[{"corr_author":"1","file_date_updated":"2024-07-22T06:16:11Z","language":[{"iso":"eng"}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","related_material":{"link":[{"url":"https://github.com/heiniglab/gaertner_megakaryocytes","relation":"software"}]},"author":[{"last_name":"Gärtner","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","full_name":"Gärtner, Florian R","first_name":"Florian R","orcid":"0000-0001-6120-3723"},{"first_name":"Hellen","last_name":"Ishikawa-Ankerhold","full_name":"Ishikawa-Ankerhold, Hellen"},{"full_name":"Stutte, Susanne","last_name":"Stutte","first_name":"Susanne"},{"last_name":"Fu","full_name":"Fu, Wenwen","first_name":"Wenwen"},{"first_name":"Jutta","full_name":"Weitz, Jutta","last_name":"Weitz"},{"first_name":"Anne","last_name":"Dueck","full_name":"Dueck, Anne"},{"last_name":"Nelakuditi","full_name":"Nelakuditi, Bhavishya","first_name":"Bhavishya"},{"last_name":"Fumagalli","full_name":"Fumagalli, Valeria","first_name":"Valeria"},{"full_name":"Van Den Heuvel, Dominic","last_name":"Van Den Heuvel","first_name":"Dominic"},{"first_name":"Larissa","full_name":"Belz, Larissa","last_name":"Belz"},{"last_name":"Sobirova","full_name":"Sobirova, Gulnoza","first_name":"Gulnoza"},{"last_name":"Zhang","full_name":"Zhang, Zhe","first_name":"Zhe"},{"full_name":"Titova, Anna","last_name":"Titova","first_name":"Anna"},{"last_name":"Navarro","full_name":"Navarro, Alejandro Martinez","first_name":"Alejandro Martinez"},{"full_name":"Pekayvaz, Kami","last_name":"Pekayvaz","first_name":"Kami"},{"first_name":"Michael","last_name":"Lorenz","full_name":"Lorenz, Michael"},{"first_name":"Louisa","last_name":"Von Baumgarten","full_name":"Von Baumgarten, Louisa"},{"first_name":"Jan","last_name":"Kranich","full_name":"Kranich, Jan"},{"full_name":"Straub, Tobias","last_name":"Straub","first_name":"Tobias"},{"last_name":"Popper","full_name":"Popper, Bastian","first_name":"Bastian"},{"last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","full_name":"Zheden, Vanessa","first_name":"Vanessa","orcid":"0000-0002-9438-4783"},{"full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","first_name":"Walter"},{"last_name":"Guo","full_name":"Guo, Chenglong","first_name":"Chenglong"},{"first_name":"Guido","last_name":"Piontek","full_name":"Piontek, Guido"},{"first_name":"Saskia","full_name":"Von Stillfried, Saskia","last_name":"Von Stillfried"},{"first_name":"Peter","full_name":"Boor, Peter","last_name":"Boor"},{"first_name":"Marco","last_name":"Colonna","full_name":"Colonna, Marco"},{"first_name":"Sebastian","last_name":"Clauß","full_name":"Clauß, Sebastian"},{"first_name":"Christian","full_name":"Schulz, Christian","last_name":"Schulz"},{"first_name":"Thomas","full_name":"Brocker, Thomas","last_name":"Brocker"},{"first_name":"Barbara","last_name":"Walzog","full_name":"Walzog, Barbara"},{"last_name":"Scheiermann","full_name":"Scheiermann, Christoph","first_name":"Christoph"},{"last_name":"Aird","full_name":"Aird, William C.","first_name":"William C."},{"first_name":"Claus","last_name":"Nerlov","full_name":"Nerlov, Claus"},{"full_name":"Stark, Konstantin","last_name":"Stark","first_name":"Konstantin"},{"first_name":"Tobias","full_name":"Petzold, Tobias","last_name":"Petzold"},{"full_name":"Engelhardt, Stefan","last_name":"Engelhardt","first_name":"Stefan"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"},{"orcid":"0000-0001-9843-3522","first_name":"Robert","full_name":"Hauschild, Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rudelius, Martina","last_name":"Rudelius","first_name":"Martina"},{"last_name":"Oostendorp","full_name":"Oostendorp, Robert A.J.","first_name":"Robert A.J."},{"last_name":"Iannacone","full_name":"Iannacone, Matteo","first_name":"Matteo"},{"full_name":"Heinig, Matthias","last_name":"Heinig","first_name":"Matthias"},{"last_name":"Massberg","full_name":"Massberg, Steffen","first_name":"Steffen"}],"department":[{"_id":"EM-Fac"},{"_id":"MiSi"},{"_id":"Bio"}],"date_created":"2024-07-21T22:01:02Z","acknowledgement":"We thank S. Helmer, N. Blount, E. Raatz and Z. Sisic for technical assistance. This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) SFB 1123 (S.M. project B06); SFB 914 (S.M. projects B02 and Z01, H.I.-A. project Z01, S.S. project A06, K.S. project B02, C. Schulz project A10, B.W. project A02, C. Scheiermann project B09); SFB 1054 (T.B. project B03); FOR2033 (F.G., R.A.J.O., S.M.); Individual research grant project ID: 514478744 (F.G.); Heisenberg Programme project ID: 514477451 (F.G.); the DZHK (German Center for Cardiovascular Research) (MHA 1.4VD (S.M.), Postdoc Start-up Grant, 81×3600213 (F.G.)); and LMUexcellence NFF (F.G.). W.F. received funding from China Scholarship Council (CSC, no. 201306270012). P.B. is supported by the German Research Foundation (DFG, project IDs 322900939, 432698239 and 445703531), European Research Council (ERC Consolidator grant no. 101001791) and the Federal Ministry of Education and Research (BMBF, STOP-FSGS-01GM2202C and NATON within the framework of the Network of University Medicine, no. 01KX2121). S.v.S. is supported by the START-Program of the Faculty of Medicine of the RWTH Aachen University (AZ 125/17). A.D. and S.E. are supported by the German Research Foundation (SFB TRR 267); S.E. by the BMBF in the framework of the Cluster4future program (CNATM—Cluster for Nucleic Acid Therapeutics Munich). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 833440 to S.M.). F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687. The project is funded by the European Union (ERC, MEKanics, 101078110). Views and opinions expressed are those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.","scopus_import":"1","_id":"17284","doi":"10.1038/s41586-024-07671-y","has_accepted_license":"1","ddc":["570"],"title":"Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis","ec_funded":1,"abstract":[{"text":"Platelet homeostasis is essential for vascular integrity and immune defence1,2. Although the process of platelet formation by fragmenting megakaryocytes (MKs; thrombopoiesis) has been extensively studied, the cellular and molecular mechanisms required to constantly replenish the pool of MKs by their progenitor cells (megakaryopoiesis) remains unclear3,4. Here we use intravital imaging to track the cellular dynamics of megakaryopoiesis over days. We identify plasmacytoid dendritic cells (pDCs) as homeostatic sensors that monitor the bone marrow for apoptotic MKs and deliver IFNα to the MK niche triggering local on-demand proliferation and maturation of MK progenitors. This pDC-dependent feedback loop is crucial for MK and platelet homeostasis at steady state and under stress. pDCs are best known for their ability to function as vigilant detectors of viral infection5. We show that virus-induced activation of pDCs interferes with their function as homeostatic sensors of megakaryopoiesis. Consequently, activation of pDCs by SARS-CoV-2 leads to excessive megakaryopoiesis. Together, we identify a pDC-dependent homeostatic circuit that involves innate immune sensing and demand-adapted release of inflammatory mediators to maintain homeostasis of the megakaryocytic lineage.","lang":"eng"}],"publication":"Nature","status":"public","publication_status":"published","date_updated":"2025-09-08T08:14:25Z","day":"18","oa_version":"Published Version","date_published":"2024-07-18T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","publisher":"Springer Nature","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":631,"oa":1,"intvolume":" 631","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"quality_controlled":"1","month":"07","type":"journal_article","external_id":{"isi":["001281636500020"],"pmid":["38987596"]},"page":"645-653","file":[{"file_name":"2024_Nature_Gaertner.pdf","checksum":"aa004afc72d2489f0fb0fcbc9919fbbd","file_id":"17286","creator":"dernst","content_type":"application/pdf","date_created":"2024-07-22T06:16:11Z","relation":"main_file","success":1,"date_updated":"2024-07-22T06:16:11Z","file_size":15704819,"access_level":"open_access"}],"pmid":1,"citation":{"ista":"Gärtner FR, Ishikawa-Ankerhold H, Stutte S, Fu W, Weitz J, Dueck A, Nelakuditi B, Fumagalli V, Van Den Heuvel D, Belz L, Sobirova G, Zhang Z, Titova A, Navarro AM, Pekayvaz K, Lorenz M, Von Baumgarten L, Kranich J, Straub T, Popper B, Zheden V, Kaufmann W, Guo C, Piontek G, Von Stillfried S, Boor P, Colonna M, Clauß S, Schulz C, Brocker T, Walzog B, Scheiermann C, Aird WC, Nerlov C, Stark K, Petzold T, Engelhardt S, Sixt MK, Hauschild R, Rudelius M, Oostendorp RAJ, Iannacone M, Heinig M, Massberg S. 2024. Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis. Nature. 631, 645–653.","chicago":"Gärtner, Florian R, Hellen Ishikawa-Ankerhold, Susanne Stutte, Wenwen Fu, Jutta Weitz, Anne Dueck, Bhavishya Nelakuditi, et al. “Plasmacytoid Dendritic Cells Control Homeostasis of Megakaryopoiesis.” Nature. Springer Nature, 2024. https://doi.org/10.1038/s41586-024-07671-y.","ieee":"F. R. Gärtner et al., “Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis,” Nature, vol. 631. Springer Nature, pp. 645–653, 2024.","short":"F.R. Gärtner, H. Ishikawa-Ankerhold, S. Stutte, W. Fu, J. Weitz, A. Dueck, B. Nelakuditi, V. Fumagalli, D. Van Den Heuvel, L. Belz, G. Sobirova, Z. Zhang, A. Titova, A.M. Navarro, K. Pekayvaz, M. Lorenz, L. Von Baumgarten, J. Kranich, T. Straub, B. Popper, V. Zheden, W. Kaufmann, C. Guo, G. Piontek, S. Von Stillfried, P. Boor, M. Colonna, S. Clauß, C. Schulz, T. Brocker, B. Walzog, C. Scheiermann, W.C. Aird, C. Nerlov, K. Stark, T. Petzold, S. Engelhardt, M.K. Sixt, R. Hauschild, M. Rudelius, R.A.J. Oostendorp, M. Iannacone, M. Heinig, S. Massberg, Nature 631 (2024) 645–653.","mla":"Gärtner, Florian R., et al. “Plasmacytoid Dendritic Cells Control Homeostasis of Megakaryopoiesis.” Nature, vol. 631, Springer Nature, 2024, pp. 645–53, doi:10.1038/s41586-024-07671-y.","ama":"Gärtner FR, Ishikawa-Ankerhold H, Stutte S, et al. Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis. Nature. 2024;631:645-653. doi:10.1038/s41586-024-07671-y","apa":"Gärtner, F. R., Ishikawa-Ankerhold, H., Stutte, S., Fu, W., Weitz, J., Dueck, A., … Massberg, S. (2024). Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis. Nature. Springer Nature. https://doi.org/10.1038/s41586-024-07671-y"},"project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020","grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"}],"article_type":"original"},{"title":"Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat","abstract":[{"lang":"eng","text":"Winter plants rely on vernalization, a crucial process for adapting to cold conditions and ensuring successful reproduction. However, understanding the role of histone modifications in guiding the vernalization process in winter wheat remains limited. In this study, we investigated the transcriptome and chromatin dynamics in the shoot apex throughout the life cycle of winter wheat in the field. Two core histone modifications, H3K27me3 and H3K36me3, exhibited opposite patterns on the key vernalization gene VERNALIZATION1 (VRN1), correlating with its induction during cold exposure. Moreover, the H3K36me3 level remained high at VRN1 after cold exposure, which may maintain its active state. Mutations in FERTILIZATION-INDEPENDENT ENDOSPERM (TaFIE) and SET DOMAIN GROUP 8/EARLY FLOWERING IN SHORT DAYS (TaSDG8/TaEFS), components of the writer complex for H3K27me3 and H3K36me3, respectively, affected flowering time. Intriguingly, VRN1 lost its high expression after the cold exposure memory in the absence of H3K36me3. During embryo development, VRN1 was silenced with the removal of active histone modifications in both winter and spring wheat, with selective restoration of H3K27me3 in winter wheat. The mutant of Tafie-cr-87, a component of H3K27me3 “writer” complex, did not influence the silence of VRN1 during embryo development, but rather attenuated the cold exposure requirement of winter wheat. Integrating gene expression with H3K27me3 and H3K36me3 patterns identified potential regulators of flowering. This study unveils distinct roles of H3K27me3 and H3K36me3 in controlling vernalization response, maintenance, and resetting in winter wheat."