[{"abstract":[{"lang":"eng","text":"Brachyury, a member of T-box gene family, is widely known for its major role in mesoderm specification in bilaterians. It is also present in non-bilaterian metazoans, such as cnidarians, where it acts as a component of an axial patterning system. In this study, we present a phylogenetic analysis of Brachyury genes within phylum Cnidaria, investigate differential expression and address a functional framework of Brachyury paralogs in hydrozoan Dynamena pumila. Our analysis indicates two duplication events of Brachyury within the cnidarian lineage. The first duplication likely appeared in the medusozoan ancestor, resulting in two copies in medusozoans, while the second duplication arose in the hydrozoan ancestor, resulting in three copies in hydrozoans. Brachyury1 and 2 display a conservative expression pattern marking the oral pole of the body axis in D. pumila. On the contrary, Brachyury3 expression was detected in scattered presumably nerve cells of the D. pumila larva. Pharmacological modulations indicated that Brachyury3 is not under regulation of cWnt signaling in contrast to the other two Brachyury genes. Divergence in expression patterns and regulation suggest neofunctionalization of Brachyury3 in hydrozoans."}],"article_type":"original","external_id":{"pmid":["37296138"],"isi":["001006690200045"]},"quality_controlled":"1","oa_version":"Published Version","day":"09","volume":13,"title":"The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization","isi":1,"article_number":"9382","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2023-08-02T06:17:18Z","month":"06","department":[{"_id":"GradSch"}],"publication_status":"published","publisher":"Springer Nature","publication_identifier":{"eissn":["2045-2322"]},"article_processing_charge":"No","doi":"10.1038/s41598-023-35979-8","date_published":"2023-06-09T00:00:00Z","year":"2023","citation":{"ista":"Vetrova AA, Kupaeva DM, Kizenko A, Lebedeva TS, Walentek P, Tsikolia N, Kremnyov SV. 2023. The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. 13, 9382.","ieee":"A. A. Vetrova <i>et al.</i>, “The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization,” <i>Scientific Reports</i>, vol. 13. Springer Nature, 2023.","mla":"Vetrova, Alexandra A., et al. “The Evolutionary History of Brachyury Genes in Hydrozoa Involves Duplications, Divergence, and Neofunctionalization.” <i>Scientific Reports</i>, vol. 13, 9382, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41598-023-35979-8\">10.1038/s41598-023-35979-8</a>.","short":"A.A. Vetrova, D.M. Kupaeva, A. Kizenko, T.S. Lebedeva, P. Walentek, N. Tsikolia, S.V. Kremnyov, Scientific Reports 13 (2023).","apa":"Vetrova, A. A., Kupaeva, D. M., Kizenko, A., Lebedeva, T. S., Walentek, P., Tsikolia, N., &#38; Kremnyov, S. V. (2023). The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-023-35979-8\">https://doi.org/10.1038/s41598-023-35979-8</a>","ama":"Vetrova AA, Kupaeva DM, Kizenko A, et al. The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. <i>Scientific Reports</i>. 2023;13. doi:<a href=\"https://doi.org/10.1038/s41598-023-35979-8\">10.1038/s41598-023-35979-8</a>","chicago":"Vetrova, Alexandra A., Daria M. Kupaeva, Alena Kizenko, Tatiana S. Lebedeva, Peter Walentek, Nikoloz Tsikolia, and Stanislav V. Kremnyov. “The Evolutionary History of Brachyury Genes in Hydrozoa Involves Duplications, Divergence, and Neofunctionalization.” <i>Scientific Reports</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41598-023-35979-8\">https://doi.org/10.1038/s41598-023-35979-8</a>."},"intvolume":"        13","pmid":1,"file":[{"success":1,"access_level":"open_access","relation":"main_file","file_size":4844149,"date_created":"2023-06-26T09:58:53Z","checksum":"baddf6b2fa9adf88263d4a3b0998f0f2","creator":"dernst","file_id":"13170","file_name":"2023_ScientificReports_Vetrova.pdf","date_updated":"2023-06-26T09:58:53Z","content_type":"application/pdf"}],"ddc":["570"],"has_accepted_license":"1","publication":"Scientific Reports","language":[{"iso":"eng"}],"status":"public","scopus_import":"1","date_created":"2023-06-25T22:00:46Z","author":[{"first_name":"Alexandra A.","last_name":"Vetrova","full_name":"Vetrova, Alexandra A."},{"first_name":"Daria M.","last_name":"Kupaeva","full_name":"Kupaeva, Daria M."},{"first_name":"Alena","last_name":"Kizenko","id":"a521c60b-0815-11ed-9b02-b8bd522477c8","full_name":"Kizenko, Alena"},{"first_name":"Tatiana S.","last_name":"Lebedeva","full_name":"Lebedeva, Tatiana S."},{"last_name":"Walentek","full_name":"Walentek, Peter","first_name":"Peter"},{"first_name":"Nikoloz","full_name":"Tsikolia, Nikoloz","last_name":"Tsikolia"},{"full_name":"Kremnyov, Stanislav V.","last_name":"Kremnyov","first_name":"Stanislav V."}],"acknowledgement":"We thank N.A. Pertsov White Sea Biological Station of Moscow State University for the help and support in obtaining samples and providing access to all required facilities and equipment of the “Center of Microscopy WSBS MSU”. We are grateful to Dr. Amro Hamdoun for pCS2+8 plasmid (Addgene plasmid # 34931).\r\nWork in the Walentek lab is supported by the Deutsche Forschungsgemeinschaft (DFG) under the Emmy Noether Programme (grant WA3365/2-2) and under Germany’s Excellence Strategy (CIBSS-EXC-2189-Project ID 390939984). SK is supported by the project No. 0088-2021-0009 of the Koltzov Institute of Developmental Biology of the RAS. The study of molecular patterning of D. pumila colony was funded by RFBR, project number 20-04-00978a (to S.K.).","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","file_date_updated":"2023-06-26T09:58:53Z","_id":"13166","oa":1},{"oa":1,"_id":"13168","file_date_updated":"2023-06-26T10:15:44Z","author":[{"full_name":"Xu, Jiayuan","last_name":"Xu","first_name":"Jiayuan"},{"first_name":"Nana","last_name":"Liu","full_name":"Liu, Nana"},{"full_name":"Polemiti, Elli","last_name":"Polemiti","first_name":"Elli"},{"last_name":"Garcia-Mondragon","full_name":"Garcia-Mondragon, Liliana","first_name":"Liliana"},{"first_name":"Jie","full_name":"Tang, Jie","last_name":"Tang"},{"last_name":"Liu","full_name":"Liu, Xiaoxuan","first_name":"Xiaoxuan"},{"first_name":"Tristram","full_name":"Lett, Tristram","last_name":"Lett"},{"last_name":"Yu","full_name":"Yu, Le","first_name":"Le"},{"last_name":"Nöthen","full_name":"Nöthen, Markus M.","first_name":"Markus M."},{"last_name":"Feng","full_name":"Feng, Jianfeng","first_name":"Jianfeng"},{"first_name":"Chunshui","last_name":"Yu","full_name":"Yu, Chunshui"},{"full_name":"Marquand, Andre","last_name":"Marquand","first_name":"Andre"},{"full_name":"Schumann, Gunter","last_name":"Schumann","first_name":"Gunter"},{"full_name":"Walter, Henrik","last_name":"Walter","first_name":"Henrik"},{"first_name":"Andreas","full_name":"Heinz, Andreas","last_name":"Heinz"},{"first_name":"Markus","last_name":"Ralser","full_name":"Ralser, Markus"},{"full_name":"Twardziok, Sven","last_name":"Twardziok","first_name":"Sven"},{"last_name":"Vaidya","full_name":"Vaidya, Nilakshi","first_name":"Nilakshi"},{"full_name":"Serin, Emin","last_name":"Serin","first_name":"Emin"},{"full_name":"Jentsch, Marcel","last_name":"Jentsch","first_name":"Marcel"},{"last_name":"Hitchen","full_name":"Hitchen, Esther","first_name":"Esther"},{"full_name":"Eils, Roland","last_name":"Eils","first_name":"Roland"},{"last_name":"Taron","full_name":"Taron, Ulrike Helene","first_name":"Ulrike Helene"},{"first_name":"Tatjana","last_name":"Schütz","full_name":"Schütz, Tatjana"},{"first_name":"Kerstin","full_name":"Schepanski, Kerstin","last_name":"Schepanski"},{"first_name":"Jamie","full_name":"Banks, Jamie","last_name":"Banks"},{"full_name":"Banaschewski, Tobias","last_name":"Banaschewski","first_name":"Tobias"},{"last_name":"Jansone","full_name":"Jansone, Karina","first_name":"Karina"},{"last_name":"Christmann","full_name":"Christmann, Nina","first_name":"Nina"},{"first_name":"Andreas","last_name":"Meyer-Lindenberg","full_name":"Meyer-Lindenberg, Andreas"},{"first_name":"Heike","full_name":"Tost, Heike","last_name":"Tost"},{"full_name":"Holz, Nathalie","last_name":"Holz","first_name":"Nathalie"},{"first_name":"Emanuel","last_name":"Schwarz","full_name":"Schwarz, Emanuel"},{"last_name":"Stringaris","full_name":"Stringaris, Argyris","first_name":"Argyris"},{"first_name":"Maja","full_name":"Neidhart, Maja","last_name":"Neidhart"},{"last_name":"Nees","full_name":"Nees, Frauke","first_name":"Frauke"},{"last_name":"Siehl","full_name":"Siehl, Sebastian","first_name":"Sebastian"},{"first_name":"Ole","full_name":"A. Andreassen, Ole","last_name":"A. Andreassen"},{"last_name":"T. Westlye","full_name":"T. Westlye, Lars","first_name":"Lars"},{"first_name":"Dennis","full_name":"Van Der Meer, Dennis","last_name":"Van Der Meer"},{"full_name":"Fernandez, Sara","last_name":"Fernandez","first_name":"Sara"},{"first_name":"Rikka","last_name":"Kjelkenes","full_name":"Kjelkenes, Rikka"},{"last_name":"Ask","full_name":"Ask, Helga","first_name":"Helga"},{"last_name":"Rapp","full_name":"Rapp, Michael","first_name":"Michael"},{"first_name":"Mira","last_name":"Tschorn","full_name":"Tschorn, Mira"},{"full_name":"Böttger, Sarah Jane","last_name":"Böttger","first_name":"Sarah Jane"},{"last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","first_name":"Gaia"},{"id":"4406F586-F248-11E8-B48F-1D18A9856A87","full_name":"Marr, Lena","last_name":"Marr","first_name":"Lena"},{"first_name":"Mel","full_name":"Slater, Mel","last_name":"Slater"},{"first_name":"Guillem Feixas","last_name":"Viapiana","full_name":"Viapiana, Guillem Feixas"},{"first_name":"Francisco Eiroa","last_name":"Orosa","full_name":"Orosa, Francisco Eiroa"},{"full_name":"Gallego, Jaime","last_name":"Gallego","first_name":"Jaime"},{"full_name":"Pastor, Alvaro","last_name":"Pastor","first_name":"Alvaro"},{"first_name":"Andreas","full_name":"Forstner, Andreas","last_name":"Forstner"},{"last_name":"Hoffmann","full_name":"Hoffmann, Per","first_name":"Per"},{"full_name":"M. Nöthen, Markus","last_name":"M. Nöthen","first_name":"Markus"},{"last_name":"J. Forstner","full_name":"J. Forstner, Andreas","first_name":"Andreas"},{"last_name":"Claus","full_name":"Claus, Isabelle","first_name":"Isabelle"},{"full_name":"Miller, Abbi","last_name":"Miller","first_name":"Abbi"},{"first_name":"Stefanie","full_name":"Heilmann-Heimbach, Stefanie","last_name":"Heilmann-Heimbach"},{"last_name":"Sommer","full_name":"Sommer, Peter","first_name":"Peter"},{"full_name":"Boye, Mona","last_name":"Boye","first_name":"Mona"},{"first_name":"Johannes","last_name":"Wilbertz","full_name":"Wilbertz, Johannes"},{"first_name":"Karen","full_name":"Schmitt, Karen","last_name":"Schmitt"},{"first_name":"Viktor","last_name":"Jirsa","full_name":"Jirsa, Viktor"},{"full_name":"Petkoski, Spase","last_name":"Petkoski","first_name":"Spase"},{"first_name":"Séverine","last_name":"Pitel","full_name":"Pitel, Séverine"},{"first_name":"Lisa","last_name":"Otten","full_name":"Otten, Lisa"},{"first_name":"Anastasios Polykarpos","full_name":"Athanasiadis, Anastasios Polykarpos","last_name":"Athanasiadis"},{"first_name":"Charlie","last_name":"Pearmund","full_name":"Pearmund, Charlie"},{"first_name":"Bernhard","last_name":"Spanlang","full_name":"Spanlang, Bernhard"},{"last_name":"Alvarez","full_name":"Alvarez, Elena","first_name":"Elena"},{"first_name":"Mavi","last_name":"Sanchez","full_name":"Sanchez, Mavi"},{"first_name":"Arantxa","last_name":"Giner","full_name":"Giner, Arantxa"},{"last_name":"Hese","full_name":"Hese, Sören","first_name":"Sören"},{"first_name":"Paul","full_name":"Renner, Paul","last_name":"Renner"},{"first_name":"Tianye","last_name":"Jia","full_name":"Jia, Tianye"},{"last_name":"Gong","full_name":"Gong, Yanting","first_name":"Yanting"},{"last_name":"Xia","full_name":"Xia, Yunman","first_name":"Yunman"},{"first_name":"Xiao","full_name":"Chang, Xiao","last_name":"Chang"},{"last_name":"Calhoun","full_name":"Calhoun, Vince","first_name":"Vince"},{"full_name":"Liu, Jingyu","last_name":"Liu","first_name":"Jingyu"},{"last_name":"Thompson","full_name":"Thompson, Paul","first_name":"Paul"},{"first_name":"Nicholas","full_name":"Clinton, Nicholas","last_name":"Clinton"},{"last_name":"Desrivieres","full_name":"Desrivieres, Sylvane","first_name":"Sylvane"},{"first_name":"Allan","last_name":"H. Young","full_name":"H. Young, Allan"},{"first_name":"Bernd","full_name":"Stahl, Bernd","last_name":"Stahl"},{"first_name":"George","last_name":"Ogoh","full_name":"Ogoh, George"}],"acknowledgement":"This work received support from the European Union-funded Horizon Europe project ‘environMENTAL’ (no. 101057429 to G.S., A.M. and M.M.N.) and cofunding by UK Research and Innovation under the UK Government’s Horizon Europe funding guarantee (nos. 10041392 and 10038599) for study design and data analysis; the Horizon 2020-funded European Research Council Advanced Grant ‘STRATIFY’ (no. 695313 to G.S. for study design and data analysis); the Human Brain Project (HBP SGA3, no. 945539 to G.S. for study design and data analysis); the National Institutes of Health (grant no. R01DA049238 to G.S. for study design and data analysis); the German Research Foundation (COPE; grant no. 675346 to G.S. for study design and data analysis); the National Natural Science Foundation of China (grant no. 82001797 to J.X., grant no. 82030053 to C.Y., grant no. 82202093 to J.T. and grant no. 82150710554 to G.S. for study design, data analysis and preparation of the manuscript); National Key Research and Development Program of China (grant no. 2018YFC1314301 to C.Y. for study design and data analysis); Tianjin Applied Basic Research Diversified Investment Foundation (grant no. 21JCYBJC01360 to J.X. for study design and data analysis); Tianjin Health Technology Project (grant no. TJWJ2021QN002 to J.X. for preparation of the manuscript); Science & Technology Development Fund of the Tianjin Education Commission for Higher Education (grant no. 2019KJ195 to J.X. for preparation of the manuscript); the Tianjin Medical University ‘Clinical Talent Training 123 Climbing Plan’ to J.X. for the preparation of the manuscript; Tianjin Key Medical Discipline (Specialty) Construction Project (grant no. TJYXZDXK-001A to C.Y. for preparation of the manuscript); the National Key R&D Program of China (grant no. 2022YFE0209400 to L.Y. for study design and data analysis); the Tsinghua University Initiative Scientific Research Program (grant no. 2021Z11GHX002 to L.Y. for study design and data analysis); the National Key Scientific and Technological Infrastructure Project ‘Earth System Science Numerical Simulator Facility’ (EarthLab to L.Y. for study design and data analysis); the Chinese National High-end Foreign Expert Recruitment Plan to G.S.; and the Alexander von Humboldt Foundation to G.S. for study design and data analysis.