[{"article_number":"649433","citation":{"ama":"Bolger-Munro M, Choi K, Cheung F, et al. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental Biology. 2021;9. doi:10.3389/fcell.2021.649433","apa":"Bolger-Munro, M., Choi, K., Cheung, F., Liu, Y. T., Dang-Lawson, M., Deretic, N., … Gold, M. R. (2021). The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental Biology. Frontiers Media. https://doi.org/10.3389/fcell.2021.649433","ieee":"M. Bolger-Munro et al., “The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse,” Frontiers in Cell and Developmental Biology, vol. 9. Frontiers Media, 2021.","short":"M. Bolger-Munro, K. Choi, F. Cheung, Y.T. Liu, M. Dang-Lawson, N. Deretic, C. Keane, M.R. Gold, Frontiers in Cell and Developmental Biology 9 (2021).","mla":"Bolger-Munro, Madison, et al. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” Frontiers in Cell and Developmental Biology, vol. 9, 649433, Frontiers Media, 2021, doi:10.3389/fcell.2021.649433.","ista":"Bolger-Munro M, Choi K, Cheung F, Liu YT, Dang-Lawson M, Deretic N, Keane C, Gold MR. 2021. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental Biology. 9, 649433.","chicago":"Bolger-Munro, Madison, Kate Choi, Faith Cheung, Yi Tian Liu, May Dang-Lawson, Nikola Deretic, Connor Keane, and Michael R. Gold. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” Frontiers in Cell and Developmental Biology. Frontiers Media, 2021. https://doi.org/10.3389/fcell.2021.649433."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000644419500001"],"pmid":["33928084"]},"article_processing_charge":"No","author":[{"id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E","first_name":"Madison","orcid":"0000-0002-8176-4824","full_name":"Bolger-Munro, Madison","last_name":"Bolger-Munro"},{"first_name":"Kate","full_name":"Choi, Kate","last_name":"Choi"},{"full_name":"Cheung, Faith","last_name":"Cheung","first_name":"Faith"},{"full_name":"Liu, Yi Tian","last_name":"Liu","first_name":"Yi Tian"},{"full_name":"Dang-Lawson, May","last_name":"Dang-Lawson","first_name":"May"},{"full_name":"Deretic, Nikola","last_name":"Deretic","first_name":"Nikola"},{"first_name":"Connor","last_name":"Keane","full_name":"Keane, Connor"},{"first_name":"Michael R.","last_name":"Gold","full_name":"Gold, Michael R."}],"title":"The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse","acknowledgement":"We thank the UBC Life Sciences Institute Imaging Facility andthe UBC Flow Cytometry Facility.","oa":1,"quality_controlled":"1","publisher":"Frontiers Media","year":"2021","has_accepted_license":"1","isi":1,"publication":"Frontiers in Cell and Developmental Biology","day":"13","date_created":"2021-05-09T22:01:37Z","date_published":"2021-04-13T00:00:00Z","doi":"10.3389/fcell.2021.649433","_id":"9379","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["B cell","actin","immune synapse","cell spreading","cofilin","WDR1 (AIP1)","LIM domain kinase","B cell receptor (BCR)"],"status":"public","date_updated":"2023-10-18T08:19:49Z","ddc":["570"],"file_date_updated":"2021-05-11T15:09:23Z","department":[{"_id":"CaHe"}],"abstract":[{"lang":"eng","text":"When B cells encounter membrane-bound antigens, the formation and coalescence of B cell antigen receptor (BCR) microclusters amplifies BCR signaling. The ability of B cells to probe the surface of antigen-presenting cells (APCs) and respond to APC-bound antigens requires remodeling of the actin cytoskeleton. Initial BCR signaling stimulates actin-related protein (Arp) 2/3 complex-dependent actin polymerization, which drives B cell spreading as well as the centripetal movement and coalescence of BCR microclusters at the B cell-APC synapse. Sustained actin polymerization depends on concomitant actin filament depolymerization, which enables the recycling of actin monomers and Arp2/3 complexes. Cofilin-mediated severing of actin filaments is a rate-limiting step in