}],"publication_status":"published","status":"public","publication":"Science China Life Sciences","date_published":"2024-10-01T00:00:00Z","article_processing_charge":"No","oa_version":"Preprint","date_updated":"2025-09-08T08:15:08Z","day":"01","publication_identifier":{"eissn":["1869-1889"],"issn":["1674-7305"]},"OA_place":"repository","intvolume":" 67","oa":1,"publisher":"Springer Nature","volume":67,"page":"2251-2266","external_id":{"isi":["001268807700002"],"pmid":["38987431"]},"month":"10","type":"journal_article","quality_controlled":"1","pmid":1,"citation":{"apa":"Liu, X., Deng, M., Shi, B., Zhu, K., Chen, J., Xu, S., … Xiao, J. (2024). Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat. Science China Life Sciences. Springer Nature. https://doi.org/10.1007/s11427-024-2664-0","ama":"Liu X, Deng M, Shi B, et al. Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat. Science China Life Sciences. 2024;67:2251-2266. doi:10.1007/s11427-024-2664-0","mla":"Liu, Xuemei, et al. “Distinct Roles of H3K27me3 and H3K36me3 in Vernalization Response, Maintenance, and Resetting in Winter Wheat.” Science China Life Sciences, vol. 67, Springer Nature, 2024, pp. 2251–66, doi:10.1007/s11427-024-2664-0.","short":"X. Liu, M. Deng, B. Shi, K. Zhu, J. Chen, S. Xu, X. Bie, X. Zhang, X. Lin, J. Xiao, Science China Life Sciences 67 (2024) 2251–2266.","ieee":"X. Liu et al., “Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat,” Science China Life Sciences, vol. 67. Springer Nature, pp. 2251–2266, 2024.","chicago":"Liu, Xuemei, Min Deng, Bingxin Shi, Kehui Zhu, Jinchao Chen, Shujuan Xu, Xiaomin Bie, Xiansheng Zhang, Xuelei Lin, and Jun Xiao. “Distinct Roles of H3K27me3 and H3K36me3 in Vernalization Response, Maintenance, and Resetting in Winter Wheat.” Science China Life Sciences. Springer Nature, 2024. https://doi.org/10.1007/s11427-024-2664-0.","ista":"Liu X, Deng M, Shi B, Zhu K, Chen J, Xu S, Bie X, Zhang X, Lin X, Xiao J. 2024. Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat. Science China Life Sciences. 67, 2251–2266."},"article_type":"original","OA_type":"green","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.12.19.572364"}],"year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"date_created":"2024-07-21T22:01:02Z","department":[{"_id":"XiFe"}],"author":[{"first_name":"Xuemei","full_name":"Liu, Xuemei","last_name":"Liu"},{"last_name":"Deng","full_name":"Deng, Min","first_name":"Min"},{"first_name":"Bingxin","full_name":"Shi, Bingxin","last_name":"Shi"},{"first_name":"Kehui","full_name":"Zhu, Kehui","last_name":"Zhu"},{"last_name":"Chen","full_name":"Chen, Jinchao","first_name":"Jinchao"},{"last_name":"Xu","id":"9724dd9d-f591-11ee-bd51-e97ed0652286","full_name":"Xu, Shujuan","first_name":"Shujuan"},{"first_name":"Xiaomin","full_name":"Bie, Xiaomin","last_name":"Bie"},{"first_name":"Xiansheng","full_name":"Zhang, Xiansheng","last_name":"Zhang"},{"full_name":"Lin, Xuelei","last_name":"Lin","first_name":"Xuelei"},{"last_name":"Xiao","full_name":"Xiao, Jun","first_name":"Jun"}],"scopus_import":"1","acknowledgement":"We thank Prof. Kang Chong from Institute of Botany, the Chinese Academy of Science for valuable comments, Dr. Haoran Li for the help with western blot of H3K36me3 in Tasdg8-cr lines. This research was supported by National Natural Science Foundation (31970529), Beijing Natural Science Foundation Outstanding Youth Project (JQ23026), National Key Research and Development Program of China (2021YFD1201500), and the Major Basic Research Program of Shandong Natural Science Foundation (ZR2019ZD15).","doi":"10.1007/s11427-024-2664-0","_id":"17285"},{"article_number":"107708","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","related_material":{"record":[{"status":"public","id":"17042","relation":"research_data"}]},"language":[{"iso":"eng"}],"OA_type":"hybrid","corr_author":"1","file_date_updated":"2024-07-23T06:23:51Z","_id":"17291","has_accepted_license":"1","doi":"10.1016/j.jmr.2024.107708","acknowledgement":"This research was supported by the French Agence Nationale de la Recherche (\r\nANR-16-CE11-0030-12, TransPepNMR). This work used the platforms of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI, France (ANR-10-INBS-0005-02\r\n) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche), CBH-EUR-GS (ANR-17-EURE-0003). Financial support from the IR INFRANALYTICS FR2054 for conducting the research and intramural funding by the Institute of Science and Technology Austria (ISTA) are gratefully acknowledged.","scopus_import":"1","author":[{"first_name":"Alicia","full_name":"Vallet, Alicia","last_name":"Vallet"},{"full_name":"Ayala, Isabel","last_name":"Ayala","first_name":"Isabel"},{"first_name":"Barbara","full_name":"Perrone, Barbara","last_name":"Perrone"},{"first_name":"Alia","last_name":"Hassan","full_name":"Hassan, Alia"},{"first_name":"Jean-Pierre","full_name":"Simorre, Jean-Pierre","last_name":"Simorre"},{"full_name":"Bougault, Catherine","last_name":"Bougault","first_name":"Catherine"},{"last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","first_name":"Paul","orcid":"0000-0002-9350-7606"}],"department":[{"_id":"PaSc"}],"date_created":"2024-07-22T07:44:10Z","day":"01","date_updated":"2025-09-09T12:01:41Z","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","date_published":"2024-07-01T00:00:00Z","publication":"Journal of Magnetic Resonance","publication_status":"published","status":"public","abstract":[{"text":"Bacterial cell walls are gigadalton-large cross-linked polymers with a wide range of motional amplitudes, including rather rigid as well as highly flexible parts. Magic-angle spinning NMR is a powerful method to obtain atomic-level information about intact cell walls. Here we investigate sensitivity and information content of different homonuclear 13Csingle bond13C and heteronuclear 1Hsingle bond15N, 1Hsingle bond13C and 15Nsingle bond13C correlation experiments. We demonstrate that a CPMAS CryoProbe yields ca. 8-fold increased signal-to-noise over a room-temperature probe, or a ca. 3–4-fold larger per-mass sensitivity. The increased sensitivity allowed to obtain high-resolution spectra even on intact bacteria. Moreover, we compare resolution and sensitivity of 1H MAS experiments obtained at 100 kHz vs. 55 kHz. Our study provides useful hints for choosing experiments to extract atomic-level details on cell-wall samples.","lang":"eng"}],"ddc":["570"],"title":"MAS NMR experiments of corynebacterial cell walls: Complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments","article_type":"original","file":[{"creator":"dernst","date_created":"2024-07-23T06:23:51Z","content_type":"application/pdf","file_name":"2024_JourMagneticResonance_Vallet.pdf","checksum":"4b59f4f0c287ecbafd808da1212ced38","file_id":"17316","date_updated":"2024-07-23T06:23:51Z","access_level":"open_access","file_size":2236665,"relation":"main_file","success":1}],"citation":{"ama":"Vallet A, Ayala I, Perrone B, et al. MAS NMR experiments of corynebacterial cell walls: Complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments. Journal of Magnetic Resonance. 2024;364. doi:10.1016/j.jmr.2024.107708","apa":"Vallet, A., Ayala, I., Perrone, B., Hassan, A., Simorre, J.-P., Bougault, C., & Schanda, P. (2024). MAS NMR experiments of corynebacterial cell walls: Complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments. Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2024.107708","ieee":"A. Vallet et al., “MAS NMR experiments of corynebacterial cell walls: Complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments,” Journal of Magnetic Resonance, vol. 364. Elsevier, 2024.","ista":"Vallet A, Ayala I, Perrone B, Hassan A, Simorre J-P, Bougault C, Schanda P. 2024. MAS NMR experiments of corynebacterial cell walls: Complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments. Journal of Magnetic Resonance. 364, 107708.","chicago":"Vallet, Alicia, Isabel Ayala, Barbara Perrone, Alia Hassan, Jean-Pierre Simorre, Catherine Bougault, and Paul Schanda. “MAS NMR Experiments of Corynebacterial Cell Walls: Complementary 1H- and CPMAS CryoProbe-Enhanced 13C-Detected Experiments.” Journal of Magnetic Resonance. Elsevier, 2024. https://doi.org/10.1016/j.jmr.2024.107708.","mla":"Vallet, Alicia, et al. “MAS NMR Experiments of Corynebacterial Cell Walls: Complementary 1H- and CPMAS CryoProbe-Enhanced 13C-Detected Experiments.” Journal of Magnetic Resonance, vol. 364, 107708, Elsevier, 2024, doi:10.1016/j.jmr.2024.107708.","short":"A. Vallet, I. Ayala, B. Perrone, A. Hassan, J.-P. Simorre, C. Bougault, P. Schanda, Journal of Magnetic Resonance 364 (2024)."},"pmid":1,"quality_controlled":"1","external_id":{"pmid":["38901173"],"isi":["001259302800001"]},"type":"journal_article","month":"07","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Elsevier","volume":364,"oa":1,"intvolume":" 364","OA_place":"publisher","publication_identifier":{"issn":["1090-7807"]}},{"date_created":"2024-07-22T09:46:52Z","department":[{"_id":"FrPe"}],"author":[{"full_name":"van Tiel, Marit","last_name":"van Tiel","first_name":"Marit"},{"last_name":"Aubry-Wake","full_name":"Aubry-Wake, Caroline","first_name":"Caroline"},{"full_name":"Somers, Lauren","last_name":"Somers","first_name":"Lauren"},{"full_name":"Andermann, Christoff","last_name":"Andermann","first_name":"Christoff"},{"first_name":"Francesco","full_name":"Avanzi, Francesco","last_name":"Avanzi"},{"full_name":"Baraer, Michel","last_name":"Baraer","first_name":"Michel"},{"first_name":"Gabriele","last_name":"Chiogna","full_name":"Chiogna, Gabriele"},{"full_name":"Daigre, Clémence","last_name":"Daigre","first_name":"Clémence"},{"last_name":"Das","full_name":"Das, Soumik","first_name":"Soumik"},{"last_name":"Drenkhan","full_name":"Drenkhan, Fabian","first_name":"Fabian"},{"full_name":"Farinotti, Daniel","last_name":"Farinotti","first_name":"Daniel"},{"first_name":"Catriona Louise","id":"001b0422-8d15-11ed-bc51-cab6c037a228","last_name":"Fyffe","full_name":"Fyffe, Catriona Louise"},{"first_name":"Inge","full_name":"de Graaf, Inge","last_name":"de Graaf"},{"first_name":"Sarah","last_name":"Hanus","full_name":"Hanus, Sarah"},{"first_name":"Walter","last_name":"Immerzeel","full_name":"Immerzeel, Walter"},{"full_name":"Koch, Franziska","last_name":"Koch","first_name":"Franziska"},{"first_name":"Jeffrey M.","last_name":"McKenzie","full_name":"McKenzie, Jeffrey M."},{"full_name":"Müller, Tom","last_name":"Müller","first_name":"Tom"},{"last_name":"Popp","full_name":"Popp, Andrea L.","first_name":"Andrea L."},{"first_name":"Zarina","full_name":"Saidaliyeva, Zarina","last_name":"Saidaliyeva"},{"first_name":"Bettina","full_name":"Schaefli, Bettina","last_name":"Schaefli"},{"last_name":"Schilling","full_name":"Schilling, Oliver S.","first_name":"Oliver S."},{"first_name":"Kapiolani","last_name":"Teagai","full_name":"Teagai, Kapiolani"},{"last_name":"Thornton","full_name":"Thornton, James M.","first_name":"James M."