[{"date_updated":"2023-08-02T06:17:18Z","oa":1,"month":"06","intvolume":"        13","date_published":"2023-06-09T00:00:00Z","article_number":"9382","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.).","year":"2023","external_id":{"pmid":["37296138"],"isi":["001006690200045"]},"license":"https://creativecommons.org/licenses/by/4.0/","date_created":"2023-06-25T22:00:46Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"day":"09","status":"public","pmid":1,"volume":13,"isi":1,"oa_version":"Published Version","doi":"10.1038/s41598-023-35979-8","publication":"Scientific Reports","file":[{"date_updated":"2023-06-26T09:58:53Z","date_created":"2023-06-26T09:58:53Z","file_name":"2023_ScientificReports_Vetrova.pdf","success":1,"checksum":"baddf6b2fa9adf88263d4a3b0998f0f2","access_level":"open_access","relation":"main_file","creator":"dernst","file_size":4844149,"content_type":"application/pdf","file_id":"13170"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Vetrova","first_name":"Alexandra A.","full_name":"Vetrova, Alexandra A."},{"full_name":"Kupaeva, Daria M.","last_name":"Kupaeva","first_name":"Daria M."},{"last_name":"Kizenko","id":"a521c60b-0815-11ed-9b02-b8bd522477c8","first_name":"Alena","full_name":"Kizenko, Alena"},{"full_name":"Lebedeva, Tatiana S.","first_name":"Tatiana S.","last_name":"Lebedeva"},{"full_name":"Walentek, Peter","first_name":"Peter","last_name":"Walentek"},{"first_name":"Nikoloz","last_name":"Tsikolia","full_name":"Tsikolia, Nikoloz"},{"full_name":"Kremnyov, Stanislav V.","first_name":"Stanislav V.","last_name":"Kremnyov"}],"title":"The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization","has_accepted_license":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"GradSch"}],"_id":"13166","quality_controlled":"1","publication_identifier":{"eissn":["2045-2322"]},"citation":{"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.","short":"A.A. Vetrova, D.M. Kupaeva, A. Kizenko, T.S. Lebedeva, P. Walentek, N. Tsikolia, S.V. Kremnyov, Scientific Reports 13 (2023).","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.","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>.","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>","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>."},"file_date_updated":"2023-06-26T09:58:53Z","type":"journal_article","abstract":[{"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.","lang":"eng"}],"scopus_import":"1","publication_status":"published"},{"external_id":{"isi":["001013172700001"]},"page":"1456-1467","year":"2023","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.","date_published":"2023-06-15T00:00:00Z","intvolume":"        29","month":"06","oa":1,"date_updated":"2023-12-13T11:25:55Z","publication":"Nature Medicine","doi":"10.1038/s41591-023-02365-w","oa_version":"Published Version","isi":1,"volume":29,"day":"15","status":"public","date_created":"2023-06-25T22:00:46Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"department":[{"_id":"GaNo"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"publisher":"Springer Nature","has_accepted_license":"1","title":"Effects of urban living environments on mental health in adults","author":[{"full_name":"Xu, Jiayuan","last_name":"Xu","first_name":"Jiayuan"},{"first_name":"Nana","last_name":"Liu","full_name":"Liu, Nana"},{"last_name":"Polemiti","first_name":"Elli","full_name":"Polemiti, Elli"},{"full_name":"Garcia-Mondragon, Liliana","last_name":"Garcia-Mondragon","first_name":"Liliana"},{"first_name":"Jie","last_name":"Tang","full_name":"Tang, Jie"},{"full_name":"Liu, Xiaoxuan","first_name":"Xiaoxuan","last_name":"Liu"},{"last_name":"Lett","first_name":"Tristram","full_name":"Lett, Tristram"},{"last_name":"Yu","first_name":"Le","full_name":"Yu, Le"},{"full_name":"Nöthen, Markus M.","first_name":"Markus M.","last_name":"Nöthen"},{"first_name":"Jianfeng","last_name":"Feng","full_name":"Feng, Jianfeng"},{"full_name":"Yu, Chunshui","first_name":"Chunshui","last_name":"Yu"},{"full_name":"Marquand, Andre","first_name":"Andre","last_name":"Marquand"},{"full_name":"Schumann, Gunter","last_name":"Schumann","first_name":"Gunter"},{"first_name":"Henrik","last_name":"Walter","full_name":"Walter, Henrik"},{"last_name":"Heinz","first_name":"Andreas","full_name":"Heinz, Andreas"},{"last_name":"Ralser","first_name":"Markus","full_name":"Ralser, Markus"},{"first_name":"Sven","last_name":"Twardziok","full_name":"Twardziok, Sven"},{"last_name":"Vaidya","first_name":"Nilakshi","full_name":"Vaidya, Nilakshi"},{"full_name":"Serin, Emin","last_name":"Serin","first_name":"Emin"},{"full_name":"Jentsch, Marcel","last_name":"Jentsch","first_name":"Marcel"},{"full_name":"Hitchen, Esther","last_name":"Hitchen","first_name":"Esther"},{"full_name":"Eils, Roland","first_name":"Roland","last_name":"Eils"},{"last_name":"Taron","first_name":"Ulrike Helene","full_name":"Taron, Ulrike Helene"},{"last_name":"Schütz","first_name":"Tatjana","full_name":"Schütz, Tatjana"},{"full_name":"Schepanski, Kerstin","first_name":"Kerstin","last_name":"Schepanski"},{"full_name":"Banks, Jamie","last_name":"Banks","first_name":"Jamie"},{"last_name":"Banaschewski","first_name":"Tobias","full_name":"Banaschewski, Tobias"},{"full_name":"Jansone, Karina","first_name":"Karina","last_name":"Jansone"},{"last_name":"Christmann","first_name":"Nina","full_name":"Christmann, Nina"},{"first_name":"Andreas","last_name":"Meyer-Lindenberg","full_name":"Meyer-Lindenberg, Andreas"},{"last_name":"Tost","first_name":"Heike","full_name":"Tost, Heike"},{"full_name":"Holz, Nathalie","last_name":"Holz","first_name":"Nathalie"},{"last_name":"Schwarz","first_name":"Emanuel","full_name":"Schwarz, Emanuel"},{"last_name":"Stringaris","first_name":"Argyris","full_name":"Stringaris, Argyris"},{"first_name":"Maja","last_name":"Neidhart","full_name":"Neidhart, Maja"},{"first_name":"Frauke","last_name":"Nees","full_name":"Nees, Frauke"},{"full_name":"Siehl, Sebastian","first_name":"Sebastian","last_name":"Siehl"},{"last_name":"A. Andreassen","first_name":"Ole","full_name":"A. Andreassen, Ole"},{"first_name":"Lars","last_name":"T. Westlye","full_name":"T. Westlye, Lars"},{"full_name":"Van Der Meer, Dennis","last_name":"Van Der Meer","first_name":"Dennis"},{"full_name":"Fernandez, Sara","last_name":"Fernandez","first_name":"Sara"},{"first_name":"Rikka","last_name":"Kjelkenes","full_name":"Kjelkenes, Rikka"},{"full_name":"Ask, Helga","first_name":"Helga","last_name":"Ask"},{"full_name":"Rapp, Michael","first_name":"Michael","last_name":"Rapp"},{"full_name":"Tschorn, Mira","last_name":"Tschorn","first_name":"Mira"},{"full_name":"Böttger, Sarah Jane","last_name":"Böttger","first_name":"Sarah Jane"},{"full_name":"Novarino, Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marr, Lena","last_name":"Marr","first_name":"Lena","id":"4406F586-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mel","last_name":"Slater","full_name":"Slater, Mel"},{"full_name":"Viapiana, Guillem Feixas","first_name":"Guillem Feixas","last_name":"Viapiana"},{"first_name":"Francisco Eiroa","last_name":"Orosa","full_name":"Orosa, Francisco Eiroa"},{"last_name":"Gallego","first_name":"Jaime","full_name":"Gallego, Jaime"},{"last_name":"Pastor","first_name":"Alvaro","full_name":"Pastor, Alvaro"},{"last_name":"Forstner","first_name":"Andreas","full_name":"Forstner, Andreas"},{"last_name":"Hoffmann","first_name":"Per","full_name":"Hoffmann, Per"},{"first_name":"Markus","last_name":"M. Nöthen","full_name":"M. Nöthen, Markus"},{"first_name":"Andreas","last_name":"J. Forstner","full_name":"J. Forstner, Andreas"},{"full_name":"Claus, Isabelle","last_name":"Claus","first_name":"Isabelle"},{"last_name":"Miller","first_name":"Abbi","full_name":"Miller, Abbi"},{"full_name":"Heilmann-Heimbach, Stefanie","last_name":"Heilmann-Heimbach","first_name":"Stefanie"},{"full_name":"Sommer, Peter","last_name":"Sommer","first_name":"Peter"},{"full_name":"Boye, Mona","last_name":"Boye","first_name":"Mona"},{"full_name":"Wilbertz, Johannes","first_name":"Johannes","last_name":"Wilbertz"},{"full_name":"Schmitt, Karen","last_name":"Schmitt","first_name":"Karen"},{"last_name":"Jirsa","first_name":"Viktor","full_name":"Jirsa, Viktor"},{"last_name":"Petkoski","first_name":"Spase","full_name":"Petkoski, Spase"},{"last_name":"Pitel","first_name":"Séverine","full_name":"Pitel, Séverine"},{"full_name":"Otten, Lisa","first_name":"Lisa","last_name":"Otten"},{"full_name":"Athanasiadis, Anastasios Polykarpos","last_name":"Athanasiadis","first_name":"Anastasios