[{"issue":"3","page":"237-246","quality_controlled":"1","publisher":"American Chemical Society","publication":"ACS Physical Chemistry Au","intvolume":"         2","title":"1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives","status":"public","oa":1,"author":[{"first_name":"Romeo C. A.","last_name":"Dubini","full_name":"Dubini, Romeo C. A."},{"full_name":"Korytiaková, Eva","last_name":"Korytiaková","first_name":"Eva"},{"first_name":"Thea","last_name":"Schinkel","full_name":"Schinkel, Thea"},{"last_name":"Heinrichs","first_name":"Pia","full_name":"Heinrichs, Pia"},{"last_name":"Carell","first_name":"Thomas","full_name":"Carell, Thomas"},{"full_name":"Rovo, Petra","id":"c316e53f-b965-11eb-b128-bb26acc59c00","first_name":"Petra","orcid":"0000-0001-8729-7326","last_name":"Rovo"}],"related_material":{"link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.12.14.472563","relation":"earlier_version"}]},"citation":{"chicago":"Dubini, Romeo C. A., Eva Korytiaková, Thea Schinkel, Pia Heinrichs, Thomas Carell, and Petra Rovo. “1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives.” <i>ACS Physical Chemistry Au</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acsphyschemau.1c00050\">https://doi.org/10.1021/acsphyschemau.1c00050</a>.","mla":"Dubini, Romeo C. A., et al. “1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives.” <i>ACS Physical Chemistry Au</i>, vol. 2, no. 3, American Chemical Society, 2022, pp. 237–46, doi:<a href=\"https://doi.org/10.1021/acsphyschemau.1c00050\">10.1021/acsphyschemau.1c00050</a>.","ama":"Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. <i>ACS Physical Chemistry Au</i>. 2022;2(3):237-246. doi:<a href=\"https://doi.org/10.1021/acsphyschemau.1c00050\">10.1021/acsphyschemau.1c00050</a>","ista":"Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 2022. 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. 2(3), 237–246.","ieee":"R. C. A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, and P. Rovo, “1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives,” <i>ACS Physical Chemistry Au</i>, vol. 2, no. 3. American Chemical Society, pp. 237–246, 2022.","short":"R.C.A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, P. Rovo, ACS Physical Chemistry Au 2 (2022) 237–246.","apa":"Dubini, R. C. A., Korytiaková, E., Schinkel, T., Heinrichs, P., Carell, T., &#38; Rovo, P. (2022). 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. <i>ACS Physical Chemistry Au</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsphyschemau.1c00050\">https://doi.org/10.1021/acsphyschemau.1c00050</a>"},"day":"11","file":[{"date_updated":"2022-07-29T07:53:20Z","file_name":"2022_ACSPhysChemAU_Dubini.pdf","success":1,"checksum":"5ce3f907848f5c7caf77f1adfe5826c6","file_size":2351220,"creator":"dernst","file_id":"11692","relation":"main_file","date_created":"2022-07-29T07:53:20Z","content_type":"application/pdf","access_level":"open_access"}],"date_updated":"2023-01-31T07:33:07Z","has_accepted_license":"1","article_type":"original","volume":2,"date_created":"2022-02-16T11:18:21Z","license":"https://creativecommons.org/licenses/by/4.0/","date_published":"2022-02-11T00:00:00Z","month":"02","_id":"10758","language":[{"iso":"eng"}],"ddc":["540"],"publication_status":"published","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"external_id":{"pmid":["35637781"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NMR"}],"abstract":[{"lang":"eng","text":"5-Carboxycytosine (5caC) is a rare epigenetic modification found in nucleic acids of all domains of life. Despite its sparse genomic abundance, 5caC is presumed to play essential regulatory roles in transcription, maintenance and base-excision processes in DNA. In this work, we utilize nuclear magnetic resonance (NMR) spectroscopy to address the effects of 5caC incorporation into canonical DNA strands at multiple pH and temperature conditions. Our results demonstrate that 5caC has a pH-dependent global destabilizing and a base-pair mobility enhancing local impact on dsDNA, albeit without any detectable influence on the ground-state B-DNA structure. Measurement of hybridization thermodynamics and kinetics of 5caC-bearing DNA duplexes highlighted how acidic environment (pH 5.8 and 4.7) destabilizes the double-stranded structure by ∼10–20 kJ mol–1 at 37 °C when compared to the same sample at neutral pH. Protonation of 5caC results in a lower activation energy for the dissociation process and a higher barrier for annealing. Studies on conformational exchange on the microsecond time scale regime revealed a sharply localized base-pair motion involving exclusively the modified site and its immediate surroundings. By direct comparison with canonical and 5-formylcytosine (5fC)-edited strands, we were able to address the impact of the two most oxidized naturally occurring cytosine derivatives in the genome. These insights on 5caC’s subtle sensitivity to acidic pH contribute to the long-standing questions of its capacity as a substrate in base excision repair processes and its purpose as an independent, stable epigenetic mark."}],"file_date_updated":"2022-07-29T07:53:20Z","publication_identifier":{"eissn":["2694-2445"]},"article_processing_charge":"Yes (via OA deal)","acknowledgement":"We thank Markus Müller for valued discussions and Felix Xu for assistance in the measurement of UV/vis melting profiles. This work was supported in part by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – SFB 1309-325871075, EU-ITN LightDyNAmics (ID: 765266), the ERC-AG EpiR (ID: 741912), the Center for NanoScience, the Excellence Clusters CIPSM, and the Fonds der Chemischen Industrie. Open access funding provided by Institute of Science and Technology Austria (ISTA).\r\n\r\n","year":"2022","type":"journal_article","scopus_import":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1021/acsphyschemau.1c00050","oa_version":"Published Version","pmid":1},{"publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2022-02-22T07:20:12Z","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"In this Thesis, I study composite quantum impurities with variational techniques, both inspired by machine learning as well as fully analytic. I supplement this with exploration of other applications of machine learning, in particular artificial neural networks, in many-body physics. In Chapters 3 and 4, I study quasiparticle systems with variational approach. I derive a Hamiltonian describing the angulon quasiparticle in the presence of a magnetic field. I apply analytic variational treatment to this Hamiltonian. Then, I introduce a variational approach for non-additive systems, based on artificial neural networks. I exemplify this approach on the example of the polaron quasiparticle (Fröhlich Hamiltonian). In Chapter 5, I continue using artificial neural networks, albeit in a different setting. I apply artificial neural networks to detect phases from snapshots of two types physical systems. Namely, I study Monte Carlo snapshots of multilayer classical spin models as well as molecular dynamics maps of colloidal systems. The main type of networks that I use here are convolutional neural networks, known for their applicability to image data."}],"ec_funded":1,"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"GradSch"},{"_id":"MiLe"}],"publication_status":"published","ddc":["530"],"language":[{"iso":"eng"}],"_id":"10759","oa_version":"Published Version","supervisor":[{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"}],"doi":"10.15479/at:ista:10759","year":"2022","type":"dissertation","oa":1,"author":[{"full_name":"Rzadkowski, Wojciech","id":"48C55298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1106-4419","last_name":"Rzadkowski","first_name":"Wojciech"}],"title":"Analytic and machine learning approaches to composite quantum impurities","status":"public","publisher":"Institute of Science and Technology Austria","page":"120","date_created":"2022-02-16T13:27:37Z","date_published":"2022-02-21T00:00:00Z","month":"02","has_accepted_license":"1","degree_awarded":"PhD","file":[{"relation":"source_file","creator":"wrzadkow","file_id":"10785","file_size":17668233,"date_created":"2022-02-21T13:58:16Z","content_type":"application/zip","access_level":"closed","date_updated":"2022-02-22T07:20:12Z","file_name":"Rzadkowski_thesis_final_source.zip","checksum":"0fc54ad1eaede879c665ac9b53c93e22"},{"checksum":"22d2d7af37ca31f6b1730c26cac7bced","success":1,"file_name":"Rzadkowski_thesis_final.pdf","date_updated":"2022-02-21T14:02:54Z","access_level":"open_access","content_type":"application/pdf","date_created":"2022-02-21T14:02:54Z","file_id":"10786","relation":"main_file","creator":"wrzadkow","file_size":13307331}],"citation":{"chicago":"Rzadkowski, Wojciech. “Analytic and Machine Learning Approaches to Composite Quantum Impurities.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:10759\">https://doi.org/10.15479/at:ista:10759</a>.","mla":"Rzadkowski, Wojciech. <i>Analytic and Machine Learning Approaches to Composite Quantum Impurities</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:10759\">10.15479/at:ista:10759</a>.","ista":"Rzadkowski W. 2022. Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria.","ama":"Rzadkowski W. Analytic and machine learning approaches to composite quantum impurities. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:10759\">10.15479/at:ista:10759</a>","ieee":"W. Rzadkowski, “Analytic and machine learning approaches to composite quantum impurities,” Institute of Science and Technology Austria, 2022.","short":"W. Rzadkowski, Analytic and Machine Learning Approaches to Composite Quantum Impurities, Institute of Science and Technology Austria, 2022.","apa":"Rzadkowski, W. (2022). <i>Analytic and machine learning approaches to composite quantum impurities</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10759\">https://doi.org/10.15479/at:ista:10759</a>"},"day":"21","date_updated":"2024-08-07T07:16:53Z","related_material":{"record":[{"id":"10762","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"7956","relation":"part_of_dissertation"},{"status":"public","id":"415","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8644","status":"public"}]}},{"article_number":"734","title":"Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor","status":"public","oa":1,"author":[{"first_name":"Beatriz","last_name":"Herguedas","full_name":"Herguedas, Beatriz"},{"first_name":"Bianka K.","last_name":"Kohegyi","full_name":"Kohegyi, Bianka K."},{"full_name":"Dohrke, Jan Niklas","first_name":"Jan Niklas","last_name":"Dohrke"},{"last_name":"Watson","orcid":"0000-0002-8698-3823","first_name":"Jake","full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"full_name":"Zhang, Danyang","first_name":"Danyang","last_name":"Zhang"},{"full_name":"Ho, Hinze","first_name":"Hinze","last_name":"Ho"},{"full_name":"Shaikh, Saher A.","first_name":"Saher A.","last_name":"Shaikh"},{"first_name":"Remigijus","last_name":"Lape","full_name":"Lape, Remigijus"},{"full_name":"Krieger, James M.","first_name":"James M.","last_name":"Krieger"},{"first_name":"Ingo H.","last_name":"Greger","full_name":"Greger, Ingo H."}],"publisher":"Springer Nature","quality_controlled":"1","intvolume":"        13","publication":"Nature Communications","has_accepted_license":"1","article_type":"original","volume":13,"date_published":"2022-02-08T00:00:00Z","date_created":"2022-02-20T23:01:30Z","month":"02","file":[{"access_level":"open_access","content_type":"application/pdf","date_created":"2022-02-21T07:59:32Z","creator":"dernst","file_id":"10778","relation":"main_file","file_size":2625540,"checksum":"d86ee8eabe8b794730729ffbb1a8832e","file_name":"2022_NatureCommunications_Herguedas.pdf","success":1,"date_updated":"2022-02-21T07:59:32Z"}],"day":"08","citation":{"mla":"Herguedas, Beatriz, et al. “Mechanisms Underlying TARP Modulation of the GluA1/2-Γ8 AMPA Receptor.” <i>Nature Communications</i>, vol. 13, 734, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-28404-7\">10.1038/s41467-022-28404-7</a>.","ista":"Herguedas B, Kohegyi BK, Dohrke JN, Watson J, Zhang D, Ho H, Shaikh SA, Lape R, Krieger JM, Greger IH. 2022. Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor. Nature Communications. 13, 734.","ama":"Herguedas B, Kohegyi BK, Dohrke JN, et al. Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-28404-7\">10.1038/s41467-022-28404-7</a>","chicago":"Herguedas, Beatriz, Bianka K. Kohegyi, Jan Niklas Dohrke, Jake Watson, Danyang Zhang, Hinze Ho, Saher A. Shaikh, Remigijus Lape, James M. Krieger, and Ingo H. Greger. “Mechanisms Underlying TARP Modulation of the GluA1/2-Γ8 AMPA Receptor.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-28404-7\">https://doi.org/10.1038/s41467-022-28404-7</a>.","ieee":"B. Herguedas <i>et al.</i>, “Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","short":"B. Herguedas, B.K. Kohegyi, J.N. Dohrke, J. Watson, D. Zhang, H. Ho, S.A. Shaikh, R. Lape, J.M. Krieger, I.H. Greger, Nature Communications 13 (2022).","apa":"Herguedas, B., Kohegyi, B. K., Dohrke, J. N., Watson, J., Zhang, D., Ho, H., … Greger, I. H. (2022). Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-28404-7\">https://doi.org/10.1038/s41467-022-28404-7</a>"},"date_updated":"2023-08-02T14:25:33Z","abstract":[{"text":"AMPA-type glutamate receptors (AMPARs) mediate rapid signal transmission at excitatory\r\nsynapses in the brain. Glutamate binding to the receptor’s ligand-binding domains (LBDs)\r\nleads to ion channel activation and desensitization. Gating kinetics shape synaptic transmission\r\nand are strongly modulated by transmembrane AMPAR regulatory proteins (TARPs)\r\nthrough currently incompletely resolved mechanisms. Here, electron cryo-microscopy\r\nstructures of the GluA1/2 TARP-γ8 complex, in both open and desensitized states\r\n(at 3.5 Å), reveal state-selective engagement of the LBDs by the large TARP-γ8 loop (‘β1’),\r\nelucidating how this TARP stabilizes specific gating states. We further show how TARPs alter\r\nchannel rectification, by interacting with the pore helix of the selectivity filter. Lastly, we\r\nreveal that the Q/R-editing site couples the channel constriction at the filter entrance to the\r\ngate, and forms the major cation binding site in the conduction path. Our results provide a\r\nmechanistic framework of how TARPs modulate AMPAR gating and conductance.","lang":"eng"}],"publication_identifier":{"eissn":["20411723"]},"file_date_updated":"2022-02-21T07:59:32Z","acknowledgement":"We thank Ondrej Cais for critical reading of the manuscript. We are grateful to LMB\r\nscientific computing and the EM facility for support, Paul Emsley for help with model\r\nbuilding and Takanori Nakane for helpful comments with Relion 3.1. This work was\r\nsupported by grants from the Medical Research Council (MC_U105174197) and BBSRC\r\n(BB/N002113/1) to I.H.G, and grants from the MCIN/AEI/ 10.13039/501100011033 and\r\n“ESF Investing in your future” to B.H (PID2019-106284GA-I00 and RYC2018-025720-I).","article_processing_charge":"No","publication_status":"published","ddc":["570"],"language":[{"iso":"eng"}],"_id":"10763","external_id":{"pmid":["35136046"],"isi":["000757297200008"]},"department":[{"_id":"PeJo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41467-022-28404-7","oa_version":"Published Version","pmid":1,"scopus_import":"1","isi":1,"type":"journal_article","year":"2022"},{"isi":1,"year":"2022","type":"journal_article","scopus_import":"1","oa_version":"Published Version","pmid":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41467-022-28331-7","external_id":{"isi":["000757297200017"],"pmid":["35136061"]},"department":[{"_id":"SiHi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10764","language":[{"iso":"eng"}],"ddc":["570"],"publication_status":"published","file_date_updated":"2022-02-21T07:51:33Z","publication_identifier":{"eissn":["20411723"]},"acknowledgement":"We thank D. Mazaud and. J. Cazères for technical assistance. This work was supported by grants from the European Research Council (Consolidator grant #683154) and European Union’s Horizon 2020 research and innovation program (Marie Sklodowska-Curie Innovative Training Networks, grant #722053, EU-GliaPhD) to N.R. and from FP7-PEOPLE Marie Curie Intra-European Fellowship for career development (grant #622289) to G.C.","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Presynaptic glutamate replenishment is fundamental to brain function. In high activity regimes, such as epileptic episodes, this process is thought to rely on the glutamate-glutamine cycle between neurons and astrocytes. However the presence of an astroglial glutamine supply, as well as its functional relevance in vivo in the healthy brain remain controversial, partly due to a lack of tools that can directly examine glutamine transfer. Here, we generated a fluorescent probe that tracks glutamine in live cells, which provides direct visual evidence of an activity-dependent glutamine supply from astroglial networks to presynaptic structures under physiological conditions. This mobilization is mediated by connexin43, an astroglial protein with both gap-junction and hemichannel functions, and is essential for synaptic transmission and object recognition memory. Our findings uncover an indispensable recruitment of astroglial glutamine in physiological synaptic activity and memory via an unconventional pathway, thus providing an astrocyte basis for cognitive processes."}],"day":"08","citation":{"chicago":"Cheung, Giselle T, Danijela Bataveljic, Josien Visser, Naresh Kumar, Julien Moulard, Glenn Dallérac, Daria Mozheiko, et al. “Physiological Synaptic Activity and Recognition Memory Require Astroglial Glutamine.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-28331-7\">https://doi.org/10.1038/s41467-022-28331-7</a>.","mla":"Cheung, Giselle T., et al. “Physiological Synaptic Activity and Recognition Memory Require Astroglial Glutamine.” <i>Nature Communications</i>, vol. 13, 753, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-28331-7\">10.1038/s41467-022-28331-7</a>.","ista":"Cheung GT, Bataveljic D, Visser J, Kumar N, Moulard J, Dallérac G, Mozheiko D, Rollenhagen A, Ezan P, Mongin C, Chever O, Bemelmans AP, Lübke J, Leray I, Rouach N. 2022. Physiological synaptic activity and recognition memory require astroglial glutamine. Nature Communications. 13, 753.","ama":"Cheung GT, Bataveljic D, Visser J, et al. Physiological synaptic activity and recognition memory require astroglial glutamine. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-28331-7\">10.1038/s41467-022-28331-7</a>","ieee":"G. T. Cheung <i>et al.</i>, “Physiological synaptic activity and recognition memory require astroglial glutamine,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","short":"G.T. Cheung, D. Bataveljic, J. Visser, N. Kumar, J. Moulard, G. Dallérac, D. Mozheiko, A. Rollenhagen, P. Ezan, C. Mongin, O. Chever, A.P. Bemelmans, J. Lübke, I. Leray, N. Rouach, Nature Communications 13 (2022).","apa":"Cheung, G. T., Bataveljic, D., Visser, J., Kumar, N., Moulard, J., Dallérac, G., … Rouach, N. (2022). Physiological synaptic activity and recognition memory require astroglial glutamine. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-28331-7\">https://doi.org/10.1038/s41467-022-28331-7</a>"},"file":[{"checksum":"51d580aff2327dd957946208a9749e1a","date_updated":"2022-02-21T07:51:33Z","file_name":"2022_NatureCommunications_Cheung.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","file_size":7910519,"relation":"main_file","file_id":"10777","creator":"dernst","date_created":"2022-02-21T07:51:33Z"}],"date_updated":"2023-08-02T14:25:01Z","date_published":"2022-02-08T00:00:00Z","date_created":"2022-02-20T23:01:30Z","month":"02","has_accepted_license":"1","article_type":"original","volume":13,"quality_controlled":"1","publisher":"Springer Nature","publication":"Nature Communications","intvolume":"        13","oa":1,"author":[{"last_name":"Cheung","first_name":"Giselle T","full_name":"Cheung, Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bataveljic, Danijela","last_name":"Bataveljic","first_name":"Danijela"},{"first_name":"Josien","last_name":"Visser","full_name":"Visser, Josien"},{"full_name":"Kumar, Naresh","first_name":"Naresh","last_name":"Kumar"},{"full_name":"Moulard, Julien","last_name":"Moulard","first_name":"Julien"},{"first_name":"Glenn","last_name":"Dallérac","full_name":"Dallérac, Glenn"},{"first_name":"Daria","last_name":"Mozheiko","full_name":"Mozheiko, Daria"},{"full_name":"Rollenhagen, Astrid","last_name":"Rollenhagen","first_name":"Astrid"},{"last_name":"Ezan","first_name":"Pascal","full_name":"Ezan, Pascal"},{"full_name":"Mongin, Cédric","first_name":"Cédric","last_name":"Mongin"},{"full_name":"Chever, Oana","last_name":"Chever","first_name":"Oana"},{"first_name":"Alexis Pierre","last_name":"Bemelmans","full_name":"Bemelmans, Alexis Pierre"},{"full_name":"Lübke, Joachim","first_name":"Joachim","last_name":"Lübke"},{"first_name":"Isabelle","last_name":"Leray","full_name":"Leray, Isabelle"},{"full_name":"Rouach, Nathalie","last_name":"Rouach","first_name":"Nathalie"}],"title":"Physiological synaptic activity and recognition memory require astroglial glutamine","article_number":"753","status":"public"},{"oa_version":"Preprint","doi":"10.1016/j.aim.2022.108236","isi":1,"year":"2022","arxiv":1,"type":"journal_article","scopus_import":"1","publication_identifier":{"issn":["0001-8708"],"eissn":["1090-2082"]},"acknowledgement":"We are grateful to Mikhail Borovoi, Zeev Rudnick and Olivier Wienberg for their interest in our\r\nwork. We would like to address our gratitude to Ulrich Derenthal for his generous support at Leibniz Universitat Hannover. We are in debt to Tim Browning for an enlightening discussion and to the anonymous referees for critical comments, which lead to overall improvements of various preliminary versions of this paper. Part of this work was carried out and reported during a visit to the University of Science and Technology of China. We thank Yongqi Liang for offering warm hospitality. The first author was supported by a Humboldt-Forschungsstipendium. The second author was supported by grant DE 1646/4-2 of the Deutsche Forschungsgemeinschaft.","article_processing_charge":"No","abstract":[{"lang":"eng","text":"We establish the Hardy-Littlewood property (à la Borovoi-Rudnick) for Zariski open subsets in affine quadrics of the form q(x1,...,xn)=m, where q is a non-degenerate integral quadratic form in  n>3 variables and m is a non-zero integer. This gives asymptotic formulas for the density of integral points taking coprime polynomial values, which is a quantitative version of the arithmetic purity of strong approximation property off infinity for affine quadrics."}],"external_id":{"arxiv":["2003.07287"],"isi":["000792517300014"]},"department":[{"_id":"TiBr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"_id":"10765","publication_status":"published","date_published":"2022-03-26T00:00:00Z","date_created":"2022-02-20T23:01:30Z","month":"03","article_type":"original","volume":398,"day":"26","citation":{"short":"Y. Cao, Z. Huang, Advances in Mathematics 398 (2022).","apa":"Cao, Y., &#38; Huang, Z. (2022). Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2022.108236\">https://doi.org/10.1016/j.aim.2022.108236</a>","ieee":"Y. Cao and Z. Huang, “Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics,” <i>Advances in Mathematics</i>, vol. 398, no. 3. Elsevier, 2022.","ista":"Cao Y, Huang Z. 2022. Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics. Advances in Mathematics. 398(3), 108236.","ama":"Cao Y, Huang Z. Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics. <i>Advances in Mathematics</i>. 2022;398(3). doi:<a href=\"https://doi.org/10.1016/j.aim.2022.108236\">10.1016/j.aim.2022.108236</a>","mla":"Cao, Yang, and Zhizhong Huang. “Arithmetic Purity of the Hardy-Littlewood Property and Geometric Sieve for Affine Quadrics.” <i>Advances in Mathematics</i>, vol. 398, no. 3, 108236, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.aim.2022.108236\">10.1016/j.aim.2022.108236</a>.","chicago":"Cao, Yang, and Zhizhong Huang. “Arithmetic Purity of the Hardy-Littlewood Property and Geometric Sieve for Affine Quadrics.” <i>Advances in Mathematics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.aim.2022.108236\">https://doi.org/10.1016/j.aim.2022.108236</a>."