},{"first_name":"Vadim","full_name":"Yapiyev, Vadim","last_name":"Yapiyev"}],"scopus_import":"1","acknowledgement":"We acknowledge the Mountain Research Initiative (MRI) for sponsoring the workshop ‘Cryosphere-groundwater Interactions: A Missing Link in Mountain Water Research’ via their funding from the Swiss Academy of Sciences (SCNAT) under project no. FNW0004 004-2019-00. M.v.T. was supported by a Walter Benjamin fellowship from the German Research Foundation (DFG) under project no. 510684314. C.A.-W. was supported by the Banting Postdoctoral Fellowships programme, administered by the government of Canada. G.C. acknowledges the support of the DFG research unit (FOR2793/2) investigating the ‘Sensitivity of High Alpine Geosystems to Climate Change since 1850’ (SEHAG) under grant CH981/3-2. F.D. acknowledges funding from the Dirección de Fomento de la Investigación at PUCP. I.d.G. acknowledges funding from the European Research Council (ERC) under grant agreement GROW-101041110. V.Y. was supported by Nazarbayev University under CRP research grant no. 021220CRP2122. We thank D. Masovic of VAW, ETH Zurich, for drawing Fig. 1.","doi":"10.1038/s44221-024-00277-8","_id":"17302","OA_type":"green","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://insu.hal.science/insu-04674297","open_access":"1"}],"year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"publication_identifier":{"issn":["2731-6084"]},"intvolume":" 2","OA_place":"repository","publisher":"Springer Nature","volume":2,"oa":1,"page":"624-637","month":"07","type":"journal_article","external_id":{"isi":["001390137500016"]},"quality_controlled":"1","citation":{"short":"M. van Tiel, C. Aubry-Wake, L. Somers, C. Andermann, F. Avanzi, M. Baraer, G. Chiogna, C. Daigre, S. Das, F. Drenkhan, D. Farinotti, C.L. Fyffe, I. de Graaf, S. Hanus, W. Immerzeel, F. Koch, J.M. McKenzie, T. Müller, A.L. Popp, Z. Saidaliyeva, B. Schaefli, O.S. Schilling, K. Teagai, J.M. Thornton, V. Yapiyev, Nature Water 2 (2024) 624–637.","mla":"van Tiel, Marit, et al. “Cryosphere–Groundwater Connectivity Is a Missing Link in the Mountain Water Cycle.” Nature Water, vol. 2, Springer Nature, 2024, pp. 624–37, doi:10.1038/s44221-024-00277-8.","ista":"van Tiel M, Aubry-Wake C, Somers L, Andermann C, Avanzi F, Baraer M, Chiogna G, Daigre C, Das S, Drenkhan F, Farinotti D, Fyffe CL, de Graaf I, Hanus S, Immerzeel W, Koch F, McKenzie JM, Müller T, Popp AL, Saidaliyeva Z, Schaefli B, Schilling OS, Teagai K, Thornton JM, Yapiyev V. 2024. Cryosphere–groundwater connectivity is a missing link in the mountain water cycle. Nature Water. 2, 624–637.","chicago":"Tiel, Marit van, Caroline Aubry-Wake, Lauren Somers, Christoff Andermann, Francesco Avanzi, Michel Baraer, Gabriele Chiogna, et al. “Cryosphere–Groundwater Connectivity Is a Missing Link in the Mountain Water Cycle.” Nature Water. Springer Nature, 2024. https://doi.org/10.1038/s44221-024-00277-8.","ieee":"M. van Tiel et al., “Cryosphere–groundwater connectivity is a missing link in the mountain water cycle,” Nature Water, vol. 2. Springer Nature, pp. 624–637, 2024.","apa":"van Tiel, M., Aubry-Wake, C., Somers, L., Andermann, C., Avanzi, F., Baraer, M., … Yapiyev, V. (2024). Cryosphere–groundwater connectivity is a missing link in the mountain water cycle. Nature Water. Springer Nature. https://doi.org/10.1038/s44221-024-00277-8","ama":"van Tiel M, Aubry-Wake C, Somers L, et al. Cryosphere–groundwater connectivity is a missing link in the mountain water cycle. Nature Water. 2024;2:624-637. doi:10.1038/s44221-024-00277-8"},"article_type":"original","title":"Cryosphere–groundwater connectivity is a missing link in the mountain water cycle","abstract":[{"lang":"eng","text":"The mountain cryosphere and groundwater play pivotal roles in shaping the hydrological cycle, yet their connectivity remains incompletely understood. Current knowledge on meltwater recharge and consequent groundwater discharge processes is better developed for snow–groundwater connectivity than for glacier–groundwater connectivity. Estimates of meltwater recharge vary considerably, which is probably a function of not only inherent catchment characteristics but also of the different spatio-temporal scales involved and the uncertainties in the methods used. This hinders a comprehensive understanding of the mountain water cycle. As glaciers retreat, permafrost thaws and snowpack diminishes, the relative importance of mountain groundwater is expected to increase. However, shifting and declining recharge from the cryosphere may decrease absolute groundwater amounts and fluxes with as-yet unknown effects on catchment-scale hydrological processes. We therefore stress the need to better quantify mountain cryosphere–groundwater connectivity to predict climate change impacts on mountain water supply and to support sustainable water resource management of downstream socio-ecological systems."}],"publication_status":"published","status":"public","publication":"Nature Water","article_processing_charge":"No","date_published":"2024-07-19T00:00:00Z","oa_version":"Submitted Version","date_updated":"2025-12-02T13:42:28Z","day":"19"},{"author":[{"first_name":"Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","full_name":"Cheng, Bingqing"}],"department":[{"_id":"BiCh"}],"date_created":"2024-07-28T22:01:08Z","acknowledgement":"B.C. thanks Ralf Drautz and Ngoc Cuong Nguyen for illuminating discussions.","scopus_import":"1","_id":"17322","DOAJ_listed":"1","has_accepted_license":"1","doi":"10.1038/s41524-024-01332-4","corr_author":"1","OA_type":"gold","file_date_updated":"2025-01-09T12:36:48Z","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"157","isi":1,"year":"2024","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Springer Nature","volume":10,"oa":1,"publication_identifier":{"eissn":["2057-3960"]},"intvolume":" 10","OA_place":"publisher","quality_controlled":"1","month":"07","external_id":{"arxiv":["2402.07472"],"isi":["001271730700001"]},"type":"journal_article","citation":{"apa":"Cheng, B. (2024). Cartesian atomic cluster expansion for machine learning interatomic potentials. Npj Computational Materials. Springer Nature. https://doi.org/10.1038/s41524-024-01332-4","ama":"Cheng B. Cartesian atomic cluster expansion for machine learning interatomic potentials. npj Computational Materials. 2024;10. doi:10.1038/s41524-024-01332-4","short":"B. Cheng, Npj Computational Materials 10 (2024).","mla":"Cheng, Bingqing. “Cartesian Atomic Cluster Expansion for Machine Learning Interatomic Potentials.” Npj Computational Materials, vol. 10, 157, Springer Nature, 2024, doi:10.1038/s41524-024-01332-4.","chicago":"Cheng, Bingqing. “Cartesian Atomic Cluster Expansion for Machine Learning Interatomic Potentials.” Npj Computational Materials. Springer Nature, 2024. https://doi.org/10.1038/s41524-024-01332-4.","ista":"Cheng B. 2024. Cartesian atomic cluster expansion for machine learning interatomic potentials. npj Computational Materials. 10, 157.","ieee":"B. Cheng, “Cartesian atomic cluster expansion for machine learning interatomic potentials,” npj Computational Materials, vol. 10. Springer Nature, 2024."},"file":[{"file_id":"18813","file_name":"2024_npjComputationalMaterials_Cheng.pdf","checksum":"e6b4d1a45a9ef1e9be35b313d96ebd6f","content_type":"application/pdf","date_created":"2025-01-09T12:36:48Z","creator":"dernst","success":1,"relation":"main_file","date_updated":"2025-01-09T12:36:48Z","file_size":1659509,"access_level":"open_access"}],"article_type":"original","title":"Cartesian atomic cluster expansion for machine learning interatomic potentials","ddc":["000"],"abstract":[{"lang":"eng","text":"Machine learning interatomic potentials are revolutionizing large-scale, accurate atomistic modeling in material science and chemistry. Many potentials use atomic cluster expansion or equivariant message-passing frameworks. Such frameworks typically use spherical harmonics as angular basis functions, followed by Clebsch-Gordan contraction to maintain rotational symmetry. We propose a mathematically equivalent and simple alternative that performs all operations in the Cartesian coordinates. This approach provides a complete set of polynormially independent features of atomic environments while maintaining interaction body orders. Additionally, we integrate low-dimensional embeddings of various chemical elements, trainable radial channel coupling, and inter-atomic message passing. The resulting potential, named Cartesian Atomic Cluster Expansion (CACE), exhibits good accuracy, stability, and generalizability. We validate its performance in diverse systems, including bulk water, small molecules, and 25-element high-entropy alloys."}],"arxiv":1,"publication":"npj Computational Materials","status":"public","publication_status":"published","oa_version":"Published Version","date_updated":"2025-09-08T08:43:34Z","day":"18","date_published":"2024-07-18T00:00:00Z","article_processing_charge":"Yes"},{"year":"2024","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"file_date_updated":"2024-07-29T10:56:01Z","doi":"10.1146/annurev-biophys-030822-032215","has_accepted_license":"1","_id":"17325","scopus_import":"1","acknowledgement":"We would like to thank all members of the Pilizota lab, as well as Calin Guet, Orkun Soyer, Munehiro Asally, Peter Swain, and in particular Matt Scott and Ariel Amir, for their support, comments, and useful discussions. T.P. and W.-C.L. were supported by the Leverhulme Trust, grant RPG-2019-187, and T.P. is supported by EPSRC Fellowship EP/V03264X/1. E.K. was supported by a European Molecular Biology Organization Long-Term Postdoctoral Fellowship, ALTF 44-2021.","department":[{"_id":"CaGu"}],"date_created":"2024-07-28T22:01:09Z","author":[{"first_name":"Wei Chang","last_name":"Lo","full_name":"Lo, Wei Chang"},{"first_name":"Ekaterina","full_name":"Krasnopeeva, Ekaterina","last_name":"Krasnopeeva","id":"1F1EE44A-BF83-11EA-B3C1-BB9CC619BF3A"},{"first_name":"Teuta","full_name":"Pilizota, Teuta","last_name":"Pilizota"}],"article_processing_charge":"Yes (in subscription journal)","date_published":"2024-07-01T00:00:00Z","date_updated":"2025-09-08T08:34:43Z","day":"01","oa_version":"Published Version","publication":"Annual Review of Biophysics","status":"public","publication_status":"published","abstract":[{"text":"Bacterial ion fluxes are involved in the generation of energy, transport, and motility. As such, bacterial electrophysiology is fundamentally important for the bacterial life cycle, but it is often neglected and consequently, by and large, not understood. Arguably, the two main reasons for this are the complexity of measuring relevant variables in small cells with a cell envelope that contains the cell wall and the fact that, in a unicellular organism, relevant variables become intertwined in a nontrivial manner. To help give bacterial electrophysiology studies a firm footing, in this review, we go back to basics. We look first at the biophysics of bacterial membrane potential, and then at the approaches and models developed mostly for the study of neurons and eukaryotic mitochondria. We discuss their applicability to bacterial cells. Finally, we connect bacterial membrane potential with other relevant (electro)physiological variables and summarize methods that can be used to both measure and influence bacterial electrophysiology.","lang":"eng"}],"ddc":["570"],"title":"Bacterial Electrophysiology","project":[{"_id":"eb872896-77a9-11ec-83b8-f59a38ec17f8","grant_number":"ALTF 44-2021","name":"Bacterial cytoplasm glass transition: passive physiological switch or active survival strategy"}],"article_type":"original","file":[{"success":1,"relation":"main_file","access_level":"open_access","file_size":1276645,"date_updated":"2024-07-29T10:56:01Z","file_id":"17339","checksum":"e0505553b3cee624fa865f0cc5a99ecc","file_name":"2024_AnnualReviewBiophys_Lo.pdf","date_created":"2024-07-29T10:56:01Z","content_type":"application/pdf","creator":"dernst"}],"pmid":1,"citation":{"ieee":"W. C. Lo, E. Krasnopeeva, and T. Pilizota, “Bacterial Electrophysiology,” Annual Review of Biophysics, vol. 53. Annual Reviews, pp. 487–510, 2024.","chicago":"Lo, Wei Chang, Ekaterina Krasnopeeva, and Teuta Pilizota. “Bacterial Electrophysiology.” Annual Review of Biophysics. Annual Reviews, 2024. https://doi.org/10.1146/annurev-biophys-030822-032215.","ista":"Lo WC, Krasnopeeva E, Pilizota T. 2024. Bacterial Electrophysiology. Annual Review of Biophysics. 