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","date_created":"2023-06-25T22:00:46Z","scopus_import":"1","publication":"Nature Medicine","language":[{"iso":"eng"}],"has_accepted_license":"1","ddc":["570"],"file":[{"checksum":"bcd3225b2731c3442fa98987fd3bd46d","date_created":"2023-06-26T10:15:44Z","relation":"main_file","file_size":7365360,"access_level":"open_access","success":1,"content_type":"application/pdf","file_name":"2023_NatureMedicine_Xu.pdf","date_updated":"2023-06-26T10:15:44Z","file_id":"13171","creator":"dernst"}],"intvolume":"        29","page":"1456-1467","date_published":"2023-06-15T00:00:00Z","year":"2023","citation":{"apa":"Xu, J., Liu, N., Polemiti, E., Garcia-Mondragon, L., Tang, J., Liu, X., … Ogoh, G. (2023). Effects of urban living environments on mental health in adults. <i>Nature Medicine</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41591-023-02365-w\">https://doi.org/10.1038/s41591-023-02365-w</a>","short":"J. Xu, N. Liu, E. Polemiti, L. Garcia-Mondragon, J. Tang, X. Liu, T. Lett, L. Yu, M.M. Nöthen, J. Feng, C. Yu, A. Marquand, G. Schumann, H. Walter, A. Heinz, M. Ralser, S. Twardziok, N. Vaidya, E. Serin, M. Jentsch, E. Hitchen, R. Eils, U.H. Taron, T. Schütz, K. Schepanski, J. Banks, T. Banaschewski, K. Jansone, N. Christmann, A. Meyer-Lindenberg, H. Tost, N. Holz, E. Schwarz, A. Stringaris, M. Neidhart, F. Nees, S. Siehl, O. A. Andreassen, L. T. Westlye, D. Van Der Meer, S. Fernandez, R. Kjelkenes, H. Ask, M. Rapp, M. Tschorn, S.J. Böttger, G. Novarino, L. Marr, M. Slater, G.F. Viapiana, F.E. Orosa, J. Gallego, A. Pastor, A. Forstner, P. Hoffmann, M. M. Nöthen, A. J. Forstner, I. Claus, A. Miller, S. Heilmann-Heimbach, P. Sommer, M. Boye, J. Wilbertz, K. Schmitt, V. Jirsa, S. Petkoski, S. Pitel, L. Otten, A.P. Athanasiadis, C. Pearmund, B. Spanlang, E. Alvarez, M. Sanchez, A. Giner, S. Hese, P. Renner, T. Jia, Y. Gong, Y. Xia, X. Chang, V. Calhoun, J. Liu, P. Thompson, N. Clinton, S. Desrivieres, A. H. Young, B. Stahl, G. Ogoh, Nature Medicine 29 (2023) 1456–1467.","chicago":"Xu, Jiayuan, Nana Liu, Elli Polemiti, Liliana Garcia-Mondragon, Jie Tang, Xiaoxuan Liu, Tristram Lett, et al. “Effects of Urban Living Environments on Mental Health in Adults.” <i>Nature Medicine</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41591-023-02365-w\">https://doi.org/10.1038/s41591-023-02365-w</a>.","ama":"Xu J, Liu N, Polemiti E, et al. Effects of urban living environments on mental health in adults. <i>Nature Medicine</i>. 2023;29:1456-1467. doi:<a href=\"https://doi.org/10.1038/s41591-023-02365-w\">10.1038/s41591-023-02365-w</a>","ista":"Xu J, Liu N, Polemiti E, Garcia-Mondragon L, Tang J, Liu X, Lett T, Yu L, Nöthen MM, Feng J, Yu C, Marquand A, Schumann G, Walter H, Heinz A, Ralser M, Twardziok S, Vaidya N, Serin E, Jentsch M, Hitchen E, Eils R, Taron UH, Schütz T, Schepanski K, Banks J, Banaschewski T, Jansone K, Christmann N, Meyer-Lindenberg A, Tost H, Holz N, Schwarz E, Stringaris A, Neidhart M, Nees F, Siehl S, A. Andreassen O, T. Westlye L, Van Der Meer D, Fernandez S, Kjelkenes R, Ask H, Rapp M, Tschorn M, Böttger SJ, Novarino G, Marr L, Slater M, Viapiana GF, Orosa FE, Gallego J, Pastor A, Forstner A, Hoffmann P, M. Nöthen M, J. Forstner A, Claus I, Miller A, Heilmann-Heimbach S, Sommer P, Boye M, Wilbertz J, Schmitt K, Jirsa V, Petkoski S, Pitel S, Otten L, Athanasiadis AP, Pearmund C, Spanlang B, Alvarez E, Sanchez M, Giner A, Hese S, Renner P, Jia T, Gong Y, Xia Y, Chang X, Calhoun V, Liu J, Thompson P, Clinton N, Desrivieres S, H. Young A, Stahl B, Ogoh G. 2023. Effects of urban living environments on mental health in adults. Nature Medicine. 29, 1456–1467.","mla":"Xu, Jiayuan, et al. “Effects of Urban Living Environments on Mental Health in Adults.” <i>Nature Medicine</i>, vol. 29, Springer Nature, 2023, pp. 1456–67, doi:<a href=\"https://doi.org/10.1038/s41591-023-02365-w\">10.1038/s41591-023-02365-w</a>.","ieee":"J. Xu <i>et al.</i>, “Effects of urban living environments on mental health in adults,” <i>Nature Medicine</i>, vol. 29. Springer Nature, pp. 1456–1467, 2023."},"publication_identifier":{"issn":["1078-8956"],"eissn":["1546-170X"]},"publisher":"Springer Nature","article_processing_charge":"No","doi":"10.1038/s41591-023-02365-w","publication_status":"published","date_updated":"2023-12-13T11:25:55Z","month":"06","department":[{"_id":"GaNo"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"title":"Effects of urban living environments on mental health in adults","volume":29,"oa_version":"Published Version","day":"15","external_id":{"isi":["001013172700001"]},"quality_controlled":"1","article_type":"original","abstract":[{"text":"Urban-living individuals are exposed to many environmental factors that may combine and interact to influence mental health. While individual factors of an urban environment have been investigated in isolation, no attempt has been made to model how complex, real-life exposure to living in the city relates to brain and mental health, and how this is moderated by genetic factors. Using the data of 156,075 participants from the UK Biobank, we carried out sparse canonical correlation analyses to investigate the relationships between urban environments and psychiatric symptoms. We found an environmental profile of social deprivation, air pollution, street network and urban land-use density that was positively correlated with an affective symptom group (r = 0.22, Pperm < 0.001), mediated by brain volume differences consistent with reward processing, and moderated by genes enriched for stress response, including CRHR1, explaining 2.01% of the variance in brain volume differences. Protective factors such as greenness and generous destination accessibility were negatively correlated with an anxiety symptom group (r = 0.10, Pperm < 0.001), mediated by brain regions necessary for emotion regulation and moderated by EXD3, explaining 1.65% of the variance. The third urban environmental profile was correlated with an emotional instability symptom group (r = 0.03, Pperm < 0.001). Our findings suggest that different environmental profiles of urban living may influence specific psychiatric symptom groups through distinct neurobiological pathways.","lang":"eng"}]},{"oa_version":"Published Version","day":"29","date_created":"2023-06-29T13:16:42Z","status":"public","keyword":["medial habenula","GABAB receptor","vesicle release","Flash and Freeze","Flash and Freeze-fracture"],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles at the presynaptic active zone (AZ). Strikingly, tonic and phasic release exhibit distinct coupling distances and are selectively affected by deletion of synaptoporin (SPO) and Ca2+-dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. Double pre-embedding immunolabeling confirmed the co-localization of CAPS2 and SPO inside the same terminal. The cytosolic protein CAPS2 showed a synaptic vesicle (SV)-associated distribution similar to the vesicular transmembrane protein SPO. A newly developed “Flash and Freeze-fracture” method revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to a persistent RRP increase. Thus, we discovered structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals."}],"file":[{"title":"Outdated Version","file_id":"13174","creator":"shigemot","date_updated":"2023-11-17T14:30:44Z","file_name":"Raw data for Koppensteiner et al.zip","description":"After review an updated version of the data is provided","content_type":"application/x-zip-compressed","access_level":"closed","file_size":542873672,"relation":"main_file","date_created":"2023-06-29T13:11:22Z","checksum":"ed59170869ba621f89f7c1894092192f"},{"date_created":"2023-11-17T14:13:02Z","checksum":"c07860eb82b4d367245f1b589fe5c250","access_level":"open_access","success":1,"file_size":915079,"relation":"main_file","date_updated":"2023-11-17T14:13:02Z","file_name":"11-17-23 Updated Koppensteiner et al. raw data.xlsx","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","creator":"patrickd","file_id":"14550"},{"creator":"dernst","file_id":"14942","content_type":"application/x-zip-compressed","file_name":"EM_Images.zip","date_updated":"2024-02-06T07:21:43Z","file_size":544868924,"relation":"main_file","success":1,"access_level":"open_access","checksum":"abf84b1699edac4349dc3a92d466fb7b","date_created":"2024-02-06T07:21:43Z"}],"ddc":["571"],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"15084"}]},"year":"2023","date_published":"2023-07-29T00:00:00Z","oa":1,"citation":{"ista":"Shigemoto R. 2023. Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:13173\">10.15479/AT:ISTA:13173</a>.","mla":"Shigemoto, Ryuichi. <i>Transition from Tonic to Phasic Neurotransmitter Release by Presynaptic GABAB Receptor Activation in Medial Habenula Terminals</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13173\">10.15479/AT:ISTA:13173</a>.","ieee":"R. Shigemoto, “Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals.” Institute of Science and Technology Austria, 2023.","apa":"Shigemoto, R. (2023). Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:13173\">https://doi.org/10.15479/AT:ISTA:13173</a>","short":"R. Shigemoto, (2023).","chicago":"Shigemoto, Ryuichi. “Transition from Tonic to Phasic Neurotransmitter Release by Presynaptic GABAB Receptor Activation in Medial Habenula Terminals.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:13173\">https://doi.org/10.15479/AT:ISTA:13173</a>.","ama":"Shigemoto R. Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13173\">10.15479/AT:ISTA:13173</a>"},"_id":"13173","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","doi":"10.15479/AT:ISTA:13173","file_date_updated":"2024-02-06T07:21:43Z","tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"date_updated":"2025-09-04T12:16:24Z","corr_author":"1","department":[{"_id":"RySh"}],"month":"07","title":"Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals","author":[{"first_name":"Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data"},{"quality_controlled":"1","external_id":{"isi":["000988204400001"],"arxiv":["1804.08353"]},"volume":151,"day":"01","oa_version":"Preprint","article_type":"original","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1804.08353","open_access":"1"}],"abstract":[{"text":"In this note we study the eigenvalue growth of infinite graphs with discrete spectrum. We assume that the corresponding Dirichlet forms satisfy certain Sobolev-type inequalities and that the total measure is finite. In this sense, the associated operators on these graphs display similarities to elliptic operators on bounded domains in the continuum. Specifically, we prove lower bounds on the eigenvalue growth and show by examples that corresponding upper bounds cannot be established.","lang":"eng"}],"doi":"10.1090/proc/14361","publisher":"American Mathematical Society","publication_identifier":{"issn":["0002-9939"],"eissn":["1088-6826"]},"article_processing_charge":"No","publication_status":"published","citation":{"apa":"Hua, B., Keller, M., Schwarz, M., &#38; Wirth, M. (2023). Sobolev-type inequalities and eigenvalue growth on graphs with finite measure. <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/proc/14361\">https://doi.org/10.1090/proc/14361</a>","short":"B. Hua, M. Keller, M. Schwarz, M. Wirth, Proceedings of the American Mathematical Society 151 (2023) 3401–3414.","chicago":"Hua, Bobo, Matthias Keller, Michael Schwarz, and Melchior Wirth. “Sobolev-Type Inequalities and Eigenvalue Growth on Graphs with Finite Measure.” <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society, 2023. <a href=\"https://doi.org/10.1090/proc/14361\">https://doi.org/10.1090/proc/14361</a>.","ama":"Hua B, Keller M, Schwarz M, Wirth M. Sobolev-type inequalities and eigenvalue growth on graphs with finite measure. <i>Proceedings of the American Mathematical Society</i>. 2023;151(8):3401-3414. doi:<a href=\"https://doi.org/10.1090/proc/14361\">10.1090/proc/14361</a>","ista":"Hua B, Keller M, Schwarz M, Wirth M. 2023. Sobolev-type inequalities and eigenvalue growth on graphs with finite measure. Proceedings of the American Mathematical Society. 151(8), 3401–3414.","mla":"Hua, Bobo, et al. “Sobolev-Type Inequalities and Eigenvalue Growth on Graphs with Finite Measure.” <i>Proceedings of the American Mathematical Society</i>, vol. 151, no. 8, American Mathematical Society, 2023, pp. 3401–14, doi:<a href=\"https://doi.org/10.1090/proc/14361\">10.1090/proc/14361</a>.","ieee":"B. Hua, M. Keller, M. Schwarz, and M. Wirth, “Sobolev-type inequalities and eigenvalue growth on graphs with finite measure,” <i>Proceedings of the American Mathematical Society</i>, vol. 151, no. 8. American Mathematical Society, pp. 3401–3414, 2023."