Polykarpos"},{"last_name":"Pearmund","first_name":"Charlie","full_name":"Pearmund, Charlie"},{"full_name":"Spanlang, Bernhard","last_name":"Spanlang","first_name":"Bernhard"},{"first_name":"Elena","last_name":"Alvarez","full_name":"Alvarez, Elena"},{"full_name":"Sanchez, Mavi","first_name":"Mavi","last_name":"Sanchez"},{"first_name":"Arantxa","last_name":"Giner","full_name":"Giner, Arantxa"},{"full_name":"Hese, Sören","first_name":"Sören","last_name":"Hese"},{"last_name":"Renner","first_name":"Paul","full_name":"Renner, Paul"},{"first_name":"Tianye","last_name":"Jia","full_name":"Jia, Tianye"},{"full_name":"Gong, Yanting","last_name":"Gong","first_name":"Yanting"},{"last_name":"Xia","first_name":"Yunman","full_name":"Xia, Yunman"},{"full_name":"Chang, Xiao","first_name":"Xiao","last_name":"Chang"},{"full_name":"Calhoun, Vince","first_name":"Vince","last_name":"Calhoun"},{"full_name":"Liu, Jingyu","last_name":"Liu","first_name":"Jingyu"},{"last_name":"Thompson","first_name":"Paul","full_name":"Thompson, Paul"},{"last_name":"Clinton","first_name":"Nicholas","full_name":"Clinton, Nicholas"},{"full_name":"Desrivieres, Sylvane","first_name":"Sylvane","last_name":"Desrivieres"},{"last_name":"H. Young","first_name":"Allan","full_name":"H. Young, Allan"},{"last_name":"Stahl","first_name":"Bernd","full_name":"Stahl, Bernd"},{"last_name":"Ogoh","first_name":"George","full_name":"Ogoh, George"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2023-06-26T10:15:44Z","date_updated":"2023-06-26T10:15:44Z","success":1,"file_name":"2023_NatureMedicine_Xu.pdf","access_level":"open_access","relation":"main_file","checksum":"bcd3225b2731c3442fa98987fd3bd46d","content_type":"application/pdf","file_id":"13171","creator":"dernst","file_size":7365360}],"publication_status":"published","scopus_import":"1","abstract":[{"lang":"eng","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."}],"type":"journal_article","file_date_updated":"2023-06-26T10:15:44Z","citation":{"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>","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.","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.","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.","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>.","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>"},"publication_identifier":{"eissn":["1546-170X"],"issn":["1078-8956"]},"quality_controlled":"1","_id":"13168"},{"keyword":["medial habenula","GABAB receptor","vesicle release","Flash and Freeze","Flash and Freeze-fracture"],"date_updated":"2024-02-21T12:19:26Z","oa":1,"title":"Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"}],"file":[{"file_name":"Raw data for Koppensteiner et al.zip","description":"After review an updated version of the data is provided","title":"Outdated Version","date_created":"2023-06-29T13:11:22Z","date_updated":"2023-11-17T14:30:44Z","content_type":"application/x-zip-compressed","file_id":"13174","file_size":542873672,"creator":"shigemot","checksum":"ed59170869ba621f89f7c1894092192f","access_level":"closed","relation":"main_file"},{"date_updated":"2023-11-17T14:13:02Z","date_created":"2023-11-17T14:13:02Z","success":1,"file_name":"11-17-23 Updated Koppensteiner et al. raw data.xlsx","relation":"main_file","access_level":"open_access","checksum":"c07860eb82b4d367245f1b589fe5c250","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_id":"14550","file_size":915079,"creator":"patrickd"},{"date_created":"2024-02-06T07:21:43Z","date_updated":"2024-02-06T07:21:43Z","file_name":"EM_Images.zip","success":1,"access_level":"open_access","relation":"main_file","checksum":"abf84b1699edac4349dc3a92d466fb7b","file_size":544868924,"creator":"dernst","file_id":"14942","content_type":"application/x-zip-compressed"}],"date_published":"2023-07-29T00:00:00Z","has_accepted_license":"1","month":"07","publisher":"Institute of Science and Technology Austria","year":"2023","article_processing_charge":"No","license":"https://creativecommons.org/licenses/by-nc/4.0/","department":[{"_id":"RySh"}],"date_created":"2023-06-29T13:16:42Z","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"_id":"13173","ddc":["571"],"day":"29","status":"public","citation":{"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>.","short":"R. Shigemoto, (2023).","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>.","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.","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>","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>.","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>"},"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_date_updated":"2024-02-06T07:21:43Z","type":"research_data","oa_version":"Published Version","doi":"10.15479/AT:ISTA:13173"},{"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"oa":1,"date_updated":"2024-10-29T09:11:06Z","keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"month":"05","date_published":"2023-05-05T00:00:00Z","alternative_title":["ISTA Thesis"],"year":"2023","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","page":"202","supervisor":[{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink"}],"day":"05","status":"public","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"date_created":"2023-06-30T08:07:43Z","ddc":["537","535","539"],"ec_funded":1,"oa_version":"Published Version","related_material":{"record":[{"id":"12900","status":"public","relation":"old_edition"},{"id":"9114","relation":"part_of_dissertation","status":"public"},{"id":"10924","relation":"part_of_dissertation","status":"public"}]},"doi":"10.15479/at:ista:13175","degree_awarded":"PhD","file":[{"date_updated":"2023-06-30T08:17:25Z","date_created":"2023-06-30T08:17:25Z","file_name":"thesis_pdfa.pdf","success":1,"access_level":"open_access","checksum":"7d03f1a5a5258ee43dfc3323dea4e08f","relation":"main_file","creator":"cchlebak","file_size":18688376,"content_type":"application/pdf","file_id":"13176"},{"file_name":"thesis.zip","date_updated":"2023-07-06T11:35:15Z","date_created":"2023-07-06T11:35:15Z","creator":"cchlebak","file_size":37847025,"file_id":"13196","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","checksum":"c3b45317ae58e0527533f98c202d81b7"}],"title":"Cavity quantum electrooptics","author":[{"last_name":"Sahu","orcid":"0000-0001-6264-2162","first_name":"Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","full_name":"Sahu, Rishabh"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"JoFi"}],"article_processing_charge":"No","_id":"13175","file_date_updated":"2023-07-06T11:35:15Z","type":"dissertation","abstract":[{"lang":"eng","text":"About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. "}],"citation":{"ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13175\">10.15479/at:ista:13175</a>","short":"R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023.","ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria.","ieee":"R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023.","chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13175\">https://doi.org/10.15479/at:ista:13175</a>.","apa":"Sahu, R. (2023). <i>Cavity quantum electrooptics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13175\">https://doi.org/10.15479/at:ista:13175</a>","mla":"Sahu, Rishabh. <i>Cavity Quantum Electrooptics</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13175\">10.15479/at:ista:13175</a>."},"publication_identifier":{"issn":["2663 - 337X"],"isbn":["978-3-99078-030-5"]},"publication_status":"published","project":[{"name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","call_identifier":"H2020"},{"grant_number":"899354","call_identifier":"H2020","name":"Quantum Local Area Networks with Superconducting Qubits","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}]},{"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"JaMa"}],"author":[{"full_name":"Hua, Bobo","first_name":"Bobo","last_name":"Hua"},{"last_name":"Keller","first_name":"Matthias","full_name":"Keller, Matthias"},{"last_name":"Schwarz","first_name":"Michael","full_name":"Schwarz, Michael"},{"full_name":"Wirth, Melchior","last_name":"Wirth","orcid":"0000-0002-0519-4241","first_name":"Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Sobolev-type inequalities and eigenvalue growth on graphs with finite measure","publisher":"American Mathematical Society","publication_status":"published","_id":"13177","quality_controlled":"1","citation":{"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.","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.","short":"B. Hua, M. Keller, M. Schwarz, M. Wirth, Proceedings of the American Mathematical Society 151 (2023) 