},"date_updated":"2023-08-02T14:24:18Z","oa":1,"author":[{"full_name":"Cao, Yang","last_name":"Cao","first_name":"Yang"},{"first_name":"Zhizhong","last_name":"Huang","full_name":"Huang, Zhizhong","id":"21f1b52f-2fd1-11eb-a347-a4cdb9b18a51"}],"title":"Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics","article_number":"108236","status":"public","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/2003.07287","open_access":"1"}],"publisher":"Elsevier","publication":"Advances in Mathematics","intvolume":"       398","issue":"3"},{"issue":"8","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"intvolume":"       119","publication":"Proceedings of the National Academy of Sciences of the United States of America","publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","status":"public","article_number":"e2122030119","title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells","author":[{"first_name":"Jana","last_name":"Slovakova","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","full_name":"Slovakova, Jana"},{"first_name":"Mateusz K","last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K"},{"first_name":"Feyza N","last_name":"Arslan","orcid":"0000-0001-5809-9566","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","full_name":"Arslan, Feyza N"},{"id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","full_name":"Caballero Mancebo, Silvia","first_name":"Silvia","orcid":"0000-0002-5223-3346","last_name":"Caballero Mancebo"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens","first_name":"Gabriel"},{"orcid":"0000-0001-9735-5315","last_name":"Kaufmann","first_name":"Walter","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jack","last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"oa":1,"related_material":{"record":[{"id":"9750","relation":"earlier_version","status":"public"}]},"date_updated":"2023-08-02T14:26:51Z","file":[{"content_type":"application/pdf","access_level":"open_access","file_id":"10780","relation":"main_file","creator":"dernst","file_size":1609678,"date_created":"2022-02-21T08:45:11Z","checksum":"d49f83c3580613966f71768ddb9a55a5","date_updated":"2022-02-21T08:45:11Z","success":1,"file_name":"2022_PNAS_Slovakova.pdf"}],"day":"14","citation":{"chicago":"Slovakova, Jana, Mateusz K Sikora, Feyza N Arslan, Silvia Caballero Mancebo, Gabriel Krens, Walter Kaufmann, Jack Merrin, and Carl-Philipp J Heisenberg. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122030119\">https://doi.org/10.1073/pnas.2122030119</a>.","mla":"Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 8, e2122030119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122030119\">10.1073/pnas.2122030119</a>.","ista":"Slovakova J, Sikora MK, Arslan FN, Caballero Mancebo S, Krens G, Kaufmann W, Merrin J, Heisenberg C-PJ. 2022. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America. 119(8), e2122030119.","ama":"Slovakova J, Sikora MK, Arslan FN, et al. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(8). doi:<a href=\"https://doi.org/10.1073/pnas.2122030119\">10.1073/pnas.2122030119</a>","ieee":"J. Slovakova <i>et al.</i>, “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 8. Proceedings of the National Academy of Sciences, 2022.","apa":"Slovakova, J., Sikora, M. K., Arslan, F. N., Caballero Mancebo, S., Krens, G., Kaufmann, W., … Heisenberg, C.-P. J. (2022). Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122030119\">https://doi.org/10.1073/pnas.2122030119</a>","short":"J. Slovakova, M.K. Sikora, F.N. Arslan, S. Caballero Mancebo, G. Krens, W. Kaufmann, J. Merrin, C.-P.J. Heisenberg, Proceedings of the National Academy of Sciences of the United States of America 119 (2022)."},"article_type":"original","volume":119,"has_accepted_license":"1","month":"02","date_published":"2022-02-14T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_created":"2022-02-20T23:01:31Z","ddc":["570"],"publication_status":"published","_id":"10766","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}],"external_id":{"isi":["000766926900009"]},"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"name":"Modulation of adhesion function in cell-cell contact formation by cortical tension","grant_number":"187-2013","_id":"2521E28E-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"abstract":[{"text":"Tension of the actomyosin cell cortex plays a key role in determining cell–cell contact growth and size. The level of cortical tension outside of the cell–cell contact, when pulling at the contact edge, scales with the total size to which a cell–cell contact can grow [J.-L. Maître et al., Science 338, 253–256 (2012)]. Here, we show in zebrafish primary germ-layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell–cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. After tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell–cell contact size is limited by tension-stabilizing E-cadherin–actin complexes at the contact.","lang":"eng"}],"acknowledgement":"We thank Guillaume Salbreaux, Silvia Grigolon, Edouard Hannezo, and Vanessa Barone for discussions and comments on the manuscript and Shayan Shamipour and Daniel Capek for help with data analysis. We also thank the Imaging & Optics, Electron Microscopy, and Zebrafish Facility Scientific Service Units at the Institute of Science and Technology Austria (ISTA)Nasser Darwish-Miranda  for continuous support. We acknowledge Hitoshi Morita for the gift of VinculinB-GFP plasmid. This research was supported by an ISTA Fellow Marie-Curie Co-funding of regional, national, and international programmes Grant P_IST_EU01 (to J.S.), European Molecular Biology Organization Long-Term Fellowship Grant, ALTF reference number: 187-2013 (to M.S.), Schroedinger Fellowship J4332-B28 (to M.S.), and European Research Council Advanced Grant (MECSPEC; to C.-P.H.).","article_processing_charge":"No","publication_identifier":{"eissn":["10916490"]},"file_date_updated":"2022-02-21T08:45:11Z","scopus_import":"1","year":"2022","type":"journal_article","isi":1,"doi":"10.1073/pnas.2122030119","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"oa_version":"Published Version"},{"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1098/rspb.2021.1985","oa_version":"Published Version","pmid":1,"scopus_import":"1","isi":1,"type":"journal_article","year":"2022","abstract":[{"text":"The t-haplotype of mice is a classical model for autosomal transmission distortion. A largely non-recombining variant of the proximal region of chromosome 17, it is transmitted to more than 90% of the progeny of heterozygous males through the disabling of sperm carrying a standard chromosome. While extensive genetic and functional work has shed light on individual genes involved in drive, much less is known about the evolution and function of the rest of its hundreds of genes. Here, we characterize the sequence and expression of dozens of t-specific transcripts and of their chromosome 17 homologues. Many genes showed reduced expression of the t-allele, but an equal number of genes showed increased expression of their t-copy, consistent with increased activity or a newly evolved function. Genes on the t-haplotype had a significantly higher non-synonymous substitution rate than their homologues on the standard chromosome, with several genes harbouring dN/dS ratios above 1. Finally, the t-haplotype has acquired at least two genes from other chromosomes, which show high and tissue-specific expression. These results provide a first overview of the gene content of this selfish element, and support a more dynamic evolutionary scenario than expected of a large genomic region with almost no recombination.","lang":"eng"}],"ec_funded":1,"publication_identifier":{"eissn":["14712954"]},"file_date_updated":"2022-02-21T08:17:38Z","article_processing_charge":"No","acknowledgement":"This project has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 715257) and from the Swiss National Science Foundation (grant no. 310030_189145).\r\nWe thank Jari Garbely of the Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland, for conducting the PCR verification. Barbara\r\nKonig, Gabi Stichel and A.K.L. collected mouse tissue samples, from the field study led by R.K.K. ","publication_status":"published","ddc":["570"],"_id":"10767","language":[{"iso":"eng"}],"external_id":{"pmid":["35135349"],"isi":["000752812800012"]},"project":[{"call_identifier":"H2020","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"BeVi"}],"has_accepted_license":"1","article_type":"original","volume":289,"date_created":"2022-02-20T23:01:31Z","date_published":"2022-02-09T00:00:00Z","month":"02","file":[{"content_type":"application/pdf","access_level":"open_access","file_size":2366976,"creator":"dernst","relation":"main_file","file_id":"10779","date_created":"2022-02-21T08:17:38Z","checksum":"27042a3706ae52a919fed1ac114bf7bb","date_updated":"2022-02-21T08:17:38Z","success":1,"file_name":"2022_ProceedingsRoyalSocB_Kelemen.pdf"}],"citation":{"ieee":"R. K. Kelemen, M. N. Elkrewi, A. K. Lindholm, and B. Vicoso, “Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome,” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 289, no. 1968. The Royal Society, p. 20211985, 2022.","apa":"Kelemen, R. K., Elkrewi, M. N., Lindholm, A. K., &#38; Vicoso, B. (2022). Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2021.1985\">https://doi.org/10.1098/rspb.2021.1985</a>","short":"R.K. Kelemen, M.N. Elkrewi, A.K. Lindholm, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 289 (2022) 20211985.","chicago":"Kelemen, Réka K, Marwan N Elkrewi, Anna K. Lindholm, and Beatriz Vicoso. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society, 2022. <a href=\"https://doi.org/10.1098/rspb.2021.1985\">https://doi.org/10.1098/rspb.2021.1985</a>.","mla":"Kelemen, Réka K., et al. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 289, no. 1968, The Royal Society, 2022, p. 20211985, doi:<a href=\"https://doi.org/10.1098/rspb.2021.1985\">10.1098/rspb.2021.1985</a>.","ama":"Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. <i>Proceedings of the Royal Society B: Biological Sciences</i>. 2022;289(1968):20211985. doi:<a href=\"https://doi.org/10.1098/rspb.2021.1985\">10.1098/rspb.2021.1985</a>","ista":"Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. 2022. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. Proceedings of the Royal Society B: Biological Sciences. 289(1968), 20211985."},"day":"09","date_updated":"2023-08-02T14:26:07Z","title":"Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome","status":"public","oa":1,"author":[{"first_name":"Réka K","last_name":"Kelemen","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","full_name":"Kelemen, Réka K"},{"first_name":"Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"first_name":"Anna K.","last_name":"Lindholm","full_name":"Lindholm, Anna K."},{"first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"issue":"1968","publisher":"The Royal Society","quality_controlled":"1","page":"20211985","intvolume":"       289","publication":"Proceedings of the Royal Society B: Biological Sciences"},{"date_updated":"2023-08-02T14:29:12Z","file":[{"checksum":"f1ee02b6fb4200934eeb31fa69120885","file_name":"2022_CurrentOpPlantBiology_Hajny.pdf","success":1,"date_updated":"2022-03-10T13:34:09Z","access_level":"open_access","content_type":"application/pdf","date_created":"2022-03-10T13:34:09Z","file_size":820322,"file_id":"10844","creator":"dernst","relation":"main_file"}],"citation":{"chicago":"Hajny, Jakub, Shutang Tan, and Jiří Friml. “Auxin Canalization: From Speculative Models toward Molecular Players.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.pbi.2022.102174\">https://doi.org/10.1016/j.pbi.2022.102174</a>.","ista":"Hajny J, Tan S, Friml J. 2022. Auxin canalization: From speculative models toward molecular players. Current Opinion in Plant Biology. 65(2), 102174.","ama":"Hajny J, Tan S, Friml J. Auxin canalization: From speculative models toward molecular players. <i>Current Opinion in Plant Biology</i>. 