the morphological changes that occur during immune synapse formation. Hence, regulators of cofilin activity such as WD repeat-containing protein 1 (Wdr1), LIM domain kinase (LIMK), and coactosin-like 1 (Cotl1) may also be essential for actin-dependent processes in B cells. Wdr1 enhances cofilin-mediated actin disassembly. Conversely, Cotl1 competes with cofilin for binding to actin and LIMK phosphorylates cofilin and prevents it from binding to actin filaments. We now show that Wdr1 and LIMK have distinct roles in BCR-induced assembly of the peripheral actin structures that drive B cell spreading, and that cofilin, Wdr1, and LIMK all contribute to the actin-dependent amplification of BCR signaling at the immune synapse. Depleting Cotl1 had no effect on these processes. Thus, the Wdr1-LIMK-cofilin axis is critical for BCR-induced actin remodeling and for B cell responses to APC-bound antigens."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 9","month":"04","publication_status":"published","publication_identifier":{"eissn":["2296-634X"]},"language":[{"iso":"eng"}],"file":[{"checksum":"8c8a03575d2f7583f88dc3b658b0976b","file_id":"9386","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-05-11T15:09:23Z","file_name":"2021_Frontiers_Cell_Bolger-Munro.pdf","date_updated":"2021-05-11T15:09:23Z","file_size":4076024,"creator":"kschuh"}],"volume":9},{"ddc":["570"],"date_updated":"2023-10-18T08:17:42Z","file_date_updated":"2021-05-04T13:22:19Z","department":[{"_id":"GaTk"}],"_id":"9362","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"file_size":2768282,"date_updated":"2021-05-04T13:22:19Z","creator":"kschuh","file_name":"2021_pone_Chalk.pdf","date_created":"2021-05-04T13:22:19Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9371","checksum":"c52da133850307d2031f552d998f00e8"}],"publication_status":"published","publication_identifier":{"eissn":["19326203"]},"volume":16,"issue":"4","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"A central goal in systems neuroscience is to understand the functions performed by neural circuits. Previous top-down models addressed this question by comparing the behaviour of an ideal model circuit, optimised to perform a given function, with neural recordings. However, this requires guessing in advance what function is being performed, which may not be possible for many neural systems. To address this, we propose an inverse reinforcement learning (RL) framework for inferring the function performed by a neural network from data. We assume that the responses of each neuron in a network are optimised so as to drive the network towards ‘rewarded’ states, that are desirable for performing a given function. We then show how one can use inverse RL to infer the reward function optimised by the network from observing its responses. This inferred reward function can be used to predict how the neural network should adapt its dynamics to perform the same function when the external environment or network structure changes. This could lead to theoretical predictions about how neural network dynamics adapt to deal with cell death and/or varying sensory stimulus statistics."}],"intvolume":" 16","month":"04","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Chalk, M. J., Tkačik, G., & Marre, O. (2021). Inferring the function performed by a recurrent neural network. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0248940","ama":"Chalk MJ, Tkačik G, Marre O. Inferring the function performed by a recurrent neural network. PLoS ONE. 2021;16(4). doi:10.1371/journal.pone.0248940","ieee":"M. J. Chalk, G. Tkačik, and O. Marre, “Inferring the function performed by a recurrent neural network,” PLoS ONE, vol. 16, no. 4. Public Library of Science, 2021.","short":"M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021).","mla":"Chalk, Matthew J., et al. “Inferring the Function Performed by a Recurrent Neural Network.” PLoS ONE, vol. 16, no. 4, e0248940, Public Library of Science, 2021, doi:10.1371/journal.pone.0248940.","ista":"Chalk MJ, Tkačik G, Marre O. 2021. Inferring the function performed by a recurrent neural network. PLoS ONE. 16(4), e0248940.","chicago":"Chalk, Matthew J, Gašper Tkačik, and Olivier Marre. “Inferring the Function Performed by a Recurrent Neural Network.