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>.","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>"},"publication_identifier":{"eissn":["1088-6826"],"issn":["0002-9939"]},"scopus_import":"1","arxiv":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"}],"type":"journal_article","year":"2023","external_id":{"isi":["000988204400001"],"arxiv":["1804.08353"]},"page":"3401-3414","date_updated":"2023-11-14T13:07:09Z","oa":1,"issue":"8","date_published":"2023-08-01T00:00:00Z","month":"08","intvolume":"       151","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.","oa_version":"Preprint","isi":1,"publication":"Proceedings of the American Mathematical Society","doi":"10.1090/proc/14361","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1804.08353","open_access":"1"}],"date_created":"2023-07-02T22:00:43Z","status":"public","day":"01","volume":151},{"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"Yes","department":[{"_id":"RoSe"}],"file":[{"checksum":"f672eb7dd015c472c9a04f1b9bf9df7d","relation":"main_file","access_level":"open_access","file_id":"13186","content_type":"application/pdf","creator":"alisjak","file_size":943192,"date_created":"2023-07-03T10:36:25Z","date_updated":"2023-07-03T10:36:25Z","success":1,"file_name":"2023_ForumofMathematics.Sigma_Mitrouskas.pdf"}],"author":[{"full_name":"Mitrouskas, David Johannes","last_name":"Mitrouskas","first_name":"David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d"},{"first_name":"Krzysztof","id":"316457FC-F248-11E8-B48F-1D18A9856A87","last_name":"Mysliwy","full_name":"Mysliwy, Krzysztof"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"title":"Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","publisher":"Cambridge University Press","project":[{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227"}],"publication_status":"published","_id":"13178","quality_controlled":"1","citation":{"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>","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>.","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>","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.","short":"D.J. Mitrouskas, K. Mysliwy, R. Seiringer, Forum of Mathematics 11 (2023) 1–52.","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.","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>."},"publication_identifier":{"eissn":["2050-5094"]},"type":"journal_article","file_date_updated":"2023-07-03T10:36:25Z","abstract":[{"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.","lang":"eng"}],"scopus_import":"1","arxiv":1,"year":"2023","external_id":{"isi":["001005008800001"],"arxiv":["2203.02454"]},"page":"1-52","date_updated":"2023-11-02T12:30:50Z","oa":1,"intvolume":"        11","month":"06","date_published":"2023-06-13T00:00:00Z","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.).","isi":1,"oa_version":"Published Version","ec_funded":1,"doi":"10.1017/fms.2023.45","publication":"Forum of Mathematics","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2023-07-02T22:00:43Z","ddc":["500"],"status":"public","day":"13","volume":11},{"article_number":"116","date_published":"2023-06-06T00:00:00Z","month":"06","intvolume":"         7","oa":1,"date_updated":"2023-07-17T08:43:19Z","year":"2023","volume":7,"day":"06","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"],"date_created":"2023-07-02T22:00:43Z","publication":"Proceedings of the ACM on Programming Languages","doi":"10.1145/3591230","oa_version":"Published Version","publisher":"Association for Computing Machinery ","has_accepted_license":"1","title":"CQS: A formally-verified framework for fair and abortable synchronization","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Koval, Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","first_name":"Nikita","last_name":"Koval"},{"full_name":"Khalanskiy, Dmitry","first_name":"Dmitry","last_name":"Khalanskiy"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","last_name":"Alistarh"}],"file":[{"date_created":"2023-07-03T13:09:39Z","date_updated":"2023-07-03T13:09:39Z","file_name":"2023_ACMProgram.Lang._Koval.pdf","success":1,"checksum":"5dba6e73f0ed79adbdae14d165bc2f68","relation":"main_file","access_level":"open_access","file_size":1266773,"creator":"alisjak","content_type":"application/pdf","file_id":"13187"}],"department":[{"_id":"DaAl"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","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."}],"scopus_import":"1","file_date_updated":"2023-07-03T13:09:39Z","type":"journal_article","publication_identifier":{"eissn":["2475-1421"]},"citation":{"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>.","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>","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.","short":"N. Koval, D. Khalanskiy, D.-A. Alistarh, Proceedings of the ACM on Programming Languages 7 (2023).","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.","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>.","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>"},"quality_controlled":"1","_id":"13179","publication_status":"published"},{"date_updated":"2023-07-17T08:39:19Z","issue":"2","oa":1,"intvolume":"        16","month":"05","date_published":"2023-05-26T00:00:00Z","year":"2023","external_id":{"arxiv":["2203.06881"]},"page":"331-342","date_created":"2023-07-02T22:00:43Z","status":"public","day":"26","volume":16,"oa_version":"Preprint","doi":"10.2140/involve.2023.16.331","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2203.06881"}],"publication":"Involve","title":"Local solubility for a family of quadrics over a split quadric surface","author":[{"full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D"},{"last_name":"Lyczak","id":"3572849A-F248-11E8-B48F-1D18A9856A87","first_name":"Julian","full_name":"Lyczak, Julian"},{"full_name":"Sarapin, Roman","last_name":"Sarapin","first_name":"Roman"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Mathematical Sciences Publishers","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"TiBr"}],"_id":"13180","quality_controlled":"1","publication_identifier":{"issn":["1944-4176"],"eissn":["1944-4184"]},"citation":{"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>.","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>","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>.","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.","short":"T.D. Browning, J. Lyczak, R. Sarapin, Involve 16 (2023) 331–342.","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.","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>"},"type":"journal_article","arxiv":1,"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"}],"scopus_import":"1","publication_status":"published"},{"project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183","call_identifier":"H2020"},{"name":"Discretization in Geometry and Dynamics","_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","grant_number":"I4887"},{"name":"The Wittgenstein Prize","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","call_identifier":"FWF"}],"publication_status":"epub_ahead","_id":"13182","quality_controlled":"1","citation":{"chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “Geometric Characterization of the Persistence of 1D Maps.” <i>Journal of Applied and Computational Topology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s41468-023-00126-9\">https://doi.org/10.1007/s41468-023-00126-9</a>.","ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Geometric characterization of the persistence of 1D maps. <i>Journal of Applied and Computational Topology</i>. 2023. doi:<a href=\"https://doi.org/10.1007/s41468-023-00126-9\">10.1007/s41468-023-00126-9</a>","ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. 2023. Geometric characterization of the persistence of 1D maps. Journal of Applied and Computational Topology.","ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Geometric characterization of the persistence of 1D maps,” <i>Journal of Applied and Computational Topology</i>. Springer Nature, 2023.