2022;65(2). doi:<a href=\"https://doi.org/10.1016/j.pbi.2022.102174\">10.1016/j.pbi.2022.102174</a>","mla":"Hajny, Jakub, et al. “Auxin Canalization: From Speculative Models toward Molecular Players.” <i>Current Opinion in Plant Biology</i>, vol. 65, no. 2, 102174, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.pbi.2022.102174\">10.1016/j.pbi.2022.102174</a>.","short":"J. Hajny, S. Tan, J. Friml, Current Opinion in Plant Biology 65 (2022).","apa":"Hajny, J., Tan, S., &#38; Friml, J. (2022). Auxin canalization: From speculative models toward molecular players. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2022.102174\">https://doi.org/10.1016/j.pbi.2022.102174</a>","ieee":"J. Hajny, S. Tan, and J. Friml, “Auxin canalization: From speculative models toward molecular players,” <i>Current Opinion in Plant Biology</i>, vol. 65, no. 2. Elsevier, 2022."},"day":"01","volume":65,"article_type":"original","has_accepted_license":"1","month":"02","date_created":"2022-02-20T23:01:32Z","date_published":"2022-02-01T00:00:00Z","issue":"2","intvolume":"        65","publication":"Current Opinion in Plant Biology","publisher":"Elsevier","quality_controlled":"1","status":"public","article_number":"102174","title":"Auxin canalization: From speculative models toward molecular players","author":[{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub","first_name":"Jakub","last_name":"Hajny","orcid":"0000-0003-2140-7195"},{"orcid":"0000-0002-0471-8285","last_name":"Tan","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"oa":1,"scopus_import":"1","isi":1,"year":"2022","type":"journal_article","doi":"10.1016/j.pbi.2022.102174","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pmid":1,"oa_version":"Published Version","publication_status":"published","ddc":["580"],"language":[{"iso":"eng"}],"_id":"10768","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JiFr"}],"external_id":{"isi":["000758724700004"],"pmid":["35123880"]},"abstract":[{"lang":"eng","text":"Among the most fascinated properties of the plant hormone auxin is its ability to promote formation of its own directional transport routes. These gradually narrowing auxin channels form from the auxin source toward the sink and involve coordinated, collective polarization of individual cells. Once established, the channels provide positional information, along which new vascular strands form, for example, during organogenesis, regeneration, or leave venation. The main prerequisite of this still mysterious auxin canalization mechanism is a feedback between auxin signaling and its directional transport. This is manifested by auxin-induced re-arrangements of polar, subcellular localization of PIN-FORMED (PIN) auxin exporters. Immanent open questions relate to how position of auxin source and sink as well as tissue context are sensed and translated into tissue polarization and how cells communicate to polarize coordinately. Recently, identification of the first molecular players opens new avenues into molecular studies of this intriguing example of self-organizing plant development."}],"acknowledgement":"The authors apologize to those researchers whose work was not cited. In addition, exciting topics such as PIN polarization in context of phyllotaxis, shoot branching and termination of gravitropic bending, or role of additional auxin transporters could not have been included owing to lack of space. This work was supported by the Czech Science Foundation GAČR (GA18-26981S). The authors also acknowledge the EMBO for supporting J.H. with a long-term fellowship (ALTF217-2021).","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"issn":["1369-5266"]},"file_date_updated":"2022-03-10T13:34:09Z"},{"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.31527/analesafa.2021.32.4.93","oa_version":"Published Version","year":"2022","type":"journal_article","scopus_import":"1","abstract":[{"text":"studiamos aspectos de Teoría Cuántica de Campos a densidad finita usando técnicas y conceptos de información cuántica. Nos enfocamos en fermiones de Dirac masivos con potencial químico en 1+1 dimensiones espacio-temporales. Usando la entropía de entrelazamiento en un intervalo, construimos la función c entrópica que es finita. Esta función c no es monótona, e incorpora el entrelazamiento de largo alcance proveniente de la superficie de Fermi. Motivados por trabajos previos de modelos en la red, calculamos numéricamente las entropías de Renyi y encontramos oscilaciones de Friedel. Seguidamente, analizamos la información mutua como una medida de correlación entre diferentes regiones. Usando una expansión de distancia grande desarrollada por Cardy, argumentamos que la información mutua detecta las correlaciones inducidas por la superficie de Fermi todavía al orden dominante en la expansión. Finalmente, analizamos la entropía relativa y sus generalizaciones de Renyi para distinguir estados con diferente carga. Encontramos que estados en diferentes sectores de superselección dan origen a un comportamiento super-extensivo en la entropía relativa.","lang":"eng"}],"file_date_updated":"2022-02-21T09:32:44Z","publication_identifier":{"eissn":["18501168"]},"acknowledgement":"Se agradece a Horacio Casini por distintas discusiones y comentarios a lo largo del trabajo. LD cuenta con el apoyo de CNEA y UNCuyo, Inst. GT cuenta con el apoyo de CONICET,\r\nANPCyT, CNEA, y UNCuyo, Inst. Balseiro. RM cuenta con el apoyo de IST Austria. MS cuenta con el apoyode CONICET y UNCuyo, Inst. Balseiro. También se agradece a la Asociación Argentina de Física por la posibilidad de presentar este artículo en el marco de una Mención Especial por el Premio Luis Másperi 2020.","article_processing_charge":"No","_id":"10769","language":[{"iso":"spa"}],"publication_status":"published","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MaSe"}],"has_accepted_license":"1","article_type":"original","volume":32,"date_published":"2022-01-13T00:00:00Z","date_created":"2022-02-20T23:01:32Z","month":"01","citation":{"chicago":"Daguerre, L., G. Torroba, Raimel A Medina Ramos, and M. Solís. “Non relativistic quantum field theory: Dynamics and irreversibility.” <i>Anales de la Asociacion Fisica Argentina</i>. Asociación Física Argentina, 2022. <a href=\"https://doi.org/10.31527/analesafa.2021.32.4.93\">https://doi.org/10.31527/analesafa.2021.32.4.93</a>.","mla":"Daguerre, L., et al. “Non relativistic quantum field theory: Dynamics and irreversibility.” <i>Anales de la Asociacion Fisica Argentina</i>, vol. 32, no. 4, Asociación Física Argentina, 2022, pp. 93–98, doi:<a href=\"https://doi.org/10.31527/analesafa.2021.32.4.93\">10.31527/analesafa.2021.32.4.93</a>.","ista":"Daguerre L, Torroba G, Medina Ramos RA, Solís M. 2022. Non relativistic quantum field theory: Dynamics and irreversibility. Anales de la Asociacion Fisica Argentina. 32(4), 93–98.","ama":"Daguerre L, Torroba G, Medina Ramos RA, Solís M. Non relativistic quantum field theory: Dynamics and irreversibility. <i>Anales de la Asociacion Fisica Argentina</i>. 2022;32(4):93-98. doi:<a href=\"https://doi.org/10.31527/analesafa.2021.32.4.93\">10.31527/analesafa.2021.32.4.93</a>","ieee":"L. Daguerre, G. Torroba, R. A. Medina Ramos, and M. Solís, “Non relativistic quantum field theory: Dynamics and irreversibility,” <i>Anales de la Asociacion Fisica Argentina</i>, vol. 32, no. 4. Asociación Física Argentina, pp. 93–98, 2022.","short":"L. Daguerre, G. Torroba, R.A. Medina Ramos, M. Solís, Anales de la Asociacion Fisica Argentina 32 (2022) 93–98.","apa":"Daguerre, L., Torroba, G., Medina Ramos, R. A., &#38; Solís, M. (2022). Non relativistic quantum field theory: Dynamics and irreversibility. <i>Anales de la Asociacion Fisica Argentina</i>. Asociación Física Argentina. <a href=\"https://doi.org/10.31527/analesafa.2021.32.4.93\">https://doi.org/10.31527/analesafa.2021.32.4.93</a>"},"day":"13","file":[{"date_updated":"2022-02-21T09:32:44Z","success":1,"file_name":"2022_AnalesAFA_Daguerre.pdf","checksum":"ca66a3017205677c5b4d22b3bb74fb0b","file_id":"10782","relation":"main_file","creator":"dernst","file_size":4505751,"date_created":"2022-02-21T09:32:44Z","content_type":"application/pdf","access_level":"open_access"}],"date_updated":"2022-02-21T09:36:01Z","title":"Non relativistic quantum field theory: Dynamics and irreversibility","status":"public","oa":1,"author":[{"full_name":"Daguerre, L.","first_name":"L.","last_name":"Daguerre"},{"full_name":"Torroba, G.","last_name":"Torroba","first_name":"G."},{"id":"CE680B90-D85A-11E9-B684-C920E6697425","full_name":"Medina Ramos, Raimel A","first_name":"Raimel A","last_name":"Medina Ramos"},{"full_name":"Solís, M.","last_name":"Solís","first_name":"M."}],"issue":"4","quality_controlled":"1","page":"93-98","publisher":"Asociación Física Argentina","publication":"Anales de la Asociacion Fisica Argentina","intvolume":"        32"},{"status":"public","article_number":"2106629","title":"Theory of chirality induced spin selectivity: Progress and challenges","author":[{"full_name":"Evers, Ferdinand","first_name":"Ferdinand","last_name":"Evers"},{"full_name":"Aharony, Amnon","last_name":"Aharony","first_name":"Amnon"},{"full_name":"Bar-Gill, Nir","first_name":"Nir","last_name":"Bar-Gill"},{"first_name":"Ora","last_name":"Entin-Wohlman","full_name":"Entin-Wohlman, Ora"},{"last_name":"Hedegård","first_name":"Per","full_name":"Hedegård, Per"},{"full_name":"Hod, Oded","last_name":"Hod","first_name":"Oded"},{"first_name":"Pavel","last_name":"Jelinek","full_name":"Jelinek, Pavel"},{"full_name":"Kamieniarz, Grzegorz","first_name":"Grzegorz","last_name":"Kamieniarz"},{"orcid":"0000-0002-6990-7802","last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Michaeli, Karen","first_name":"Karen","last_name":"Michaeli"},{"full_name":"Mujica, Vladimiro","first_name":"Vladimiro","last_name":"Mujica"},{"first_name":"Ron","last_name":"Naaman","full_name":"Naaman, Ron"},{"full_name":"Paltiel, Yossi","first_name":"Yossi","last_name":"Paltiel"},{"first_name":"Sivan","last_name":"Refaely-Abramson","full_name":"Refaely-Abramson, Sivan"},{"full_name":"Tal, Oren","first_name":"Oren","last_name":"Tal"},{"last_name":"Thijssen","first_name":"Jos","full_name":"Thijssen, Jos"},{"first_name":"Michael","last_name":"Thoss","full_name":"Thoss, Michael"},{"first_name":"Jan M.","last_name":"Van Ruitenbeek","full_name":"Van Ruitenbeek, Jan M."},{"last_name":"Venkataraman","first_name":"Latha","full_name":"Venkataraman, Latha"},{"full_name":"Waldeck, David H.","first_name":"David H.","last_name":"Waldeck"},{"last_name":"Yan","first_name":"Binghai","full_name":"Yan, Binghai"},{"first_name":"Leeor","last_name":"Kronik","full_name":"Kronik, Leeor"}],"oa":1,"issue":"13","intvolume":"        34","publication":"Advanced Materials","publisher":"Wiley","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2108.09998"}],"article_type":"review","volume":34,"month":"04","date_published":"2022-04-01T00:00:00Z","date_created":"2022-02-20T23:01:33Z","date_updated":"2023-08-02T14:30:22Z","citation":{"chicago":"Evers, Ferdinand, Amnon Aharony, Nir Bar-Gill, Ora Entin-Wohlman, Per Hedegård, Oded Hod, Pavel Jelinek, et al. “Theory of Chirality Induced Spin Selectivity: Progress and Challenges.” <i>Advanced Materials</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/adma.202106629\">https://doi.org/10.1002/adma.202106629</a>.","mla":"Evers, Ferdinand, et al. “Theory of Chirality Induced Spin Selectivity: Progress and Challenges.” <i>Advanced Materials</i>, vol. 34, no. 13, 2106629, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/adma.202106629\">10.1002/adma.202106629</a>.","ista":"Evers F, Aharony A, Bar-Gill N, Entin-Wohlman O, Hedegård P, Hod O, Jelinek P, Kamieniarz G, Lemeshko M, Michaeli K, Mujica V, Naaman R, Paltiel Y, Refaely-Abramson S, Tal O, Thijssen J, Thoss M, Van Ruitenbeek JM, Venkataraman L, Waldeck DH, Yan B, Kronik L. 2022. Theory of chirality induced spin selectivity: Progress and challenges. Advanced Materials. 34(13), 2106629.","ama":"Evers F, Aharony A, Bar-Gill N, et al. Theory of chirality induced spin selectivity: Progress and challenges. <i>Advanced Materials</i>. 2022;34(13). doi:<a href=\"https://doi.org/10.1002/adma.202106629\">10.1002/adma.202106629</a>","ieee":"F. Evers <i>et al.