53, 487–510.","mla":"Lo, Wei Chang, et al. “Bacterial Electrophysiology.” Annual Review of Biophysics, vol. 53, Annual Reviews, 2024, pp. 487–510, doi:10.1146/annurev-biophys-030822-032215.","short":"W.C. Lo, E. Krasnopeeva, T. Pilizota, Annual Review of Biophysics 53 (2024) 487–510.","ama":"Lo WC, Krasnopeeva E, Pilizota T. Bacterial Electrophysiology. Annual Review of Biophysics. 2024;53:487-510. doi:10.1146/annurev-biophys-030822-032215","apa":"Lo, W. C., Krasnopeeva, E., & Pilizota, T. (2024). Bacterial Electrophysiology. Annual Review of Biophysics. Annual Reviews. https://doi.org/10.1146/annurev-biophys-030822-032215"},"type":"journal_article","external_id":{"isi":["001278237500021"],"pmid":["38382113"]},"month":"07","page":"487-510","quality_controlled":"1","intvolume":" 53","publication_identifier":{"eissn":["1936-1238"],"issn":["1936-122X"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":53,"publisher":"Annual Reviews","oa":1},{"external_id":{"arxiv":["2404.17167"],"isi":["001270972500001"]},"type":"journal_article","month":"07","quality_controlled":"1","intvolume":" 970","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"oa":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"IOP Publishing","volume":970,"project":[{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020"}],"article_type":"original","file":[{"access_level":"open_access","file_size":3912290,"date_updated":"2024-07-29T11:02:48Z","relation":"main_file","success":1,"creator":"dernst","date_created":"2024-07-29T11:02:48Z","content_type":"application/pdf","file_name":"2024_AstrophysicalJourn_Bhattacharya.pdf","checksum":"acb42a87deecbc9228fbbe6a48a37ec6","file_id":"17340"}],"citation":{"mla":"Bhattacharya, Shatanik, et al. “Detectability of Axisymmetric Magnetic Fields from the Core to the Surface of Oscillating Post-Main-Sequence Stars.” Astrophysical Journal, vol. 970, no. 1, 42, IOP Publishing, 2024, doi:10.3847/1538-4357/ad4708.","short":"S. Bhattacharya, S.B. Das, L.A. Bugnet, S. Panda, S.M. Hanasoge, Astrophysical Journal 970 (2024).","ieee":"S. Bhattacharya, S. B. Das, L. A. Bugnet, S. Panda, and S. M. Hanasoge, “Detectability of axisymmetric magnetic fields from the core to the surface of oscillating post-main-sequence stars,” Astrophysical Journal, vol. 970, no. 1. IOP Publishing, 2024.","ista":"Bhattacharya S, Das SB, Bugnet LA, Panda S, Hanasoge SM. 2024. Detectability of axisymmetric magnetic fields from the core to the surface of oscillating post-main-sequence stars. Astrophysical Journal. 970(1), 42.","chicago":"Bhattacharya, Shatanik, Srijan B Das, Lisa Annabelle Bugnet, Subrata Panda, and Shravan M. Hanasoge. “Detectability of Axisymmetric Magnetic Fields from the Core to the Surface of Oscillating Post-Main-Sequence Stars.” Astrophysical Journal. IOP Publishing, 2024. https://doi.org/10.3847/1538-4357/ad4708.","apa":"Bhattacharya, S., Das, S. B., Bugnet, L. A., Panda, S., & Hanasoge, S. M. (2024). Detectability of axisymmetric magnetic fields from the core to the surface of oscillating post-main-sequence stars. Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ad4708","ama":"Bhattacharya S, Das SB, Bugnet LA, Panda S, Hanasoge SM. Detectability of axisymmetric magnetic fields from the core to the surface of oscillating post-main-sequence stars. Astrophysical Journal. 2024;970(1). doi:10.3847/1538-4357/ad4708"},"arxiv":1,"abstract":[{"lang":"eng","text":"Magnetic fields in the stellar interiors are key candidates to explain observed core rotation rates inside solar-like stars along their evolution. Recently, asteroseismic estimates of radial magnetic field amplitudes near the hydrogen-burning shell (H-shell) inside about 24 red giants (RGs) have been obtained by measuring frequency splittings from their power spectra. Using general Lorentz-stress (magnetic) kernels, we investigated the potential for detectability of near-surface magnetism in a 1.3 M⊙ star of supersolar metallicity as it evolves from a mid subgiant to a late subgiant into an RG. Based on these sensitivity kernels, we decompose an RG into three zones—deep core, H-shell, and near-surface. The subgiants instead required decomposition into an inner core, an outer core, and a near-surface layer. Additionally, we find that for a low-frequency g-dominated dipolar mode in the presence of a typical stable magnetic field, ∼25% of the frequency shift comes from the H-shell and the remaining from deeper layers. The ratio of the subsurface tangential field to the radial field in the H-burning shell decides if subsurface fields may be potentially detectable. For p-dominated dipole modes close to vmax, this ratio is around two orders of magnitude smaller in subgiant phases than the corresponding RG. Further, with the availability of magnetic kernels, we propose lower limits of field strengths in crucial layers in our stellar model during its evolutionary phases. The theoretical prescription outlined here provides the first formal way to devise inverse problems for stellar magnetism and can be seamlessly employed for slow rotators."}],"ec_funded":1,"ddc":["520"],"title":"Detectability of axisymmetric magnetic fields from the core to the surface of oscillating post-main-sequence stars","article_processing_charge":"Yes","date_published":"2024-07-15T00:00:00Z","day":"15","date_updated":"2025-09-08T08:42:20Z","oa_version":"Published Version","publication":"Astrophysical Journal","status":"public","publication_status":"published","date_created":"2024-07-28T22:01:09Z","department":[{"_id":"LiBu"}],"author":[{"full_name":"Bhattacharya, Shatanik","last_name":"Bhattacharya","first_name":"Shatanik"},{"orcid":"0000-0003-0896-7972","first_name":"Srijan B","full_name":"Das, Srijan B","id":"9ce7c423-dacf-11ed-8942-e09c6cb27149","last_name":"Das"},{"first_name":"Lisa Annabelle","orcid":"0000-0003-0142-4000","id":"d9edb345-f866-11ec-9b37-d119b5234501","last_name":"Bugnet","full_name":"Bugnet, Lisa Annabelle"},{"last_name":"Panda","full_name":"Panda, Subrata","first_name":"Subrata"},{"first_name":"Shravan M.","last_name":"Hanasoge","full_name":"Hanasoge, Shravan M."}],"has_accepted_license":"1","doi":"10.3847/1538-4357/ad4708","DOAJ_listed":"1","_id":"17326","scopus_import":"1","acknowledgement":"This project has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 101034413. S.\r\nB.D. acknowledges Prof. Jeroen Tromp at Princeton University for supporting a part of this work. S.M.H., S.B., and S.P. acknowledge support from the Department of Atomic Energy,\r\nGovernment of India, under Project Identification No. RTI 4002. The authors would like to thank the reviewer(s) and data editor for their constructive comments and suggestions. The\r\ngeneration of the stellar models was done using the Modules for Experiments in Stellar Astrophysics (MESA Paxton et al. 2011, 2013, 2015, 2018, 2019; we have used MESA version\r\nr22.05.1 for RG and r23.05.1 for SG models, MESA-SDK version x86_64-linux-22.6.1). The eigenfrequencies and eigenfunctions for this model were calculated using the GYRE\r\n(Townsend & Teitler 2013) code. The code to calculate the kernels and the splittings has been written completely in Python 3.8.16.","issue":"1","language":[{"iso":"eng"}],"file_date_updated":"2024-07-29T11:02:48Z","year":"2024","isi":1,"article_number":"42","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"file":[{"content_type":"application/pdf","date_created":"2024-07-29T11:15:59Z","creator":"dernst","file_id":"17341","checksum":"cc6bb89be0eaa404a6ce019392cd293e","file_name":"2024_LIPICs_Cano.pdf","date_updated":"2024-07-29T11:15:59Z","file_size":1391381,"access_level":"open_access","success":1,"relation":"main_file"}],"citation":{"apa":"Cano, F., Henzinger, T. A., Könighofer, B., Kueffner, K., & Mallik, K. (2024). Abstraction-based decision making for statistical properties. In 9th International Conference on Formal Structures for Computation and Deduction (Vol. 299). Tallinn, Estonia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.FSCD.2024.2","ama":"Cano F, Henzinger TA, Könighofer B, Kueffner K, Mallik K. Abstraction-based decision making for statistical properties. In: 9th International Conference on Formal Structures for Computation and Deduction. Vol 299. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.FSCD.2024.2","mla":"Cano, Filip, et al. “Abstraction-Based Decision Making for Statistical Properties.” 9th International Conference on Formal Structures for Computation and Deduction, vol. 299, 2, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.FSCD.2024.2.","short":"F. Cano, T.A. Henzinger, B. Könighofer, K. Kueffner, K. Mallik, in:, 9th International Conference on Formal Structures for Computation and Deduction, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","ieee":"F. Cano, T. A. Henzinger, B. Könighofer, K. Kueffner, and K. Mallik, “Abstraction-based decision making for statistical properties,” in 9th International Conference on Formal Structures for Computation and Deduction, Tallinn, Estonia, 2024, vol. 299.","ista":"Cano F, Henzinger TA, Könighofer B, Kueffner K, Mallik K. 2024. Abstraction-based decision making for statistical properties. 9th International Conference on Formal Structures for Computation and Deduction. FSCD: Conference on Formal Structures for Computation and Deduction, LIPIcs, vol. 299, 2.","chicago":"Cano, Filip, Thomas A Henzinger, Bettina Könighofer, Konstantin Kueffner, and Kaushik Mallik. “Abstraction-Based Decision Making for Statistical Properties.” In 9th International Conference on Formal Structures for Computation and Deduction, Vol. 299. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.FSCD.2024.2."