:19Z","creator":"dernst","access_level":"open_access"}],"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.","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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>.","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.","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).","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>","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>."},"publication":"Astronomy and Astrophysics","month":"08","oa":1,"article_number":"L9","oa_version":"Published Version","status":"public","file_date_updated":"2023-09-06T07:13:19Z","_id":"14256","ddc":["520"],"intvolume":"       676","scopus_import":"1","doi":"10.1051/0004-6361/202346832","date_created":"2023-09-03T22:01:15Z","volume":676,"author":[{"last_name":"Mathis","full_name":"Mathis, S.","first_name":"S."},{"full_name":"Bugnet, Lisa Annabelle","last_name":"Bugnet","orcid":"0000-0003-0142-4000","id":"d9edb345-f866-11ec-9b37-d119b5234501","first_name":"Lisa Annabelle"}],"day":"01","publisher":"EDP Sciences","article_type":"letter_note","department":[{"_id":"LiBu"}],"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","language":[{"iso":"eng"}],"year":"2023"},{"oa":1,"month":"09","_id":"14258","file_date_updated":"2024-01-30T13:20:35Z","ddc":["570"],"status":"public","oa_version":"Published Version","doi":"10.1016/j.ajhg.2023.07.006","scopus_import":"1","intvolume":"       110","author":[{"full_name":"Ojavee, Sven E.","last_name":"Ojavee","first_name":"Sven E."},{"first_name":"Liza","last_name":"Darrous","full_name":"Darrous, Liza"},{"full_name":"Patxot, Marion","last_name":"Patxot","first_name":"Marion"},{"last_name":"Läll","full_name":"Läll, Kristi","first_name":"Kristi"},{"full_name":"Fischer, Krista","last_name":"Fischer","first_name":"Krista"},{"last_name":"Mägi","full_name":"Mägi, Reedik","first_name":"Reedik"},{"first_name":"Zoltan","full_name":"Kutalik, Zoltan","last_name":"Kutalik"},{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","last_name":"Robinson","full_name":"Robinson, Matthew Richard"}],"volume":110,"date_created":"2023-09-03T22:01:15Z","article_type":"original","publisher":"Elsevier","day":"07","issue":"9","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","department":[{"_id":"MaRo"}],"year":"2023","language":[{"iso":"eng"}],"page":"1549-1563","corr_author":"1","publication_identifier":{"issn":["0002-9297"],"eissn":["1537-6605"]},"publication_status":"published","title":"Genetic insights into the age-specific biological mechanisms governing human ovarian aging","date_updated":"2025-09-09T12:51:20Z","date_published":"2023-09-07T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001074842500001"],"pmid":["37543033"]},"isi":1,"abstract":[{"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.","lang":"eng"}],"quality_controlled":"1","file":[{"file_size":2551276,"file_id":"14912","checksum":"4108b031dc726ae6b4a5ae7e021ba188","relation":"main_file","content_type":"application/pdf","file_name":"2023_AJHG_Ojavee.pdf","date_created":"2024-01-30T13:20:35Z","creator":"dernst","access_level":"open_access","date_updated":"2024-01-30T13:20:35Z","success":1}],"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.","type":"journal_article","citation":{"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.","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>","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>.","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.","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>.","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>","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."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"publication":"American Journal of Human Genetics"},{"publisher":"Springer Nature","day":"17","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","department":[{"_id":"KrCh"}],"year":"2023","language":[{"iso":"eng"}],"page":"390-414","oa":1,"month":"07","ddc":["000"],"_id":"14259","file_date_updated":"2023-09-06T08:25:50Z","oa_version":"Published Version","status":"public","doi":"10.1007/978-3-031-37706-8_20","scopus_import":"1","intvolume":"     13964","author":[{"first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","last_name":"Kretinsky"},{"orcid":"0000-0002-1712-2165","last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias","first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1"},{"first_name":"Maximilian","last_name":"Prokop","full_name":"Prokop, Maximilian"},{"last_name":"Rieder","full_name":"Rieder, Sabine","first_name":"Sabine"}],"volume":13964,"date_created":"2023-09-03T22:01:16Z","file":[{"file_name":"2023_LNCS_CAV_Kretinsky.pdf","date_created":"2023-09-06T08:25:50Z","success":1,"date_updated":"2023-09-06T08:25:50Z","access_level":"open_access","creator":"dernst","file_id":"14276","file_size":428354,"relation":"main_file","content_type":"application/pdf","checksum":"ed66278b61bb869e1baba3d9b9081271"}],"alternative_title":["LNCS"],"acknowledgement":"This research was funded in part by the German Research Foundation (DFG) project 427755713 Group-By Objectives in Probabilistic Verification (GOPro).","type":"conference","conference":{"name":"CAV: Computer Aided Verification","end_date":"2023-07-22","start_date":"2023-07-17","location":"Paris, France"},"citation":{"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>","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.","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.","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>","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>.","short":"J. Kretinsky, T. Meggendorfer, M. Prokop, S. Rieder, in:, 35th International Conference on Computer Aided Verification , Springer Nature, 2023, pp. 390–414."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"35th International Conference on Computer Aided Verification ","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783031377051"]},"title":"Guessing winning policies in LTL synthesis by semantic learning","publication_status":"published","date_updated":"2025-09-09T12:52:34Z","date_published":"2023-07-17T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"external_id":{"isi":["001310786500020"]},"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."