</i>, “Theory of chirality induced spin selectivity: Progress and challenges,” <i>Advanced Materials</i>, vol. 34, no. 13. Wiley, 2022.","short":"F. Evers, A. Aharony, N. Bar-Gill, O. Entin-Wohlman, P. Hedegård, O. Hod, P. Jelinek, G. Kamieniarz, M. Lemeshko, K. Michaeli, V. Mujica, R. Naaman, Y. Paltiel, S. Refaely-Abramson, O. Tal, J. Thijssen, M. Thoss, J.M. Van Ruitenbeek, L. Venkataraman, D.H. Waldeck, B. Yan, L. Kronik, Advanced Materials 34 (2022).","apa":"Evers, F., Aharony, A., Bar-Gill, N., Entin-Wohlman, O., Hedegård, P., Hod, O., … Kronik, L. (2022). Theory of chirality induced spin selectivity: Progress and challenges. <i>Advanced Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adma.202106629\">https://doi.org/10.1002/adma.202106629</a>"},"day":"01","abstract":[{"lang":"eng","text":"A critical overview of the theory of the chirality-induced spin selectivity (CISS) effect, that is, phenomena in which the chirality of molecular species imparts significant spin selectivity to various electron processes, is provided. Based on discussions in a recently held workshop, and further work published since, the status of CISS effects—in electron transmission, electron transport, and chemical reactions—is reviewed. For each, a detailed discussion of the state-of-the-art in theoretical understanding is provided and remaining challenges and research opportunities are identified."}],"article_processing_charge":"No","publication_identifier":{"issn":["09359648"],"eissn":["15214095"]},"publication_status":"published","_id":"10771","language":[{"iso":"eng"}],"department":[{"_id":"MiLe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["2108.09998"],"isi":["000753795900001"]},"doi":"10.1002/adma.202106629","oa_version":"Preprint","scopus_import":"1","type":"journal_article","isi":1,"year":"2022","arxiv":1},{"scopus_import":"1","year":"2022","type":"journal_article","arxiv":1,"isi":1,"oa_version":"Published Version","doi":"10.1112/jlms.12515","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"TaHa"}],"external_id":{"arxiv":["1712.10260"],"isi":["000751600600001"]},"publication_status":"published","ddc":["510"],"_id":"10772","language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)","acknowledgement":"This paper is based on my PhD thesis, which would not be possible without the support of my advisor Bernd Siebert. I also thank Dan Abramovich, Mohammed Abouzaid, Mark Gross, Tom Coates and Dimitri Zvonkine for many useful conversations. Finally, I thank the anonymous referees for their many insightful comments and valuable suggestions which have resulted in major improvements to this article. This project has received funding from the EuropeanResearch Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement Number: 682603), and from Fondation Mathématique Jacques Hadamard. ","publication_identifier":{"issn":["0024-6107"],"eissn":["1469-7750"]},"file_date_updated":"2022-02-21T11:22:58Z","abstract":[{"text":"We introduce tropical corals, balanced trees in a half-space, and show that they correspond to holomorphic polygons capturing the product rule in Lagrangian Floer theory for the elliptic curve. We then prove a correspondence theorem equating counts of tropical corals to punctured log Gromov–Witten invariants of the Tate curve. This implies that the homogeneous coordinate ring of the mirror to the Tate curve is isomorphic to the degree-zero part of symplectic cohomology, confirming a prediction of homological mirror symmetry.","lang":"eng"}],"date_updated":"2023-08-02T14:29:50Z","file":[{"file_name":"2022_JournLondonMathSociety_Arguez.pdf","success":1,"date_updated":"2022-02-21T11:22:58Z","checksum":"8bd0fd9694be894a191857ddf27678f0","date_created":"2022-02-21T11:22:58Z","file_id":"10783","creator":"dernst","relation":"main_file","file_size":936873,"access_level":"open_access","content_type":"application/pdf"}],"citation":{"ieee":"N. H. Arguez, “Mirror symmetry for the Tate curve via tropical and log corals,” <i>Journal of the London Mathematical Society</i>, vol. 105, no. 1. London Mathematical Society, pp. 343–411, 2022.","short":"N.H. Arguez, Journal of the London Mathematical Society 105 (2022) 343–411.","apa":"Arguez, N. H. (2022). Mirror symmetry for the Tate curve via tropical and log corals. <i>Journal of the London Mathematical Society</i>. London Mathematical Society. <a href=\"https://doi.org/10.1112/jlms.12515\">https://doi.org/10.1112/jlms.12515</a>","mla":"Arguez, Nuroemuer Huelya. “Mirror Symmetry for the Tate Curve via Tropical and Log Corals.” <i>Journal of the London Mathematical Society</i>, vol. 105, no. 1, London Mathematical Society, 2022, pp. 343–411, doi:<a href=\"https://doi.org/10.1112/jlms.12515\">10.1112/jlms.12515</a>.","ama":"Arguez NH. Mirror symmetry for the Tate curve via tropical and log corals. <i>Journal of the London Mathematical Society</i>. 2022;105(1):343-411. doi:<a href=\"https://doi.org/10.1112/jlms.12515\">10.1112/jlms.12515</a>","ista":"Arguez NH. 2022. Mirror symmetry for the Tate curve via tropical and log corals. Journal of the London Mathematical Society. 105(1), 343–411.","chicago":"Arguez, Nuroemuer Huelya. “Mirror Symmetry for the Tate Curve via Tropical and Log Corals.” <i>Journal of the London Mathematical Society</i>. London Mathematical Society, 2022. <a href=\"https://doi.org/10.1112/jlms.12515\">https://doi.org/10.1112/jlms.12515</a>."},"day":"05","month":"02","date_created":"2022-02-20T23:01:33Z","date_published":"2022-02-05T00:00:00Z","volume":105,"article_type":"original","has_accepted_license":"1","intvolume":"       105","publication":"Journal of the London Mathematical Society","publisher":"London Mathematical Society","quality_controlled":"1","page":"343-411","issue":"1","author":[{"last_name":"Arguez","first_name":"Nuroemuer Huelya","full_name":"Arguez, Nuroemuer Huelya","id":"3c26b22e-c843-11eb-aa56-d38ffa0bdd08"}],"oa":1,"status":"public","title":"Mirror symmetry for the Tate curve via tropical and log corals"},{"scopus_import":"1","year":"2022","type":"journal_article","isi":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1007/s00454-022-00371-2","oa_version":"Published Version","publication_status":"published","ddc":["510"],"_id":"10773","language":[{"iso":"eng"}],"external_id":{"isi":["000752175300002"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"HeEd"}],"abstract":[{"lang":"eng","text":"The Voronoi tessellation in Rd is defined by locally minimizing the power distance to given weighted points. Symmetrically, the Delaunay mosaic can be defined by locally maximizing the negative power distance to other such points. We prove that the average of the two piecewise quadratic functions is piecewise linear, and that all three functions have the same critical points and values. Discretizing the two piecewise quadratic functions, we get the alpha shapes as sublevel sets of the discrete function on the Delaunay mosaic, and analogous shapes as superlevel sets of the discrete function on the Voronoi tessellation. For the same non-critical value, the corresponding shapes are disjoint, separated by a narrow channel that contains no critical points but the entire level set of the piecewise linear function."}],"publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"file_date_updated":"2022-08-02T06:07:55Z","acknowledgement":"Open access funding provided by the Institute of Science and Technology (IST Austria).","article_processing_charge":"Yes (via OA deal)","file":[{"date_updated":"2022-08-02T06:07:55Z","success":1,"file_name":"2022_DiscreteCompGeometry_Biswas.pdf","checksum":"9383d3b70561bacee905e335dc922680","relation":"main_file","creator":"dernst","file_id":"11718","file_size":2518111,"date_created":"2022-08-02T06:07:55Z","content_type":"application/pdf","access_level":"open_access"}],"citation":{"ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Continuous and discrete radius functions on Voronoi tessellations and Delaunay mosaics,” <i>Discrete and Computational Geometry</i>, vol. 67. Springer Nature, pp. 811–842, 2022.","apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (2022). Continuous and discrete radius functions on Voronoi tessellations and Delaunay mosaics. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-022-00371-2\">https://doi.org/10.1007/s00454-022-00371-2</a>","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Discrete and Computational Geometry 67 (2022) 811–842.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “Continuous and Discrete Radius Functions on Voronoi Tessellations and Delaunay Mosaics.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00454-022-00371-2\">https://doi.org/10.1007/s00454-022-00371-2</a>.","mla":"Biswas, Ranita, et al. “Continuous and Discrete Radius Functions on Voronoi Tessellations and Delaunay Mosaics.” <i>Discrete and Computational Geometry</i>, vol. 67, Springer Nature, 2022, pp. 811–42, doi:<a href=\"https://doi.org/10.1007/s00454-022-00371-2\">10.1007/s00454-022-00371-2</a>.","ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. 2022. Continuous and discrete radius functions on Voronoi tessellations and Delaunay mosaics. Discrete and Computational Geometry. 67, 811–842.","ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Continuous and discrete radius functions on Voronoi tessellations and Delaunay mosaics. <i>Discrete and Computational Geometry</i>. 2022;67:811-842. doi:<a href=\"https://doi.org/10.1007/s00454-022-00371-2\">10.1007/s00454-022-00371-2</a>"},"day":"01","date_updated":"2023-08-02T14:31:25Z","has_accepted_license":"1","volume":67,"article_type":"original","date_published":"2022-04-01T00:00:00Z","date_created":"2022-02-20T23:01:34Z","month":"04","publisher":"Springer Nature","quality_controlled":"1","page":"811-842","intvolume":"        67","publication":"Discrete and Computational Geometry","title":"Continuous and discrete radius functions on Voronoi tessellations and Delaunay mosaics","status":"public","oa":1,"author":[{"full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","last_name":"Biswas","orcid":"0000-0002-5372-7890","first_name":"Ranita"},{"id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","full_name":"Cultrera Di Montesano, Sebastiano","first_name":"Sebastiano","last_name":"Cultrera Di Montesano","orcid":"0000-0001-6249-0832"},{"first_name":"Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"full_name":"Saghafian, Morteza","last_name":"Saghafian","first_name":"Morteza"}]},{"author":[{"last_name":"Bartocci","first_name":"Ezio","full_name":"Bartocci, Ezio"},{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","full_name":"Ferrere, Thomas","last_name":"Ferrere","orcid":"0000-0001-5199-3143","first_name":"Thomas"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A"},{"first_name":"Dejan","last_name":"Nickovic","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","full_name":"Nickovic, Dejan"},{"full_name":"Da Costa, Ana Oliveira","last_name":"Da Costa","first_name":"Ana Oliveira"}],"oa":1,"status":"public","title":"Flavors of sequential information flow","intvolume":"     13182","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","publisher":"Springer Nature","page":"1-19","quality_controlled":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2105.02013","open_access":"1"}],"month":"01","date_published":"2022-01-14T00:00:00Z","date_created":"2022-02-20T23:01:34Z","volume":13182,"date_updated":"2022-08-05T09:02:56Z","citation":{"short":"E. Bartocci, T. Ferrere, T.A. Henzinger, D. Nickovic, A.O. Da Costa, in:, Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer Nature, 2022, pp. 1–19.","apa":"Bartocci, E., Ferrere, T., Henzinger, T. A., Nickovic, D., &#38; Da Costa, A. O. (2022). Flavors of sequential information flow. In <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 13182, pp. 1–19). Philadelphia, PA, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-94583-1_1\">https://doi.org/10.1007/978-3-030-94583-1_1</a>","ieee":"E. Bartocci, T. Ferrere, T. A. Henzinger, D. Nickovic, and A. O. Da Costa, “Flavors of sequential information flow,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Philadelphia, PA, United States, 2022, vol. 13182, pp. 1–19.","ama":"Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. Flavors of sequential information flow. In: <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 13182. Springer Nature; 2022:1-19. doi:<a href=\"https://doi.org/10.1007/978-3-030-94583-1_1\">10.1007/978-3-030-94583-1_1</a>","ista":"Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. 