},"project":[{"name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":299,"oa":1,"conference":{"name":"FSCD: Conference on Formal Structures for Computation and Deduction","start_date":"2024-07-10","end_date":"2024-07-13","location":"Tallinn, Estonia"},"intvolume":" 299","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773232"]},"quality_controlled":"1","external_id":{"isi":["001587746100002"]},"month":"07","type":"conference","publication":"9th International Conference on Formal Structures for Computation and Deduction","status":"public","publication_status":"published","alternative_title":["LIPIcs"],"day":"01","date_updated":"2025-12-02T13:43:50Z","oa_version":"Published Version","article_processing_charge":"Yes","date_published":"2024-07-01T00:00:00Z","ddc":["000"],"title":"Abstraction-based decision making for statistical properties","ec_funded":1,"abstract":[{"text":"Sequential decision-making in probabilistic environments is a fundamental problem with many applications in AI and economics. In this paper, we present an algorithm for synthesizing sequential decision-making agents that optimize statistical properties such as maximum and average response times. In the general setting of sequential decision-making, the environment is modeled as a random process that generates inputs. The agent responds to each input, aiming to maximize rewards and minimize costs within a specified time horizon. The corresponding synthesis problem is known to be PSPACE-hard. We consider the special case where the input distribution, reward, and cost depend on input-output statistics specified by counter automata. For such problems, this paper presents the first PTIME synthesis algorithms. We introduce the notion of statistical abstraction, which clusters statistically indistinguishable input-output sequences into equivalence classes. This abstraction allows for a dynamic programming algorithm whose complexity grows polynomially with the considered horizon, making the statistical case exponentially more efficient than the general case. We evaluate our algorithm on three different application scenarios of a client-server protocol, where multiple clients compete via bidding to gain access to the service offered by the server. The synthesized policies optimize profit while guaranteeing that none of the server’s clients is disproportionately starved of the service.","lang":"eng"}],"acknowledgement":"This work is partly supported by the European Research Council under Grant No.: ERC2020-AdG 101020093. It is also partially supported by the State Government of Styria, Austria –\r\nDepartment Zukunftsfonds Steiermark.","scopus_import":"1","_id":"17327","doi":"10.4230/LIPIcs.FSCD.2024.2","has_accepted_license":"1","author":[{"last_name":"Cano","full_name":"Cano, Filip","first_name":"Filip"},{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Könighofer, Bettina","last_name":"Könighofer","first_name":"Bettina"},{"last_name":"Kueffner","id":"8121a2d0-dc85-11ea-9058-af578f3b4515","full_name":"Kueffner, Konstantin","first_name":"Konstantin","orcid":"0000-0001-8974-2542"},{"full_name":"Mallik, Kaushik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","last_name":"Mallik","orcid":"0000-0001-9864-7475","first_name":"Kaushik"}],"department":[{"_id":"ToHe"}],"date_created":"2024-07-28T22:01:09Z","isi":1,"article_number":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024","corr_author":"1","file_date_updated":"2024-07-29T11:15:59Z","language":[{"iso":"eng"}]},{"ddc":["000"],"title":"Game dynamics and equilibrium computation in the population protocol model","ec_funded":1,"abstract":[{"lang":"eng","text":"We initiate the study of game dynamics in the population protocol model: n agents each maintain a current local strategy and interact in pairs uniformly at random. Upon each interaction, the agents play a two-person game and receive a payoff from an underlying utility function, and they can subsequently update their strategies according to a fixed local algorithm. In this setting, we ask how the distribution over agent strategies evolves over a sequence of interactions, and we introduce a new distributional equilibrium concept to quantify the quality of such distributions. As an initial example, we study a class of repeated prisoner's dilemma games, and we consider a family of simple local update algorithms that yield non-trivial dynamics over the distribution of agent strategies. We show that these dynamics are related to a new class of high-dimensional Ehrenfest random walks, and we derive exact characterizations of their stationary distributions, bounds on their mixing times, and prove their convergence to approximate distributional equilibria. Our results highlight trade-offs between the local state space of each agent, and the convergence rate and approximation factor of the underlying dynamics. Our approach opens the door towards the further characterization of equilibrium computation for other classes of games and dynamics in the population setting."}],"publication_status":"published","publication":"Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed Computing","status":"public","day":"17","date_updated":"2025-04-14T07:52:47Z","oa_version":"Published Version","date_published":"2024-06-17T00:00:00Z","article_processing_charge":"Yes (via OA deal)","publisher":"Association for Computing Machinery","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"conference":{"location":"Nantes, France","start_date":"2024-06-17","end_date":"2024-06-21","name":"PODC: Symposium on Principles of Distributed Computing"},"publication_identifier":{"isbn":["9798400706684"]},"quality_controlled":"1","type":"conference","month":"06","page":"40-49","file":[{"date_updated":"2024-07-29T07:37:31Z","file_size":750908,"access_level":"open_access","relation":"main_file","success":1,"creator":"dernst","content_type":"application/pdf","date_created":"2024-07-29T07:37:31Z","file_name":"2024_ACMPODC_Alistarh.pdf","checksum":"65a40437f83373fa79dd999d5287509e","file_id":"17335"}],"citation":{"ama":"Alistarh D-A, Chatterjee K, Karrabi M, Lazarsfeld JM. Game dynamics and equilibrium computation in the population protocol model. In: Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2024:40-49. doi:10.1145/3662158.3662768","apa":"Alistarh, D.-A., Chatterjee, K., Karrabi, M., & Lazarsfeld, J. M. (2024). Game dynamics and equilibrium computation in the population protocol model. In Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed Computing (pp. 40–49). Nantes, France: Association for Computing Machinery. https://doi.org/10.1145/3662158.3662768","ista":"Alistarh D-A, Chatterjee K, Karrabi M, Lazarsfeld JM. 2024. Game dynamics and equilibrium computation in the population protocol model. Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 40–49.","chicago":"Alistarh, Dan-Adrian, Krishnendu Chatterjee, Mehrdad Karrabi, and John M Lazarsfeld. “Game Dynamics and Equilibrium Computation in the Population Protocol Model.” In Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed Computing, 40–49. Association for Computing Machinery, 2024. https://doi.org/10.1145/3662158.3662768.","ieee":"D.-A. Alistarh, K. Chatterjee, M. Karrabi, and J. M. Lazarsfeld, “Game dynamics and equilibrium computation in the population protocol model,” in Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed Computing, Nantes, France, 2024, pp. 40–49.","short":"D.-A. Alistarh, K. Chatterjee, M. Karrabi, J.M. Lazarsfeld, in:, Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2024, pp. 40–49.","mla":"Alistarh, Dan-Adrian, et al. “Game Dynamics and Equilibrium Computation in the Population Protocol Model.” Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2024, pp. 40–49, doi:10.1145/3662158.3662768."},"project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"corr_author":"1","file_date_updated":"2024-07-29T07:37:31Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Mehrdad","id":"67638922-f394-11eb-9cf6-f20423e08757","last_name":"Karrabi","full_name":"Karrabi, Mehrdad"},{"full_name":"Lazarsfeld, John M","id":"17ce3656-183e-11ef-84c3-8932383e1b23","last_name":"Lazarsfeld","first_name":"John M"}],"department":[{"_id":"DaAl"},{"_id":"KrCh"}],"date_created":"2024-07-28T22:01:10Z","acknowledgement":"This work was supported in part by the ERC-2020-CoG 863818 (FoRM-SMArt) grant. We thank James Aspnes and Thomas Sauerwald for several helpful discussions on Ehrenfest random walks.","scopus_import":"1","_id":"17329","has_accepted_license":"1","doi":"10.1145/3662158.3662768"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2210.07754"}],"language":[{"iso":"eng"}],"OA_type":"green","corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"year":"2024","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"14083"}]},"author":[{"first_name":"Nicolas","full_name":"Resch, Nicolas","last_name":"Resch"},{"last_name":"Yuan","full_name":"Yuan, Chen","first_name":"Chen"},{"first_name":"Yihan","orcid":"0000-0002-6465-6258","last_name":"Zhang","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","full_name":"Zhang, Yihan"}],"department":[{"_id":"MaMo"}],"date_created":"2024-07-28T22:01:10Z","_id":"17330","doi":"10.1109/TIT.2024.3430842","issue":"9","acknowledgement":"Part of this work was done while Nicolas Resch was affiliated with the Centrum Wiskunde & Informatica and supported in part by ERC H2020 grant No.74079 (ALGSTRONGCRYPTO). Chen Yuan is supported in part by the National Key Research and Development Projects under Grant 2022YFA1004900 and Grant 2021YFE0109900, the National Natural Science Foundation of China under Grant 12101403 and Grant 12031011.","scopus_import":"1","abstract":[{"lang":"eng","text":"In this work we consider the list-decodability and list-recoverability of arbitrary q -ary codes, for all integer values of q ⩾ 2. A code is called ( p , L ) q -list-decodable if every radius pn Hamming ball contains less than L codewords; ( p , ℓ, L ) q -recoverability is a generalization where we place radius pn Hamming balls on every point of a combinatorial rectangle with side length ℓ and again stipulate that there be less than L codewords. Our main contribution is to precisely calculate the maximum value of p for which there exist infinite families of positive rate ( p , ℓ, L ) q -list-recoverable codes, the quantity we call the zero-rate threshold . Denoting this value by p *, we in fact show that codes correcting a p * + ε fraction of errors must have size O ε (1), i.e., independent of n . Such a result is typically referred to as a “Plotkin bound.” To complement this, a standard random code with expurgation construction shows that there exist positive rate codes correcting a p * − ε fraction of errors. We also follow a classical proof template (typically attributed to Elias and Bassalygo) to derive from the zero-rate threshold other tradeoffs between rate and decoding radius for list-decoding and list-recovery. Technically, proving the Plotkin bound boils down to demon-strating the Schur convexity of a certain function defined on the q -simplex as well as the convexity of a univariate function derived from it. We remark that an earlier argument claimed similar results for q -ary list-decoding; however, we point out that this earlier proof is flawed."}],"arxiv":1,"title":"Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery","oa_version":"Preprint","day":"01","date_updated":"2025-09-08T08:31:53Z","article_processing_charge":"No","date_published":"2024-09-01T00:00:00Z","status":"public","publication_status":"published","publication":"IEEE Transactions on Information Theory","quality_controlled":"1","page":"6211-6238","month":"09","external_id":{"arxiv":["2210.07754"],"isi":["001299623600019"]},"type":"journal_article","oa":1,"publisher":"IEEE","volume":70,"publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"OA_place":"repository","intvolume":" 70","article_type":"original","citation":{"apa":"Resch, N., Yuan, C., & Zhang, Y. (2024). Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2024.3430842","ama":"Resch N, Yuan C, Zhang Y. Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. IEEE Transactions on Information Theory. 2024;70(9):6211-6238. doi:10.1109/TIT.2024.3430842","mla":"Resch, Nicolas, et al. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding and List-Recovery.” IEEE Transactions on Information Theory, vol. 70, no. 9, IEEE, 2024, pp. 6211–38, doi:10.1109/TIT.2024.3430842.","short":"N. Resch, C. Yuan, Y. Zhang, IEEE Transactions on Information Theory 70 (2024) 6211–6238.","ieee":"N. Resch, C. Yuan, and Y. Zhang, “Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery,” IEEE Transactions on Information Theory, vol. 70, no. 9. IEEE, pp. 6211–6238, 2024.","ista":"Resch N, Yuan C, Zhang Y. 2024. Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. IEEE Transactions on Information Theory. 70(9), 6211–6238.","chicago":"Resch, Nicolas, Chen Yuan, and Yihan Zhang. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding and List-Recovery.” IEEE Transactions on Information Theory. IEEE, 2024. https://doi.org/10.1109/TIT.2024.3430842."}},{"publication":"Proteins: Structure, Function and Bioinformatics","status":"public","publication_status":"published","article_processing_charge":"No","date_published":"2024-12-01T00:00:00Z","day":"01","date_updated":"2025-09-08T08:33:53Z","oa_version":"Preprint","title":"Hereditary amyloidosis: Insights into a fibrinogen A variant protein","abstract":[{"lang":"eng","text":"Amyloidosis are a group of diseases in which soluble proteins aggregate and deposit in fibrillar conformation extracellularly in tissues. The effectiveness of therapeutic strategies depends on the specific protein involved, being crucial to accurately determine its nature. Moreover, following the diagnosis, the search for the mutation within relatives allows the clinical advice. Here we report the precise diagnosis and explored the possible reasons of the structural pathogenicity for a renal amyloidosis related to a fibrinogen Aα-chain variant. Whole-exome sequencing and GATK calling pipeline were leveraged to characterize the protein variant present in a patient with kidney failure. Bioinformatics strategies were applied to suggest potential explanations of the variants aggregation. Our pipeline allowed the identification of a single-point variant of fibrinogen Aα-chain, which opened the possibility of curative transplantation. In silico structural analysis suggested that the pathogenicity of the variant may be attributed to a heightened susceptibility to yield a peptide prone to deposit as an oligomer with a β-sheet structure. Exploiting the comprehensive coverage of whole-genome sequencing, we managed to fill a vacant stage in the diagnosis of hereditary amyloidosis and to stimulate the advancement in biomedicine."}],"citation":{"short":"E.R. Cattaneo, R.A. Gisonno, M.C. Abba, M. Santana, S.A. Rosú, E. Nucifora, M.A. Aguirre, M.C. Giordani, M.A. Tricerri, N.A. Ramella, Proteins: Structure, Function and Bioinformatics 92 (2024) 1366–1374.","mla":"Cattaneo, Elizabeth R., et al. “Hereditary Amyloidosis: Insights into a Fibrinogen A Variant Protein.” Proteins: Structure, Function and Bioinformatics, vol. 92, no. 12, Wiley, 2024, pp. 1366–74, doi:10.1002/prot.26732.","chicago":"Cattaneo, Elizabeth R, Romina A Gisonno, Martín C Abba, Marianela Santana, Silvana A Rosú, Elsa Nucifora, María A Aguirre, María C Giordani, M. Alejandra Tricerri, and Nahuel A Ramella. “Hereditary Amyloidosis: Insights into a Fibrinogen A Variant Protein.” Proteins: Structure, Function and Bioinformatics. Wiley, 2024. https://doi.org/10.1002/prot.26732.","ista":"Cattaneo ER, Gisonno RA, Abba MC, Santana M, Rosú SA, Nucifora E, Aguirre MA, Giordani MC, Tricerri MA, Ramella NA. 2024. Hereditary amyloidosis: Insights into a fibrinogen A variant protein. Proteins: Structure, Function and Bioinformatics. 92(12), 1366–1374.","ieee":"E. R. Cattaneo et al., “Hereditary amyloidosis: Insights into a fibrinogen A variant protein,” Proteins: Structure, Function and Bioinformatics, vol. 92, no. 12. Wiley, pp. 1366–1374, 2024.","apa":"Cattaneo, E. R., Gisonno, R. A., Abba, M. C., Santana, M., Rosú, S. A., Nucifora, E., … Ramella, N. A. (2024). Hereditary amyloidosis: Insights into a fibrinogen A variant protein. Proteins: Structure, Function and Bioinformatics. Wiley. https://doi.org/10.1002/prot.26732","ama":"Cattaneo ER, Gisonno RA, Abba MC, et al. Hereditary amyloidosis: Insights into a fibrinogen A variant protein. Proteins: Structure, Function and Bioinformatics. 2024;92(12):1366-1374. doi:10.1002/prot.26732"},"pmid":1,"article_type":"original","OA_place":"repository","intvolume":" 92","publication_identifier":{"issn":["0887-3585"],"eissn":["1097-0134"]},"publisher":"Wiley","volume":92,"oa":1,"type":"journal_article","external_id":{"isi":["001272128100001"],"pmid":["39031927"]},"month":"12","page":"1366-1374","quality_controlled":"1","year":"2024","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_type":"green","main_file_link":[{"open_access":"1","url":"https://doi.org/10.22541/au.171804763.37967262/v1"}],"language":[{"iso":"eng"}],"scopus_import":"1","acknowledgement":"The authors acknowledge Rosana del Cid for her help with English corrections, Mario Ramos for the figure editions, and Gabriela Finarelli for technical assistance. S.A. Rosú, N.A. Ramella, and M.A. Tricerri acknowledge support from Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) (Grant PIP 11220200102381), Agencia Nacional de Promoción Científica y Tecnológica (PICT 2019-03592), Universidad Nacional de La Plata (UNLP) (Grants M234 and PPID M014), and Fundación Florencio Fiorini. The authors warmly thank M.P. for her willingness to conduct these studies.","issue":"12","doi":"10.1002/prot.26732","_id":"17331","department":[{"_id":"GaNo"}],"date_created":"2024-07-28T22:01:10Z","author":[{"first_name":"Elizabeth R","last_name":"Cattaneo","full_name":"Cattaneo, Elizabeth R"},{"last_name":"Gisonno","id":"a9e08d76-6a98-11ec-8f7b-c777fe5ca519","full_name":"Gisonno, Romina A","first_name":"Romina A"},{"last_name":"Abba","full_name":"Abba, Martín C","first_name":"Martín C"},{"full_name":"Santana, Marianela","last_name":"Santana","first_name":"Marianela"},{"first_name":"Silvana A","full_name":"Rosú, Silvana A","last_name":"Rosú"},{"full_name":"Nucifora, Elsa","last_name":"Nucifora","first_name":"Elsa"},{"first_name":"María A","full_name":"Aguirre, María A","last_name":"Aguirre"},{"first_name":"María C","last_name":"Giordani","full_name":"Giordani, María C"},{"first_name":"M. Alejandra","last_name":"Tricerri","full_name":"Tricerri, M. Alejandra"},{"first_name":"Nahuel A","full_name":"Ramella, Nahuel A","last_name":"Ramella"}]},{"title":"Wait-free trees with asymptotically-efficient range queries","abstract":[{"lang":"eng","text":"Tree data structures, such as red-black trees, quad trees, treaps, or tries, are fundamental tools in computer science. A classical problem in concurrency is to obtain expressive, efficient, and scalable versions of practical tree data structures. We are interested in concurrent trees supporting range queries, i.e., queries that involve multiple consecutive data items. Existing implementations with this capability can list keys in a specific range, but do not support aggregate range queries: for instance, if we want to calculate the number of keys in a range, the only choice is to retrieve a whole list and return its size. This is suboptimal: in the sequential setting, one can augment a balanced search tree with counters and, consequently, perform these aggregate requests in logarithmic rather than linear time.In this paper, we propose a generic approach to implement a broad class of range queries on concurrent trees in a way that is wait-free, asymptotically efficient, and practically scalable. The key idea is a new mechanism for maintaining metadata concurrently at tree nodes, which can be seen as a wait-free variant of hand-over-hand locking (which we call hand-over-hand helping). We did a preliminary implementation of the wait-free binary search tree and preliminary experiments have indicated the soundness of our approach."}],"arxiv":1,"publication":"2024 IEEE International Parallel and Distributed Processing Symposium","publication_status":"published","status":"public","date_published":"2024-07-08T00:00:00Z","article_processing_charge":"No","oa_version":"Preprint","date_updated":"2025-09-08T08:29:45Z","day":"08","publication_identifier":{"eissn":["1530-2075"],"isbn":["9798350337662"]},"conference":{"location":"San Francisco, CA, United States","start_date":"2024-05-27","name":"IPDPS: International Parallel and Distributed Processing Symposium","end_date":"2024-05-31"},"publisher":"IEEE","oa":1,"page":"169-179","type":"conference","external_id":{"isi":["001270389600078"],"arxiv":["2310.05293"]},"month":"07","quality_controlled":"1","citation":{"ieee":"I. Kokorin, V. Yudov, V. Aksenov, and D.-A. Alistarh, “Wait-free trees with asymptotically-efficient range queries,” in 2024 IEEE International Parallel and Distributed Processing Symposium, San Francisco, CA, United States, 2024, pp. 169–179.","ista":"Kokorin I, Yudov V, Aksenov V, Alistarh D-A. 2024. Wait-free trees with asymptotically-efficient range queries. 2024 IEEE International Parallel and Distributed Processing Symposium. IPDPS: International Parallel and Distributed Processing Symposium, 169–179.","chicago":"Kokorin, Ilya, Victor Yudov, Vitaly Aksenov, and Dan-Adrian Alistarh. “Wait-Free Trees with Asymptotically-Efficient Range Queries.” In 2024 IEEE International Parallel and Distributed Processing Symposium, 169–79. IEEE, 2024. https://doi.org/10.1109/IPDPS57955.2024.00023.","mla":"Kokorin, Ilya, et al. “Wait-Free Trees with Asymptotically-Efficient Range Queries.” 2024 IEEE International Parallel and Distributed Processing Symposium, IEEE, 2024, pp. 169–79, doi:10.1109/IPDPS57955.2024.00023.","short":"I. Kokorin, V. Yudov, V. Aksenov, D.-A. Alistarh, in:, 2024 IEEE International Parallel and Distributed Processing Symposium, IEEE, 2024, pp. 169–179.","ama":"Kokorin I, Yudov V, Aksenov V, Alistarh D-A. Wait-free trees with asymptotically-efficient range queries. In: 2024 IEEE International Parallel and Distributed Processing Symposium. IEEE; 2024:169-179. doi:10.1109/IPDPS57955.2024.00023","apa":"Kokorin, I., Yudov, V., Aksenov, V., & Alistarh, D.-A. (2024). Wait-free trees with asymptotically-efficient range queries. In 2024 IEEE International Parallel and Distributed Processing Symposium (pp. 169–179). San Francisco, CA, United States: IEEE. https://doi.org/10.1109/IPDPS57955.2024.00023"},"corr_author":"1","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2310.05293","open_access":"1"}],"year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"date_created":"2024-07-28T22:01:11Z","department":[{"_id":"DaAl"}],"author":[{"first_name":"Ilya","full_name":"Kokorin, Ilya","last_name":"Kokorin"},{"last_name":"Yudov","full_name":"Yudov, Victor","first_name":"Victor"},{"first_name":"Vitaly","full_name":"Aksenov, Vitaly","last_name":"Aksenov"},{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"}],"scopus_import":"1","acknowledgement":"We thank Trevor Brown and Yuanhao Wei for the discussion and anonymous reviewers for helping us to improve the paper. Also, we thank JetBrains and Huawei for their support.","doi":"10.1109/IPDPS57955.2024.00023","_id":"17332"},{"_id":"17333","doi":"10.1038/s41929-024-01184-7","issue":"7","scopus_import":"1","author":[{"last_name":"Mondal","id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","full_name":"Mondal, Soumyadip","first_name":"Soumyadip"},{"last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319"}],"date_created":"2024-07-29T07:05:33Z","department":[{"_id":"StFr"}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","language":[{"iso":"eng"}],"corr_author":"1","article_type":"letter_note","citation":{"mla":"Mondal, Soumyadip, and Stefan Alexander Freunberger. “Catalysing Rate and Capacity.” Nature Catalysis, vol. 7, no. 7, Springer Nature, 2024, pp. 759–60, doi:10.1038/s41929-024-01184-7.","short":"S. Mondal, S.A. Freunberger, Nature Catalysis 7 (2024) 759–760.","ieee":"S. Mondal and S. A. Freunberger, “Catalysing rate and capacity,” Nature Catalysis, vol. 7, no. 7. Springer Nature, pp. 759–760, 2024.","ista":"Mondal S, Freunberger SA. 2024. Catalysing rate and capacity. Nature Catalysis. 