},"date_published":"2023-08-01T00:00:00Z","year":"2023","isi":1,"title":"Sobolev-type inequalities and eigenvalue growth on graphs with finite measure","month":"08","department":[{"_id":"JaMa"}],"date_updated":"2024-10-09T21:05:50Z","language":[{"iso":"eng"}],"publication":"Proceedings of the American Mathematical Society","date_created":"2023-07-02T22:00:43Z","status":"public","scopus_import":"1","page":"3401-3414","intvolume":"       151","arxiv":1,"_id":"13177","oa":1,"type":"journal_article","acknowledgement":"The second author was supported by the priority program SPP2026 of the German Research Foundation (DFG). The fourth author was supported by the German Academic Scholarship Foundation (Studienstiftung des deutschen Volkes) and by the German Research Foundation (DFG) via RTG 1523/2.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Bobo","last_name":"Hua","full_name":"Hua, Bobo"},{"first_name":"Matthias","last_name":"Keller","full_name":"Keller, Matthias"},{"last_name":"Schwarz","full_name":"Schwarz, Michael","first_name":"Michael"},{"orcid":"0000-0002-0519-4241","first_name":"Melchior","last_name":"Wirth","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","full_name":"Wirth, Melchior"}],"issue":"8","corr_author":"1"},{"citation":{"chicago":"Mitrouskas, David Johannes, Krzysztof Mysliwy, and Robert Seiringer. “Optimal Parabolic Upper Bound for the Energy-Momentum Relation of a Strongly Coupled Polaron.” <i>Forum of Mathematics</i>. Cambridge University Press, 2023. <a href=\"https://doi.org/10.1017/fms.2023.45\">https://doi.org/10.1017/fms.2023.45</a>.","ama":"Mitrouskas DJ, Mysliwy K, Seiringer R. Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron. <i>Forum of Mathematics</i>. 2023;11:1-52. doi:<a href=\"https://doi.org/10.1017/fms.2023.45\">10.1017/fms.2023.45</a>","apa":"Mitrouskas, D. J., Mysliwy, K., &#38; Seiringer, R. (2023). Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron. <i>Forum of Mathematics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/fms.2023.45\">https://doi.org/10.1017/fms.2023.45</a>","short":"D.J. Mitrouskas, K. Mysliwy, R. Seiringer, Forum of Mathematics 11 (2023) 1–52.","mla":"Mitrouskas, David Johannes, et al. “Optimal Parabolic Upper Bound for the Energy-Momentum Relation of a Strongly Coupled Polaron.” <i>Forum of Mathematics</i>, vol. 11, Cambridge University Press, 2023, pp. 1–52, doi:<a href=\"https://doi.org/10.1017/fms.2023.45\">10.1017/fms.2023.45</a>.","ieee":"D. J. Mitrouskas, K. Mysliwy, and R. Seiringer, “Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron,” <i>Forum of Mathematics</i>, vol. 11. Cambridge University Press, pp. 1–52, 2023.","ista":"Mitrouskas DJ, Mysliwy K, Seiringer R. 2023. Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron. Forum of Mathematics. 11, 1–52."},"year":"2023","date_published":"2023-06-13T00:00:00Z","publication_status":"published","doi":"10.1017/fms.2023.45","article_processing_charge":"Yes","publication_identifier":{"eissn":["2050-5094"]},"publisher":"Cambridge University Press","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"month":"06","department":[{"_id":"RoSe"}],"date_updated":"2025-04-14T07:26:58Z","title":"Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron","isi":1,"day":"13","oa_version":"Published Version","volume":11,"ec_funded":1,"project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"external_id":{"isi":["001005008800001"],"arxiv":["2203.02454"]},"quality_controlled":"1","abstract":[{"lang":"eng","text":"We consider the large polaron described by the Fröhlich Hamiltonian and study its energy-momentum relation defined as the lowest possible energy as a function of the total momentum. Using a suitable family of trial states, we derive an optimal parabolic upper bound for the energy-momentum relation in the limit of strong coupling. The upper bound consists of a momentum independent term that agrees with the predicted two-term expansion for the ground state energy of the strongly coupled polaron at rest and a term that is quadratic in the momentum with coefficient given by the inverse of twice the classical effective mass introduced by Landau and Pekar."}],"article_type":"original","oa":1,"_id":"13178","arxiv":1,"file_date_updated":"2023-07-03T10:36:25Z","corr_author":"1","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Mitrouskas","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","full_name":"Mitrouskas, David Johannes","first_name":"David Johannes"},{"first_name":"Krzysztof","full_name":"Mysliwy, Krzysztof","id":"316457FC-F248-11E8-B48F-1D18A9856A87","last_name":"Mysliwy"},{"orcid":"0000-0002-6781-0521","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"acknowledgement":"This research was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme grant agreement No. 694227 (R.S.) and the Maria Skłodowska-Curie grant agreement No. 665386 (K.M.).","date_created":"2023-07-02T22:00:43Z","scopus_import":"1","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Forum of Mathematics","file":[{"file_id":"13186","creator":"alisjak","content_type":"application/pdf","file_name":"2023_ForumofMathematics.Sigma_Mitrouskas.pdf","date_updated":"2023-07-03T10:36:25Z","file_size":943192,"relation":"main_file","access_level":"open_access","success":1,"checksum":"f672eb7dd015c472c9a04f1b9bf9df7d","date_created":"2023-07-03T10:36:25Z"}],"ddc":["500"],"intvolume":"        11","page":"1-52"},{"quality_controlled":"1","oa_version":"Published Version","volume":7,"day":"06","abstract":[{"text":"Writing concurrent code that is both correct and efficient is notoriously difficult. Thus, programmers often prefer to use synchronization abstractions, which render code simpler and easier to reason about. Despite a wealth of work on this topic, there is still a gap between the rich semantics provided by synchronization abstractions in modern programming languages—specifically, fair FIFO ordering of synchronization requests and support for abortable operations—and frameworks for implementing it correctly and efficiently. Supporting such semantics is critical given the rising popularity of constructs for asynchronous programming, such as coroutines, which abort frequently and are cheaper to suspend and resume compared to native threads.\r\n\r\nThis paper introduces a new framework called CancellableQueueSynchronizer (CQS), which enables simple yet efficient implementations of a wide range of fair and abortable synchronization primitives: mutexes, semaphores, barriers, count-down latches, and blocking pools. Our main contribution is algorithmic, as implementing both fairness and abortability efficiently at this level of generality is non-trivial. Importantly, all our algorithms, including the CQS framework and the primitives built on top of it, come with formal proofs in the Iris framework for Coq for many of their properties. These proofs are modular, so it is easy to show correctness for new primitives implemented on top of CQS. From a practical perspective, implementation of CQS for native threads on the JVM improves throughput by up to two orders of magnitude over Java’s AbstractQueuedSynchronizer, the only practical abstraction offering similar semantics. Further, we successfully integrated CQS as a core component of the popular Kotlin Coroutines library, validating the framework’s practical impact and expressiveness in a real-world environment. In sum, CancellableQueueSynchronizer is the first framework to combine expressiveness with formal guarantees and solid practical performance. Our approach should be extensible to other languages and families of synchronization primitives.","lang":"eng"}],"article_type":"original","publication_status":"published","article_processing_charge":"No","publication_identifier":{"eissn":["2475-1421"]},"publisher":"Association for Computing Machinery ","doi":"10.1145/3591230","date_published":"2023-06-06T00:00:00Z","year":"2023","citation":{"ieee":"N. Koval, D. Khalanskiy, and D.-A. Alistarh, “CQS: A formally-verified framework for fair and abortable synchronization,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 7. Association for Computing Machinery , 2023.","mla":"Koval, Nikita, et al. “CQS: A Formally-Verified Framework for Fair and Abortable Synchronization.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 7, 116, Association for Computing Machinery , 2023, doi:<a href=\"https://doi.org/10.1145/3591230\">10.1145/3591230</a>.","ista":"Koval N, Khalanskiy D, Alistarh D-A. 2023. CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. 7, 116.","ama":"Koval N, Khalanskiy D, Alistarh D-A. CQS: A formally-verified framework for fair and abortable synchronization. <i>Proceedings of the ACM on Programming Languages</i>. 2023;7. doi:<a href=\"https://doi.org/10.1145/3591230\">10.1145/3591230</a>","chicago":"Koval, Nikita, Dmitry Khalanskiy, and Dan-Adrian Alistarh. “CQS: A Formally-Verified Framework for Fair and Abortable Synchronization.” <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery , 2023. <a href=\"https://doi.org/10.1145/3591230\">https://doi.org/10.1145/3591230</a>.","short":"N. Koval, D. Khalanskiy, D.-A. Alistarh, Proceedings of the ACM on Programming Languages 7 (2023).","apa":"Koval, N., Khalanskiy, D., &#38; Alistarh, D.-A. (2023). CQS: A formally-verified framework for fair and abortable synchronization. <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery . <a href=\"https://doi.org/10.1145/3591230\">https://doi.org/10.1145/3591230</a>"},"title":"CQS: A formally-verified framework for fair and abortable synchronization","article_number":"116","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2024-10-09T21:05:51Z","month":"06","department":[{"_id":"DaAl"}],"has_accepted_license":"1","publication":"Proceedings of the ACM on Programming Languages","language":[{"iso":"eng"}],"scopus_import":"1","status":"public","date_created":"2023-07-02T22:00:43Z","intvolume":"         7","file":[{"file_name":"2023_ACMProgram.Lang._Koval.pdf","date_updated":"2023-07-03T13:09:39Z","content_type":"application/pdf","creator":"alisjak","file_id":"13187","date_created":"2023-07-03T13:09:39Z","checksum":"5dba6e73f0ed79adbdae14d165bc2f68","success":1,"access_level":"open_access","file_size":1266773,"relation":"main_file"}],"ddc":["000"],"_id":"13179","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Nikita","last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita"},{"last_name":"Khalanskiy","full_name":"Khalanskiy, Dmitry","first_name":"Dmitry"},{"orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"}],"type":"journal_article","file_date_updated":"2023-07-03T13:09:39Z","corr_author":"1"},{"volume":16,"oa_version":"Preprint","day":"26","external_id":{"arxiv":["2203.06881"]},"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2203.06881"}],"abstract":[{"lang":"eng","text":"We study the density of everywhere locally soluble diagonal quadric surfaces, parameterised by rational points that lie on a split quadric surface"}],"article_type":"original","citation":{"ista":"Browning TD, Lyczak J, Sarapin R. 2023. Local solubility for a family of quadrics over a split quadric surface. Involve. 16(2), 331–342.","ieee":"T. D. Browning, J. Lyczak, and R. Sarapin, “Local solubility for a family of quadrics over a split quadric surface,” <i>Involve</i>, vol. 16, no. 2. Mathematical Sciences Publishers, pp. 331–342, 2023.","mla":"Browning, Timothy D., et al. “Local Solubility for a Family of Quadrics over a Split Quadric Surface.” <i>Involve</i>, vol. 16, no. 2, Mathematical Sciences Publishers, 2023, pp. 331–42, doi:<a href=\"https://doi.org/10.2140/involve.2023.16.331\">10.2140/involve.2023.16.331</a>.","short":"T.D. Browning, J. Lyczak, R. Sarapin, Involve 16 (2023) 331–342.","apa":"Browning, T. D., Lyczak, J., &#38; Sarapin, R. (2023). Local solubility for a family of quadrics over a split quadric surface. <i>Involve</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/involve.2023.16.331\">https://doi.org/10.2140/involve.2023.16.331</a>","ama":"Browning TD, Lyczak J, Sarapin R. Local solubility for a family of quadrics over a split quadric surface. <i>Involve</i>. 2023;16(2):331-342. doi:<a href=\"https://doi.org/10.2140/involve.2023.16.331\">10.2140/involve.2023.16.331</a>","chicago":"Browning, Timothy D, Julian Lyczak, and Roman Sarapin. “Local Solubility for a Family of Quadrics over a Split Quadric Surface.” <i>Involve</i>. Mathematical Sciences Publishers, 2023. <a href=\"https://doi.org/10.2140/involve.2023.16.331\">https://doi.org/10.2140/involve.2023.16.331</a>."