}],"quality_controlled":"1"},{"ddc":["000"],"_id":"14260","file_date_updated":"2023-09-06T08:16:25Z","oa_version":"Published Version","status":"public","oa":1,"month":"07","author":[{"first_name":"Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","last_name":"Koval","full_name":"Koval, Nikita"},{"last_name":"Fedorov","full_name":"Fedorov, Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","first_name":"Alexander"},{"first_name":"Maria","last_name":"Sokolova","full_name":"Sokolova, Maria"},{"last_name":"Tsitelov","full_name":"Tsitelov, Dmitry","first_name":"Dmitry"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"}],"volume":13964,"date_created":"2023-09-03T22:01:16Z","related_material":{"record":[{"status":"public","id":"14995","relation":"research_data"}]},"doi":"10.1007/978-3-031-37706-8_8","scopus_import":"1","intvolume":"     13964","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"publisher":"Springer Nature","day":"17","page":"156-169","year":"2023","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0302-9743"],"isbn":["9783031377051"],"eissn":["1611-3349"]},"quality_controlled":"1","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"}],"title":"Lincheck: A practical framework for testing concurrent data structures on JVM","publication_status":"published","date_updated":"2025-09-09T12:51:52Z","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2023-07-17T00:00:00Z","external_id":{"isi":["001310786500008"]},"type":"conference","conference":{"name":"CAV: Computer Aided Verification","end_date":"2023-07-22","location":"Paris, France","start_date":"2023-07-17"},"file":[{"date_created":"2023-09-06T08:16:25Z","file_name":"2023_LNCS_Koval.pdf","date_updated":"2023-09-06T08:16:25Z","success":1,"access_level":"open_access","creator":"dernst","file_id":"14275","file_size":421408,"content_type":"application/pdf","relation":"main_file","checksum":"c346016393123a0a2338ad4d976f61bc"}],"alternative_title":["LNCS"],"publication":"35th International Conference on Computer Aided Verification ","citation":{"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>","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>.","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>.","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>","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."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"language":[{"iso":"eng"}],"year":"2023","page":"7395-7403","issue":"33","day":"11","article_type":"original","publisher":"American Chemical Society","department":[{"_id":"GradSch"}],"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","intvolume":"        14","scopus_import":"1","doi":"10.1021/acs.jpclett.3c01707","date_created":"2023-09-03T22:01:16Z","volume":14,"author":[{"last_name":"Gamper","full_name":"Gamper, Jakob","first_name":"Jakob"},{"full_name":"Kluibenschedl, Florian","last_name":"Kluibenschedl","first_name":"Florian","id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9"},{"full_name":"Weiss, Alexander K.H.","last_name":"Weiss","first_name":"Alexander K.H."},{"first_name":"Thomas S.","full_name":"Hofer, Thomas S.","last_name":"Hofer"}],"month":"08","oa":1,"oa_version":"Published Version","status":"public","_id":"14261","ddc":["530","540"],"file_date_updated":"2023-09-06T07:32:39Z","pmid":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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>.","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>.","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>","short":"J. Gamper, F. Kluibenschedl, A.K.H. Weiss, T.S. Hofer, Journal of Physical Chemistry Letters 14 (2023) 7395–7403."},"publication":"Journal of Physical Chemistry Letters","file":[{"date_created":"2023-09-06T07:32:39Z","file_name":"2023_JourPhysChemistry_Gamper.pdf","date_updated":"2023-09-06T07:32:39Z","success":1,"access_level":"open_access","creator":"dernst","file_size":4986859,"file_id":"14272","content_type":"application/pdf","relation":"main_file","checksum":"637454e2b3a357498d8d622d241c4bf6"}],"type":"journal_article","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.","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2023-08-11T00:00:00Z","external_id":{"isi":["001048165800001"],"pmid":["37566743"]},"date_updated":"2023-09-06T11:04:31Z","publication_status":"published","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","abstract":[{"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.","lang":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["1948-7185"]}},{"author":[{"first_name":"Daniel R","id":"453AF628-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1585-2631","full_name":"Boocock, Daniel R","last_name":"Boocock"},{"first_name":"Tsuyoshi","last_name":"Hirashima","full_name":"Hirashima, Tsuyoshi"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"}],"date_created":"2023-09-06T08:30:59Z","volume":1,"doi":"10.1103/prxlife.1.013001","intvolume":"         1","oa_version":"Published Version","status":"public","_id":"14277","ddc":["570"],"file_date_updated":"2023-09-15T06:30:50Z","article_number":"013001","oa":1,"month":"07","language":[{"iso":"eng"}],"year":"2023","has_accepted_license":"1","article_processing_charge":"Yes","department":[{"_id":"EdHa"}],"publisher":"American Physical Society","article_type":"original","day":"20","issue":"1","abstract":[{"lang":"eng","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."}],"quality_controlled":"1","date_updated":"2025-04-14T07:52:27Z","project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288"}],"publication_status":"published","title":"Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2023-07-20T00:00:00Z","ec_funded":1,"publication_identifier":{"issn":["2835-8279"]},"corr_author":"1","publication":"PRX Life","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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>","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.","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>.","ista":"Boocock DR, Hirashima T, Hannezo EB. 2023. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 1(1), 013001.","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>.","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>","short":"D.R. Boocock, T. Hirashima, E.B. Hannezo, PRX Life 1 (2023)."},"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.","type":"journal_article","file":[{"date_created":"2023-09-15T06:30:50Z","file_name":"2023_PRXLife_Boocock.pdf","creator":"dernst","access_level":"open_access","date_updated":"2023-09-15T06:30:50Z","success":1,"file_id":"14335","file_size":2559520,"checksum":"f881d98c89eb9f1aa136d7b781511553","content_type":"application/pdf","relation":"main_file"}]},{"department":[{"_id":"EdHa"}],"type":"research_data_reference","has_accepted_license":"1","article_processing_charge":"No","day":"11","publisher":"Zenodo","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M.C. Ucar, (2023).","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>.","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>","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>.","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>.","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."