2022. Flavors of sequential information flow. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 13182, 1–19.","mla":"Bartocci, Ezio, et al. “Flavors of Sequential Information Flow.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, vol. 13182, Springer Nature, 2022, pp. 1–19, doi:<a href=\"https://doi.org/10.1007/978-3-030-94583-1_1\">10.1007/978-3-030-94583-1_1</a>.","chicago":"Bartocci, Ezio, Thomas Ferrere, Thomas A Henzinger, Dejan Nickovic, and Ana Oliveira Da Costa. “Flavors of Sequential Information Flow.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, 13182:1–19. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-94583-1_1\">https://doi.org/10.1007/978-3-030-94583-1_1</a>."},"day":"14","conference":{"end_date":"2022-01-18","location":"Philadelphia, PA, United States","start_date":"2022-01-16","name":"VMCAI: Verifcation, Model Checking, and Abstract Interpretation"},"acknowledgement":"This work was funded in part by the Wittgenstein Award Z211-N23 of the Austrian Science Fund (FWF) and by the FWF project W1255-N23.","alternative_title":["LNCS"],"article_processing_charge":"No","publication_identifier":{"isbn":["9783030945824"],"eissn":["16113349"],"issn":["03029743"]},"abstract":[{"text":"We study the problem of specifying sequential information-flow properties of systems. Information-flow properties are hyperproperties, as they compare different traces of a system. Sequential information-flow properties can express changes, over time, in the information-flow constraints. For example, information-flow constraints during an initialization phase of a system may be different from information-flow constraints that are required during the operation phase. We formalize several variants of interpreting sequential information-flow constraints, which arise from different assumptions about what can be observed of the system. For this purpose, we introduce a first-order logic, called Hypertrace Logic, with both trace and time quantifiers for specifying linear-time hyperproperties. We prove that HyperLTL, which corresponds to a fragment of Hypertrace Logic with restricted quantifier prefixes, cannot specify the majority of the studied variants of sequential information flow, including all variants in which the transition between sequential phases (such as initialization and operation) happens asynchronously. Our results rely on new equivalences between sets of traces that cannot be distinguished by certain classes of formulas from Hypertrace Logic. This presents a new approach to proving inexpressiveness results for HyperLTL.","lang":"eng"}],"department":[{"_id":"ToHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2105.02013"]},"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"publication_status":"published","language":[{"iso":"eng"}],"_id":"10774","oa_version":"Preprint","doi":"10.1007/978-3-030-94583-1_1","scopus_import":"1","arxiv":1,"year":"2022","type":"conference"},{"external_id":{"isi":["000799622500022"],"arxiv":["2012.10584"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MaKw"}],"publication_status":"published","language":[{"iso":"eng"}],"_id":"10775","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"article_processing_charge":"No","acknowledgement":"Research supported by NSF Award DMS-1953990.","abstract":[{"text":"List-decodability of Reed–Solomon codes has received a lot of attention, but the best-possible dependence between the parameters is still not well-understood. In this work, we focus on the case where the list-decoding radius is of the form r = 1-ε for ε tending to zero. Our main result states that there exist Reed–Solomon codes with rate Ω(ε) which are (1 - ε, O(1/ε))-list-decodable, meaning that any Hamming ball of radius 1-ε contains at most O(1/ε) codewords. This trade-off between rate and list-decoding radius is best-possible for any code with list size less than exponential in the block length. By achieving this trade-off between rate and list-decoding radius we improve a recent result of Guo, Li, Shangguan, Tamo, and Wootters, and resolve the main motivating question of their work. Moreover, while their result requires the field to be exponentially large in the block length, we only need the field size to be polynomially large (and in fact, almost-linear suffices). We deduce our main result from a more general theorem, in which we prove good list-decodability properties of random puncturings of any given code with very large distance.","lang":"eng"}],"scopus_import":"1","type":"journal_article","year":"2022","isi":1,"arxiv":1,"oa_version":"Preprint","doi":"10.1109/TIT.2022.3148779","publisher":"IEEE","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2012.10584"}],"quality_controlled":"1","page":"3823-3828","intvolume":"        68","publication":"IEEE Transactions on Information Theory","issue":"6","oa":1,"author":[{"last_name":"Ferber","first_name":"Asaf","full_name":"Ferber, Asaf"},{"id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan","first_name":"Matthew Alan","last_name":"Kwan","orcid":"0000-0002-4003-7567"},{"last_name":"Sauermann","first_name":"Lisa","full_name":"Sauermann, Lisa"}],"title":"List-decodability with large radius for Reed-Solomon codes","status":"public","citation":{"ama":"Ferber A, Kwan MA, Sauermann L. List-decodability with large radius for Reed-Solomon codes. <i>IEEE Transactions on Information Theory</i>. 2022;68(6):3823-3828. doi:<a href=\"https://doi.org/10.1109/TIT.2022.3148779\">10.1109/TIT.2022.3148779</a>","ista":"Ferber A, Kwan MA, Sauermann L. 2022. List-decodability with large radius for Reed-Solomon codes. IEEE Transactions on Information Theory. 68(6), 3823–3828.","mla":"Ferber, Asaf, et al. “List-Decodability with Large Radius for Reed-Solomon Codes.” <i>IEEE Transactions on Information Theory</i>, vol. 68, no. 6, IEEE, 2022, pp. 3823–28, doi:<a href=\"https://doi.org/10.1109/TIT.2022.3148779\">10.1109/TIT.2022.3148779</a>.","chicago":"Ferber, Asaf, Matthew Alan Kwan, and Lisa Sauermann. “List-Decodability with Large Radius for Reed-Solomon Codes.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2022. <a href=\"https://doi.org/10.1109/TIT.2022.3148779\">https://doi.org/10.1109/TIT.2022.3148779</a>.","short":"A. Ferber, M.A. Kwan, L. Sauermann, IEEE Transactions on Information Theory 68 (2022) 3823–3828.","apa":"Ferber, A., Kwan, M. A., &#38; Sauermann, L. (2022). List-decodability with large radius for Reed-Solomon codes. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/TIT.2022.3148779\">https://doi.org/10.1109/TIT.2022.3148779</a>","ieee":"A. Ferber, M. A. Kwan, and L. Sauermann, “List-decodability with large radius for Reed-Solomon codes,” <i>IEEE Transactions on Information Theory</i>, vol. 68, no. 6. IEEE, pp. 3823–3828, 2022."},"day":"01","date_updated":"2023-08-03T06:57:01Z","related_material":{"record":[{"status":"public","id":"11145","relation":"earlier_version"}]},"date_published":"2022-06-01T00:00:00Z","date_created":"2022-02-20T23:01:34Z","month":"06","volume":68,"article_type":"original"},{"abstract":[{"text":"Let K be a convex body in Rn (i.e., a compact convex set with nonempty interior). Given a point p in the interior of K, a hyperplane h passing through p is called barycentric if p is the barycenter of K∩h. In 1961, Grünbaum raised the question whether, for every K, there exists an interior point p through which there are at least n+1 distinct barycentric hyperplanes. Two years later, this was seemingly resolved affirmatively by showing that this is the case if p=p0 is the point of maximal depth in K. However, while working on a related question, we noticed that one of the auxiliary claims in the proof is incorrect. Here, we provide a counterexample; this re-opens Grünbaum’s question. It follows from known results that for n≥2, there are always at least three distinct barycentric cuts through the point p0∈K of maximal depth. Using tools related to Morse theory we are able to improve this bound: four distinct barycentric cuts through p0 are guaranteed if n≥3.","lang":"eng"}],"publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"acknowledgement":"The work by Zuzana Patáková has been partially supported by Charles University Research Center Program No. UNCE/SCI/022, and part of it was done during her research stay at IST Austria. The work by Martin Tancer is supported by the GAČR Grant 19-04113Y and by the Charles University Projects PRIMUS/17/SCI/3 and UNCE/SCI/004.","article_processing_charge":"No","_id":"10776","language":[{"iso":"eng"}],"publication_status":"published","external_id":{"isi":["000750681500001"],"arxiv":["2003.13536"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"UlWa"}],"doi":"10.1007/s00454-021-00364-7","oa_version":"Preprint","year":"2022","arxiv":1,"isi":1,"type":"journal_article","scopus_import":"1","title":"Barycentric cuts through a convex body","status":"public","oa":1,"author":[{"first_name":"Zuzana","last_name":"Patakova","orcid":"0000-0002-3975-1683","full_name":"Patakova, Zuzana","id":"48B57058-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tancer, Martin","first_name":"Martin","last_name":"Tancer"},{"first_name":"Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli"}],"quality_controlled":"1","page":"1133-1154","main_file_link":[{"url":"https://arxiv.org/abs/2003.13536","open_access":"1"}],"publisher":"Springer Nature","publication":"Discrete and Computational Geometry","intvolume":"        68","article_type":"original","volume":68,"date_created":"2022-02-20T23:01:35Z","date_published":"2022-12-01T00:00:00Z","month":"12","citation":{"ieee":"Z. Patakova, M. Tancer, and U. Wagner, “Barycentric cuts through a convex body,” <i>Discrete and Computational Geometry</i>, vol. 68. Springer Nature, pp. 1133–1154, 2022.","apa":"Patakova, Z., Tancer, M., &#38; Wagner, U. (2022). Barycentric cuts through a convex body. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-021-00364-7\">https://doi.org/10.1007/s00454-021-00364-7</a>","short":"Z. Patakova, M. Tancer, U. Wagner, Discrete and Computational Geometry 68 (2022) 1133–1154.","mla":"Patakova, Zuzana, et al. “Barycentric Cuts through a Convex Body.” <i>Discrete and Computational Geometry</i>, vol. 68, Springer Nature, 2022, pp. 1133–54, doi:<a href=\"https://doi.org/10.1007/s00454-021-00364-7\">10.1007/s00454-021-00364-7</a>.","ama":"Patakova Z, Tancer M, Wagner U. Barycentric cuts through a convex body. <i>Discrete and Computational Geometry</i>. 2022;68:1133-1154. doi:<a href=\"https://doi.org/10.1007/s00454-021-00364-7\">10.1007/s00454-021-00364-7</a>","ista":"Patakova Z, Tancer M, Wagner U. 2022. Barycentric cuts through a convex body. Discrete and Computational Geometry. 68, 1133–1154.","chicago":"Patakova, Zuzana, Martin Tancer, and Uli Wagner. “Barycentric Cuts through a Convex Body.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00454-021-00364-7\">https://doi.org/10.1007/s00454-021-00364-7</a>."},"day":"01","date_updated":"2023-08-02T14:38:58Z"},{"related_material":{"record":[{"relation":"dissertation_contains","id":"14711","status":"public"}]},"day":"11","citation":{"chicago":"Barton, Nicholas H, and Oluwafunmilola O Olusanya. “The Response of a Metapopulation to a Changing Environment.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. The Royal Society, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0009\">https://doi.org/10.1098/rstb.2021.0009</a>.","mla":"Barton, Nicholas H., and Oluwafunmilola O. Olusanya. “The Response of a Metapopulation to a Changing Environment.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1848, The Royal Society, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0009\">10.1098/rstb.2021.0009</a>.","ista":"Barton NH, Olusanya OO. 2022. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1848).","ama":"Barton NH, Olusanya OO. The response of a metapopulation to a changing environment. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1848). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0009\">10.1098/rstb.2021.0009</a>","ieee":"N. H. Barton and O. O. Olusanya, “The response of a metapopulation to a changing environment,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1848. The Royal Society, 2022.","apa":"Barton, N. H., &#38; Olusanya, O. O. (2022). The response of a metapopulation to a changing environment. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2021.0009\">https://doi.org/10.1098/rstb.2021.0009</a>","short":"N.H. Barton, O.O. Olusanya, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022)."},"file":[{"date_updated":"2022-08-02T06:14:32Z","success":1,"file_name":"2022_PhilosophicalTransactionsRSB_Barton.pdf","checksum":"3b0243738f01bf3c07e0d7e8dc64f71d","relation":"main_file","file_id":"11719","creator":"dernst","file_size":1349672,"date_created":"2022-08-02T06:14:32Z","content_type":"application/pdf","access_level":"open_access"}],"date_updated":"2025-05-26T09:05:09Z","has_accepted_license":"1","article_type":"original","volume":377,"date_published":"2022-04-11T00:00:00Z","date_created":"2022-02-21T16:08:10Z","month":"04","issue":"1848","quality_controlled":"1","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"publisher":"The Royal Society","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","intvolume":"       377","title":"The response of a metapopulation to a changing environment","status":"public","oa":1,"author":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","full_name":"Olusanya, Oluwafunmilola O","first_name":"Oluwafunmilola O","last_name":"Olusanya","orcid":"0000-0003-1971-8314"}],"year":"2022","type":"journal_article","isi":1,"scopus_import":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1098/rstb.2021.0009","oa_version":"Published Version","pmid":1,"_id":"10787","language":[{"iso":"eng"}],"ddc":["570"],"publication_status":"published","project":[{"name":"Causes and consequences of population fragmentation","grant_number":"P32896","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"}],"external_id":{"isi":["000758140300001"],"pmid":["35184588"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"abstract":[{"lang":"eng","text":"A species distributed across diverse environments may adapt to local conditions. We ask how quickly such a species changes its range in response to changed conditions. Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210)) used the infinite island model to find the stationary distribution of allele frequencies and deme sizes. We extend this to find how a metapopulation responds to changes in carrying capacity, selection strength, or migration rate when deme sizes are fixed. We further develop a ‘fixed-state’ approximation. Under this approximation, polymorphism is only possible for a narrow range of habitat proportions when selection is weak compared to drift, but for a much wider range otherwise. When rates of selection or migration relative to drift change in a single deme of the metapopulation, the population takes a time of order m−1 to reach the new equilibrium. However, even with many loci, there can be substantial fluctuations in net adaptation, because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation, variation may gradually be lost by chance, even if it would persist in an infinite metapopulation. When conditions change across the whole metapopulation, there can be rapid change, which is predicted well by the fixed-state approximation. This work helps towards an understanding of how metapopulations extend their range across diverse environments.\r\nThis article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’."}],"file_date_updated":"2022-08-02T06:14:32Z","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) [FWF P-32896B].","article_processing_charge":"No"},{"article_processing_charge":"No","acknowledgement":"Part of this work was conducted as a guest at the Institut de Mathématiques de Jussieu–Paris Rive Gauche invited by Antoine Chambert-Loir and funded by DAAD.\r\nDuring this time, I had interesting and fruitful discussions on the interpretation of the result for\r\nthe toric variety discussed in Section 3 with Antoine Chambert-Loir. I wish to thank him for these\r\nopportunities and for his useful remarks on earlier versions of this article. This work was partly\r\nfunded by FWF grant P 32428-N35.","author":[{"first_name":"Florian Alexander","last_name":"Wilsch","orcid":"0000-0001-7302-8256","id":"560601DA-8D36-11E9-A136-7AC1E5697425","full_name":"Wilsch, Florian Alexander"}],"oa":1,"status":"public","article_number":"2202.10909","abstract":[{"lang":"eng","text":"We determine an asymptotic formula for the number of integral points of\r\nbounded height on a certain toric variety, which is incompatible with part of a\r\npreprint by Chambert-Loir and Tschinkel. We provide an alternative\r\ninterpretation of the asymptotic formula we get. To do so, we construct an\r\nanalogue of Peyre's constant $\\alpha$ and describe its relation to a new\r\nobstruction to the Zariski density of integral points in certain regions of\r\nvarieties."}],"title":"Integral points of bounded height on a certain toric variety","department":[{"_id":"TiBr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"arXiv","external_id":{"arxiv":["2202.10909"]},"keyword":["Integral point","toric variety","Manin's conjecture"],"main_file_link":[{"url":"https://arxiv.org/abs/2202.10909","open_access":"1"}],"project":[{"_id":"26AEDAB2-B435-11E9-9278-68D0E5697425","grant_number":"P32428","call_identifier":"FWF","name":"New frontiers of the Manin conjecture"}],"publication_status":"submitted","_id":"10788","language":[{"iso":"eng"}],"month":"02","oa_version":"Preprint","date_created":"2022-02-23T09:04:43Z","date_published":"2022-02-22T00:00:00Z","doi":"10.48550/arXiv.2202.10909","date_updated":"2023-05-03T07:46:35Z","citation":{"chicago":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Certain Toric Variety.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2202.10909\">https://doi.org/10.48550/arXiv.2202.10909</a>.","ista":"Wilsch FA. Integral points of bounded height on a certain toric variety. arXiv, 2202.10909.","ama":"Wilsch FA. Integral points of bounded height on a certain toric variety. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2202.10909\">10.48550/arXiv.2202.10909</a>","mla":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Certain Toric Variety.” <i>ArXiv</i>, 2202.10909, doi:<a href=\"https://doi.org/10.48550/arXiv.2202.10909\">10.48550/arXiv.2202.10909</a>.","short":"F.A. Wilsch, ArXiv (n.d.).","apa":"Wilsch, F. A. (n.d.). Integral points of bounded height on a certain toric variety. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2202.10909\">https://doi.org/10.48550/arXiv.2202.10909</a>","ieee":"F. A. Wilsch, “Integral points of bounded height on a certain toric variety,” <i>arXiv</i>. ."},"day":"22","year":"2022","type":"preprint","arxiv":1},{"day":"07","citation":{"chicago":"Hansen, Andi H, Florian Pauler, Michael Riedl, Carmen Streicher, Anna-Magdalena Heger, Susanne Laukoter, Christoph M Sommer, et al. “Tissue-Wide Effects Override Cell-Intrinsic Gene Function in Radial Neuron Migration.” <i>Oxford Open Neuroscience</i>. Oxford Academic, 2022. <a href=\"https://doi.org/10.1093/oons/kvac009\">https://doi.org/10.1093/oons/kvac009</a>.","mla":"Hansen, Andi H., et al. “Tissue-Wide Effects Override Cell-Intrinsic Gene Function in Radial Neuron Migration.” <i>Oxford Open Neuroscience</i>, vol. 1, no. 1, kvac009, Oxford Academic, 2022, doi:<a href=\"https://doi.org/10.1093/oons/kvac009\">10.1093/oons/kvac009</a>.","ama":"Hansen AH, Pauler F, Riedl M, et al. Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. <i>Oxford Open Neuroscience</i>. 2022;1(1). doi:<a href=\"https://doi.org/10.1093/oons/kvac009\">10.1093/oons/kvac009</a>","ista":"Hansen AH, Pauler F, Riedl M, Streicher C, Heger A-M, Laukoter S, Sommer CM, Nicolas A, Hof B, Tsai LH, Rülicke T, Hippenmeyer S. 2022. Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. Oxford Open Neuroscience. 1(1), kvac009.","ieee":"A. H. Hansen <i>et al.</i>, “Tissue-wide effects override cell-intrinsic gene function in radial neuron migration,” <i>Oxford Open Neuroscience</i>, vol. 1, no. 1. Oxford Academic, 2022.","apa":"Hansen, A. H., Pauler, F., Riedl, M., Streicher, C., Heger, A.-M., Laukoter, S., … Hippenmeyer, S. (2022). Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. <i>Oxford Open Neuroscience</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/oons/kvac009\">https://doi.org/10.1093/oons/kvac009</a>","short":"A.H. Hansen, F. Pauler, M. Riedl, C. Streicher, A.-M. Heger, S. Laukoter, C.M. Sommer, A. Nicolas, B. Hof, L.H. Tsai, T. Rülicke, S. Hippenmeyer, Oxford Open Neuroscience 1 (2022)."},"file":[{"access_level":"open_access","content_type":"application/pdf","date_created":"2023-08-16T08:00:30Z","relation":"main_file","file_id":"14061","creator":"dernst","file_size":4846551,"checksum":"822e76e056c07099d1fb27d1ece5941b","file_name":"2023_OxfordOpenNeuroscience_Hansen.pdf","success":1,"date_updated":"2023-08-16T08:00:30Z"}],"date_updated":"2023-11-30T10:55:12Z","related_material":{"record":[{"status":"public","id":"12726","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"14530"}]},"date_created":"2022-02-25T07:52:11Z","date_published":"2022-07-07T00:00:00Z","month":"07","has_accepted_license":"1","volume":1,"article_type":"original","quality_controlled":"1","publisher":"Oxford Academic","publication":"Oxford Open Neuroscience","intvolume":"         1","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"Bio"}],"issue":"1","oa":1,"author":[{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H","last_name":"Hansen","first_name":"Andi H"},{"full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler"},{"full_name":"Riedl, Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","last_name":"Riedl","orcid":"0000-0003-4844-6311","first_name":"Michael"},{"last_name":"Streicher","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen"},{"last_name":"Heger","first_name":"Anna-Magdalena","id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87","full_name":"Heger, Anna-Magdalena"},{"last_name":"Laukoter","orcid":"0000-0002-7903-3010","first_name":"Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","full_name":"Laukoter, Susanne"},{"last_name":"Sommer","orcid":"0000-0003-1216-9105","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M"},{"first_name":"Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87","full_name":"Nicolas, Armel"},{"first_name":"Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"},{"last_name":"Tsai","first_name":"Li Huei","full_name":"Tsai, Li Huei"},{"first_name":"Thomas","last_name":"Rülicke","full_name":"Rülicke, Thomas"},{"first_name":"Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"}],"title":"Tissue-wide effects override cell-intrinsic gene function in radial neuron migration","article_number":"kvac009","status":"public","type":"journal_article","year":"2022","oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1093/oons/kvac009","project":[{"name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7","grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Mechanisms of Radial Neuronal Migration","_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812"}],"department":[{"_id":"SiHi"},{"_id":"BjHo"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10791","language":[{"iso":"eng"}],"ddc":["570"],"publication_status":"published","file_date_updated":"2023-08-16T08:00:30Z","publication_identifier":{"eissn":["2753-149X"]},"article_processing_charge":"No","acknowledgement":"A.H.H. was a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences. This work also received support from IST Austria institutional funds; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA grant agreement No 618444 to S.H.\r\nAPC funding was obtained by IST Austria institutional funds.