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0248940."},"title":"Inferring the function performed by a recurrent neural network","external_id":{"isi":["000641474900072"],"pmid":["33857170"]},"article_processing_charge":"No","author":[{"last_name":"Chalk","full_name":"Chalk, Matthew J","orcid":"0000-0001-7782-4436","first_name":"Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Marre","full_name":"Marre, Olivier","first_name":"Olivier"}],"article_number":"e0248940","publication":"PLoS ONE","day":"15","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-05-02T22:01:28Z","date_published":"2021-04-15T00:00:00Z","doi":"10.1371/journal.pone.0248940","acknowledgement":"The authors would like to thank Ulisse Ferrari for useful discussions and feedback.","oa":1,"publisher":"Public Library of Science","quality_controlled":"1"},{"intvolume":" 22","month":"08","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Size control is a fundamental question in biology, showing incremental complexity in plants, whose cells possess a rigid cell wall. The phytohormone auxin is a vital growth regulator with central importance for differential growth control. Our results indicate that auxin-reliant growth programs affect the molecular complexity of xyloglucans, the major type of cell wall hemicellulose in eudicots. Auxin-dependent induction and repression of growth coincide with reduced and enhanced molecular complexity of xyloglucans, respectively. In agreement with a proposed function in growth control, genetic interference with xyloglucan side decorations distinctly modulates auxin-dependent differential growth rates. Our work proposes that auxin-dependent growth programs have a spatially defined effect on xyloglucan’s molecular structure, which in turn affects cell wall mechanics and specifies differential, gravitropic hypocotyl growth."}],"volume":22,"issue":"17","language":[{"iso":"eng"}],"file":[{"file_id":"9988","checksum":"6b7055cf89f1b7ed8594c3fdf56f000b","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-09-06T12:50:19Z","file_name":"2021_IntJMolecularSciences_Velasquez.pdf","date_updated":"2021-09-07T09:04:53Z","file_size":2162247,"creator":"cchlebak"}],"publication_status":"published","publication_identifier":{"eissn":["1422-0067"],"issn":["1661-6596"]},"keyword":["auxin","growth","cell wall","xyloglucans","hypocotyls","gravitropism"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"9986","file_date_updated":"2021-09-07T09:04:53Z","department":[{"_id":"EvBe"}],"ddc":["575"],"date_updated":"2023-10-31T19:29:38Z","oa":1,"quality_controlled":"1","publisher":"MDPI","acknowledgement":"We are grateful to Paul Knox, Markus Pauly, Malcom O’Neill, and Ignacio Zarra for providing published material; the BOKU-VIBT Imaging Center for access and M. Debreczeny for expertise; J.I. Thaker and Georg Seifert for critical reading.\r\n","date_created":"2021-09-05T22:01:24Z","date_published":"2021-08-26T00:00:00Z","doi":"10.3390/ijms22179222","publication":"International Journal of Molecular Sciences","day":"26","year":"2021","has_accepted_license":"1","isi":1,"article_number":"9222","title":"Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants","external_id":{"pmid":["34502129"],"isi":["000694347100001"]},"article_processing_charge":"Yes","author":[{"full_name":"Velasquez, Silvia Melina","last_name":"Velasquez","first_name":"Silvia