},"status":"public","oa_version":"Published Version","ddc":["570"],"_id":"14279","month":"07","oa":1,"corr_author":"1","related_material":{"record":[{"id":"14274","relation":"used_in_publication","status":"public"}]},"date_created":"2023-09-06T08:39:25Z","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."}],"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133960","open_access":"1"}],"author":[{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C","full_name":"Ucar, Mehmet C","last_name":"Ucar","orcid":"0000-0003-0506-4217"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2023-07-11T00:00:00Z","date_updated":"2025-04-15T06:54:33Z","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\""},{"citation":{"ieee":"N. I. Edman <i>et al.</i>, “Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies,” <i>bioRxiv</i>. .","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>","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>.","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>.","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>","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.)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","language":[{"iso":"eng"}],"publication":"bioRxiv","day":"15","article_processing_charge":"No","type":"preprint","title":"Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies","publication_status":"submitted","doi":"10.1101/2023.03.14.532666","extern":"1","date_updated":"2023-11-07T12:21:58Z","date_published":"2023-03-15T00:00:00Z","author":[{"last_name":"Edman","full_name":"Edman, Natasha I","first_name":"Natasha I"},{"first_name":"Rachel L","full_name":"Redler, Rachel L","last_name":"Redler"},{"first_name":"Ashish","full_name":"Phal, Ashish","last_name":"Phal"},{"last_name":"Schlichthaerle","full_name":"Schlichthaerle, Thomas","first_name":"Thomas"},{"last_name":"Srivatsan","full_name":"Srivatsan, Sanjay R","first_name":"Sanjay R"},{"last_name":"Etemadi","full_name":"Etemadi, Ali","first_name":"Ali"},{"full_name":"An, Seong","last_name":"An","first_name":"Seong"},{"first_name":"Andrew","full_name":"Favor, Andrew","last_name":"Favor"},{"first_name":"Devon","full_name":"Ehnes, Devon","last_name":"Ehnes"},{"first_name":"Zhe","last_name":"Li","full_name":"Li, Zhe"},{"last_name":"Praetorius","full_name":"Praetorius, Florian M","first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"full_name":"Gordon, Max","last_name":"Gordon","first_name":"Max"},{"last_name":"Yang","full_name":"Yang, Wei","first_name":"Wei"},{"first_name":"Brian","full_name":"Coventry, Brian","last_name":"Coventry"},{"full_name":"Hicks, Derrick R","last_name":"Hicks","first_name":"Derrick R"},{"first_name":"Longxing","full_name":"Cao, Longxing","last_name":"Cao"},{"full_name":"Bethel, Neville","last_name":"Bethel","first_name":"Neville"},{"full_name":"Heine, Piper","last_name":"Heine","first_name":"Piper"},{"full_name":"Murray, Analisa N","last_name":"Murray","first_name":"Analisa N"},{"first_name":"Stacey","full_name":"Gerben, Stacey","last_name":"Gerben"},{"last_name":"Carter","full_name":"Carter, Lauren","first_name":"Lauren"},{"first_name":"Marcos","last_name":"Miranda","full_name":"Miranda, Marcos"},{"first_name":"Babak","full_name":"Negahdari, Babak","last_name":"Negahdari"},{"first_name":"Sangwon","last_name":"Lee","full_name":"Lee, Sangwon"},{"first_name":"Cole","last_name":"Trapnell","full_name":"Trapnell, Cole"},{"first_name":"Lance","full_name":"Stewart, Lance","last_name":"Stewart"},{"last_name":"Ekiert","full_name":"Ekiert, Damian C","first_name":"Damian C"},{"first_name":"Joseph","full_name":"Schlessinger, Joseph","last_name":"Schlessinger"},{"full_name":"Shendure, Jay","last_name":"Shendure","first_name":"Jay"},{"full_name":"Bhabha, Gira","last_name":"Bhabha","first_name":"Gira"},{"last_name":"Ruohola-Baker","full_name":"Ruohola-Baker, Hannele","first_name":"Hannele"},{"first_name":"David","full_name":"Baker, David","last_name":"Baker"}],"main_file_link":[{"url":"https://doi.org/10.1101/2023.03.14.532666","open_access":"1"}],"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"}],"date_created":"2023-09-06T12:31:49Z","oa":1,"month":"03","_id":"14294","oa_version":"Preprint","status":"public"},{"date_created":"2023-09-10T22:01:11Z","volume":75,"author":[{"last_name":"Fiedler","full_name":"Fiedler, Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986","first_name":"Lukas"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"        75","scopus_import":"1","doi":"10.1016/j.pbi.2023.102443","article_number":"102443","status":"public","oa_version":"Submitted Version","_id":"14313","ddc":["580"],"file_date_updated":"2023-11-02T17:03:20Z","month":"10","oa":1,"language":[{"iso":"eng"}],"year":"2023","department":[{"_id":"JiFr"}],"has_accepted_license":"1","article_processing_charge":"No","day":"01","issue":"10","publisher":"Elsevier","article_type":"review","quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"external_id":{"isi":["001080095300001"],"pmid":["37666097"]},"date_published":"2023-10-01T00:00:00Z","isi":1,"date_updated":"2025-09-09T12:54:16Z","publication_status":"published","title":"Rapid auxin signaling: Unknowns old and new","publication_identifier":{"issn":["1369-5266"]},"corr_author":"1","publication":"Current Opinion in Plant Biology","pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"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>.","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>","short":"L. Fiedler, J. Friml, Current Opinion in Plant Biology 75 (2023).","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>","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.","ista":"Fiedler L, Friml J. 2023. Rapid auxin signaling: Unknowns old and new. Current Opinion in Plant Biology. 75(10), 102443.","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>."},"type":"journal_article","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.","file":[{"file_size":737872,"file_id":"14482","content_type":"application/pdf","relation":"main_file","checksum":"1c476c3414d2dfb0c85db0cb6cfd8a28","date_created":"2023-11-02T17:03:20Z","file_name":"Fiedler CurrOpinOlantBiol 2023_revised.pdf","success":1,"date_updated":"2023-11-02T17:03:20Z","access_level":"open_access","creator":"amally"}]},{"date_updated":"2025-09-09T12:53:32Z","project":[{"call_identifier":"FP7","_id":"257BBB4C-B435-11E9-9278-68D0E5697425","name":"inter-and intracellular signalling in schizophrenia","grant_number":"607616"}],"publication_status":"published","title":"Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions","external_id":{"isi":["001068779200001"],"pmid":["37632747"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2023-09-26T00:00:00Z","isi":1,"quality_controlled":"1","abstract":[{"lang":"eng","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."