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Journal of Applied and Computational Topology (2023).","mla":"Biswas, Ranita, et al. “Geometric Characterization of the Persistence of 1D Maps.” <i>Journal of Applied and Computational Topology</i>, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s41468-023-00126-9\">10.1007/s41468-023-00126-9</a>.","apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (2023). Geometric characterization of the persistence of 1D maps. <i>Journal of Applied and Computational Topology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s41468-023-00126-9\">https://doi.org/10.1007/s41468-023-00126-9</a>"},"publication_identifier":{"eissn":["2367-1734"],"issn":["2367-1726"]},"type":"journal_article","file_date_updated":"2023-07-03T09:41:05Z","abstract":[{"text":"We characterize critical points of 1-dimensional maps paired in persistent homology\r\ngeometrically and this way get elementary proofs of theorems about the symmetry\r\nof persistence diagrams and the variation of such maps. In particular, we identify\r\nbranching points and endpoints of networks as the sole source of asymmetry and\r\nrelate the cycle basis in persistent homology with a version of the stable marriage\r\nproblem. Our analysis provides the foundations of fast algorithms for maintaining a\r\ncollection of sorted lists together with its persistence diagram.","lang":"eng"}],"scopus_import":"1","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"HeEd"}],"file":[{"file_id":"13185","content_type":"application/pdf","file_size":487355,"creator":"alisjak","relation":"main_file","access_level":"open_access","checksum":"697249d5d1c61dea4410b9f021b70fce","success":1,"file_name":"2023_Journal of Applied and Computational Topology_Biswas.pdf","date_created":"2023-07-03T09:41:05Z","date_updated":"2023-07-03T09:41:05Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Geometric characterization of the persistence of 1D maps","author":[{"full_name":"Biswas, Ranita","first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","last_name":"Biswas","orcid":"0000-0002-5372-7890"},{"first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-0832","last_name":"Cultrera Di Montesano","full_name":"Cultrera Di Montesano, Sebastiano"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"last_name":"Saghafian","first_name":"Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824","full_name":"Saghafian, Morteza"}],"has_accepted_license":"1","publisher":"Springer Nature","ec_funded":1,"oa_version":"Published Version","doi":"10.1007/s41468-023-00126-9","publication":"Journal of Applied and Computational Topology","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"],"date_created":"2023-07-02T22:00:44Z","day":"17","status":"public","year":"2023","date_updated":"2023-10-18T08:13:10Z","oa":1,"month":"06","date_published":"2023-06-17T00:00:00Z","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35. The authors of this paper thank anonymous reviewers for their constructive criticism and Monika Henzinger for detailed comments on an earlier version of this paper."},{"has_accepted_license":"1","publisher":"Association for Computing Machinery","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","full_name":"Hafner, Christian"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","last_name":"Bickel","full_name":"Bickel, Bernd"}],"title":"The design space of Kirchhoff rods","file":[{"file_name":"kirchhoff-rods.pdf","success":1,"date_created":"2023-07-04T08:11:28Z","date_updated":"2023-07-04T08:11:28Z","creator":"chafner","file_size":19635168,"content_type":"application/pdf","file_id":"13194","checksum":"4954c1cfa487725bc156dcfec872478a","access_level":"open_access","relation":"main_file"},{"date_updated":"2023-07-04T07:46:28Z","date_created":"2023-07-04T07:46:28Z","title":"Supplemental Material with Proofs","file_name":"supp-main.pdf","relation":"supplementary_material","checksum":"79c9975fbc82ff71f1767331d2204cca","access_level":"open_access","creator":"chafner","file_size":420909,"content_type":"application/pdf","file_id":"13190"},{"content_type":"application/pdf","file_id":"13191","file_size":430086,"creator":"chafner","relation":"supplementary_material","access_level":"open_access","checksum":"4ab647e4f03c711e1e6a5fc1eb8684db","file_name":"supp-cheat.pdf","title":"Cheat Sheet for Notation","date_created":"2023-07-04T07:46:30Z","date_updated":"2023-07-04T07:46:30Z"},{"file_name":"kirchhoff-video-final.mp4","date_created":"2023-07-04T07:46:39Z","date_updated":"2023-07-04T07:46:39Z","title":"Supplemental Video","creator":"chafner","file_size":268088064,"file_id":"13192","content_type":"video/mp4","checksum":"c0fd9a57d012046de90c185ffa904b76","access_level":"open_access","relation":"supplementary_material"},{"file_name":"matlab-submission.zip","title":"Matlab Source Code with Example","date_created":"2023-07-04T07:47:10Z","date_updated":"2023-07-04T07:47:10Z","file_id":"13193","content_type":"application/x-zip-compressed","file_size":25790,"creator":"chafner","checksum":"71b00712b489ada2cd9815910ee180a9","relation":"supplementary_material","access_level":"open_access"}],"article_processing_charge":"No","department":[{"_id":"BeBi"}],"language":[{"iso":"eng"}],"article_type":"original","citation":{"apa":"Hafner, C., &#38; Bickel, B. (2023). The design space of Kirchhoff rods. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3606033\">https://doi.org/10.1145/3606033</a>","mla":"Hafner, Christian, and Bernd Bickel. “The Design Space of Kirchhoff Rods.” <i>ACM Transactions on Graphics</i>, vol. 42, no. 5, 171, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3606033\">10.1145/3606033</a>.","ista":"Hafner C, Bickel B. 2023. The design space of Kirchhoff rods. ACM Transactions on Graphics. 42(5), 171.","short":"C. Hafner, B. Bickel, ACM Transactions on Graphics 42 (2023).","ieee":"C. Hafner and B. Bickel, “The design space of Kirchhoff rods,” <i>ACM Transactions on Graphics</i>, vol. 42, no. 5. Association for Computing Machinery, 2023.","ama":"Hafner C, Bickel B. The design space of Kirchhoff rods. <i>ACM Transactions on Graphics</i>. 2023;42(5). doi:<a href=\"https://doi.org/10.1145/3606033\">10.1145/3606033</a>","chicago":"Hafner, Christian, and Bernd Bickel. “The Design Space of Kirchhoff Rods.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3606033\">https://doi.org/10.1145/3606033</a>."},"publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"abstract":[{"text":"The Kirchhoff rod model describes the bending and twisting of slender elastic rods in three dimensions, and has been widely studied to enable the prediction of how a rod will deform, given its geometry and boundary conditions. In this work, we study a number of inverse problems with the goal of computing the geometry of a straight rod that will automatically deform to match a curved target shape after attaching its endpoints to a support structure. Our solution lets us finely control the static equilibrium state of a rod by varying the cross-sectional profiles along its length.\r\nWe also show that the set of physically realizable equilibrium states admits a concise geometric description in terms of linear line complexes, which leads to very efficient computational design algorithms. Implemented in an interactive software tool, they allow us to convert three-dimensional hand-drawn spline curves to elastic rods, and give feedback about the feasibility and practicality of a design in real time. We demonstrate the efficacy of our method by designing and manufacturing several physical prototypes with applications to interior design and soft robotics.","lang":"eng"}],"file_date_updated":"2023-07-04T08:11:28Z","type":"journal_article","_id":"13188","quality_controlled":"1","project":[{"call_identifier":"H2020","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"publication_status":"published","date_published":"2023-09-20T00:00:00Z","month":"09","intvolume":"        42","acknowledgement":"We thank the anonymous reviewers for their generous feedback, and Julian Fischer for his help in proving Proposition 1. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 715767).","article_number":"171","keyword":["Computer Graphics","Computational Design","Computational Geometry","Shape Modeling"],"date_updated":"2024-03-25T23:30:26Z","acknowledged_ssus":[{"_id":"M-Shop"}],"oa":1,"issue":"5","external_id":{"isi":["001086833300010"]},"year":"2023","volume":42,"ddc":["516"],"date_created":"2023-07-04T07:41:30Z","day":"20","status":"public","publication":"ACM Transactions on Graphics","doi":"10.1145/3606033","related_material":{"record":[{"id":"12897","relation":"part_of_dissertation","status":"public"}]},"ec_funded":1,"oa_version":"Submitted Version","isi":1},{"external_id":{"arxiv":["2304.12861"],"isi":["001019565900002"]},"year":"2023","date_published":"2023-06-13T00:00:00Z","intvolume":"         7","month":"06","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. ","article_number":"065601","keyword":["Physics and Astronomy (miscellaneous)","General Materials Science"],"date_updated":"2023-08-02T06:34:47Z","oa":1,"issue":"6","publication":"Physical Review Materials","doi":"10.1103/physrevmaterials.7.065601","oa_version":"Submitted Version","ec_funded":1,"isi":1,"volume":7,"date_created":"2023-07-07T12:48:01Z","ddc":["537"],"day":"13","status":"public","article_processing_charge":"No","department":[{"_id":"ScWa"}],"language":[{"iso":"eng"}],"article_type":"original","has_accepted_license":"1","publisher":"American Physical Society","title":"Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts","author":[{"orcid":"0000-0001-5154-417X","last_name":"Grosjean","first_name":"Galien M","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","full_name":"Grosjean, Galien M"},{"full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis","orcid":"0000-0002-2299-3176","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_created":"2023-07-07T12:49:51Z","date_updated":"2023-07-07T12:49:51Z","success":1,"file_name":"Mosaic_asymmetries.pdf","access_level":"open_access","checksum":"75584730d9cdd50eeccb4c52c509776d","relation":"main_file","file_id":"13198","content_type":"application/pdf","creator":"ggrosjea","file_size":1127040}],"project":[{"name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020","grant_number":"949120"},{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","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>","short":"G.M. Grosjean, S.R. Waitukaitis, Physical Review Materials 7 (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.","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.","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>.","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>"},"publication_identifier":{"issn":["2475-9953"]},"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"}],"arxiv":1,"file_date_updated":"2023-07-07T12:49:51Z","type":"journal_article","_id":"13197","quality_controlled":"1"},{"publisher":"Nature Research","has_accepted_license":"1","author":[{"full_name":"Qiu, Liu","orcid":"0000-0003-4345-4267","last_name":"Qiu","first_name":"Liu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac"},{"last_name":"Sahu","orcid":"0000-0001-6264-2162","first_name":"Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","full_name":"Sahu, Rishabh"},{"last_name":"Hease","orcid":"0000-0001-9868-2166","first_name":"William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","full_name":"Hease, William J"},{"last_name":"Arnold","orcid":"0000-0003-1397-7876","first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"title":"Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"2023_NatureComms_Qiu.pdf","success":1,"date_updated":"2023-07-10T10:10:54Z","date_created":"2023-07-10T10:10:54Z","file_size":1349134,"creator":"alisjak","file_id":"13206","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"ec7ccd2c08f90d59cab302fd0d7776a4"}],"department":[{"_id":"JoFi"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"arxiv":1,"scopus_import":"1","abstract":[{"lang":"eng","text":"Recent quantum technologies have established precise quantum control of various microscopic systems using electromagnetic waves. Interfaces based on cryogenic cavity electro-optic systems are particularly promising, due to the direct interaction between microwave and optical fields in the quantum regime. Quantum optical control of superconducting microwave circuits has been precluded so far due to the weak electro-optical coupling as well as quasi-particles induced by the pump laser. Here we report the coherent control of a superconducting microwave cavity using laser pulses in a multimode electro-optical device at millikelvin temperature with near-unity cooperativity. Both the stationary and instantaneous responses of the microwave and optical modes comply with the coherent electro-optical interaction, and reveal only minuscule amount of excess back-action with an unanticipated time delay. Our demonstration enables wide ranges of applications beyond quantum transductions, from squeezing and quantum non-demolition measurements of microwave fields, to entanglement generation and hybrid quantum networks."}],"file_date_updated":"2023-07-10T10:10:54Z","type":"journal_article","publication_identifier":{"eissn":["2041-1723"]},"citation":{"mla":"Qiu, Liu, et al. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical Dynamical Back-Action.” <i>Nature Communications</i>, vol. 14, 3784, Nature Research, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-39493-3\">10.1038/s41467-023-39493-3</a>.","apa":"Qiu, L., Sahu, R., Hease, W. J., Arnold, G. M., &#38; Fink, J. M. (2023). Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. <i>Nature Communications</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41467-023-39493-3\">https://doi.org/10.1038/s41467-023-39493-3</a>","chicago":"Qiu, Liu, Rishabh Sahu, William J Hease, Georg M Arnold, and Johannes M Fink. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical Dynamical Back-Action.” <i>Nature Communications</i>. Nature Research, 2023. <a href=\"https://doi.org/10.1038/s41467-023-39493-3\">https://doi.org/10.1038/s41467-023-39493-3</a>.","ista":"Qiu L, Sahu R, Hease WJ, Arnold GM, Fink JM. 2023. Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. Nature Communications. 14, 3784.","short":"L. Qiu, R. Sahu, W.J. Hease, G.M. Arnold, J.M. Fink, Nature Communications 14 (2023).","ieee":"L. Qiu, R. Sahu, W. J. Hease, G. M. Arnold, and J. M. Fink, “Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action,” <i>Nature Communications</i>, vol. 14. Nature Research, 2023.","ama":"Qiu L, Sahu R, Hease WJ, Arnold GM, Fink JM. Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-39493-3\">10.1038/s41467-023-39493-3</a>"},"quality_controlled":"1","_id":"13200","publication_status":"published","project":[{"grant_number":"758053","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020","grant_number":"899354"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"},{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"This work was supported by the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 899354 (FETopen SuperQuLAN), and the Austrian Science Fund (FWF) through BeyondC (F7105). L.Q. acknowledges generous support from the ISTFELLOW programme. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 754411. G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria.","article_number":"3784","date_published":"2023-06-24T00:00:00Z","month":"06","intvolume":"        14","oa":1,"date_updated":"2024-08-07T07:11:55Z","external_id":{"isi":["001018100800002"],"arxiv":["2210.12443"],"pmid":["37355691"]},"year":"2023","volume":14,"pmid":1,"status":"public","day":"24","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2023-07-09T22:01:11Z","ddc":["000"],"publication":"Nature Communications","doi":"10.1038/s41467-023-39493-3","ec_funded":1,"oa_version":"Published Version","isi":1},{"department":[{"_id":"JiFr"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","has_accepted_license":"1","file":[{"date_updated":"2023-12-13T23:30:03Z","date_created":"2023-07-10T08:48:40Z","file_name":"2023_PNAS_Wang.pdf","access_level":"open_access","relation":"main_file","checksum":"d800e06252eaefba28531fa9440f23f0","embargo":"2023-12-12","creator":"alisjak","file_size":5244581,"file_id":"13204","content_type":"application/pdf"}],"title":"The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation","author":[{"full_name":"Wang, Yalu","first_name":"Yalu","last_name":"Wang"},{"full_name":"Yuan, Zhi","first_name":"Zhi","last_name":"Yuan"},{"last_name":"Wang","first_name":"Jinyi","full_name":"Wang, Jinyi"},{"first_name":"Huixin","last_name":"Xiao","full_name":"Xiao, Huixin"},{"full_name":"Wan, Lu","last_name":"Wan","first_name":"Lu"},{"full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin","last_name":"Li","orcid":"0000-0002-5607-272X"},{"first_name":"Yan","last_name":"Guo","full_name":"Guo, Yan"},{"full_name":"Gong, Zhizhong","first_name":"Zhizhong","last_name":"Gong"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Zhang, Jing","last_name":"Zhang","first_name":"Jing"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","file_date_updated":"2023-12-13T23:30:03Z","type":"journal_article","abstract":[{"lang":"eng","text":"As a crucial nitrogen source, nitrate (NO3−) is a key nutrient for plants. Accordingly, root systems adapt to maximize NO3− availability, a developmental regulation also involving the phytohormone auxin. Nonetheless, the molecular mechanisms underlying this regulation remain poorly understood. Here, we identify low-nitrate-resistant mutant (lonr) in Arabidopsis (Arabidopsis thaliana), whose root growth fails to adapt to low-NO3− conditions. lonr2 is defective in the high-affinity NO3− transporter NRT2.1. lonr2 (nrt2.1) mutants exhibit defects in polar auxin transport, and their low-NO3−-induced root phenotype depends on the PIN7 auxin exporter activity. NRT2.1 directly associates with PIN7 and antagonizes PIN7-mediated auxin efflux depending on NO3− levels. These results reveal a mechanism by which NRT2.1 in response to NO3− limitation directly regulates auxin transport activity and, thus, root growth. This adaptive mechanism contributes to the root developmental plasticity to help plants cope with changes in NO3− availability."