7(7), 759–760.","chicago":"Mondal, Soumyadip, and Stefan Alexander Freunberger. “Catalysing Rate and Capacity.” Nature Catalysis. Springer Nature, 2024. https://doi.org/10.1038/s41929-024-01184-7.","apa":"Mondal, S., & Freunberger, S. A. (2024). Catalysing rate and capacity. Nature Catalysis. Springer Nature. https://doi.org/10.1038/s41929-024-01184-7","ama":"Mondal S, Freunberger SA. Catalysing rate and capacity. 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Now, a fast catalytic step involved in oxygen redox catalysis is shown to contribute to capacity at a high rate.","lang":"eng"}],"title":"Catalysing rate and capacity"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","supervisor":[{"first_name":"Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","full_name":"Maas, Jan"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"17351","status":"public"},{"relation":"part_of_dissertation","id":"17353","status":"public"},{"id":"17350","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"17352","status":"public"},{"status":"public","id":"17143","relation":"part_of_dissertation"}]},"year":"2024","degree_awarded":"PhD","language":[{"iso":"eng"}],"corr_author":"1","file_date_updated":"2024-08-02T09:27:15Z","_id":"17336","has_accepted_license":"1","doi":"10.15479/at:ista:17336","author":[{"id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","last_name":"Pedrotti","full_name":"Pedrotti, Francesco","first_name":"Francesco"}],"department":[{"_id":"GradSch"},{"_id":"JaMa"}],"date_created":"2024-07-29T09:14:14Z","date_updated":"2026-04-07T13:00:03Z","day":"31","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","article_processing_charge":"No","date_published":"2024-07-31T00:00:00Z","status":"public","publication_status":"published","ec_funded":1,"abstract":[{"text":"This thesis deals with the study of stochastic processes and their ergodicity properties. The\r\nvariety of problems encountered calls for a set of different approaches, ranging from classical to\r\nmodern ones: a special place is held by probabilistic methods based on couplings, by functional\r\ninequalities, and by the theory of gradient flows in the space of measures.\r\n\r\nThe material is organized as follows. Chapter 1 contains the introduction to this thesis, starting\r\nwith a general presentation of some of the relevant topics. Section 1.1 is dedicated to the\r\ntheory of gradient flows in metric spaces, and introduces the first contribution of this thesis\r\n[DSMP24], which is presented in detail in Chapter 2. Section 1.2 moves to the topic of\r\ncurvature of Markov chains, concluding with a brief description of our second contribution\r\n[Ped23], which is included in Chapter 3. Section 1.3 discusses applications of stochastic\r\nprocesses to the theory of sampling, in particular the recent framework of score-based diffusion\r\nmodels, and our contribution [PMM24], which is contained in Chapter 4. Section 1.4 discusses\r\nsome related problems, concerning the regularization properties of the heat flow. It serves\r\nas a motivation for the work [BP24], which we report in Chapter 5. Finally, Section 1.5\r\ndiscusses the last contribution of this thesis, which can be found in Chapter 6. It deals with\r\nthe convergence to equilibrium of a particular stochastic model from quantitative genetics:\r\nthis is established via some functional inequalities, which we prove with probabilistic arguments\r\nbased on couplings.\r\n","lang":"eng"}],"ddc":["500","510","515","519"],"title":"Functional inequalities and convergence of stochastic processes","project":[{"name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"716117"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"file":[{"creator":"fpedrott","date_created":"2024-08-02T09:23:26Z","content_type":"application/pdf","file_name":"thesis_final.pdf","checksum":"11650bab714ef85ad43a287060850523","file_id":"17366","file_size":2941599,"access_level":"open_access","date_updated":"2024-08-02T09:23:26Z","relation":"main_file","success":1},{"relation":"source_file","date_updated":"2024-08-02T09:27:15Z","file_size":6293375,"access_level":"closed","file_name":"thesis_final_source.zip","checksum":"c30ba5611941226cf1bfc867c25b1e80","file_id":"17367","creator":"fpedrott","date_created":"2024-08-02T09:27:15Z","content_type":"application/x-zip-compressed"}],"citation":{"ista":"Pedrotti F. 2024. 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Mathematica notebook for “Effect of assortative mating and sexual selection on polygenic barriers to gene flow.” 2024. doi:10.15479/AT:ISTA:17344","apa":"Surendranadh, P., & Sachdeva, H. (2024). Mathematica notebook for “Effect of assortative mating and sexual selection on polygenic barriers to gene flow.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:17344","chicago":"Surendranadh, Parvathy, and Himani Sachdeva. “Mathematica Notebook for ‘Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:17344.","ista":"Surendranadh P, Sachdeva H. 2024. Mathematica notebook for ‘Effect of assortative mating and sexual selection on polygenic barriers to gene flow’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:17344.","ieee":"P. Surendranadh and H. Sachdeva, “Mathematica notebook for ‘Effect of assortative mating and sexual selection on polygenic barriers to gene flow.’” Institute of Science and Technology Austria, 2024.","short":"P. Surendranadh, H. Sachdeva, (2024).","mla":"Surendranadh, Parvathy, and Himani Sachdeva. Mathematica Notebook for “Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:17344."},"file":[{"success":1,"relation":"main_file","file_size":726132,"access_level":"open_access","date_updated":"2024-07-29T13:51:11Z","file_id":"17345","checksum":"75bdbc7ad7cc6afe4459bc4a8824a302","file_name":"Submission.nb","date_created":"2024-07-29T13:51:11Z","content_type":"application/octet-stream","creator":"psurendr"}],"doi":"10.15479/AT:ISTA:17344","has_accepted_license":"1","_id":"17344","file_date_updated":"2024-07-29T13:51:11Z","title":"Mathematica notebook for 'Effect of assortative mating and sexual selection on polygenic barriers to gene flow'","ddc":["576"],"abstract":[{"text":"This file contains the Mathematica notebook associated with the paper Effect of assortative mating and sexual selection on polygenic barriers to gene flow. It contains the numerical approximations, analyses, and simulations used in the study. ","lang":"eng"}],"status":"public","date_published":"2024-07-01T00:00:00Z","article_processing_charge":"No","year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","date_updated":"2025-01-14T13:02:59Z"},{"month":"06","external_id":{"arxiv":["2305.14164"]},"department":[{"_id":"JaMa"},{"_id":"MaMo"}],"date_created":"2024-07-31T07:56:40Z","type":"preprint","author":[{"first_name":"Francesco","id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","last_name":"Pedrotti","full_name":"Pedrotti, Francesco"},{"full_name":"Maas, Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","first_name":"Jan"},{"last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","first_name":"Marco","orcid":"0000-0002-3242-7020"}],"OA_place":"repository","oa":1,"doi":"10.48550/arXiv.2305.14164","project":[{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"_id":"17350","citation":{"ista":"Pedrotti F, Maas J, Mondelli M. Improved convergence of score-based diffusion models via prediction-correction. arXiv, 10.48550/arXiv.2305.14164.","chicago":"Pedrotti, Francesco, Jan Maas, and Marco Mondelli. “Improved Convergence of Score-Based Diffusion Models via Prediction-Correction.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2305.14164.","ieee":"F. Pedrotti, J. Maas, and M. Mondelli, “Improved convergence of score-based diffusion models via prediction-correction,” arXiv. .","short":"F. Pedrotti, J. Maas, M. Mondelli, ArXiv (n.d.).","mla":"Pedrotti, Francesco, et al. “Improved Convergence of Score-Based Diffusion Models via Prediction-Correction.” ArXiv, doi:10.48550/arXiv.2305.14164.","ama":"Pedrotti F, Maas J, Mondelli M. Improved convergence of score-based diffusion models via prediction-correction. arXiv. doi:10.48550/arXiv.2305.14164","apa":"Pedrotti, F., Maas, J., & Mondelli, M. (n.d.). Improved convergence of score-based diffusion models via prediction-correction. arXiv. https://doi.org/10.48550/arXiv.2305.14164"},"abstract":[{"lang":"eng","text":"Score-based generative models (SGMs) are powerful tools to sample from\r\ncomplex data distributions. Their underlying idea is to (i) run a forward\r\nprocess for time $T_1$ by adding noise to the data, (ii) estimate its score\r\nfunction, and (iii) use such estimate to run a reverse process. As the reverse\r\nprocess is initialized with the stationary distribution of the forward one, the\r\nexisting analysis paradigm requires $T_1\\to\\infty$. This is however\r\nproblematic: from a theoretical viewpoint, for a given precision of the score\r\napproximation, the convergence guarantee fails as $T_1$ diverges; from a\r\npractical viewpoint, a large $T_1$ increases computational costs and leads to\r\nerror propagation. This paper addresses the issue by considering a version of\r\nthe popular predictor-corrector scheme: after running the forward process, we\r\nfirst estimate the final distribution via an inexact Langevin dynamics and then\r\nrevert the process. Our key technical contribution is to provide convergence\r\nguarantees which require to run the forward process only for a fixed finite\r\ntime $T_1$. Our bounds exhibit a mild logarithmic dependence on the input\r\ndimension and the subgaussian norm of the target distribution, have minimal\r\nassumptions on the data, and require only to control the $L^2$ loss on the\r\nscore approximation, which is the quantity minimized in practice."}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2305.14164","open_access":"1"}],"arxiv":1,"language":[{"iso":"eng"}],"corr_author":"1","title":"Improved convergence of score-based diffusion models via prediction-correction","date_published":"2024-06-06T00:00:00Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"18897"},{"status":"public","id":"17336","relation":"dissertation_contains"}]},"article_processing_charge":"No","year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","date_updated":"2026-04-07T13:00:02Z","day":"06","status":"public","publication_status":"draft","publication":"arXiv"},{"corr_author":"1","title":"L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher's infinitesimal model","abstract":[{"text":"We prove upper bounds on the $L^\\infty$-Wasserstein distance from optimal\r\ntransport between strongly log-concave probability densities and log-Lipschitz\r\nperturbations. In the simplest setting, such a bound amounts to a\r\ntransport-information inequality involving the $L^\\infty$-Wasserstein metric\r\nand the relative $L^\\infty$-Fisher information. We show that this inequality\r\ncan be sharpened significantly in situations where the involved densities are\r\nanisotropic. Our proof is based on probabilistic techniques using Langevin\r\ndynamics. As an application of these results, we obtain sharp exponential rates\r\nof convergence in Fisher's infinitesimal model from quantitative genetics,\r\ngeneralising recent results by Calvez, Poyato, and Santambrogio in dimension 1\r\nto arbitrary dimensions.","lang":"eng"}],"language":[{"iso":"eng"}],"arxiv":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2402.04151"}],"publication":"arXiv","publication_status":"draft","status":"public","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-04-07T13:00:02Z","day":"07","article_number":"2402.04151","date_published":"2024-02-07T00:00:00Z","related_material":{"record":[{"status":"public","id":"20050","relation":"later_version"},{"id":"17336","relation":"dissertation_contains","status":"public"}]},"year":"2024","article_processing_charge":"No","oa":1,"OA_place":"repository","author":[{"first_name":"Kseniia","orcid":"0000-0002-6246-1465","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","last_name":"Khudiakova","full_name":"Khudiakova, Kseniia"},{"full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","orcid":"0000-0002-0845-1338","first_name":"Jan"},{"first_name":"Francesco","full_name":"Pedrotti, Francesco","id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","last_name":"Pedrotti"}],"month":"02","department":[{"_id":"JaMa"}],"date_created":"2024-07-31T08:07:40Z","type":"preprint","external_id":{"arxiv":["2402.04151"]},"citation":{"mla":"Khudiakova, Kseniia, et al. “L∞-Optimal Transport of Anisotropic Log-Concave Measures and Exponential Convergence in Fisher’s Infinitesimal Model.” ArXiv, 2402.04151, doi:10.48550/arXiv.2402.04151.","short":"K. Khudiakova, J. Maas, F. Pedrotti, ArXiv (n.d.).","ieee":"K. Khudiakova, J. Maas, and F. Pedrotti, “L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model,” arXiv. .","chicago":"Khudiakova, Kseniia, Jan Maas, and Francesco Pedrotti. “L∞-Optimal Transport of Anisotropic Log-Concave Measures and Exponential Convergence in Fisher’s Infinitesimal Model.