}],"publication_identifier":{"eissn":["2211-1247"]},"corr_author":"1","ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"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>.","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>","short":"M. Nardin, K. Käfer, F. Stella, J.L. Csicsvari, Cell Reports 42 (2023).","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.","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.","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>."},"pmid":1,"publication":"Cell Reports","file":[{"file_id":"14337","file_size":4879455,"checksum":"ca77a304fb813c292550b8604b0fb41d","relation":"main_file","content_type":"application/pdf","file_name":"2023_CellPress_Nardin.pdf","date_created":"2023-09-15T07:12:46Z","access_level":"open_access","creator":"dernst","success":1,"date_updated":"2023-09-15T07:12:46Z"}],"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).","type":"journal_article","scopus_import":"1","doi":"10.1016/j.celrep.2023.113015","intvolume":"        42","author":[{"first_name":"Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570","last_name":"Nardin","full_name":"Nardin, Michele"},{"id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","first_name":"Karola","last_name":"Käfer","full_name":"Käfer, Karola"},{"first_name":"Federico","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9439-3148","last_name":"Stella","full_name":"Stella, Federico"},{"orcid":"0000-0002-5193-4036","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-09-10T22:01:11Z","volume":42,"oa":1,"month":"09","status":"public","oa_version":"Published Version","_id":"14314","ddc":["570"],"file_date_updated":"2023-09-15T07:12:46Z","article_number":"113015","language":[{"iso":"eng"}],"year":"2023","publisher":"Elsevier","article_type":"original","day":"26","issue":"9","has_accepted_license":"1","article_processing_charge":"Yes","department":[{"_id":"JoCs"}]},{"article_processing_charge":"Yes","has_accepted_license":"1","department":[{"_id":"MaHe"}],"article_type":"original","publisher":"eLife Sciences Publications","day":"04","year":"2023","language":[{"iso":"eng"}],"_id":"14315","ddc":["570"],"file_date_updated":"2023-09-15T06:59:10Z","status":"public","oa_version":"Published Version","article_number":"RP89066","oa":1,"month":"09","author":[{"first_name":"Ukrae H.","full_name":"Cho, Ukrae H.","last_name":"Cho"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"Hetzer","full_name":"Hetzer, Martin W","orcid":"0000-0002-2111-992X"}],"volume":12,"date_created":"2023-09-10T22:01:11Z","doi":"10.7554/eLife.89066","scopus_import":"1","intvolume":"        12","type":"journal_article","acknowledgement":"We thank the members of the Hetzer laboratory, Tony Hunter (Salk), Lorenzo Puri (Sanford Burnham Prebys), and Jongmin Kim (Massachusetts General Hospital) for the critical reading of the manuscript; Kenneth Diffenderfer and Aimee Pankonin (Stem Cell Core at the Salk Institute) for help with neurogenesis; Carol Marchetto and Fred Gage (Salk) for providing H9 embryonic stem cells; Lorenzo Puri, Alexandra Sacco, and Luca Caputo (Sanford Burnham Prebys) for helpful discussions and sharing mouse primary myoblasts. This work was supported by a Glenn Foundation for Medical Research Postdoctoral Fellowship in Aging Research (UHC), the NOMIS foundation (MWH), and the National Institutes of Health (R01 NS096786 to MWH and K01 AR080828 to UHC). This work was also supported by the Mass Spectrometry Core of the Salk Institute with funding from NIH-NCI CCSG: P30 014195 and the Helmsley Center for Genomic Medicine. We thank Jolene Diedrich and Antonio Pinto for technical support.","file":[{"date_updated":"2023-09-15T06:59:10Z","success":1,"creator":"dernst","access_level":"open_access","date_created":"2023-09-15T06:59:10Z","file_name":"2023_eLife_Cho.pdf","content_type":"application/pdf","relation":"main_file","checksum":"db24bf3d595507387b48d3799c33e289","file_size":3703097,"file_id":"14336"}],"publication":"eLife","citation":{"ista":"Cho UH, Hetzer M. 2023. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. eLife. 12, RP89066.","mla":"Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” <i>ELife</i>, vol. 12, RP89066, eLife Sciences Publications, 2023, doi:<a href=\"https://doi.org/10.7554/eLife.89066\">10.7554/eLife.89066</a>.","ieee":"U. H. Cho and M. Hetzer, “Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress,” <i>eLife</i>, vol. 12. eLife Sciences Publications, 2023.","ama":"Cho UH, Hetzer M. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. <i>eLife</i>. 2023;12. doi:<a href=\"https://doi.org/10.7554/eLife.89066\">10.7554/eLife.89066</a>","short":"U.H. Cho, M. Hetzer, ELife 12 (2023).","chicago":"Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” <i>ELife</i>. eLife Sciences Publications, 2023. <a href=\"https://doi.org/10.7554/eLife.89066\">https://doi.org/10.7554/eLife.89066</a>.","apa":"Cho, U. H., &#38; Hetzer, M. (2023). Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.89066\">https://doi.org/10.7554/eLife.89066</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"corr_author":"1","publication_identifier":{"eissn":["2050-084X"]},"quality_controlled":"1","abstract":[{"lang":"eng","text":"During apoptosis, caspases degrade 8 out of ~30 nucleoporins to irreversibly demolish the nuclear pore complex. However, for poorly understood reasons, caspases are also activated during cell differentiation. Here, we show that sublethal activation of caspases during myogenesis results in the transient proteolysis of four peripheral Nups and one transmembrane Nup. ‘Trimmed’ NPCs become nuclear export-defective, and we identified in an unbiased manner several classes of cytoplasmic, plasma membrane, and mitochondrial proteins that rapidly accumulate in the nucleus. NPC trimming by non-apoptotic caspases was also observed in neurogenesis and endoplasmic reticulum stress. Our results suggest that caspases can reversibly modulate nuclear transport activity, which allows them to function as agents of cell differentiation and adaptation at sublethal levels."