Melina"},{"first_name":"Xiaoyuan","last_name":"Guo","full_name":"Guo, Xiaoyuan"},{"full_name":"Gallemi, Marçal","orcid":"0000-0003-4675-6893","last_name":"Gallemi","first_name":"Marçal","id":"460C6802-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bibek","last_name":"Aryal","full_name":"Aryal, Bibek"},{"first_name":"Peter","full_name":"Venhuizen, Peter","last_name":"Venhuizen"},{"first_name":"Elke","full_name":"Barbez, Elke","last_name":"Barbez"},{"first_name":"Kai Alexander","full_name":"Dünser, Kai Alexander","last_name":"Dünser"},{"first_name":"Martin","last_name":"Darino","full_name":"Darino, Martin"},{"full_name":"Pӗnčík, Aleš","last_name":"Pӗnčík","first_name":"Aleš"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"full_name":"Kalyna, Maria","last_name":"Kalyna","first_name":"Maria"},{"full_name":"Mouille, Gregory","last_name":"Mouille","first_name":"Gregory"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková"},{"full_name":"Bhalerao, Rishikesh P.","last_name":"Bhalerao","first_name":"Rishikesh P."},{"last_name":"Mravec","full_name":"Mravec, Jozef","first_name":"Jozef"},{"first_name":"Jürgen","last_name":"Kleine-Vehn","full_name":"Kleine-Vehn, Jürgen"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"S. M. Velasquez et al., “Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants,” International Journal of Molecular Sciences, vol. 22, no. 17. MDPI, 2021.","short":"S.M. Velasquez, X. Guo, M. Gallemi, B. Aryal, P. Venhuizen, E. Barbez, K.A. Dünser, M. Darino, A. Pӗnčík, O. Novák, M. Kalyna, G. Mouille, E. Benková, R.P. Bhalerao, J. Mravec, J. Kleine-Vehn, International Journal of Molecular Sciences 22 (2021).","ama":"Velasquez SM, Guo X, Gallemi M, et al. Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. International Journal of Molecular Sciences. 2021;22(17). doi:10.3390/ijms22179222","apa":"Velasquez, S. M., Guo, X., Gallemi, M., Aryal, B., Venhuizen, P., Barbez, E., … Kleine-Vehn, J. (2021). Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms22179222","mla":"Velasquez, Silvia Melina, et al. “Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants.” International Journal of Molecular Sciences, vol. 22, no. 17, 9222, MDPI, 2021, doi:10.3390/ijms22179222.","ista":"Velasquez SM, Guo X, Gallemi M, Aryal B, Venhuizen P, Barbez E, Dünser KA, Darino M, Pӗnčík A, Novák O, Kalyna M, Mouille G, Benková E, Bhalerao RP, Mravec J, Kleine-Vehn J. 2021. Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. International Journal of Molecular Sciences. 22(17), 9222.","chicago":"Velasquez, Silvia Melina, Xiaoyuan Guo, Marçal Gallemi, Bibek Aryal, Peter Venhuizen, Elke Barbez, Kai Alexander Dünser, et al. “Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants.” International Journal of Molecular Sciences. MDPI, 2021. https://doi.org/10.3390/ijms22179222."}},{"scopus_import":"1","month":"06","intvolume":" 44","abstract":[{"lang":"eng","text":"Transposable elements exist widely throughout plant genomes and play important roles in plant evolution. Auxin is an important regulator that is traditionally associated with root development and drought stress adaptation. The DEEPER ROOTING 1 (DRO1) gene is a key component of rice drought avoidance. Here, we identified a transposon that acts as an autonomous auxin‐responsive promoter and its presence at specific genome positions conveys physiological adaptations related to drought avoidance. Rice varieties with high and auxin‐mediated transcription of DRO1 in the root tip show deeper and longer root phenotypes and are thus better adapted to drought. The INDITTO2 transposon contains an auxin response element and displays auxin‐responsive promoter activity; it is thus able to convey auxin regulation of transcription to genes in its proximity. In the rice Acuce, which displays DRO1‐mediated drought adaptation, the INDITTO2 transposon was found to be inserted at the promoter region of the DRO1 locus. Transgenesis‐based insertion of the INDITTO2 transposon into the DRO1 promoter of the non‐adapted rice variety Nipponbare was sufficient to promote its drought avoidance. Our data identify an example of how transposons can act as promoters and convey hormonal regulation to nearby loci, improving plant fitness in response to different abiotic stresses."