}],"scopus_import":"1","citation":{"ama":"Wang Y, Yuan Z, Wang J, et al. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2023;120(25). doi:<a href=\"https://doi.org/10.1073/pnas.2221313120\">10.1073/pnas.2221313120</a>","ieee":"Y. Wang <i>et al.</i>, “The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 25. National Academy of Sciences, 2023.","short":"Y. Wang, Z. Yuan, J. Wang, H. Xiao, L. Wan, L. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","ista":"Wang Y, Yuan Z, Wang J, Xiao H, Wan L, Li L, Guo Y, Gong Z, Friml J, Zhang J. 2023. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. 120(25), e2221313120.","chicago":"Wang, Yalu, Zhi Yuan, Jinyi Wang, Huixin Xiao, Lu Wan, Lanxin Li, Yan Guo, Zhizhong Gong, Jiří Friml, and Jing Zhang. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2023. <a href=\"https://doi.org/10.1073/pnas.2221313120\">https://doi.org/10.1073/pnas.2221313120</a>.","apa":"Wang, Y., Yuan, Z., Wang, J., Xiao, H., Wan, L., Li, L., … Zhang, J. (2023). The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2221313120\">https://doi.org/10.1073/pnas.2221313120</a>","mla":"Wang, Yalu, et al. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 25, e2221313120, National Academy of Sciences, 2023, doi:<a href=\"https://doi.org/10.1073/pnas.2221313120\">10.1073/pnas.2221313120</a>."},"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"quality_controlled":"1","_id":"13201","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","external_id":{"pmid":["37307446"],"isi":["001030689600003"]},"year":"2023","acknowledgement":"We are grateful to Caifu Jiang for providing ethyl metha-nesulfonate- mutagenized population, Yi Wang for providing Xenopus oocytes, Jun Fan and Zhaosheng Kong for providing tobacco BY- 2 cells, and Claus Schwechheimer, Alain Gojon, and Shutang Tan for helpful discussions. This work was supported by the National Key Research and Development Program of China (2021YFF1000500), the  National  Natural  Science  Foundation  of  China  (32170265  and  32022007),  Hainan  Provincial  Natural  Science  Foundation  of  China  (323CXTD379),  Chinese  Universities  Scientific  Fund  (2023TC019),  Beijing  Municipal  Natural  Science  Foundation  (5192011),  Beijing  Outstanding  University  Discipline  Program,  and  China Postdoctoral Science Foundation (BH2020259460).","article_number":"e2221313120","intvolume":"       120","month":"06","date_published":"2023-06-12T00:00:00Z","issue":"25","oa":1,"date_updated":"2023-12-13T23:30:04Z","doi":"10.1073/pnas.2221313120","publication":"Proceedings of the National Academy of Sciences of the United States of America","isi":1,"oa_version":"Published Version","pmid":1,"volume":120,"day":"12","status":"public","date_created":"2023-07-09T22:01:12Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"ddc":["570"]},{"article_processing_charge":"No","department":[{"_id":"RySh"}],"language":[{"iso":"eng"}],"article_type":"original","has_accepted_license":"1","publisher":"Society for Neuroscience","file":[{"file_name":"2023_JN_Eguchi.pdf","success":1,"date_created":"2023-07-10T09:04:58Z","date_updated":"2023-07-10T09:04:58Z","creator":"alisjak","file_size":7794425,"content_type":"application/pdf","file_id":"13205","access_level":"open_access","relation":"main_file","checksum":"70b2141870e0bf1c94fd343e18fdbc32"}],"author":[{"full_name":"Eguchi, Kohgaku","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","first_name":"Kohgaku","orcid":"0000-0002-6170-2546","last_name":"Eguchi"},{"full_name":"Le Monnier, Elodie","id":"3B59276A-F248-11E8-B48F-1D18A9856A87","first_name":"Elodie","last_name":"Le Monnier"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"title":"Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"2659CC84-B435-11E9-9278-68D0E5697425","name":"Ultrastructural analysis of phosphoinositides in nerve terminals: distribution, dynamics and physiological roles in synaptic transmission","grant_number":"793482","call_identifier":"H2020"},{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694539"}],"publication_status":"published","publication_identifier":{"issn":["0270-6474"],"eissn":["1529-2401"]},"citation":{"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>","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.","short":"K. Eguchi, E. Le Monnier, R. Shigemoto, The Journal of Neuroscience 43 (2023) 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>.","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>","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>."},"file_date_updated":"2023-07-10T09:04:58Z","type":"journal_article","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"}],"scopus_import":"1","_id":"13202","quality_controlled":"1","external_id":{"pmid":["37160366"],"isi":["001020132100005"]},"page":"4197-4216","year":"2023","intvolume":"        43","month":"06","date_published":"2023-06-07T00:00:00Z","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.","date_updated":"2023-10-18T07:12:47Z","issue":"23","oa":1,"acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.1523/JNEUROSCI.1514-22.2023","publication":"The Journal of Neuroscience","isi":1,"ec_funded":1,"oa_version":"Published Version","pmid":1,"volume":43,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_created":"2023-07-09T22:01:12Z","day":"07","status":"public"},{"date_published":"2023-05-18T00:00:00Z","intvolume":"        12","month":"05","acknowledgement":"We thank Egor Babaev for encouraging us to study this problem, and Rupert Frank for many fruitful discussions. scussions. Funding. Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No. 694227 (Barbara Roos and Robert Seiringer) is gratefully acknowledged.","date_updated":"2023-10-27T10:37:29Z","oa":1,"issue":"4","external_id":{"arxiv":["2201.08090"],"isi":["000997933500008"]},"page":"1507–1540","year":"2023","volume":12,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["530"],"date_created":"2023-07-10T16:35:45Z","status":"public","day":"18","publication":"Journal of Spectral Theory","doi":"10.4171/JST/439","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14374"}]},"ec_funded":1,"oa_version":"Published Version","isi":1,"has_accepted_license":"1","publisher":"EMS Press","title":"Boundary superconductivity in the BCS model","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Hainzl, Christian","first_name":"Christian","last_name":"Hainzl"},{"full_name":"Roos, Barbara","id":"5DA90512-D80F-11E9-8994-2E2EE6697425","first_name":"Barbara","orcid":"0000-0002-9071-5880","last_name":"Roos"},{"orcid":"0000-0002-6781-0521","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert"}],"file":[{"success":1,"file_name":"2023_EMS_Hainzl.pdf","date_updated":"2023-07-11T08:19:15Z","date_created":"2023-07-11T08:19:15Z","content_type":"application/pdf","file_id":"13208","creator":"alisjak","file_size":304619,"access_level":"open_access","checksum":"5501da33be010b5c81440438287584d5","relation":"main_file"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"language":[{"iso":"eng"}],"article_type":"original","publication_identifier":{"eissn":["1664-0403"],"issn":["1664-039X"]},"citation":{"short":"C. Hainzl, B. Roos, R. Seiringer, Journal of Spectral Theory 12 (2023) 1507–1540.","ieee":"C. Hainzl, B. Roos, and R. Seiringer, “Boundary superconductivity in the BCS model,” <i>Journal of Spectral Theory</i>, vol. 12, no. 4. EMS Press, pp. 1507–1540, 2023.","ista":"Hainzl C, Roos B, Seiringer R. 2023. Boundary superconductivity in the BCS model. Journal of Spectral Theory. 12(4), 1507–1540.","ama":"Hainzl C, Roos B, Seiringer R. Boundary superconductivity in the BCS model. <i>Journal of Spectral Theory</i>. 