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2402.04151.","ista":"Khudiakova K, Maas J, Pedrotti F. L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model. arXiv, 2402.04151.","apa":"Khudiakova, K., Maas, J., & Pedrotti, F. (n.d.). L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model. arXiv. https://doi.org/10.48550/arXiv.2402.04151","ama":"Khudiakova K, Maas J, Pedrotti F. L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model. arXiv. doi:10.48550/arXiv.2402.04151"},"_id":"17352","doi":"10.48550/arXiv.2402.04151","project":[{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"grant_number":"26293","_id":"34d33d68-11ca-11ed-8bc3-ec13763c0ca8","name":"The impact of deleterious mutations on small populations"}]},{"doi":"10.48550/arXiv.2404.15205","_id":"17353","citation":{"ama":"Brigati G, Pedrotti F. Heat flow, log-concavity, and Lipschitz transport maps. arXiv. doi:10.48550/arXiv.2404.15205","apa":"Brigati, G., & Pedrotti, F. (n.d.). Heat flow, log-concavity, and Lipschitz transport maps. arXiv. https://doi.org/10.48550/arXiv.2404.15205","ieee":"G. Brigati and F. Pedrotti, “Heat flow, log-concavity, and Lipschitz transport maps,” arXiv. .","chicago":"Brigati, Giovanni, and Francesco Pedrotti. “Heat Flow, Log-Concavity, and Lipschitz Transport Maps.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2404.15205.","ista":"Brigati G, Pedrotti F. Heat flow, log-concavity, and Lipschitz transport maps. arXiv, 2404.15205.","mla":"Brigati, Giovanni, and Francesco Pedrotti. “Heat Flow, Log-Concavity, and Lipschitz Transport Maps.” ArXiv, 2404.15205, doi:10.48550/arXiv.2404.15205.","short":"G. Brigati, F. Pedrotti, ArXiv (n.d.)."},"external_id":{"arxiv":["2404.15205"]},"date_created":"2024-07-31T08:17:14Z","month":"05","type":"preprint","department":[{"_id":"JaMa"}],"author":[{"first_name":"Giovanni","last_name":"Brigati","id":"63ff57e8-1fbb-11ee-88f2-f558ffc59cf1","full_name":"Brigati, Giovanni"},{"first_name":"Francesco","last_name":"Pedrotti","id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","full_name":"Pedrotti, Francesco"}],"OA_place":"repository","oa":1,"date_published":"2024-05-08T00:00:00Z","article_processing_charge":"No","year":"2024","related_material":{"record":[{"id":"20591","relation":"later_version","status":"public"},{"status":"public","relation":"dissertation_contains","id":"17336"}]},"article_number":"2404.15205","date_updated":"2026-04-07T13:00:02Z","day":"08","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"draft","status":"public","publication":"arXiv","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2404.15205"}],"arxiv":1,"language":[{"iso":"eng"}],"abstract":[{"text":"In this paper we derive estimates for the Hessian of the logarithm\r\n(log-Hessian) for solutions to the heat equation. For initial data in the form\r\nof log-Lipschitz perturbation of strongly log-concave measures, the log-Hessian\r\nadmits an explicit, uniform (in space) lower bound. This yields a new estimate\r\nfor the Lipschitz constant of a transport map pushing forward the standard\r\nGaussian to a measure in this class. Further connections are discussed with\r\nscore-based diffusion models and improved Gaussian logarithmic Sobolev\r\ninequalities. Finally, we show that assuming only fast decay of the tails of\r\nthe initial datum does not suffice to guarantee uniform log-Hessian upper\r\nbounds.","lang":"eng"}],"corr_author":"1","title":"Heat flow, log-concavity, and Lipschitz transport maps"},{"abstract":[{"text":"We present symplectic structures on the shape space of unparameterized space curves that generalize the classical Marsden-Weinstein structure. Our method integrates the Liouville 1-form of the Marsden-Weinstein structure with Riemannian structures that have been introduced in mathematical shape analysis. We also derive Hamiltonian vector fields for several classical Hamiltonian functions with respect to these new symplectic structures.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2407.19908"}],"arxiv":1,"language":[{"iso":"eng"}],"title":"Symplectic structures on the space of space curves","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Preprint","day":"29","date_updated":"2026-04-28T09:59:01Z","related_material":{"record":[{"id":"20551","relation":"dissertation_contains","status":"public"},{"id":"21743","relation":"later_version","status":"public"}]},"article_processing_charge":"No","year":"2024","date_published":"2024-07-29T00:00:00Z","keyword":["space of space curves","symplectic stuctures"],"status":"public","publication":"arXiv","publication_status":"draft","author":[{"first_name":"Martin","full_name":"Bauer, Martin","last_name":"Bauer"},{"first_name":"Sadashige","orcid":"0000-0002-3121-3100","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","last_name":"Ishida","full_name":"Ishida, Sadashige"},{"full_name":"Michor, Peter W.","last_name":"Michor","first_name":"Peter W."}],"external_id":{"arxiv":["2407.19908"]},"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"type":"preprint","month":"07","date_created":"2024-08-01T06:34:08Z","oa":1,"OA_place":"repository","_id":"17361","doi":"10.48550/arXiv.2407.19908","project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"citation":{"apa":"Bauer, M., Ishida, S., & Michor, P. W. (n.d.). Symplectic structures on the space of space curves. arXiv. https://doi.org/10.48550/arXiv.2407.19908","ama":"Bauer M, Ishida S, Michor PW. Symplectic structures on the space of space curves. arXiv. doi:10.48550/arXiv.2407.19908","mla":"Bauer, Martin, et al. “Symplectic Structures on the Space of Space Curves.” ArXiv, doi:10.48550/arXiv.2407.19908.","short":"M. Bauer, S. Ishida, P.W. Michor, ArXiv (n.d.).","ieee":"M. Bauer, S. Ishida, and P. W. Michor, “Symplectic structures on the space of space curves,” arXiv. .","chicago":"Bauer, Martin, Sadashige Ishida, and Peter W. Michor. “Symplectic Structures on the Space of Space Curves.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2407.19908.","ista":"Bauer M, Ishida S, Michor PW. Symplectic structures on the space of space curves. arXiv, 10.48550/arXiv.2407.19908."},"acknowledgement":"The authors are grateful to Boris Khesin for valuable comments on the MW symplectic structure and S. Ishida thanks Albert Chern for insightful discussions on space curves and Chris Wojtan for his continuous support. M. Bauer was partially supported by NSF grant DMS-1953244 and by the Binational Science Foundation (BSF). S. Ishida was partially supported by ERC Consolidator Grant 101045083 “CoDiNA” funded by the European Research Council. Some figures were generated by the software Houdini and its education license was provided by SideFX."},{"related_material":{"record":[{"status":"public","id":"17890","relation":"used_in_publication"}]},"year":"2024","date_published":"2024-08-05T00:00:00Z","article_processing_charge":"No","acknowledged_ssus":[{"_id":"ScienComp"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","date_updated":"2026-04-16T12:20:41Z","day":"05","status":"public","abstract":[{"text":"This is the supplementary data for the paper titled \"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome\", where we described the generation and analysis of single-nucleus expression and chromatin-accessibility data from the female reproductive system of Artemia franciscana. We compared our dataset to the published Drosophila single-nucleus data (over 400 million years of divergence) and highlighted the extreme conservation of several of the molecular pathways of oogenesis and meiosis. We found evidence of global transcriptional quiescence and chromatin condensation in late germ cells, highlighting the conserved role of this repressive stage in arthropod oogenesis. Additionally, we explored the expression patterns of the ZW sex chromosomes during oogenesis. Our data shows that the Z-chromosome is consistently downregulated in germline cells. While this is partly driven by a lack of dosage compensation in the germline, a subset of cells show stronger repression of the Z chromosome.","lang":"eng"}],"file_date_updated":"2024-08-05T23:28:52Z","corr_author":"1","title":"Data for: \"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome\"","ddc":["576"],"has_accepted_license":"1","project":[{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"}],"doi":"10.15479/AT:ISTA:17362","_id":"17362","citation":{"ama":"Elkrewi MN, Vicoso B. Data for: “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.” 2024. doi:10.15479/AT:ISTA:17362","apa":"Elkrewi, M. N., & Vicoso, B. (2024). Data for: “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:17362","ista":"Elkrewi MN, Vicoso B. 2024. Data for: ‘Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:17362.","chicago":"Elkrewi, Marwan N, and Beatriz Vicoso. “Data for: ‘Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:17362.","ieee":"M. N. Elkrewi and B. Vicoso, “Data for: ‘Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.’” Institute of Science and Technology Austria, 2024.","short":"M.N. Elkrewi, B. Vicoso, (2024).","mla":"Elkrewi, Marwan N., and Beatriz Vicoso. Data for: “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:17362."},"file":[{"date_updated":"2024-08-05T22:24:18Z","access_level":"open_access","file_size":2465,"relation":"main_file","success":1,"creator":"melkrewi","content_type":"text/plain","date_created":"2024-08-05T22:24:18Z","file_name":"README.txt","checksum":"26b5d41b3103f4284dd97d56e370a5b6","file_id":"17394"},{"creator":"melkrewi","date_created":"2024-08-05T23:28:52Z","content_type":"application/x-zip-compressed","file_name":"Data_artemia_single_nucleus_atlas.zip","checksum":"95adab5e36148015da313505e3910707","file_id":"17395","access_level":"open_access","file_size":2526735400,"date_updated":"2024-08-05T23:28:52Z","relation":"main_file","success":1}],"type":"research_data","date_created":"2024-08-02T07:27:45Z","month":"08","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"author":[{"first_name":"Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N"},{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"publisher":"Institute of Science and Technology Austria"}]