},"date_published":"2023-05-26T00:00:00Z","year":"2023","publication_status":"published","doi":"10.2140/involve.2023.16.331","publication_identifier":{"eissn":["1944-4184"],"issn":["1944-4176"]},"publisher":"Mathematical Sciences Publishers","article_processing_charge":"No","month":"05","department":[{"_id":"TiBr"}],"date_updated":"2024-10-09T21:05:51Z","title":"Local solubility for a family of quadrics over a split quadric surface","date_created":"2023-07-02T22:00:43Z","status":"public","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Involve","intvolume":"        16","page":"331-342","oa":1,"_id":"13180","arxiv":1,"issue":"2","corr_author":"1","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D"},{"last_name":"Lyczak","full_name":"Lyczak, Julian","id":"3572849A-F248-11E8-B48F-1D18A9856A87","first_name":"Julian"},{"first_name":"Roman","full_name":"Sarapin, Roman","last_name":"Sarapin"}]},{"oa":1,"_id":"13197","arxiv":1,"file_date_updated":"2023-07-07T12:49:51Z","issue":"6","corr_author":"1","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Grosjean","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","full_name":"Grosjean, Galien M","orcid":"0000-0001-5154-417X","first_name":"Galien M"},{"orcid":"0000-0002-2299-3176","first_name":"Scott R","full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis"}],"acknowledgement":"This project has received funding from the European Research Council Grant Agreement No. 949120 and from\r\nthe European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant\r\nAgreement No. 754411. ","keyword":["Physics and Astronomy (miscellaneous)","General Materials Science"],"date_created":"2023-07-07T12:48:01Z","status":"public","scopus_import":"1","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Physical Review Materials","file":[{"checksum":"75584730d9cdd50eeccb4c52c509776d","date_created":"2023-07-07T12:49:51Z","file_size":1127040,"relation":"main_file","success":1,"access_level":"open_access","content_type":"application/pdf","date_updated":"2023-07-07T12:49:51Z","file_name":"Mosaic_asymmetries.pdf","file_id":"13198","creator":"ggrosjea"}],"ddc":["537"],"intvolume":"         7","citation":{"chicago":"Grosjean, Galien M, and Scott R Waitukaitis. “Asymmetries in Triboelectric Charging: Generalizing Mosaic Models to Different-Material Samples and Sliding Contacts.” <i>Physical Review Materials</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevmaterials.7.065601\">https://doi.org/10.1103/physrevmaterials.7.065601</a>.","ama":"Grosjean GM, Waitukaitis SR. Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts. <i>Physical Review Materials</i>. 2023;7(6). doi:<a href=\"https://doi.org/10.1103/physrevmaterials.7.065601\">10.1103/physrevmaterials.7.065601</a>","apa":"Grosjean, G. M., &#38; Waitukaitis, S. R. (2023). Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts. <i>Physical Review Materials</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevmaterials.7.065601\">https://doi.org/10.1103/physrevmaterials.7.065601</a>","short":"G.M. Grosjean, S.R. Waitukaitis, Physical Review Materials 7 (2023).","mla":"Grosjean, Galien M., and Scott R. Waitukaitis. “Asymmetries in Triboelectric Charging: Generalizing Mosaic Models to Different-Material Samples and Sliding Contacts.” <i>Physical Review Materials</i>, vol. 7, no. 6, 065601, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevmaterials.7.065601\">10.1103/physrevmaterials.7.065601</a>.","ieee":"G. M. Grosjean and S. R. Waitukaitis, “Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts,” <i>Physical Review Materials</i>, vol. 7, no. 6. American Physical Society, 2023.","ista":"Grosjean GM, Waitukaitis SR. 2023. Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts. Physical Review Materials. 7(6), 065601."},"date_published":"2023-06-13T00:00:00Z","year":"2023","publication_status":"published","doi":"10.1103/physrevmaterials.7.065601","article_processing_charge":"No","publisher":"American Physical Society","publication_identifier":{"issn":["2475-9953"]},"month":"06","department":[{"_id":"ScWa"}],"date_updated":"2025-04-14T07:43:55Z","title":"Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts","article_number":"065601","isi":1,"day":"13","oa_version":"Submitted Version","volume":7,"ec_funded":1,"project":[{"grant_number":"949120","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020","name":"Tribocharge: a multi-scale approach to an enduring problem in physics"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"quality_controlled":"1","external_id":{"isi":["001019565900002"],"arxiv":["2304.12861"]},"abstract":[{"text":"Nominally identical materials exchange net electric charge during contact through a mechanism that is still debated. ‘Mosaic models’, in which surfaces are presumed to consist of a random patchwork of microscopic donor/acceptor sites, offer an appealing explanation for this phenomenon. However, recent experiments have shown that global differences persist even between same-material samples, which the standard mosaic framework does not account for. Here, we expand the mosaic framework by incorporating global differences in the densities of donor/acceptor sites. We develop\r\nan analytical model, backed by numerical simulations, that smoothly connects the global and deterministic charge transfer of different materials to the local and stochastic mosaic picture normally associated with identical materials. Going further, we extend our model to explain the effect of contact asymmetries during sliding, providing a plausible explanation for reversal of charging sign that has been observed experimentally.","lang":"eng"}],"article_type":"original"},{"status":"public","date_created":"2023-07-09T22:01:12Z","scopus_import":"1","acknowledged_ssus":[{"_id":"EM-Fac"}],"has_accepted_license":"1","publication":"The Journal of Neuroscience","language":[{"iso":"eng"}],"file":[{"file_name":"2023_JN_Eguchi.pdf","date_updated":"2023-07-10T09:04:58Z","content_type":"application/pdf","creator":"alisjak","file_id":"13205","date_created":"2023-07-10T09:04:58Z","checksum":"70b2141870e0bf1c94fd343e18fdbc32","access_level":"open_access","success":1,"file_size":7794425,"relation":"main_file"}],"ddc":["570"],"pmid":1,"intvolume":"        43","page":"4197-4216","oa":1,"_id":"13202","file_date_updated":"2023-07-10T09:04:58Z","corr_author":"1","issue":"23","author":[{"first_name":"Kohgaku","orcid":"0000-0002-6170-2546","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","full_name":"Eguchi, Kohgaku","last_name":"Eguchi"},{"last_name":"Le Monnier","id":"3B59276A-F248-11E8-B48F-1D18A9856A87","full_name":"Le Monnier, Elodie","first_name":"Elodie"},{"last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","first_name":"Ryuichi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported by The Institute of Science and Technology (IST) Austria, the European Union's Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie Grant Agreement No. 793482 (to K.E.) and by the European Research Council (ERC) Grant Agreement No. 694539 (to R.S.). We thank Nicoleta Condruz (IST Austria, Klosterneuburg, Austria) for technical assistance with sample preparation, the Electron Microscopy Facility of IST Austria (Klosterneuburg, Austria) for technical support with EM works, Natalia Baranova (University of Vienna, Vienna, Austria) and Martin Loose (IST Austria, Klosterneuburg, Austria) for advice on liposome preparation, and Yugo Fukazawa (University of Fukui, Fukui, Japan) for comments.","type":"journal_article","volume":43,"day":"07","oa_version":"Published Version","ec_funded":1,"quality_controlled":"1","external_id":{"isi":["001020132100005"],"pmid":["37160366"]},"project":[{"_id":"2659CC84-B435-11E9-9278-68D0E5697425","name":"Ultrastructural analysis of phosphoinositides in nerve terminals: distribution, dynamics and physiological roles in synaptic transmission","call_identifier":"H2020","grant_number":"793482"},{"grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"}],"abstract":[{"text":"Phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) plays an essential role in neuronal activities through interaction with various proteins involved in signaling at membranes. However, the distribution pattern of PI(4,5)P2 and the association with these proteins on the neuronal cell membranes remain elusive. In this study, we established a method for visualizing PI(4,5)P2 by SDS-digested freeze-fracture replica labeling (SDS-FRL) to investigate the quantitative nanoscale distribution of PI(4,5)P2 in cryo-fixed brain. We demonstrate that PI(4,5)P2 forms tiny clusters with a mean size of ∼1000 nm2 rather than randomly distributed in cerebellar neuronal membranes in male C57BL/6J mice. These clusters show preferential accumulation in specific membrane compartments of different cell types, in particular, in Purkinje cell (PC) spines and granule cell (GC) presynaptic active zones. Furthermore, we revealed extensive association of PI(4,5)P2 with CaV2.1 and GIRK3 across different membrane compartments, whereas its association with mGluR1α was compartment specific. These results suggest that our SDS-FRL method provides valuable insights into the physiological functions of PI(4,5)P2 in neurons.","lang":"eng"}],"article_type":"original","date_published":"2023-06-07T00:00:00Z","year":"2023","citation":{"mla":"Eguchi, Kohgaku, et al. “Nanoscale Phosphoinositide Distribution on Cell Membranes of Mouse Cerebellar Neurons.” <i>The Journal of Neuroscience</i>, vol. 43, no. 23, Society for Neuroscience, 2023, pp. 4197–216, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1514-22.2023\">10.1523/JNEUROSCI.1514-22.2023</a>.","ieee":"K. Eguchi, E. Le Monnier, and R. Shigemoto, “Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons,” <i>The Journal of Neuroscience</i>, vol. 43, no. 23. Society for Neuroscience, pp. 4197–4216, 2023.","ista":"Eguchi K, Le Monnier E, Shigemoto R. 2023. Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons. The Journal of Neuroscience. 43(23), 4197–4216.","chicago":"Eguchi, Kohgaku, Elodie Le Monnier, and Ryuichi Shigemoto. “Nanoscale Phosphoinositide Distribution on Cell Membranes of Mouse Cerebellar Neurons.” <i>The Journal of Neuroscience</i>. Society for Neuroscience, 2023. <a href=\"https://doi.org/10.1523/JNEUROSCI.1514-22.2023\">https://doi.org/10.1523/JNEUROSCI.1514-22.2023</a>.","ama":"Eguchi K, Le Monnier E, Shigemoto R. Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons. <i>The Journal of Neuroscience</i>. 2023;43(23):4197-4216. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1514-22.2023\">10.1523/JNEUROSCI.1514-22.2023</a>","apa":"Eguchi, K., Le Monnier, E., &#38; Shigemoto, R. (2023). Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons. <i>The Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.1514-22.2023\">https://doi.org/10.1523/JNEUROSCI.1514-22.2023</a>","short":"K. Eguchi, E. Le Monnier, R. Shigemoto, The Journal of Neuroscience 43 (2023) 4197–4216."},"publication_status":"published","article_processing_charge":"No","publisher":"Society for Neuroscience","publication_identifier":{"issn":["0270-6474"],"eissn":["1529-2401"]},"doi":"10.1523/JNEUROSCI.1514-22.2023","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2025-04-14T07:27:15Z","month":"06","department":[{"_id":"RySh"}],"title":"Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons","isi":1},{"publisher":"Elsevier ","publication_identifier":{"eissn":["2590-3462"]},"article_processing_charge":"Yes","doi":"10.1016/j.xplc.2023.100632","publication_status":"published","year":"2023","date_published":"2023-11-13T00:00:00Z","citation":{"short":"J. Xia, M. Kong, Z. Yang, L. Sun, Y. Peng, Y. Mao, H. Wei, W. Ying, Y. Gao, J. Friml, J. Weng, X. Liu, L. Sun, S. Tan, Plant Communications 4 (2023).","apa":"Xia, J., Kong, M., Yang, Z., Sun, L., Peng, Y., Mao, Y., … Tan, S. (2023). Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen. <i>Plant Communications</i>. Elsevier . <a href=\"https://doi.org/10.1016/j.xplc.2023.100632\">https://doi.org/10.1016/j.xplc.2023.100632</a>","ama":"Xia J, Kong M, Yang Z, et al. Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen. <i>Plant Communications</i>. 2023;4(6). doi:<a href=\"https://doi.org/10.1016/j.xplc.2023.100632\">10.1016/j.xplc.2023.100632</a>","chicago":"Xia, Jing, Mengjuan Kong, Zhisen Yang, Lianghanxiao Sun, Yakun Peng, Yanbo Mao, Hong Wei, et al. “Chemical Inhibition of Arabidopsis PIN-FORMED Auxin Transporters by the Anti-Inflammatory Drug Naproxen.” <i>Plant Communications</i>. Elsevier , 2023. <a href=\"https://doi.org/10.1016/j.xplc.2023.100632\">https://doi.org/10.1016/j.xplc.2023.100632</a>.","ista":"Xia J, Kong M, Yang Z, Sun L, Peng Y, Mao Y, Wei H, Ying W, Gao Y, Friml J, Weng J, Liu X, Sun L, Tan S. 2023. Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen. Plant Communications. 4(6), 100632.","ieee":"J. Xia <i>et al.</i>, “Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen,” <i>Plant Communications</i>, vol. 4, no. 6. Elsevier , 2023.","mla":"Xia, Jing, et al. “Chemical Inhibition of Arabidopsis PIN-FORMED Auxin Transporters by the Anti-Inflammatory Drug Naproxen.” <i>Plant Communications</i>, vol. 4, no. 6, 100632, Elsevier , 2023, doi:<a href=\"https://doi.org/10.1016/j.xplc.2023.100632\">10.1016/j.xplc.2023.100632</a>."