}],"title":"Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress","publication_status":"published","date_updated":"2024-10-09T21:06:57Z","date_published":"2023-09-04T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37665327"]}},{"publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"publication_status":"published","title":"Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway","date_updated":"2025-09-09T12:56:46Z","external_id":{"pmid":["37539494"],"isi":["001112832300005"]},"date_published":"2023-09-01T00:00:00Z","isi":1,"quality_controlled":"1","abstract":[{"text":"Clathrin-mediated vesicle trafficking plays central roles in post-Golgi transport. In yeast (Saccharomyces cerevisiae), the AP-1 complex and GGA adaptors are predicted to generate distinct transport vesicles at the trans-Golgi network (TGN), and the epsin-related proteins Ent3p and Ent5p (collectively Ent3p/5p) act as accessories for these adaptors. Recently, we showed that vesicle transport from the TGN is crucial for yeast Rab5 (Vps21p)-mediated endosome formation, and that Ent3p/5p are crucial for this process, whereas AP-1 and GGA adaptors are dispensable. However, these observations were incompatible with previous studies showing that these adaptors are required for Ent3p/5p recruitment to the TGN, and thus the overall mechanism responsible for regulation of Vps21p activity remains ambiguous. Here, we investigated the functional relationships between clathrin adaptors in post-Golgi-mediated Vps21p activation. We show that AP-1 disruption in the ent3Δ5Δ mutant impaired transport of the Vps21p guanine nucleotide exchange factor Vps9p transport to the Vps21p compartment and severely reduced Vps21p activity. Additionally, GGA adaptors, the phosphatidylinositol-4-kinase Pik1p and Rab11 GTPases Ypt31p and Ypt32p were found to have partially overlapping functions for recruitment of AP-1 and Ent3p/5p to the TGN. These findings suggest a distinct role of clathrin adaptors for Vps21p activation in the TGN–endosome trafficking pathway.","lang":"eng"}],"type":"journal_article","citation":{"chicago":"Nagano, Makoto, Kaito Aoshima, Hiroki Shimamura, Daria E Siekhaus, Junko Y. Toshima, and Jiro Toshima. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” <i>Journal of Cell Science</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/jcs.261448\">https://doi.org/10.1242/jcs.261448</a>.","apa":"Nagano, M., Aoshima, K., Shimamura, H., Siekhaus, D. E., Toshima, J. Y., &#38; Toshima, J. (2023). Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.261448\">https://doi.org/10.1242/jcs.261448</a>","short":"M. Nagano, K. Aoshima, H. Shimamura, D.E. Siekhaus, J.Y. Toshima, J. Toshima, Journal of Cell Science 136 (2023).","ieee":"M. Nagano, K. Aoshima, H. Shimamura, D. E. Siekhaus, J. Y. Toshima, and J. Toshima, “Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway,” <i>Journal of Cell Science</i>, vol. 136, no. 17. The Company of Biologists, 2023.","ama":"Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. <i>Journal of Cell Science</i>. 2023;136(17). doi:<a href=\"https://doi.org/10.1242/jcs.261448\">10.1242/jcs.261448</a>","ista":"Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. 2023. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. Journal of Cell Science. 136(17), jcs261448.","mla":"Nagano, Makoto, et al. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” <i>Journal of Cell Science</i>, vol. 136, no. 17, jcs261448, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/jcs.261448\">10.1242/jcs.261448</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"publication":"Journal of Cell Science","oa":1,"month":"09","_id":"14316","oa_version":"Preprint","status":"public","article_number":"jcs261448","doi":"10.1242/jcs.261448","scopus_import":"1","intvolume":"       136","author":[{"last_name":"Nagano","full_name":"Nagano, Makoto","first_name":"Makoto"},{"last_name":"Aoshima","full_name":"Aoshima, Kaito","first_name":"Kaito"},{"full_name":"Shimamura, Hiroki","last_name":"Shimamura","first_name":"Hiroki"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353"},{"first_name":"Junko Y.","last_name":"Toshima","full_name":"Toshima, Junko Y."},{"first_name":"Jiro","full_name":"Toshima, Jiro","last_name":"Toshima"}],"main_file_link":[{"url":"https://doi.org/10.1101/2023.03.27.534325","open_access":"1"}],"volume":136,"date_created":"2023-09-10T22:01:12Z","publisher":"The Company of Biologists","article_type":"original","issue":"17","day":"01","article_processing_charge":"No","department":[{"_id":"DaSi"}],"year":"2023","language":[{"iso":"eng"}]},{"abstract":[{"text":"Markov decision processes can be viewed as transformers of probability distributions. While this view is useful from a practical standpoint to reason about trajectories of distributions, basic reachability and safety problems are known to be computationally intractable (i.e., Skolem-hard) to solve in such models. Further, we show that even for simple examples of MDPs, strategies for safety objectives over distributions can require infinite memory and randomization.\r\nIn light of this, we present a novel overapproximation approach to synthesize strategies in an MDP, such that a safety objective over the distributions is met. More precisely, we develop a new framework for template-based synthesis of certificates as affine distributional and inductive invariants for safety objectives in MDPs. We provide two algorithms within this framework. One can only synthesize memoryless strategies, but has relative completeness guarantees, while the other can synthesize general strategies. The runtime complexity of both algorithms is in PSPACE. We implement these algorithms and show that they can solve several non-trivial examples.","lang":"eng"}],"quality_controlled":"1","title":"MDPs as distribution transformers: Affine invariant synthesis for safety objectives","publication_status":"published","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818"}],"date_updated":"2025-09-09T12:56:00Z","date_published":"2023-07-17T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001310805600005"]},"isi":1,"ec_funded":1,"publication_identifier":{"issn":["0302-9743"],"isbn":["9783031377082"],"eissn":["1611-3349"]},"publication":"International Conference on Computer Aided Verification","citation":{"chicago":"Akshay, S., Krishnendu Chatterjee, Tobias Meggendorfer, and Dorde Zikelic. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” In <i>International Conference on Computer Aided Verification</i>, 13966:86–112. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">https://doi.org/10.1007/978-3-031-37709-9_5</a>.","apa":"Akshay, S., Chatterjee, K., Meggendorfer, T., &#38; Zikelic, D. (2023). MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In <i>International Conference on Computer Aided Verification</i> (Vol. 13966, pp. 86–112). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">https://doi.org/10.1007/978-3-031-37709-9_5</a>","short":"S. Akshay, K. Chatterjee, T. Meggendorfer, D. Zikelic, in:, International Conference on Computer Aided Verification, Springer Nature, 2023, pp. 86–112.","ama":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In: <i>International Conference on Computer Aided Verification</i>. Vol 13966. Springer Nature; 2023:86-112. doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">10.1007/978-3-031-37709-9_5</a>","ieee":"S. Akshay, K. Chatterjee, T. Meggendorfer, and D. Zikelic, “MDPs as distribution transformers: Affine invariant synthesis for safety objectives,” in <i>International Conference on Computer Aided Verification</i>, Paris, France, 2023, vol. 13966, pp. 86–112.","ista":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. 