2023;12(4):1507–1540. doi:<a href=\"https://doi.org/10.4171/JST/439\">10.4171/JST/439</a>","chicago":"Hainzl, Christian, Barbara Roos, and Robert Seiringer. “Boundary Superconductivity in the BCS Model.” <i>Journal of Spectral Theory</i>. EMS Press, 2023. <a href=\"https://doi.org/10.4171/JST/439\">https://doi.org/10.4171/JST/439</a>.","apa":"Hainzl, C., Roos, B., &#38; Seiringer, R. (2023). Boundary superconductivity in the BCS model. <i>Journal of Spectral Theory</i>. EMS Press. <a href=\"https://doi.org/10.4171/JST/439\">https://doi.org/10.4171/JST/439</a>","mla":"Hainzl, Christian, et al. “Boundary Superconductivity in the BCS Model.” <i>Journal of Spectral Theory</i>, vol. 12, no. 4, EMS Press, 2023, pp. 1507–1540, doi:<a href=\"https://doi.org/10.4171/JST/439\">10.4171/JST/439</a>."},"abstract":[{"lang":"eng","text":"We consider the linear BCS equation, determining the BCS critical temperature, in the presence of a boundary, where Dirichlet boundary conditions are imposed. In the one-dimensional case with point interactions, we prove that the critical temperature is strictly larger than the bulk value, at least at weak coupling. In particular, the Cooper-pair wave function localizes near the boundary, an effect that cannot be modeled by effective Neumann boundary conditions on the order parameter as often imposed in Ginzburg–Landau theory. We also show that the relative shift in critical temperature vanishes if the coupling constant either goes to zero or to infinity."}],"arxiv":1,"type":"journal_article","file_date_updated":"2023-07-11T08:19:15Z","_id":"13207","quality_controlled":"1","project":[{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","call_identifier":"H2020"}],"publication_status":"published"},{"oa_version":"Published Version","isi":1,"publication":"Plant Communications","doi":"10.1016/j.xplc.2023.100632","status":"public","day":"13","date_created":"2023-07-12T07:32:00Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"ddc":["580"],"volume":4,"pmid":1,"year":"2023","external_id":{"pmid":["37254481"],"isi":["001113003000001"]},"oa":1,"issue":"6","date_updated":"2024-01-30T10:55:34Z","article_number":"100632","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. ","date_published":"2023-11-13T00:00:00Z","intvolume":"         4","month":"11","publication_status":"published","quality_controlled":"1","_id":"13209","abstract":[{"lang":"eng","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."}],"type":"journal_article","file_date_updated":"2024-01-30T10:54:40Z","publication_identifier":{"eissn":["2590-3462"]},"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).","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.","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.","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>.","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>","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_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"article_processing_charge":"Yes","title":"Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Xia, Jing","last_name":"Xia","first_name":"Jing"},{"last_name":"Kong","first_name":"Mengjuan","full_name":"Kong, Mengjuan"},{"full_name":"Yang, Zhisen","last_name":"Yang","first_name":"Zhisen"},{"full_name":"Sun, Lianghanxiao","first_name":"Lianghanxiao","last_name":"Sun"},{"last_name":"Peng","first_name":"Yakun","full_name":"Peng, Yakun"},{"full_name":"Mao, Yanbo","first_name":"Yanbo","last_name":"Mao"},{"full_name":"Wei, Hong","first_name":"Hong","last_name":"Wei"},{"last_name":"Ying","first_name":"Wei","full_name":"Ying, Wei"},{"last_name":"Gao","first_name":"Yongxiao","full_name":"Gao, Yongxiao"},{"full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"full_name":"Weng, Jianping","first_name":"Jianping","last_name":"Weng"},{"full_name":"Liu, Xin","last_name":"Liu","first_name":"Xin"},{"full_name":"Sun, Linfeng","last_name":"Sun","first_name":"Linfeng"},{"last_name":"Tan","first_name":"Shutang","full_name":"Tan, Shutang"}],"file":[{"checksum":"f8ef92af6096834f91ce38587fb1db9f","access_level":"open_access","relation":"main_file","file_id":"14900","content_type":"application/pdf","file_size":1434862,"creator":"dernst","date_created":"2024-01-30T10:54:40Z","date_updated":"2024-01-30T10:54:40Z","success":1,"file_name":"2023_PlantCommunications_Xia.pdf"}],"publisher":"Elsevier ","has_accepted_license":"1"},{"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_created":"2023-07-12T07:32:46Z","ddc":["580"],"day":"01","status":"public","pmid":1,"volume":16,"isi":1,"oa_version":"Published Version","ec_funded":1,"doi":"10.1016/j.molp.2023.06.007","publication":"Molecular Plant","date_updated":"2024-01-29T10:38:57Z","issue":"7","oa":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"month":"07","intvolume":"        16","date_published":"2023-07-01T00:00:00Z","acknowledgement":"We thank all the authors for sharing the published materials. This research was supported by the Lab Support Facility and the Imaging and Optics Facility of ISTA. We thank Lukáš Fiedler (ISTA) for critical reading of the manuscript. This project was funded by the European Research Council Advanced Grant (ETAP-742985).","year":"2023","external_id":{"pmid":["37393433"],"isi":["001044410900001"]},"page":"1117-1119","_id":"13212","quality_controlled":"1","publication_identifier":{"eissn":["1674-2052"],"issn":["1752-9867"]},"citation":{"ama":"Chen H, Li L, Zou M, Qi L, Friml J. Distinct functions of TIR1 and AFB1 receptors in auxin signalling. <i>Molecular Plant</i>. 2023;16(7):1117-1119. doi:<a href=\"https://doi.org/10.1016/j.molp.2023.06.007\">10.1016/j.molp.2023.06.007</a>","ista":"Chen H, Li L, Zou M, Qi L, Friml J. 2023. Distinct functions of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. 16(7), 1117–1119.","short":"H. Chen, L. Li, M. Zou, L. Qi, J. Friml, Molecular Plant 16 (2023) 1117–1119.","ieee":"H. Chen, L. Li, M. Zou, L. Qi, and J. Friml, “Distinct functions of TIR1 and AFB1 receptors in auxin signalling.,” <i>Molecular Plant</i>, vol. 16, no. 7. Elsevier , pp. 1117–1119, 2023.","chicago":"Chen, Huihuang, Lanxin Li, Minxia Zou, Linlin Qi, and Jiří Friml. “Distinct Functions of TIR1 and AFB1 Receptors in Auxin Signalling.” <i>Molecular Plant</i>. Elsevier , 2023. <a href=\"https://doi.org/10.1016/j.molp.2023.06.007\">https://doi.org/10.1016/j.molp.2023.06.007</a>.","apa":"Chen, H., Li, L., Zou, M., Qi, L., &#38; Friml, J. (2023). Distinct functions of TIR1 and AFB1 receptors in auxin signalling. <i>Molecular Plant</i>. Elsevier . <a href=\"https://doi.org/10.1016/j.molp.2023.06.007\">https://doi.org/10.1016/j.molp.2023.06.007</a>","mla":"Chen, Huihuang, et al. “Distinct Functions of TIR1 and AFB1 Receptors in Auxin Signalling.” <i>Molecular Plant</i>, vol. 16, no. 7, Elsevier , 2023, pp. 1117–19, doi:<a href=\"https://doi.org/10.1016/j.molp.2023.06.007\">10.1016/j.molp.2023.06.007</a>."},"type":"journal_article","file_date_updated":"2024-01-29T10:37:05Z","scopus_import":"1","abstract":[{"lang":"eng","text":"Auxin is the major plant hormone regulating growth and development (Friml, 2022). Forward genetic approaches in the model plant Arabidopsis thaliana have identified major components of auxin signalling and established the canonical mechanism mediating transcriptional and thus developmental reprogramming. In this textbook view, TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFBs) are auxin receptors, which act as F-box subunits determining the substrate specificity of the Skp1-Cullin1-F box protein (SCF) type E3 ubiquitin ligase complex. Auxin acts as a “molecular glue” increasing the affinity between TIR1/AFBs and the Aux/IAA repressors. Subsequently, Aux/IAAs are ubiquitinated and degraded, thus releasing auxin transcription factors from their repression making them free to mediate transcription of auxin response genes (Yu et al., 2022). Nonetheless, accumulating evidence suggests existence of rapid, non-transcriptional responses downstream of TIR1/AFBs such as auxin-induced cytosolic calcium (Ca2+) transients, plasma membrane depolarization and apoplast alkalinisation, all converging on the process of root growth inhibition and root gravitropism (Li et al., 2022). Particularly, these rapid responses are mostly contributed by predominantly cytosolic AFB1, while the long-term growth responses are mediated by mainly nuclear TIR1 and AFB2-AFB5 (Li et al., 2021; Prigge et al., 2020; Serre et al., 2021). How AFB1 conducts auxin-triggered rapid responses and how it is different from TIR1 and AFB2-AFB5 remains elusive. Here, we compare the roles of TIR1 and AFB1 in transcriptional and rapid responses by modulating their subcellular localization in Arabidopsis and by testing their ability to mediate transcriptional responses when part of the minimal auxin circuit reconstituted in yeast."