},"article_number":"100632","isi":1,"title":"Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen","date_updated":"2024-10-21T06:01:37Z","month":"11","department":[{"_id":"JiFr"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"quality_controlled":"1","external_id":{"pmid":["37254481"],"isi":["001113003000001"]},"oa_version":"Published Version","day":"13","volume":4,"article_type":"original","abstract":[{"text":"The phytohormone auxin plays central roles in many growth and developmental processes in plants. Development of chemical tools targeting the auxin pathway is useful for both plant biology and agriculture. Here we reveal that naproxen, a synthetic compound with anti-inflammatory activity in humans, acts as an auxin transport inhibitor targeting PIN-FORMED (PIN) transporters in plants. Physiological experiments indicate that exogenous naproxen treatment affects pleiotropic auxin-regulated developmental processes. Additional cellular and biochemical evidence indicates that naproxen suppresses auxin transport, specifically PIN-mediated auxin efflux. Moreover, biochemical and structural analyses confirm that naproxen binds directly to PIN1 protein via the same binding cavity as the indole-3-acetic acid substrate. Thus, by combining cellular, biochemical, and structural approaches, this study clearly establishes that naproxen is a PIN inhibitor and elucidates the underlying mechanisms. Further use of this compound may advance our understanding of the molecular mechanisms of PIN-mediated auxin transport and expand our toolkit in auxin biology and agriculture.","lang":"eng"}],"_id":"13209","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Xia, Jing","last_name":"Xia","first_name":"Jing"},{"full_name":"Kong, Mengjuan","last_name":"Kong","first_name":"Mengjuan"},{"full_name":"Yang, Zhisen","last_name":"Yang","first_name":"Zhisen"},{"first_name":"Lianghanxiao","full_name":"Sun, Lianghanxiao","last_name":"Sun"},{"last_name":"Peng","full_name":"Peng, Yakun","first_name":"Yakun"},{"first_name":"Yanbo","full_name":"Mao, Yanbo","last_name":"Mao"},{"last_name":"Wei","full_name":"Wei, Hong","first_name":"Hong"},{"first_name":"Wei","last_name":"Ying","full_name":"Ying, Wei"},{"full_name":"Gao, Yongxiao","last_name":"Gao","first_name":"Yongxiao"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"first_name":"Jianping","last_name":"Weng","full_name":"Weng, Jianping"},{"first_name":"Xin","full_name":"Liu, Xin","last_name":"Liu"},{"first_name":"Linfeng","last_name":"Sun","full_name":"Sun, Linfeng"},{"full_name":"Tan, Shutang","last_name":"Tan","first_name":"Shutang"}],"acknowledgement":"This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB37020103 to Linfeng Sun); research funds from the Center for Advanced Interdisciplinary Science\r\nand Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China (QYPY20220012 to S.T.); start-up funding from the University of Science and Technology of China and the\r\nChinese Academy of Sciences (GG9100007007, KY9100000026,KY9100000051, and KJ2070000079 to S.T.); the National Natural Science Foundation of China (31900885 to X.L. and 31870732 to Linfeng Sun); the Natural Science Foundation of Anhui Province (2008085MC90 to X.L. and 2008085J15 to Linfeng Sun); the Fundamental Research Funds for the Central Universities (WK9100000021 to S.T. and WK9100000031 to Linfeng Sun); and the USTC Research Funds of the Double First-Class Initiative (YD9100002016 to S.T. and YD9100002004 to Linfeng Sun). Linfeng Sun is supported by an Outstanding Young Scholar Award from the Qiu Shi Science and Technologies Foundation and a Young Scholar Award from the Cyrus Tang Foundation.We thank Dr. Yang Zhao for sharing published materials (Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences) and the Cryo-EM Center of the University of Science and Technology of China for the EM facility support. We are grateful to Y. Gao and all other staff members for their technical support on cryo-EM data collection. ","type":"journal_article","issue":"6","file_date_updated":"2024-01-30T10:54:40Z","publication":"Plant Communications","language":[{"iso":"eng"}],"has_accepted_license":"1","date_created":"2023-07-12T07:32:00Z","scopus_import":"1","status":"public","pmid":1,"intvolume":"         4","ddc":["580"],"file":[{"access_level":"open_access","success":1,"file_size":1434862,"relation":"main_file","date_created":"2024-01-30T10:54:40Z","checksum":"f8ef92af6096834f91ce38587fb1db9f","creator":"dernst","file_id":"14900","file_name":"2023_PlantCommunications_Xia.pdf","date_updated":"2024-01-30T10:54:40Z","content_type":"application/pdf"}]},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2024-10-21T06:01:27Z","month":"07","department":[{"_id":"JiFr"}],"title":"Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots","isi":1,"year":"2023","date_published":"2023-07-01T00:00:00Z","citation":{"short":"C. Chen, Y. Zhang, J. Cai, Y. Qiu, L. Li, C. Gao, Y. Gao, M. Ke, S. Wu, C. Wei, J. Chen, T. Xu, J. Friml, J. Wang, R. Li, D. Chao, B. Zhang, X. Chen, Z. Gao, Plant Physiology 192 (2023) 2243–2260.","apa":"Chen, C., Zhang, Y., Cai, J., Qiu, Y., Li, L., Gao, C., … Gao, Z. (2023). Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1093/plphys/kiad207\">https://doi.org/10.1093/plphys/kiad207</a>","ama":"Chen C, Zhang Y, Cai J, et al. Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. <i>Plant Physiology</i>. 2023;192(3):2243-2260. doi:<a href=\"https://doi.org/10.1093/plphys/kiad207\">10.1093/plphys/kiad207</a>","chicago":"Chen, C, Y Zhang, J Cai, Y Qiu, L Li, C Gao, Y Gao, et al. “Multi-Copper Oxidases SKU5 and SKS1 Coordinate Cell Wall Formation Using Apoplastic Redox-Based Reactions in Roots.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2023. <a href=\"https://doi.org/10.1093/plphys/kiad207\">https://doi.org/10.1093/plphys/kiad207</a>.","ista":"Chen C, Zhang Y, Cai J, Qiu Y, Li L, Gao C, Gao Y, Ke M, Wu S, Wei C, Chen J, Xu T, Friml J, Wang J, Li R, Chao D, Zhang B, Chen X, Gao Z. 2023. Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. 192(3), 2243–2260.","ieee":"C. Chen <i>et al.</i>, “Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots,” <i>Plant Physiology</i>, vol. 192, no. 3. American Society of Plant Biologists, pp. 2243–2260, 2023.","mla":"Chen, C., et al. “Multi-Copper Oxidases SKU5 and SKS1 Coordinate Cell Wall Formation Using Apoplastic Redox-Based Reactions in Roots.” <i>Plant Physiology</i>, vol. 192, no. 3, American Society of Plant Biologists, 2023, pp. 2243–60, doi:<a href=\"https://doi.org/10.1093/plphys/kiad207\">10.1093/plphys/kiad207</a>."},"publication_status":"published","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"publisher":"American Society of Plant Biologists","article_processing_charge":"No","doi":"10.1093/plphys/kiad207","abstract":[{"lang":"eng","text":"The primary cell wall is a fundamental plant constituent that is flexible but sufficiently rigid to support the plant cell shape. Although many studies have demonstrated that reactive oxygen species (ROS) serve as important signaling messengers to modify the cell wall structure and affect cellular growth, the regulatory mechanism underlying the spatial-temporal regulation of ROS activity for cell wall maintenance remains largely unclear. Here, we demonstrate the role of the Arabidopsis (Arabidopsis thaliana) multicopper oxidase-like protein skewed 5 (SKU5) and its homolog SKU5-similar 1 (SKS1) in root cell wall formation through modulating ROS homeostasis. Loss of SKU5 and SKS1 function resulted in aberrant division planes, protruding cell walls, ectopic deposition of iron, and reduced nicotinamide adeninedinucleotide phosphate (NADPH) oxidase-dependent ROS overproduction in the root epidermis–cortex and cortex–endodermis junctions. A decrease in ROS level or inhibition of NADPH oxidase activity rescued the cell wall defects of sku5 sks1 double mutants. SKU5 and SKS1 proteins were activated by iron treatment, and iron over-accumulated in the walls between the root epidermis and cortex cell layers of sku5 sks1. The glycosylphosphatidylinositol-anchored motif was crucial for membrane association and functionality of SKU5 and SKS1. Overall, our results identified SKU5 and SKS1 as regulators of ROS at the cell surface for regulation of cell wall structure and root cell growth."}],"article_type":"original","day":"01","oa_version":"Published Version","volume":192,"quality_controlled":"1","external_id":{"pmid":["37010107"],"isi":["000971795800001"]},"file_date_updated":"2023-07-13T13:26:33Z","issue":"3","author":[{"first_name":"C","full_name":"Chen, C","last_name":"Chen"},{"first_name":"Y","full_name":"Zhang, Y","last_name":"Zhang"},{"last_name":"Cai","full_name":"Cai, J","first_name":"J"},{"last_name":"Qiu","full_name":"Qiu, Y","first_name":"Y"},{"last_name":"Li","full_name":"Li, L","first_name":"L"},{"first_name":"C","last_name":"Gao","full_name":"Gao, C"},{"first_name":"Y","last_name":"Gao","full_name":"Gao, Y"},{"first_name":"M","full_name":"Ke, M","last_name":"Ke"},{"first_name":"S","last_name":"Wu","full_name":"Wu, S"},{"full_name":"Wei, C","last_name":"Wei","first_name":"C"},{"first_name":"J","full_name":"Chen, J","last_name":"Chen"},{"first_name":"T","full_name":"Xu, T","last_name":"Xu"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"J","last_name":"Wang","full_name":"Wang, J"},{"last_name":"Li","full_name":"Li, R","first_name":"R"},{"first_name":"D","last_name":"Chao","full_name":"Chao, D"},{"first_name":"B","full_name":"Zhang, B","last_name":"Zhang"},{"full_name":"Chen, X","last_name":"Chen","first_name":"X"},{"first_name":"Z","full_name":"Gao, Z","last_name":"Gao"}],"acknowledgement":"We thank Dong liu for offering iron staining technique; ZhiChang Chen and Zhenbiao Yang for discussion; Dandan Zheng for earlier attempt; Liwen Jiang and Dingquan Huang for initial tests of the TEM experiment; John C. Sedbrook for a donation of sku5 and pSKU5::SKU5-GFP seeds; Catherine Perrot-Rechenmann and Ke Zhou for the donation of sks1, sks2, and sku5 sks1 seeds; Zengyu Liu and Zhongquan Lin for live-imaging microscopy assistance. We are grateful to Can Peng, and Xixia Li for helping with sample preparation, and taking TEM images, at the Center for Biological Imaging (CBI), Institute of Biophysics, Chinese Academy of Science.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","oa":1,"_id":"13213","file":[{"file_id":"13220","creator":"cchlebak","content_type":"application/pdf","date_updated":"2023-07-13T13:26:33Z","file_name":"2023_PlantPhys_Chen.pdf","relation":"main_file","file_size":2076977,"success":1,"access_level":"open_access","checksum":"5492e1d18ac3eaf202633d210fa0fb75","date_created":"2023-07-13T13:26:33Z"}],"ddc":["575"],"intvolume":"       192","pmid":1,"page":"2243-2260","scopus_import":"1","status":"public","date_created":"2023-07-12T07:32:58Z","has_accepted_license":"1","publication":"Plant Physiology","language":[{"iso":"eng"}]},{"day":"13","volume":12,"oa_version":"Published Version","project":[{"_id":"62883ed7-2b32-11ec-9570-93580204e56b","name":"Functional asymmetry of medial habenula outputs in mice","grant_number":"26130"}],"external_id":{"isi":["001017033600001"],"pmid":["37371083"]},"quality_controlled":"1","article_type":"review","abstract":[{"lang":"eng","text":"Nitrogen is an important macronutrient required for plant growth and development, thus directly impacting agricultural productivity. In recent years, numerous studies have shown that nitrogen-driven growth depends on pathways that control nitrate/nitrogen homeostasis and hormonal networks that act both locally and systemically to coordinate growth and development of plant organs. In this review, we will focus on recent advances in understanding the role of the plant hormones auxin and cytokinin and their crosstalk in nitrate-regulated growth and discuss the significance of novel findings and possible missing links."}],"citation":{"apa":"Abualia, R., Riegler, S., &#38; Benková, E. (2023). Nitrate, auxin and cytokinin - a trio to tango. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells12121613\">https://doi.org/10.3390/cells12121613</a>","short":"R. Abualia, S. Riegler, E. Benková, Cells 12 (2023).","chicago":"Abualia, R, Stefan Riegler, and Eva Benková. “Nitrate, Auxin and Cytokinin - a Trio to Tango.” <i>Cells</i>. MDPI, 2023. <a href=\"https://doi.org/10.3390/cells12121613\">https://doi.org/10.3390/cells12121613</a>.","ama":"Abualia R, Riegler S, Benková E. Nitrate, auxin and cytokinin - a trio to tango. <i>Cells</i>. 2023;12(12). doi:<a href=\"https://doi.org/10.3390/cells12121613\">10.3390/cells12121613</a>","ista":"Abualia R, Riegler S, Benková E. 2023. Nitrate, auxin and cytokinin - a trio to tango. Cells. 12(12), 1613.","mla":"Abualia, R., et al. “Nitrate, Auxin and Cytokinin - a Trio to Tango.” <i>Cells</i>, vol. 12, no. 12, 1613, MDPI, 2023, doi:<a href=\"https://doi.org/10.3390/cells12121613\">10.3390/cells12121613</a>.","ieee":"R. Abualia, S. Riegler, and E. Benková, “Nitrate, auxin and cytokinin - a trio to tango,” <i>Cells</i>, vol. 12, no. 12. MDPI, 2023."},"year":"2023","date_published":"2023-06-13T00:00:00Z","doi":"10.3390/cells12121613","publisher":"MDPI","article_processing_charge":"Yes","publication_identifier":{"issn":["2073-4409"]},"publication_status":"published","department":[{"_id":"EvBe"}],"month":"06","date_updated":"2025-04-15T06:27:18Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"article_number":"1613","title":"Nitrate, auxin and cytokinin - a trio to tango","status":"public","scopus_import":"1","date_created":"2023-07-12T07:41:25Z","language":[{"iso":"eng"}],"publication":"Cells","has_accepted_license":"1","ddc":["570"],"file":[{"access_level":"open_access","success":1,"relation":"main_file","file_size":1066802,"date_created":"2023-07-12T10:01:54Z","checksum":"6dc9df5f4f59fc27c509c275060354a5","creator":"alisjak","file_id":"13218","date_updated":"2023-07-12T10:01:54Z","file_name":"2023_cells_Abualia.pdf","content_type":"application/pdf"}],"intvolume":"        12","pmid":1,"oa":1,"_id":"13214","issue":"12","corr_author":"1","file_date_updated":"2023-07-12T10:01:54Z","type":"journal_article","author":[{"first_name":"R","last_name":"Abualia","full_name":"Abualia, R"},{"first_name":"Stefan","orcid":"0000-0003-3413-1343","last_name":"Riegler","full_name":"Riegler, Stefan","id":"FF6018E0-D806-11E9-8E43-0B14E6697425"},{"first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","last_name":"Benková"}],"acknowledgement":"This work was supported by the Austrian Academy of Sciences ÖAW: Doc fellowship (26130) to Stefan Riegler.