\r\nWe thank A. Sommer and C. Czepe (VBCF GmbH, NGS Unit), L. Andersen, J. Sonntag and J. Renno for technical support and/or initial experiments; M. Sixt, J. Nimpf and all members of the Hippenmeyer lab for discussion. This research was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging and Optics Facility, Lab Support Facility and Preclinical Facility.","abstract":[{"lang":"eng","text":"The mammalian neocortex is composed of diverse neuronal and glial cell classes that broadly arrange in six distinct laminae. Cortical layers emerge during development and defects in the developmental programs that orchestrate cortical lamination are associated with neurodevelopmental diseases. The developmental principle of cortical layer formation depends on concerted radial projection neuron migration, from their birthplace to their final target position. Radial migration occurs in defined sequential steps, regulated by a large array of signaling pathways. However, based on genetic loss-of-function experiments, most studies have thus far focused on the role of cell-autonomous gene function. Yet, cortical neuron migration in situ is a complex process and migrating neurons traverse along diverse cellular compartments and environments. The role of tissue-wide properties and genetic state in radial neuron migration is however not clear. Here we utilized mosaic analysis with double markers (MADM) technology to either sparsely or globally delete gene function, followed by quantitative single-cell phenotyping. The MADM-based gene ablation paradigms in combination with computational modeling demonstrated that global tissue-wide effects predominate cell-autonomous gene function albeit in a gene-specific manner. Our results thus suggest that the genetic landscape in a tissue critically affects the overall migration phenotype of individual cortical projection neurons. In a broader context, our findings imply that global tissue-wide effects represent an essential component of the underlying etiology associated with focal malformations of cortical development in particular, and neurological diseases in general."}],"ec_funded":1},{"_id":"10792","language":[{"iso":"eng"}],"publication_status":"submitted","main_file_link":[{"url":"https://doi.org/10.21203/rs.3.rs-1316167/v1","open_access":"1"}],"page":"30","publisher":"Research Square","external_id":{"pmid":["PPR454733"]},"department":[{"_id":"SiHi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Background\r\nProper cerebral cortical development depends on the tightly orchestrated migration of newly born neurons from the inner ventricular and subventricular zones to the outer cortical plate. Any disturbance in this process during prenatal stages may lead to neuronal migration disorders (NMDs), which can vary in extent from focal to global. Furthermore, NMDs show a substantial comorbidity with other neurodevelopmental disorders, notably autism spectrum disorders (ASDs). Our previous work demonstrated focal neuronal migration defects in mice carrying loss-of-function alleles of the recognized autism risk gene WDFY3. However, the cellular origins of these defects in Wdfy3 mutant mice remain elusive and uncovering it will provide critical insight into WDFY3-dependent disease pathology .\r\nMethods\r\nHere, in an effort to untangle the origins of NMDs in Wdfy3lacZ mice, we employed mosaic analysis with double markers (MADM). MADM technology enabled us to genetically distinctly track and phenotypically analyze mutant and wild type cells concomitantly in vivo using immunofluorescent techniques.\r\nResults\r\nWe revealed a cell autonomous requirement of WDFY3 for accurate laminar positioning of cortical projection neurons and elimination of mispositioned cells during early postnatal life. In addition, we identified significant deviations in dendritic arborization, as well as synaptic density and morphology between wild type, heterozygous, and homozygous Wdfy3 mutant neurons in Wdfy3-MADM reporter mice at postnatal stages. Limitations While Wdfy3 mutant mice have provided valuable insight into prenatal aspects of ASD pathology that remain inaccessible to investigation in humans, like most animal models, they do not a perfectly replicate all aspects of human ASD biology. The lack of human data makes it indeterminate whether morphological deviations described here apply to ASD patients.\r\nConclusions\r\nOur genetic approach revealed several cell autonomous requirements of Wdfy3 in neuronal development that could underly the pathogenic mechanisms of WDFY3-related ASD conditions. The results are also consistent with findings in other ASD animal models and patients and suggest an important role for Wdfy3 in regulating neuronal function and interconnectivity in postnatal life.","lang":"eng"}],"title":"WDFY3 cell autonomously controls neuronal migration","status":"public","oa":1,"publication_identifier":{"eissn":["2693-5015"]},"author":[{"full_name":"Schaaf, Zachary","last_name":"Schaaf","first_name":"Zachary"},{"last_name":"Tat","first_name":"Lyvin","full_name":"Tat, Lyvin"},{"full_name":"Cannizzaro, Noemi","last_name":"Cannizzaro","first_name":"Noemi"},{"full_name":"Green, Ralph","last_name":"Green","first_name":"Ralph"},{"last_name":"Rülicke","first_name":"Thomas","full_name":"Rülicke, Thomas"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon"},{"full_name":"Zarbalis, K","last_name":"Zarbalis","first_name":"K"}],"article_processing_charge":"No","year":"2022","type":"preprint","citation":{"apa":"Schaaf, Z., Tat, L., Cannizzaro, N., Green, R., Rülicke, T., Hippenmeyer, S., &#38; Zarbalis, K. (n.d.). WDFY3 cell autonomously controls neuronal migration. Research Square. <a href=\"https://doi.org/10.21203/rs.3.rs-1316167/v1\">https://doi.org/10.21203/rs.3.rs-1316167/v1</a>","short":"Z. Schaaf, L. Tat, N. Cannizzaro, R. Green, T. Rülicke, S. Hippenmeyer, K. Zarbalis, (n.d.).","ieee":"Z. Schaaf <i>et al.</i>, “WDFY3 cell autonomously controls neuronal migration.” Research Square.","ista":"Schaaf Z, Tat L, Cannizzaro N, Green R, Rülicke T, Hippenmeyer S, Zarbalis K. WDFY3 cell autonomously controls neuronal migration. <a href=\"https://doi.org/10.21203/rs.3.rs-1316167/v1\">10.21203/rs.3.rs-1316167/v1</a>.","ama":"Schaaf Z, Tat L, Cannizzaro N, et al. WDFY3 cell autonomously controls neuronal migration. doi:<a href=\"https://doi.org/10.21203/rs.3.rs-1316167/v1\">10.21203/rs.3.rs-1316167/v1</a>","mla":"Schaaf, Zachary, et al. <i>WDFY3 Cell Autonomously Controls Neuronal Migration</i>. Research Square, doi:<a href=\"https://doi.org/10.21203/rs.3.rs-1316167/v1\">10.21203/rs.3.rs-1316167/v1</a>.","chicago":"Schaaf, Zachary, Lyvin Tat, Noemi Cannizzaro, Ralph Green, Thomas Rülicke, Simon Hippenmeyer, and K Zarbalis. “WDFY3 Cell Autonomously Controls Neuronal Migration.” Research Square, n.d. <a href=\"https://doi.org/10.21203/rs.3.rs-1316167/v1\">https://doi.org/10.21203/rs.3.rs-1316167/v1</a>."},"day":"16","date_updated":"2023-10-17T13:06:52Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.21203/rs.3.rs-1316167/v1","date_created":"2022-02-25T07:53:26Z","date_published":"2022-02-16T00:00:00Z","oa_version":"Preprint","pmid":1,"month":"02"},{"abstract":[{"text":"We consider symmetric partial exclusion and inclusion processes in a general graph in contact with reservoirs, where we allow both for edge disorder and well-chosen site disorder. We extend the classical dualities to this context and then we derive new orthogonal polynomial dualities. From the classical dualities, we derive the uniqueness of the non-equilibrium steady state and obtain correlation inequalities. Starting from the orthogonal polynomial dualities, we show universal properties of n-point correlation functions in the non-equilibrium steady state for systems with at most two different reservoir parameters, such as a chain with reservoirs at left and right ends.","lang":"eng"},{"lang":"fre","text":"Nous considérons des processus d’exclusion partielle, et des processus d’inclusion sur un graphe général en contact avec des réservoirs. Nous autorisons la présence de inhomogenéités sur les arrêts ainsi que sur les sommets du graph. Nous généralisons les “dualités classiques” dans ce contexte et nous démontrons des nouvelles dualités orthogonales. À partir des dualités classiques, nous démontrons l’unicité de l’état stationnaire non-équilibre, ainsi que des inégalités de corrélation. À partir des dualités orthogonales nous démontrons des propriétés universelles des fonctions de corrélation à n points dans l’état stationnaire non-équilibre pour des systèmes avec deux paramètres de réservoirs inégaux, comme par exemple une chaîne avec des réservoirs à droite et à gauche."}],"ec_funded":1,"publication_identifier":{"issn":["0246-0203"]},"acknowledgement":"The authors would like to thank Gioia Carinci and Cristian Giardinà for useful discussions. F.R. and S.F. thank Jean-René Chazottes for a stay at CPHT (Institut Polytechnique de Paris), in the realm of Chaire d’Alembert (Paris-Saclay University), where part of this work was performed. S.F. acknowledges Simona Villa for her support in creating the picture. S.F. acknowledges financial support from NWO via the grant TOP1.17.019. F.S. acknowledges financial support from the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411.","article_processing_charge":"No","publication_status":"published","_id":"10797","language":[{"iso":"eng"}],"external_id":{"isi":["000752489300010"],"arxiv":["2007.08272"]},"project":[{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JaMa"}],"doi":"10.1214/21-AIHP1163","oa_version":"Preprint","scopus_import":"1","arxiv":1,"isi":1,"type":"journal_article","year":"2022","title":"Orthogonal polynomial duality of boundary driven particle systems and non-equilibrium correlations","status":"public","oa":1,"author":[{"full_name":"Floreani, Simone","first_name":"Simone","last_name":"Floreani"},{"first_name":"Frank","last_name":"Redig","full_name":"Redig, Frank"},{"last_name":"Sau","first_name":"Federico","id":"E1836206-9F16-11E9-8814-AEFDE5697425","full_name":"Sau, Federico"}],"issue":"1","publisher":"Institute of Mathematical Statistics","quality_controlled":"1","page":"220-247","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.08272"}],"intvolume":"        58","publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","article_type":"original","volume":58,"date_created":"2022-02-27T23:01:50Z","date_published":"2022-02-01T00:00:00Z","month":"02","day":"01","citation":{"short":"S. Floreani, F. Redig, F. Sau, Annales de l’institut Henri Poincare (B) Probability and Statistics 58 (2022) 220–247.","apa":"Floreani, S., Redig, F., &#38; Sau, F. (2022). Orthogonal polynomial duality of boundary driven particle systems and non-equilibrium correlations. <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-AIHP1163\">https://doi.org/10.1214/21-AIHP1163</a>","ieee":"S. Floreani, F. Redig, and F. Sau, “Orthogonal polynomial duality of boundary driven particle systems and non-equilibrium correlations,” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>, vol. 58, no. 1. Institute of Mathematical Statistics, pp. 220–247, 2022.","ista":"Floreani S, Redig F, Sau F. 2022. Orthogonal polynomial duality of boundary driven particle systems and non-equilibrium correlations. Annales de l’institut Henri Poincare (B) Probability and Statistics. 58(1), 220–247.","ama":"Floreani S, Redig F, Sau F. Orthogonal polynomial duality of boundary driven particle systems and non-equilibrium correlations. <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. 2022;58(1):220-247. doi:<a href=\"https://doi.org/10.1214/21-AIHP1163\">10.1214/21-AIHP1163</a>","mla":"Floreani, Simone, et al. “Orthogonal Polynomial Duality of Boundary Driven Particle Systems and Non-Equilibrium Correlations.” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>, vol. 58, no. 1, Institute of Mathematical Statistics, 2022, pp. 220–47, doi:<a href=\"https://doi.org/10.1214/21-AIHP1163\">10.1214/21-AIHP1163</a>.","chicago":"Floreani, Simone, Frank Redig, and Federico Sau. “Orthogonal Polynomial Duality of Boundary Driven Particle Systems and Non-Equilibrium Correlations.” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. Institute of Mathematical Statistics, 2022. <a href=\"https://doi.org/10.1214/21-AIHP1163\">https://doi.org/10.1214/21-AIHP1163</a>."},"date_updated":"2023-10-17T12:49:43Z"}]