2023. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 86–112.","mla":"Akshay, S., et al. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” <i>International Conference on Computer Aided Verification</i>, vol. 13966, Springer Nature, 2023, pp. 86–112, doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">10.1007/978-3-031-37709-9_5</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"This work was supported in part by the ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 as well as DST/CEFIPRA/INRIA project EQuaVE and SERB Matrices grant MTR/2018/00074.","type":"conference","conference":{"name":"CAV: Computer Aided Verification","end_date":"2023-07-22","start_date":"2023-07-17","location":"Paris, France"},"file":[{"date_created":"2023-09-20T08:46:43Z","file_name":"2023_LNCS_Akshay.pdf","access_level":"open_access","creator":"dernst","success":1,"date_updated":"2023-09-20T08:46:43Z","file_size":531745,"file_id":"14349","checksum":"f143c8eedf609f20f2aad2eeb496d53f","content_type":"application/pdf","relation":"main_file"}],"alternative_title":["LNCS"],"author":[{"first_name":"S.","full_name":"Akshay, S.","last_name":"Akshay"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0002-1712-2165","last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias","first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1"},{"orcid":"0000-0002-4681-1699","last_name":"Zikelic","full_name":"Zikelic, Dorde","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"}],"volume":13966,"date_created":"2023-09-10T22:01:12Z","doi":"10.1007/978-3-031-37709-9_5","scopus_import":"1","intvolume":"     13966","_id":"14317","ddc":["000"],"file_date_updated":"2023-09-20T08:46:43Z","oa_version":"Published Version","status":"public","oa":1,"month":"07","page":"86-112","year":"2023","language":[{"iso":"eng"}],"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","day":"17"},{"publication_identifier":{"isbn":["9783031377082"],"issn":["0302-9743"],"eissn":["1611-3349"]},"ec_funded":1,"date_published":"2023-07-17T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"external_id":{"isi":["001310805600002"]},"date_updated":"2025-09-09T12:55:28Z","title":"Automated tail bound analysis for probabilistic recurrence relations","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"publication_status":"published","abstract":[{"text":"Probabilistic recurrence relations (PRRs) are a standard formalism for describing the runtime of a randomized algorithm. Given a PRR and a time limit κ, we consider the tail probability Pr[T≥κ], i.e., the probability that the randomized runtime T of the PRR exceeds κ. Our focus is the formal analysis of tail bounds that aims at finding a tight asymptotic upper bound u≥Pr[T≥κ]. To address this problem, the classical and most well-known approach is the cookbook method by Karp (JACM 1994), while other approaches are mostly limited to deriving tail bounds of specific PRRs via involved custom analysis.\r\nIn this work, we propose a novel approach for deriving the common exponentially-decreasing tail bounds for PRRs whose preprocessing time and random passed sizes observe discrete or (piecewise) uniform distribution and whose recursive call is either a single procedure call or a divide-and-conquer. We first establish a theoretical approach via Markov’s inequality, and then instantiate the theoretical approach with a template-based algorithmic approach via a refined treatment of exponentiation. Experimental evaluation shows that our algorithmic approach is capable of deriving tail bounds that are (i) asymptotically tighter than Karp’s method, (ii) match the best-known manually-derived asymptotic tail bound for QuickSelect, and (iii) is only slightly worse (with a loglogn factor) than the manually-proven optimal asymptotic tail bound for QuickSort. Moreover, our algorithmic approach handles all examples (including realistic PRRs such as QuickSort, QuickSelect, DiameterComputation, etc.) in less than 0.1 s, showing that our approach is efficient in practice.","lang":"eng"}],"quality_controlled":"1","alternative_title":["LNCS"],"file":[{"content_type":"application/pdf","relation":"main_file","checksum":"42917e086f8c7699f3bccf84f74fe000","file_id":"14348","file_size":624647,"date_updated":"2023-09-20T08:24:47Z","success":1,"creator":"dernst","access_level":"open_access","date_created":"2023-09-20T08:24:47Z","file_name":"2023_LNCS_Sun.pdf"}],"conference":{"start_date":"2023-07-17","location":"Paris, France","end_date":"2023-07-22","name":"CAV: Computer Aided Verification"},"acknowledgement":"We thank Prof. Bican Xia for valuable information on the exponential theory of reals. The work is partially supported by the National Natural Science Foundation of China (NSFC) with Grant No. 62172271, ERC CoG 863818 (ForM-SMArt), the Hong Kong Research Grants Council ECS Project Number 26208122, the HKUST-Kaisa Joint Research Institute Project Grant HKJRI3A-055 and the HKUST Startup Grant R9272.","type":"conference","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"short":"Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Computer Aided Verification, Springer Nature, 2023, pp. 16–39.","chicago":"Sun, Yican, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” In <i>Computer Aided Verification</i>, 13966:16–39. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">https://doi.org/10.1007/978-3-031-37709-9_2</a>.","apa":"Sun, Y., Fu, H., Chatterjee, K., &#38; Goharshady, A. K. (2023). Automated tail bound analysis for probabilistic recurrence relations. In <i>Computer Aided Verification</i> (Vol. 13966, pp. 16–39). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">https://doi.org/10.1007/978-3-031-37709-9_2</a>","ista":"Sun Y, Fu H, Chatterjee K, Goharshady AK. 2023. Automated tail bound analysis for probabilistic recurrence relations. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 16–39.","mla":"Sun, Yican, et al. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” <i>Computer Aided Verification</i>, vol. 13966, Springer Nature, 2023, pp. 16–39, doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">10.1007/978-3-031-37709-9_2</a>.","ieee":"Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Automated tail bound analysis for probabilistic recurrence relations,” in <i>Computer Aided Verification</i>, Paris, France, 2023, vol. 13966, pp. 16–39.","ama":"Sun Y, Fu H, Chatterjee K, Goharshady AK. Automated tail bound analysis for probabilistic recurrence relations. In: <i>Computer Aided Verification</i>. Vol 13966. Springer Nature; 2023:16-39. doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">10.1007/978-3-031-37709-9_2</a>"},"publication":"Computer Aided Verification","month":"07","oa":1,"status":"public","oa_version":"Published Version","_id":"14318","file_date_updated":"2023-09-20T08:24:47Z","ddc":["000"],"intvolume":"     13966","scopus_import":"1","doi":"10.1007/978-3-031-37709-9_2","related_material":{"link":[{"url":"https://github.com/boyvolcano/PRR","relation":"software"}]},"date_created":"2023-09-10T22:01:12Z","volume":13966,"author":[{"full_name":"Sun, Yican","last_name":"Sun","first_name":"Yican"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar"}],"day":"17","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","language":[{"iso":"eng"}],"year":"2023","page":"16-39"},{"year":"2023","language":[{"iso":"eng"}],"department":[{"_id":"MaKw"}],"article_processing_charge":"Yes","has_accepted_license":"1","day":"28","issue":"3","publisher":"Electronic Journal of Combinatorics","article_type":"original","volume":30,"date_created":"2023-09-10T22:01:12Z","author":[{"first_name":"Michael","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","full_name":"Anastos, Michael","last_name":"Anastos"},{"first_name":"David","last_name":"Fabian","full_name":"Fabian, David"},{"full_name":"Müyesser, Alp","last_name":"Müyesser","first_name":"Alp"},{"last_name":"Szabó","full_name":"Szabó, Tibor","first_name":"Tibor"}],"intvolume":"        30","doi":"10.37236/11714","scopus_import":"1","article_number":"P3.10","_id":"14319","ddc":["510"],"file_date_updated":"2023-09-15T08:02:09Z","status":"public","oa_version":"Published Version","month":"07","oa":1,"publication":"Electronic Journal of Combinatorics","citation":{"short":"M. Anastos, D. Fabian, A. Müyesser, T. Szabó, Electronic Journal of Combinatorics 30 (2023).","apa":"Anastos, M., Fabian, D., Müyesser, A., &#38; Szabó, T. (2023). Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics. <a href=\"https://doi.org/10.37236/11714\">https://doi.org/10.37236/11714</a>","chicago":"Anastos, Michael, David Fabian, Alp Müyesser, and Tibor Szabó. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics, 2023. <a href=\"https://doi.org/10.37236/11714\">https://doi.org/10.37236/11714</a>.","ista":"Anastos M, Fabian D, Müyesser A, Szabó T. 2023. Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics. 30(3), P3.10.","mla":"Anastos, Michael, et al. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” <i>Electronic Journal of Combinatorics</i>, vol. 30, no. 3, P3.10, Electronic Journal of Combinatorics, 2023, doi:<a href=\"https://doi.org/10.37236/11714\">10.37236/11714</a>.","ama":"Anastos M, Fabian D, Müyesser A, Szabó T. Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. <i>Electronic Journal of Combinatorics</i>. 2023;30(3). doi:<a href=\"https://doi.org/10.37236/11714\">10.37236/11714</a>","ieee":"M. Anastos, D. Fabian, A. Müyesser, and T. Szabó, “Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets,” <i>Electronic Journal of Combinatorics</i>, vol. 30, no. 3. Electronic Journal of Combinatorics, 2023."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","acknowledgement":"Anastos has received funding from the European Union’s Horizon 2020 research and in-novation programme under the Marie Sk lodowska-Curie grant agreement No 101034413.Fabian’s research is supported by the Deutsche Forschungsgemeinschaft (DFG, GermanResearch Foundation) Graduiertenkolleg “Facets of Complexity” (GRK 2434).","file":[{"content_type":"application/pdf","relation":"main_file","checksum":"52c46c8cb329f9aaee9ade01525f317b","file_id":"14338","file_size":247917,"date_updated":"2023-09-15T08:02:09Z","success":1,"access_level":"open_access","creator":"dernst","date_created":"2023-09-15T08:02:09Z","file_name":"2023_elecJournCombinatorics_Anastos.pdf"}],"quality_controlled":"1","abstract":[{"text":"We study multigraphs whose edge-sets are the union of three perfect matchings, M1, M2, and M3. Given such a graph G and any a1; a2; a3 2 N with a1 +a2 +a3 6 n - 2, we show there exists a matching M of G with jM \\ Mij = ai for each i 2 f1; 2; 3g. The bound n - 2 in the theorem is best possible in general. We conjecture however that if G is bipartite, the same result holds with n - 2 replaced by n - 1. We give a construction that shows such a result would be tight. We\r\nalso make a conjecture generalising the Ryser-Brualdi-Stein conjecture with colour\r\nmultiplicities.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png"},"isi":1,"date_published":"2023-07-28T00:00:00Z","external_id":{"isi":["001042382200001"],"arxiv":["2212.03100"]},"project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"title":"Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets","publication_status":"published","date_updated":"2025-09-09T12:54:51Z","arxiv":1,"ec_funded":1,"publication_identifier":{"eissn":["1077-8926"]}},{"language":[{"iso":"eng"}],"year":"2023","article_processing_charge":"No","department":[{"_id":"MaSe"},{"_id":"ChLa"},{"_id":"MiLe"}],"article_type":"original","publisher":"American Physical Society","day":"15","issue":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2210.06310"}],"author":[{"id":"13C09E74-18D9-11E9-8878-32CFE5697425","first_name":"Paul M","last_name":"Henderson","full_name":"Henderson, Paul M","orcid":"0000-0002-5198-7445"},{"orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander A.","full_name":"Zibrov, Alexander A.","last_name":"Zibrov"},{"first_name":"Andrea F.","full_name":"Young, Andrea F.","last_name":"Young"},{"orcid":"0000-0002-2399-5827","last_name":"Serbyn","full_name":"Serbyn, Maksym","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-09-12T07:12:12Z","volume":108,"scopus_import":"1","doi":"10.1103/physrevb.108.125411","intvolume":"       108","status":"public","oa_version":"Preprint","_id":"14320","article_number":"125411","oa":1,"month":"09","publication":"Physical Review B","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"P. M. Henderson, A. Ghazaryan, A. A. Zibrov, A. F. Young, and M. Serbyn, “Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene,” <i>Physical Review B</i>, vol. 108, no. 12. American Physical Society, 2023.","ama":"Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. <i>Physical Review B</i>. 2023;108(12). doi:<a href=\"https://doi.org/10.1103/physrevb.108.125411\">10.1103/physrevb.108.125411</a>","ista":"Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. 2023. Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. Physical Review B. 108(12), 125411.","mla":"Henderson, Paul M., et al. “Deep Learning Extraction of Band Structure Parameters from Density of States: A Case Study on Trilayer Graphene.” <i>Physical Review B</i>, vol. 108, no. 12, 125411, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevb.108.125411\">10.1103/physrevb.108.125411</a>.","apa":"Henderson, P. M., Ghazaryan, A., Zibrov, A. A., Young, A. F., &#38; Serbyn, M. (2023). Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.108.125411\">https://doi.org/10.1103/physrevb.108.125411</a>","chicago":"Henderson, Paul M, Areg Ghazaryan, Alexander A. Zibrov, Andrea F. Young, and Maksym Serbyn. “Deep Learning Extraction of Band Structure Parameters from Density of States: A Case Study on Trilayer Graphene.” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevb.108.125411\">https://doi.org/10.1103/physrevb.108.125411</a>.","short":"P.M. Henderson, A. Ghazaryan, A.A. Zibrov, A.F. Young, M. Serbyn, Physical Review B 108 (2023)."},"type":"journal_article","acknowledgement":"A.F.Y. acknowledges primary support from the Department of Energy under award DE-SC0020043, and additional support from the Gordon and Betty Moore Foundation under award GBMF9471 for group operations.","quality_controlled":"1","abstract":[{"lang":"eng","text":"The development of two-dimensional materials has resulted in a diverse range of novel, high-quality compounds with increasing complexity. A key requirement for a comprehensive quantitative theory is the accurate determination of these materials' band structure parameters. However, this task is challenging due to the intricate band structures and the indirect nature of experimental probes. In this work, we introduce a general framework to derive band structure parameters from experimental data using deep neural networks. We applied our method to the penetration field capacitance measurement of trilayer graphene, an effective probe of its density of states. First, we demonstrate that a trained deep network gives accurate predictions for the penetration field capacitance as a function of tight-binding parameters. Next, we use the fast and accurate predictions from the trained network to automatically determine tight-binding parameters directly from experimental data, with extracted parameters being in a good agreement with values in the literature. We conclude by discussing potential applications of our method to other materials and experimental techniques beyond penetration field capacitance."}],"date_updated":"2023-09-20T09:38:24Z","publication_status":"published","title":"Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene","date_published":"2023-09-15T00:00:00Z","external_id":{"arxiv":["2210.06310"]},"arxiv":1,"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]}},{"scopus_import":"1","doi":"10.1063/5.0165806","intvolume":"       159","author":[{"first_name":"Ragheed","id":"d1c405be-ae15-11ed-8510-ccf53278162e","last_name":"Al Hyder","full_name":"Al Hyder, Ragheed"},{"id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","first_name":"Alberto","last_name":"Cappellaro","full_name":"Cappellaro, Alberto","orcid":"0000-0001-6110-2359"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802"},{"first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","last_name":"Volosniev","full_name":"Volosniev, Artem"}],"date_created":"2023-09-13T09:25:09Z","volume":159,"oa":1,"month":"09","status":"public","oa_version":"Published Version","file_date_updated":"2023-09-13T09:34:20Z","_id":"14321","ddc":["530"],"article_number":"104103","language":[{"iso":"eng"}],"year":"2023","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"article_type":"original","publisher":"AIP Publishing","issue":"10","day":"11","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"MiLe"}],"date_updated":"2025-09-09T12:57:42Z","title":"Achiral dipoles on a ferromagnet can affect its magnetization direction","project":[{"grant_number":"101062862","name":"Non-Equilibrium Field Theory of Molecular Rotations","_id":"bd7b5202-d553-11ed-ba76-9b1c1b258338"},{"call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770"}],"publication_status":"published","date_published":"2023-09-11T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2306.17592"],"pmid":["37694742"],"isi":["001133333600011"]},"isi":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"We demonstrate the possibility of a coupling between the magnetization direction of a ferromagnet and the tilting angle of adsorbed achiral molecules. To illustrate the mechanism of the coupling, we analyze a minimal Stoner model that includes Rashba spin–orbit coupling due to the electric field on the surface of the ferromagnet. The proposed mechanism allows us to study magnetic anisotropy of the system with an extended Stoner–Wohlfarth model and argue that adsorbed achiral molecules can change magnetocrystalline anisotropy of the substrate. Our research aims to motivate further experimental studies of the current-free chirality induced spin selectivity effect involving both enantiomers."}],"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"corr_author":"1","ec_funded":1,"arxiv":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"chicago":"Al Hyder, Ragheed, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0165806\">https://doi.org/10.1063/5.0165806</a>.","apa":"Al Hyder, R., Cappellaro, A., Lemeshko, M., &#38; Volosniev, A. (2023). Achiral dipoles on a ferromagnet can affect its magnetization direction. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0165806\">https://doi.org/10.1063/5.0165806</a>","short":"R. Al Hyder, A. Cappellaro, M. Lemeshko, A. Volosniev, The Journal of Chemical Physics 159 (2023).","ieee":"R. Al Hyder, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Achiral dipoles on a ferromagnet can affect its magnetization direction,” <i>The Journal of Chemical Physics</i>, vol. 159, no. 10. AIP Publishing, 2023.","ama":"Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. Achiral dipoles on a ferromagnet can affect its magnetization direction. <i>The Journal of Chemical Physics</i>. 2023;159(10). doi:<a href=\"https://doi.org/10.1063/5.0165806\">10.1063/5.0165806</a>","ista":"Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. 2023. Achiral dipoles on a ferromagnet can affect its magnetization direction. The Journal of Chemical Physics. 159(10), 104103.","mla":"Al Hyder, Ragheed, et al. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” <i>The Journal of Chemical Physics</i>, vol. 159, no. 10, 104103, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0165806\">10.1063/5.0165806</a>."},"pmid":1,"publication":"The Journal of Chemical Physics","file":[{"relation":"main_file","content_type":"application/pdf","checksum":"507ab65ab29e2c987c94cabad7c5370b","file_size":5749653,"file_id":"14322","date_updated":"2023-09-13T09:34:20Z","success":1,"creator":"acappell","access_level":"open_access","file_name":"104103_1_5.0165806.pdf","date_created":"2023-09-13T09:34:20Z"}],"acknowledgement":"We thank Zhanybek Alpichshev, Mohammad Reza Safari, Binghai Yan, and Yossi Paltiel for enlightening discussions.\r\nM.L. acknowledges support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A. C. received funding from the European Union’s Horizon Europe research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101062862 - NeqMolRot.","type":"journal_article"}]