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"oa":1,"_id":"13216","issue":"27","corr_author":"1","file_date_updated":"2023-07-12T10:22:04Z","type":"journal_article","author":[{"id":"91deeae8-1207-11ec-b130-c194ad5b50c6","full_name":"Bunting, Rhys","last_name":"Bunting","first_name":"Rhys","orcid":"0000-0001-6928-074X"},{"orcid":"0009-0000-1457-795X","first_name":"Felix","last_name":"Wodaczek","id":"8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e","full_name":"Wodaczek, Felix"},{"first_name":"Tina","last_name":"Torabi","full_name":"Torabi, Tina"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632","first_name":"Bingqing"}],"acknowledgement":"B.C. acknowledges resources provided by the Cambridge Tier2 system operated by the University of Cambridge Research\r\nComputing Service funded by EPSRC Tier-2 capital grant EP/\r\nP020259/1.","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"date_created":"2023-07-12T09:16:40Z","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Journal of the American Chemical Society","has_accepted_license":"1","ddc":["540"],"file":[{"file_id":"13219","creator":"cchlebak","file_name":"2023_JACS_Bunting.pdf","date_updated":"2023-07-12T10:22:04Z","content_type":"application/pdf","success":1,"access_level":"open_access","relation":"main_file","file_size":3155843,"date_created":"2023-07-12T10:22:04Z","checksum":"e07d5323f9c0e5cbd1ad6453f29440ab"}],"page":"14894-14902","pmid":1,"intvolume":"       145","citation":{"apa":"Bunting, R., Wodaczek, F., Torabi, T., &#38; Cheng, B. (2023). Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.3c04030\">https://doi.org/10.1021/jacs.3c04030</a>","short":"R. Bunting, F. Wodaczek, T. Torabi, B. Cheng, Journal of the American Chemical Society 145 (2023) 14894–14902.","chicago":"Bunting, Rhys, Felix Wodaczek, Tina Torabi, and Bingqing Cheng. “Reactivity of Single-Atom Alloy Nanoparticles: Modeling the Dehydrogenation of Propane.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/jacs.3c04030\">https://doi.org/10.1021/jacs.3c04030</a>.","ama":"Bunting R, Wodaczek F, Torabi T, Cheng B. Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. <i>Journal of the American Chemical Society</i>. 2023;145(27):14894-14902. doi:<a href=\"https://doi.org/10.1021/jacs.3c04030\">10.1021/jacs.3c04030</a>","ista":"Bunting R, Wodaczek F, Torabi T, Cheng B. 2023. Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. Journal of the American Chemical Society. 145(27), 14894–14902.","mla":"Bunting, Rhys, et al. “Reactivity of Single-Atom Alloy Nanoparticles: Modeling the Dehydrogenation of Propane.” <i>Journal of the American Chemical Society</i>, vol. 145, no. 27, American Chemical Society, 2023, pp. 14894–902, doi:<a href=\"https://doi.org/10.1021/jacs.3c04030\">10.1021/jacs.3c04030</a>.","ieee":"R. Bunting, F. Wodaczek, T. Torabi, and B. Cheng, “Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane,” <i>Journal of the American Chemical Society</i>, vol. 145, no. 27. American Chemical Society, pp. 14894–14902, 2023."},"year":"2023","date_published":"2023-06-30T00:00:00Z","doi":"10.1021/jacs.3c04030","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"article_processing_charge":"Yes (via OA deal)","publisher":"American Chemical Society","publication_status":"published","month":"06","department":[{"_id":"MaIb"},{"_id":"BiCh"}],"date_updated":"2024-10-21T06:01:30Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"title":"Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane","oa_version":"Published Version","volume":145,"day":"30","quality_controlled":"1","external_id":{"pmid":["37390457"],"isi":["001020623900001"]},"article_type":"original","abstract":[{"lang":"eng","text":"Physical catalysts often have multiple sites where reactions can take place. One prominent example is single-atom alloys, where the reactive dopant atoms can preferentially locate in the bulk or at different sites on the surface of the nanoparticle. However, ab initio modeling of catalysts usually only considers one site of the catalyst, neglecting the effects of multiple sites. Here, nanoparticles of copper doped with single-atom rhodium or palladium are modeled for the dehydrogenation of propane. Single-atom alloy nanoparticles are simulated at 400–600 K, using machine learning potentials trained on density functional theory calculations, and then the occupation of different single-atom active sites is identified using a similarity kernel. Further, the turnover frequency for all possible sites is calculated for propane dehydrogenation to propene through microkinetic modeling using density functional theory calculations. The total turnover frequencies of the whole nanoparticle are then described from both the population and the individual turnover frequency of each site. Under operating conditions, rhodium as a dopant is found to almost exclusively occupy (111) surface sites while palladium as a dopant occupies a greater variety of facets. Undercoordinated dopant surface sites are found to tend to be more reactive for propane dehydrogenation compared to the (111) surface. It is found that considering the dynamics of the single-atom alloy nanoparticle has a profound effect on the calculated catalytic activity of single-atom alloys by several orders of magnitude."}]},{"department":[{"_id":"RoSe"}],"month":"08","date_updated":"2025-04-14T07:26:58Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_number":"65","isi":1,"title":"Correlation energy of a weakly interacting Fermi gas with large interaction potential","citation":{"short":"N.P. Benedikter, M. Porta, B. Schlein, R. Seiringer, Archive for Rational Mechanics and Analysis 247 (2023).","apa":"Benedikter, N. P., Porta, M., Schlein, B., &#38; Seiringer, R. (2023). Correlation energy of a weakly interacting Fermi gas with large interaction potential. <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00205-023-01893-6\">https://doi.org/10.1007/s00205-023-01893-6</a>","ama":"Benedikter NP, Porta M, Schlein B, Seiringer R. Correlation energy of a weakly interacting Fermi gas with large interaction potential. <i>Archive for Rational Mechanics and Analysis</i>. 2023;247(4). doi:<a href=\"https://doi.org/10.1007/s00205-023-01893-6\">10.1007/s00205-023-01893-6</a>","chicago":"Benedikter, Niels P, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Correlation Energy of a Weakly Interacting Fermi Gas with Large Interaction Potential.” <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00205-023-01893-6\">https://doi.org/10.1007/s00205-023-01893-6</a>.","ista":"Benedikter NP, Porta M, Schlein B, Seiringer R. 2023. Correlation energy of a weakly interacting Fermi gas with large interaction potential. Archive for Rational Mechanics and Analysis. 247(4), 65.","ieee":"N. P. Benedikter, M. Porta, B. Schlein, and R. Seiringer, “Correlation energy of a weakly interacting Fermi gas with large interaction potential,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 247, no. 4. Springer Nature, 2023.","mla":"Benedikter, Niels P., et al. “Correlation Energy of a Weakly Interacting Fermi Gas with Large Interaction Potential.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 247, no. 4, 65, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s00205-023-01893-6\">10.1007/s00205-023-01893-6</a>."},"date_published":"2023-08-01T00:00:00Z","year":"2023","doi":"10.1007/s00205-023-01893-6","publisher":"Springer Nature","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"publication_status":"published","article_type":"original","abstract":[{"text":"Recently the leading order of the correlation energy of a Fermi gas in a coupled mean-field and semiclassical scaling regime has been derived, under the assumption of an interaction potential with a small norm and with compact support in Fourier space. We generalize this result to large interaction potentials, requiring only |⋅|V^∈ℓ1(Z3). Our proof is based on approximate, collective bosonization in three dimensions. Significant improvements compared to recent work include stronger bounds on non-bosonizable terms and more efficient control on the bosonization of the kinetic energy.","lang":"eng"}],"ec_funded":1,"day":"01","oa_version":"Published Version","volume":247,"project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"quality_controlled":"1","external_id":{"isi":["001024369000001"],"arxiv":["2106.13185"]},"issue":"4","file_date_updated":"2023-11-14T13:12:12Z","type":"journal_article","author":[{"last_name":"Benedikter","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","full_name":"Benedikter, Niels P","first_name":"Niels P","orcid":"0000-0002-1071-6091"},{"first_name":"Marcello","full_name":"Porta, Marcello","last_name":"Porta"},{"first_name":"Benjamin","last_name":"Schlein","full_name":"Schlein, Benjamin"},{"orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"RS was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 694227). MP acknowledges financial support from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (ERC StG MaMBoQ, Grant Agreement No. 802901). BS acknowledges financial support from the NCCR SwissMAP, from the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose-Einstein condensates” and from the European Research Council through the ERC AdG CLaQS (Grant Agreement No. 834782). NB and MP were supported by Gruppo Nazionale per la Fisica Matematica (GNFM) of Italy. NB was supported by the European Research Council’s Starting Grant FERMIMATH (Grant Agreement No. 101040991).\r\nOpen access funding provided by Università degli Studi di Milano within the CRUI-CARE Agreement.","oa":1,"arxiv":1,"_id":"13225","ddc":["510"],"file":[{"creator":"dernst","file_id":"14535","file_name":"2023_ArchiveRationalMechAnalysis_Benedikter.pdf","date_updated":"2023-11-14T13:12:12Z","content_type":"application/pdf","access_level":"open_access","success":1,"relation":"main_file","file_size":851626,"date_created":"2023-11-14T13:12:12Z","checksum":"2b45828d854a253b14bf7aa196ec55e9"}],"intvolume":"       247","date_created":"2023-07-16T22:01:08Z","status":"public","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Archive for Rational Mechanics and Analysis","has_accepted_license":"1"},{"arxiv":1,"OA_place":"publisher","_id":"13226","oa":1,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"It is a pleasure to thank Martin Kolb, Simone Rademacher, Robert Seiringer and Stefan Teufel for helpful discussions. Moreover, we thank the referee for many constructive comments. L.B. gratefully acknowledges funding from the German Research Foundation within the Munich Center of Quantum Science and Technology (EXC 2111) and from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. We thank the Mathematical Research Institute Oberwolfach, where part of this work was done, for their hospitality.\r\nOpen Access funding enabled and organized by Projekt DEAL.","author":[{"last_name":"Bossmann","full_name":"Bossmann, Lea","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","first_name":"Lea","orcid":"0000-0002-6854-1343"},{"first_name":"Sören P","orcid":"0000-0002-9166-5889","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrat, Sören P","last_name":"Petrat"}],"issue":"4","corr_author":"1","file_date_updated":"2025-06-25T06:20:02Z","language":[{"iso":"eng"}],"publication":"Letters in Mathematical Physics","has_accepted_license":"1","date_created":"2023-07-16T22:01:08Z","scopus_import":"1","status":"public","intvolume":"       113","ddc":["510"],"file":[{"date_updated":"2025-06-25T06:20:02Z","file_name":"2023_LettersMathPhysics_Bossmann.pdf","content_type":"application/pdf","file_id":"19898","creator":"dernst","date_created":"2025-06-25T06:20:02Z","checksum":"995c902a989a6769fd3db456cfd41111","access_level":"open_access","success":1,"file_size":586698,"relation":"main_file"}],"doi":"10.1007/s11005-023-01698-4","publisher":"Springer Nature","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"eissn":["1573-0530"],"issn":["0377-9017"]},"publication_status":"published","citation":{"ama":"Bossmann L, Petrat SP. Weak Edgeworth expansion for the mean-field Bose gas. <i>Letters in Mathematical Physics</i>. 2023;113(4). doi:<a href=\"https://doi.org/10.1007/s11005-023-01698-4\">10.1007/s11005-023-01698-4</a>","chicago":"Bossmann, Lea, and Sören P Petrat. “Weak Edgeworth Expansion for the Mean-Field Bose Gas.” <i>Letters in Mathematical Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s11005-023-01698-4\">https://doi.org/10.1007/s11005-023-01698-4</a>.","short":"L. Bossmann, S.P. Petrat, Letters in Mathematical Physics 113 (2023).","apa":"Bossmann, L., &#38; Petrat, S. P. (2023). Weak Edgeworth expansion for the mean-field Bose gas. <i>Letters in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11005-023-01698-4\">https://doi.org/10.1007/s11005-023-01698-4</a>","ieee":"L. Bossmann and S. P. Petrat, “Weak Edgeworth expansion for the mean-field Bose gas,” <i>Letters in Mathematical Physics</i>, vol. 113, no. 4. Springer Nature, 2023.","mla":"Bossmann, Lea, and Sören P. Petrat. “Weak Edgeworth Expansion for the Mean-Field Bose Gas.” <i>Letters in Mathematical Physics</i>, vol. 113, no. 4, 77, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s11005-023-01698-4\">10.1007/s11005-023-01698-4</a>.","ista":"Bossmann L, Petrat SP. 2023. Weak Edgeworth expansion for the mean-field Bose gas. Letters in Mathematical Physics. 113(4), 77."