}],"project":[{"call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","file":[{"checksum":"6012b7e4a2f680ee6c1f84001e2b945f","relation":"main_file","access_level":"open_access","file_size":1000871,"creator":"dernst","file_id":"14894","content_type":"application/pdf","date_updated":"2024-01-29T10:37:05Z","date_created":"2024-01-29T10:37:05Z","file_name":"2023_MolecularPlant_Chen.pdf","success":1}],"title":"Distinct functions of TIR1 and AFB1 receptors in auxin signalling.","author":[{"last_name":"Chen","first_name":"Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f","full_name":"Chen, Huihuang"},{"full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","last_name":"Li","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zou, Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","first_name":"Minxia","last_name":"Zou"},{"first_name":"Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","orcid":"0000-0001-5187-8401","last_name":"Qi","full_name":"Qi, Linlin"},{"full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","publisher":"Elsevier ","language":[{"iso":"eng"}],"article_type":"letter_note","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"JiFr"}]},{"publisher":"American Society of Plant Biologists","has_accepted_license":"1","title":"Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Chen, C","last_name":"Chen","first_name":"C"},{"last_name":"Zhang","first_name":"Y","full_name":"Zhang, Y"},{"last_name":"Cai","first_name":"J","full_name":"Cai, J"},{"first_name":"Y","last_name":"Qiu","full_name":"Qiu, Y"},{"full_name":"Li, L","last_name":"Li","first_name":"L"},{"first_name":"C","last_name":"Gao","full_name":"Gao, C"},{"first_name":"Y","last_name":"Gao","full_name":"Gao, Y"},{"last_name":"Ke","first_name":"M","full_name":"Ke, M"},{"full_name":"Wu, S","last_name":"Wu","first_name":"S"},{"full_name":"Wei, C","last_name":"Wei","first_name":"C"},{"last_name":"Chen","first_name":"J","full_name":"Chen, J"},{"last_name":"Xu","first_name":"T","full_name":"Xu, T"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří"},{"first_name":"J","last_name":"Wang","full_name":"Wang, J"},{"full_name":"Li, R","first_name":"R","last_name":"Li"},{"first_name":"D","last_name":"Chao","full_name":"Chao, D"},{"first_name":"B","last_name":"Zhang","full_name":"Zhang, B"},{"full_name":"Chen, X","last_name":"Chen","first_name":"X"},{"last_name":"Gao","first_name":"Z","full_name":"Gao, Z"}],"file":[{"file_name":"2023_PlantPhys_Chen.pdf","success":1,"date_created":"2023-07-13T13:26:33Z","date_updated":"2023-07-13T13:26:33Z","file_size":2076977,"creator":"cchlebak","file_id":"13220","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"5492e1d18ac3eaf202633d210fa0fb75"}],"department":[{"_id":"JiFr"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"abstract":[{"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.","lang":"eng"}],"file_date_updated":"2023-07-13T13:26:33Z","type":"journal_article","publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"citation":{"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>","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.","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.","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>.","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>","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>."},"quality_controlled":"1","_id":"13213","publication_status":"published","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.","date_published":"2023-07-01T00:00:00Z","intvolume":"       192","month":"07","oa":1,"issue":"3","date_updated":"2023-08-02T06:27:55Z","external_id":{"isi":["000971795800001"],"pmid":["37010107"]},"page":"2243-2260","year":"2023","volume":192,"pmid":1,"day":"01","status":"public","date_created":"2023-07-12T07:32:58Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["575"],"publication":"Plant Physiology","doi":"10.1093/plphys/kiad207","oa_version":"Published Version","isi":1},{"external_id":{"isi":["001017033600001"],"pmid":["37371083"]},"year":"2023","article_number":"1613","acknowledgement":"This work was supported by the Austrian Academy of Sciences ÖAW: Doc fellowship (26130) to Stefan Riegler.","date_published":"2023-06-13T00:00:00Z","intvolume":"        12","month":"06","oa":1,"issue":"12","date_updated":"2024-03-06T14:00:33Z","publication":"Cells","doi":"10.3390/cells12121613","oa_version":"Published Version","isi":1,"volume":12,"pmid":1,"status":"public","day":"13","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_created":"2023-07-12T07:41:25Z","department":[{"_id":"EvBe"}],"article_processing_charge":"Yes","article_type":"review","language":[{"iso":"eng"}],"publisher":"MDPI","has_accepted_license":"1","author":[{"full_name":"Abualia, R","last_name":"Abualia","first_name":"R"},{"full_name":"Riegler, Stefan","first_name":"Stefan","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","orcid":"0000-0003-3413-1343","last_name":"Riegler"},{"full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","last_name":"Benková"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Nitrate, auxin and cytokinin - a trio to tango","file":[{"file_name":"2023_cells_Abualia.pdf","success":1,"date_updated":"2023-07-12T10:01:54Z","date_created":"2023-07-12T10:01:54Z","creator":"alisjak","file_size":1066802,"content_type":"application/pdf","file_id":"13218","relation":"main_file","checksum":"6dc9df5f4f59fc27c509c275060354a5","access_level":"open_access"}],"publication_status":"published","project":[{"name":"Functional asymmetry of medial habenula outputs in mice","_id":"62883ed7-2b32-11ec-9570-93580204e56b","grant_number":"26130"}],"abstract":[{"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.","lang":"eng"}],"file_date_updated":"2023-07-12T10:01:54Z","type":"journal_article","publication_identifier":{"issn":["2073-4409"]},"citation":{"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>.","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>","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>.","short":"R. Abualia, S. Riegler, E. Benková, Cells 12 (2023).","ista":"Abualia R, Riegler S, Benková E. 2023. Nitrate, auxin and cytokinin - a trio to tango. Cells. 12(12), 1613.","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.","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>"},"quality_controlled":"1","_id":"13214"},{"issue":"27","oa":1,"date_updated":"2023-10-11T08:45:10Z","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"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.","intvolume":"       145","month":"06","date_published":"2023-06-30T00:00:00Z","year":"2023","external_id":{"pmid":["37390457"],"isi":["001020623900001"]},"page":"14894-14902","status":"public","day":"30","ddc":["540"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2023-07-12T09:16:40Z","pmid":1,"volume":145,"isi":1,"oa_version":"Published Version","doi":"10.1021/jacs.3c04030","publication":"Journal of the American Chemical Society","file":[{"success":1,"file_name":"2023_JACS_Bunting.pdf","date_created":"2023-07-12T10:22:04Z","date_updated":"2023-07-12T10:22:04Z","file_id":"13219","content_type":"application/pdf","creator":"cchlebak","file_size":3155843,"relation":"main_file","access_level":"open_access","checksum":"e07d5323f9c0e5cbd1ad6453f29440ab"}],"title":"Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane","author":[{"first_name":"Rhys","id":"91deeae8-1207-11ec-b130-c194ad5b50c6","last_name":"Bunting","orcid":"0000-0001-6928-074X","full_name":"Bunting, Rhys"},{"full_name":"Wodaczek, Felix","last_name":"Wodaczek","orcid":"0009-0000-1457-795X","first_name":"Felix","id":"8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e"},{"last_name":"Torabi","first_name":"Tina","full_name":"Torabi, Tina"},{"full_name":"Cheng, Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"American Chemical Society","has_accepted_license":"1","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"MaIb"},{"_id":"BiCh"}],"article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","_id":"13216","type":"journal_article","file_date_updated":"2023-07-12T10:22:04Z","abstract":[{"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.","lang":"eng"}],"publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"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>","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.","short":"R. Bunting, F. Wodaczek, T. Torabi, B. Cheng, Journal of the American Chemical Society 145 (2023) 14894–14902.","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.","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>","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>."},"publication_status":"published"}]