},"year":"2023","date_published":"2023-07-03T00:00:00Z","article_number":"77","isi":1,"title":"Weak Edgeworth expansion for the mean-field Bose gas","month":"07","department":[{"_id":"RoSe"}],"date_updated":"2025-06-25T06:20:15Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"external_id":{"arxiv":["2208.00199"],"isi":["001022878900002"]},"quality_controlled":"1","ec_funded":1,"oa_version":"Published Version","volume":113,"day":"03","OA_type":"hybrid","article_type":"original","abstract":[{"text":"We consider the ground state and the low-energy excited states of a system of N identical bosons with interactions in the mean-field scaling regime. For the ground state, we derive a weak Edgeworth expansion for the fluctuations of bounded one-body operators, which yields corrections to a central limit theorem to any order in 1/N−−√. For suitable excited states, we show that the limiting distribution is a polynomial times a normal distribution, and that higher-order corrections are given by an Edgeworth-type expansion.","lang":"eng"}]},{"publication_status":"published","doi":"10.1145/3593013.3594028","publication_identifier":{"isbn":["9781450372527"]},"article_processing_charge":"Yes (via OA deal)","publisher":"Association for Computing Machinery","citation":{"ista":"Henzinger TA, Karimi M, Kueffner K, Mallik K. 2023. Runtime monitoring of dynamic fairness properties. FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency. FAccT: Conference on Fairness, Accountability and Transparency, 604–614.","ieee":"T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Runtime monitoring of dynamic fairness properties,” in <i>FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency</i>, Chicago, IL, United States, 2023, pp. 604–614.","mla":"Henzinger, Thomas A., et al. “Runtime Monitoring of Dynamic Fairness Properties.” <i>FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency</i>, Association for Computing Machinery, 2023, pp. 604–14, doi:<a href=\"https://doi.org/10.1145/3593013.3594028\">10.1145/3593013.3594028</a>.","short":"T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency, Association for Computing Machinery, 2023, pp. 604–614.","apa":"Henzinger, T. A., Karimi, M., Kueffner, K., &#38; Mallik, K. (2023). Runtime monitoring of dynamic fairness properties. In <i>FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency</i> (pp. 604–614). Chicago, IL, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3593013.3594028\">https://doi.org/10.1145/3593013.3594028</a>","ama":"Henzinger TA, Karimi M, Kueffner K, Mallik K. Runtime monitoring of dynamic fairness properties. In: <i>FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency</i>. Association for Computing Machinery; 2023:604-614. doi:<a href=\"https://doi.org/10.1145/3593013.3594028\">10.1145/3593013.3594028</a>","chicago":"Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik. “Runtime Monitoring of Dynamic Fairness Properties.” In <i>FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency</i>, 604–14. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3593013.3594028\">https://doi.org/10.1145/3593013.3594028</a>."},"year":"2023","date_published":"2023-06-12T00:00:00Z","title":"Runtime monitoring of dynamic fairness properties","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"ToHe"}],"month":"06","date_updated":"2026-01-21T07:23:43Z","project":[{"grant_number":"101020093","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"external_id":{"arxiv":["2305.04699"],"isi":["001062819300057"]},"quality_controlled":"1","oa_version":"Published Version","day":"12","ec_funded":1,"conference":{"name":"FAccT: Conference on Fairness, Accountability and Transparency","end_date":"2023-06-15","start_date":"2023-06-12","location":"Chicago, IL, United States"},"abstract":[{"lang":"eng","text":"A machine-learned system that is fair in static decision-making tasks may have biased societal impacts in the long-run. This may happen when the system interacts with humans and feedback patterns emerge, reinforcing old biases in the system and creating new biases. While existing works try to identify and mitigate long-run biases through smart system design, we introduce techniques for monitoring fairness in real time. Our goal is to build and deploy a monitor that will continuously observe a long sequence of events generated by the system in the wild, and will output, with each event, a verdict on how fair the system is at the current point in time. The advantages of monitoring are two-fold. Firstly, fairness is evaluated at run-time, which is important because unfair behaviors may not be eliminated a priori, at design-time, due to partial knowledge about the system and the environment, as well as uncertainties and dynamic changes in the system and the environment, such as the unpredictability of human behavior. Secondly, monitors are by design oblivious to how the monitored system is constructed, which makes them suitable to be used as trusted third-party fairness watchdogs. They function as computationally lightweight statistical estimators, and their correctness proofs rely on the rigorous analysis of the stochastic process that models the assumptions about the underlying dynamics of the system. We show, both in theory and experiments, how monitors can warn us (1) if a bank’s credit policy over time has created an unfair distribution of credit scores among the population, and (2) if a resource allocator’s allocation policy over time has made unfair allocations. Our experiments demonstrate that the monitors introduce very low overhead. We believe that runtime monitoring is an important and mathematically rigorous new addition to the fairness toolbox."}],"_id":"13228","arxiv":1,"oa":1,"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-2985-7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"full_name":"Karimi, Mahyar","id":"6e5417ba-5355-11ee-ae5a-94c2e510b26b","last_name":"Karimi","orcid":"0009-0005-0820-1696","first_name":"Mahyar"},{"first_name":"Konstantin","orcid":"0000-0001-8974-2542","id":"8121a2d0-dc85-11ea-9058-af578f3b4515","full_name":"Kueffner, Konstantin","last_name":"Kueffner"},{"last_name":"Mallik","full_name":"Mallik, Kaushik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","first_name":"Kaushik","orcid":"0000-0001-9864-7475"}],"acknowledgement":"The authors would like to thank the anonymous reviewers for their valuable comments and helpful suggestions. This work is supported by the European Research Council under Grant No.: ERC-2020-AdG 101020093.","file_date_updated":"2023-07-18T07:43:10Z","corr_author":"1","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"FAccT '23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency","status":"public","date_created":"2023-07-16T22:01:09Z","scopus_import":"1","page":"604-614","file":[{"creator":"dernst","file_id":"13245","content_type":"application/pdf","file_name":"2023_ACM_HenzingerT.pdf","date_updated":"2023-07-18T07:43:10Z","file_size":4100596,"relation":"main_file","access_level":"open_access","success":1,"checksum":"96c759db9cdf94b81e37871a66a6ff48","date_created":"2023-07-18T07:43:10Z"}],"ddc":["000"]},{"acknowledgement":"This work was supported by funding from the European Union (European Research Council Advanced grant 742573) to C.-P.H. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Shamipour","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan","first_name":"Shayan"},{"first_name":"Laura","full_name":"Hofmann, Laura","id":"b88d43f2-dc74-11ea-a0a7-e41b7912e031","last_name":"Hofmann"},{"last_name":"Steccari","full_name":"Steccari, Irene","id":"2705C766-9FE2-11EA-B224-C6773DDC885E","first_name":"Irene"},{"full_name":"Kardos, Roland","id":"4039350E-F248-11E8-B48F-1D18A9856A87","last_name":"Kardos","first_name":"Roland"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"type":"journal_article","file_date_updated":"2023-07-18T07:59:58Z","corr_author":"1","issue":"6","_id":"13229","oa":1,"page":"e3002146","pmid":1,"intvolume":"        21","file":[{"creator":"dernst","file_id":"13246","content_type":"application/pdf","file_name":"2023_PloSBiology_Shamipour.pdf","date_updated":"2023-07-18T07:59:58Z","file_size":4431723,"relation":"main_file","success":1,"access_level":"open_access","checksum":"8e88cb0e5a6433a2f1939a9030bed384","date_created":"2023-07-18T07:59:58Z"}],"ddc":["570"],"has_accepted_license":"1","publication":"PLoS Biology","language":[{"iso":"eng"}],"date_created":"2023-07-16T22:01:09Z","status":"public","scopus_import":"1","title":"Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2025-04-14T07:46:59Z","month":"06","department":[{"_id":"CaHe"}],"publication_status":"published","publisher":"Public Library of Science","article_processing_charge":"No","publication_identifier":{"eissn":["1545-7885"]},"doi":"10.1371/journal.pbio.3002146","year":"2023","date_published":"2023-06-08T00:00:00Z","citation":{"ieee":"S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, and C.-P. J. Heisenberg, “Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes,” <i>PLoS Biology</i>, vol. 21, no. 6. Public Library of Science, p. e3002146, 2023.","mla":"Shamipour, Shayan, et al. “Yolk Granule Fusion and Microtubule Aster Formation Regulate Cortical Granule Translocation and Exocytosis in Zebrafish Oocytes.” <i>PLoS Biology</i>, vol. 21, no. 6, Public Library of Science, 2023, p. e3002146, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002146\">10.1371/journal.pbio.3002146</a>.","ista":"Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. 2023. Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. 21(6), e3002146.","ama":"Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. <i>PLoS Biology</i>. 2023;21(6):e3002146. doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002146\">10.1371/journal.pbio.3002146</a>","chicago":"Shamipour, Shayan, Laura Hofmann, Irene Steccari, Roland Kardos, and Carl-Philipp J Heisenberg. “Yolk Granule Fusion and Microtubule Aster Formation Regulate Cortical Granule Translocation and Exocytosis in Zebrafish Oocytes.” <i>PLoS Biology</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pbio.3002146\">https://doi.org/10.1371/journal.pbio.3002146</a>.","short":"S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, C.-P.J. Heisenberg, PLoS Biology 21 (2023) e3002146.","apa":"Shamipour, S., Hofmann, L., Steccari, I., Kardos, R., &#38; Heisenberg, C.-P. J. (2023). Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3002146\">https://doi.org/10.1371/journal.pbio.3002146</a>"},"abstract":[{"text":"Dynamic reorganization of the cytoplasm is key to many core cellular processes, such as cell division, cell migration, and cell polarization. Cytoskeletal rearrangements are thought to constitute the main drivers of cytoplasmic flows and reorganization. In contrast, remarkably little is known about how dynamic changes in size and shape of cell organelles affect cytoplasmic organization. Here, we show that within the maturing zebrafish oocyte, the surface localization of exocytosis-competent cortical granules (Cgs) upon germinal vesicle breakdown (GVBD) is achieved by the combined activities of yolk granule (Yg) fusion and microtubule aster formation and translocation. We find that Cgs are moved towards the oocyte surface through radially outward cytoplasmic flows induced by Ygs fusing and compacting towards the oocyte center in response to GVBD. We further show that vesicles decorated with the small Rab GTPase Rab11, a master regulator of vesicular trafficking and exocytosis, accumulate together with Cgs at the oocyte surface. This accumulation is achieved by Rab11-positive vesicles being transported by acentrosomal microtubule asters, the formation of which is induced by the release of CyclinB/Cdk1 upon GVBD, and which display a net movement towards the oocyte surface by preferentially binding to the oocyte actin cortex. We finally demonstrate that the decoration of Cgs by Rab11 at the oocyte surface is needed for Cg exocytosis and subsequent chorion elevation, a process central in egg activation. Collectively, these findings unravel a yet unrecognized role of organelle fusion, functioning together with cytoskeletal rearrangements, in orchestrating cytoplasmic organization during oocyte maturation.","lang":"eng"}],"article_type":"original","external_id":{"isi":["001003199100005"],"pmid":["37289834"]},"quality_controlled":"1","project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"}],"volume":21,"day":"08","oa_version":"Published Version","ec_funded":1},{"article_type":"original","abstract":[{"lang":"eng","text":"To interpret the sensory environment, the brain combines ambiguous sensory measurements with knowledge that reflects context-specific prior experience. But environmental contexts can change abruptly and unpredictably, resulting in uncertainty about the current context. Here we address two questions: how should context-specific prior knowledge optimally guide the interpretation of sensory stimuli in changing environments, and do human decision-making strategies resemble this optimum? We probe these questions with a task in which subjects report the orientation of ambiguous visual stimuli that were drawn from three dynamically switching distributions, representing different environmental contexts. We derive predictions for an ideal Bayesian observer that leverages knowledge about the statistical structure of the task to maximize decision accuracy, including knowledge about the dynamics of the environment. We show that its decisions are biased by the dynamically changing task context. The magnitude of this decision bias depends on the observer’s continually evolving belief about the current context. The model therefore not only predicts that decision bias will grow as the context is indicated more reliably, but also as the stability of the environment increases, and as the number of trials since the last context switch grows. Analysis of human choice data validates all three predictions, suggesting that the brain leverages knowledge of the statistical structure of environmental change when interpreting ambiguous sensory signals."}],"oa_version":"Published Version","volume":19,"day":"08","quality_controlled":"1","external_id":{"isi":["001003410200003"],"pmid":["37289753"]},"month":"06","department":[{"_id":"MaJö"}],"date_updated":"2023-08-02T06:33:50Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"article_number":"e1011104","title":"Environmental dynamics shape perceptual decision bias","citation":{"chicago":"Charlton, Julie A., Wiktor F Mlynarski, Yoon H. Bai, Ann M. Hermundstad, and Robbe L.T. Goris. “Environmental Dynamics Shape Perceptual Decision Bias.” <i>PLoS Computational Biology</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pcbi.1011104\">https://doi.org/10.1371/journal.pcbi.1011104</a>.","ama":"Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. Environmental dynamics shape perceptual decision bias. <i>PLoS Computational Biology</i>. 2023;19(6). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1011104\">10.1371/journal.pcbi.1011104</a>","apa":"Charlton, J. A., Mlynarski, W. F., Bai, Y. H., Hermundstad, A. M., &#38; Goris, R. L. T. (2023). Environmental dynamics shape perceptual decision bias. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1011104\">https://doi.org/10.1371/journal.pcbi.1011104</a>","short":"J.A. Charlton, W.F. Mlynarski, Y.H. Bai, A.M. Hermundstad, R.L.T. Goris, PLoS Computational Biology 19 (2023).","mla":"Charlton, Julie A., et al. “Environmental Dynamics Shape Perceptual Decision Bias.” <i>PLoS Computational Biology</i>, vol. 19, no. 6, e1011104, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1011104\">10.1371/journal.pcbi.1011104</a>.","ieee":"J. A. Charlton, W. F. Mlynarski, Y. H. Bai, A. M. Hermundstad, and R. L. T. Goris, “Environmental dynamics shape perceptual decision bias,” <i>PLoS Computational Biology</i>, vol. 19, no. 6. Public Library of Science, 2023.","ista":"Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. 2023. Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. 19(6), e1011104."},"year":"2023","date_published":"2023-06-08T00:00:00Z","doi":"10.1371/journal.pcbi.1011104","publisher":"Public Library of Science","article_processing_charge":"No","publication_identifier":{"eissn":["1553-7358"]},"publication_status":"published","ddc":["570"],"file":[{"date_created":"2023-07-18T08:07:59Z","checksum":"800761fa2c647fabd6ad034589bc526e","success":1,"access_level":"open_access","file_size":2281868,"relation":"main_file","file_name":"2023_PloSCompBio_Charlton.pdf","date_updated":"2023-07-18T08:07:59Z","content_type":"application/pdf","creator":"dernst","file_id":"13247"}],"intvolume":"        19","pmid":1,"date_created":"2023-07-16T22:01:09Z","scopus_import":"1","status":"public","language":[{"iso":"eng"}],"publication":"PLoS Computational Biology","has_accepted_license":"1","issue":"6","file_date_updated":"2023-07-18T08:07:59Z","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Charlton","full_name":"Charlton, Julie A.","first_name":"Julie A."},{"last_name":"Mlynarski","id":"358A453A-F248-11E8-B48F-1D18A9856A87","full_name":"Mlynarski, Wiktor F","first_name":"Wiktor F"},{"first_name":"Yoon H.","last_name":"Bai","full_name":"Bai, Yoon H."},{"full_name":"Hermundstad, Ann M.","last_name":"Hermundstad","first_name":"Ann M."},{"full_name":"Goris, Robbe L.T.","last_name":"Goris","first_name":"Robbe L.T."}],"acknowledgement":"The authors thank Corey Ziemba and Zoe Boundy-Singer for valuable discussion and feedback.","oa":1,"_id":"13230"},{"status":"public","scopus_import":"1","date_created":"2023-07-16T22:01:10Z","language":[{"iso":"eng"}],"publication":"Physical Review E","pmid":1,"intvolume":"       107","oa":1,"_id":"13231","arxiv":1,"issue":"6","type":"journal_article","author":[{"last_name":"Schörner","full_name":"Schörner, Maximilian","first_name":"Maximilian"},{"last_name":"Bethkenhagen","full_name":"Bethkenhagen, Mandy","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","orcid":"0000-0002-1838-2129","first_name":"Mandy"},{"first_name":"Tilo","full_name":"Döppner, Tilo","last_name":"Döppner"},{"first_name":"Dominik","last_name":"Kraus","full_name":"Kraus, Dominik"},{"full_name":"Fletcher, Luke B.","last_name":"Fletcher","first_name":"Luke B."},{"last_name":"Glenzer","full_name":"Glenzer, Siegfried H.","first_name":"Siegfried H."},{"first_name":"Ronald","last_name":"Redmer","full_name":"Redmer, Ronald"}],"acknowledgement":"We want to thank P. Sperling, B. Witte, M. French, G. Röpke, H. J. Lee and A. Cangi for many helpful discussions. M. S. and R. R. acknowledge support by the Deutsche Forschungsgemeinschaft (DFG) within the Research Unit FOR 2440. All simulations and analyses were performed at the North-German Supercomputing Alliance (HLRN) and the ITMZ of the University of Rostock. M. B. gratefully acknowledges support by the European Horizon 2020 programme within the Marie Sklodowska-Curie actions (xICE grant 894725) and the\r\nNOMIS foundation. The work of T. D. was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","volume":107,"day":"14","external_id":{"pmid":["37464593"],"isi":["001020265000002"],"arxiv":["2301.01545"]},"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.01545"}],"abstract":[{"text":"We study ab initio approaches for calculating x-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula that expresses the inelastic contribution in terms of the dielectric function. We study the electronic dynamic structure factor computed from the Mermin dielectric function using an ab initio electron-ion collision frequency in comparison to computations using a linear-response time-dependent density functional theory (LR-TDDFT) framework for hydrogen and beryllium and investigate the dispersion of free-free and bound-free contributions to the scattering signal. A separate treatment of these contributions, where only the free-free part follows the Mermin dispersion, shows good agreement with LR-TDDFT results for ambient-density beryllium, but breaks down for highly compressed matter where the bound states become pressure ionized. LR-TDDFT is used to reanalyze x-ray Thomson scattering experiments on beryllium demonstrating strong deviations from the plasma conditions inferred with traditional analytic models at small scattering angles.","lang":"eng"}],"article_type":"original","citation":{"chicago":"Schörner, Maximilian, Mandy Bethkenhagen, Tilo Döppner, Dominik Kraus, Luke B. Fletcher, Siegfried H. Glenzer, and Ronald Redmer. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” <i>Physical Review E</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevE.107.065207\">https://doi.org/10.1103/PhysRevE.107.065207</a>.","ama":"Schörner M, Bethkenhagen M, Döppner T, et al. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. <i>Physical Review E</i>. 2023;107(6). doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.065207\">10.1103/PhysRevE.107.065207</a>","apa":"Schörner, M., Bethkenhagen, M., Döppner, T., Kraus, D., Fletcher, L. B., Glenzer, S. H., &#38; Redmer, R. (2023). X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.107.065207\">https://doi.org/10.1103/PhysRevE.107.065207</a>","short":"M. Schörner, M. Bethkenhagen, T. Döppner, D. Kraus, L.B. Fletcher, S.H. Glenzer, R. Redmer, Physical Review E 107 (2023).","mla":"Schörner, Maximilian, et al. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” <i>Physical Review E</i>, vol. 107, no. 6, 065207, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.065207\">10.1103/PhysRevE.107.065207</a>.","ieee":"M. Schörner <i>et al.</i>, “X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula,” <i>Physical Review E</i>, vol. 107, no. 6. American Physical Society, 2023.","ista":"Schörner M, Bethkenhagen M, Döppner T, Kraus D, Fletcher LB, Glenzer SH, Redmer R. 2023. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. 107(6), 065207."},"date_published":"2023-06-14T00:00:00Z","year":"2023","publication_status":"published","doi":"10.1103/PhysRevE.107.065207","article_processing_charge":"No","publisher":"American Physical Society","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"department":[{"_id":"BiCh"}],"month":"06","date_updated":"2025-03-06T14:02:33Z","title":"X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula","article_number":"065207","isi":1},{"file":[{"content_type":"application/pdf","date_updated":"2023-07-18T07:25:43Z","file_name":"2023_Vaccines_Dormeshkin.pdf","creator":"dernst","file_id":"13244","checksum":"8f484c0f30f8699c589b1c29a0fd7d7f","date_created":"2023-07-18T07:25:43Z","relation":"main_file","file_size":2339746,"success":1,"access_level":"open_access"}],"ddc":["570"],"intvolume":"        11","pmid":1,"scopus_import":"1","status":"public","date_created":"2023-07-16T22:01:10Z","has_accepted_license":"1","publication":"Vaccines","language":[{"iso":"eng"}],"file_date_updated":"2023-07-18T07:25:43Z","issue":"6","author":[{"first_name":"Dmitri","last_name":"Dormeshkin","full_name":"Dormeshkin, Dmitri"},{"full_name":"Katsin, Mikalai","last_name":"Katsin","first_name":"Mikalai"},{"first_name":"Maria","last_name":"Stegantseva","full_name":"Stegantseva, Maria"},{"last_name":"Golenchenko","full_name":"Golenchenko, Sergey","first_name":"Sergey"},{"first_name":"Michail","full_name":"Shapira, Michail","last_name":"Shapira"},{"full_name":"Dubovik, Simon","last_name":"Dubovik","first_name":"Simon"},{"first_name":"Dzmitry","last_name":"Lutskovich","full_name":"Lutskovich, Dzmitry"},{"first_name":"Anton","orcid":"0000-0003-2091-526X","last_name":"Kavaleuski","id":"62304f89-eb97-11eb-a6c2-8903dd183976","full_name":"Kavaleuski, Anton"},{"first_name":"Alexander","last_name":"Meleshko","full_name":"Meleshko, Alexander"}],"acknowledgement":"The authors declare that this study received funding from Immunofusion. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article, or the decision to submit it for publication. The authors express their gratitude to the Institute of Physiology of the National Academy of Sciences of Belarus for providing assistance in keeping laboratory animals.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","oa":1,"_id":"13232","abstract":[{"text":"The potential of immune-evasive mutation accumulation in the SARS-CoV-2 virus has led to its rapid spread, causing over 600 million confirmed cases and more than 6.5 million confirmed deaths. The huge demand for the rapid development and deployment of low-cost and effective vaccines against emerging variants has renewed interest in DNA vaccine technology. Here, we report the rapid generation and immunological evaluation of novel DNA vaccine candidates against the Wuhan-Hu-1 and Omicron variants based on the RBD protein fused with the Potato virus X coat protein (PVXCP). The delivery of DNA vaccines using electroporation in a two-dose regimen induced high-antibody titers and profound cellular responses in mice. The antibody titers induced against the Omicron variant of the vaccine were sufficient for effective protection against both Omicron and Wuhan-Hu-1 virus infections. The PVXCP protein in the vaccine construct shifted the immune response to the favorable Th1-like type and provided the oligomerization of RBD-PVXCP protein. Naked DNA delivery by needle-free injection allowed us to achieve antibody titers comparable with mRNA-LNP delivery in rabbits. These data identify the RBD-PVXCP DNA vaccine platform as a promising solution for robust and effective SARS-CoV-2 protection, supporting further translational study.","lang":"eng"}],"article_type":"original","volume":11,"day":"01","oa_version":"Published Version","quality_controlled":"1","external_id":{"isi":["001017740000001"],"pmid":["37376403"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2025-04-23T13:01:23Z","department":[{"_id":"LeSa"}],"month":"06","title":"Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein","isi":1,"article_number":"1014","year":"2023","date_published":"2023-06-01T00:00:00Z","citation":{"mla":"Dormeshkin, Dmitri, et al. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” <i>Vaccines</i>, vol. 11, no. 6, 1014, MDPI, 2023, doi:<a href=\"https://doi.org/10.3390/vaccines11061014\">10.3390/vaccines11061014</a>.","ieee":"D. Dormeshkin <i>et al.</i>, “Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein,” <i>Vaccines</i>, vol. 11, no. 6. MDPI, 2023.","ista":"Dormeshkin D, Katsin M, Stegantseva M, Golenchenko S, Shapira M, Dubovik S, Lutskovich D, Kavaleuski A, Meleshko A. 2023. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 11(6), 1014.","chicago":"Dormeshkin, Dmitri, Mikalai Katsin, Maria Stegantseva, Sergey Golenchenko, Michail Shapira, Simon Dubovik, Dzmitry Lutskovich, Anton Kavaleuski, and Alexander Meleshko. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” <i>Vaccines</i>. MDPI, 2023. <a href=\"https://doi.org/10.3390/vaccines11061014\">https://doi.org/10.3390/vaccines11061014</a>.","ama":"Dormeshkin D, Katsin M, Stegantseva M, et al. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. <i>Vaccines</i>. 2023;11(6). doi:<a href=\"https://doi.org/10.3390/vaccines11061014\">10.3390/vaccines11061014</a>","apa":"Dormeshkin, D., Katsin, M., Stegantseva, M., Golenchenko, S., Shapira, M., Dubovik, S., … Meleshko, A. (2023). Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. <i>Vaccines</i>. MDPI. <a href=\"https://doi.org/10.3390/vaccines11061014\">https://doi.org/10.3390/vaccines11061014</a>","short":"D. Dormeshkin, M. Katsin, M. Stegantseva, S. Golenchenko, M. Shapira, S. Dubovik, D. Lutskovich, A. Kavaleuski, A. Meleshko, Vaccines 11 (2023)."},"publication_status":"published","article_processing_charge":"No","publication_identifier":{"eissn":["2076-393X"]},"publisher":"MDPI","doi":"10.3390/vaccines11061014"}]