}],"oa_version":"Submitted Version","pmid":1,"volume":44,"issue":"6","publication_identifier":{"issn":["0140-7791"],"eissn":["1365-3040"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"a812418fede076741c9c4dc07f317068","file_id":"14481","success":1,"creator":"amally","date_updated":"2023-11-02T17:02:11Z","file_size":8437528,"date_created":"2023-11-02T17:02:11Z","file_name":"Zhao PlantCellEnv 2021_accepted.pdf"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"9189","file_date_updated":"2023-11-02T17:02:11Z","department":[{"_id":"JiFr"}],"date_updated":"2023-11-07T08:18:36Z","ddc":["580"],"publisher":"Wiley","quality_controlled":"1","oa":1,"page":"1846-1857","doi":"10.1111/pce.14029","date_published":"2021-06-01T00:00:00Z","date_created":"2021-02-24T10:07:21Z","isi":1,"has_accepted_license":"1","year":"2021","day":"01","publication":"Plant, Cell & Environment","author":[{"last_name":"Zhao","full_name":"Zhao, Y","first_name":"Y"},{"full_name":"Wu, L","last_name":"Wu","first_name":"L"},{"first_name":"Q","full_name":"Fu, Q","last_name":"Fu"},{"full_name":"Wang, D","last_name":"Wang","first_name":"D"},{"full_name":"Li, J","last_name":"Li","first_name":"J"},{"first_name":"B","full_name":"Yao, B","last_name":"Yao"},{"first_name":"S","last_name":"Yu","full_name":"Yu, S"},{"full_name":"Jiang, L","last_name":"Jiang","first_name":"L"},{"first_name":"J","full_name":"Qian, J","last_name":"Qian"},{"first_name":"X","full_name":"Zhou, X","last_name":"Zhou"},{"last_name":"Han","full_name":"Han, L","first_name":"L"},{"full_name":"Zhao, S","last_name":"Zhao","first_name":"S"},{"first_name":"C","last_name":"Ma","full_name":"Ma, C"},{"full_name":"Zhang, Y","last_name":"Zhang","first_name":"Y"},{"first_name":"C","last_name":"Luo","full_name":"Luo, C"},{"full_name":"Dong, Q","last_name":"Dong","first_name":"Q"},{"last_name":"Li","full_name":"Li, S","first_name":"S"},{"first_name":"L","full_name":"Zhang, L","last_name":"Zhang"},{"last_name":"Jiang","full_name":"Jiang, X","first_name":"X"},{"first_name":"Y","last_name":"Li","full_name":"Li, Y"},{"first_name":"H","last_name":"Luo","full_name":"Luo, H"},{"first_name":"K","last_name":"Li","full_name":"Li, K"},{"full_name":"Yang, J","last_name":"Yang","first_name":"J"},{"last_name":"Luo","full_name":"Luo, Q","first_name":"Q"},{"first_name":"L","full_name":"Li, L","last_name":"Li"},{"first_name":"S","full_name":"Peng, S","last_name":"Peng"},{"full_name":"Huang, H","last_name":"Huang","first_name":"H"},{"full_name":"Zuo, Z","last_name":"Zuo","first_name":"Z"},{"last_name":"Liu","full_name":"Liu, C","first_name":"C"},{"last_name":"Wang","full_name":"Wang, L","first_name":"L"},{"last_name":"Li","full_name":"Li, C","first_name":"C"},{"first_name":"X","last_name":"He","full_name":"He, X"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Y","last_name":"Du","full_name":"Du, Y"}],"external_id":{"pmid":["33576018"],"isi":["000625398600001"]},"article_processing_charge":"No","title":"INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance","citation":{"ieee":"Y. Zhao et al., “INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance,” Plant, Cell & Environment, vol. 44, no. 6. Wiley, pp. 1846–1857, 2021.","short":"Y. Zhao, L. Wu, Q. Fu, D. Wang, J. Li, B. Yao, S. Yu, L. Jiang, J. Qian, X. Zhou, L. Han, S. Zhao, C. Ma, Y. Zhang, C. Luo, Q. Dong, S. Li, L. Zhang, X. Jiang, Y. Li, H. Luo, K. Li, J. Yang, Q. Luo, L. Li, S. Peng, H. Huang, Z. Zuo, C. Liu, L. Wang, C. Li, X. He, J. Friml, Y. Du, Plant, Cell & Environment 44 (2021) 1846–1857.","ama":"Zhao Y, Wu L, Fu Q, et al. INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant, Cell & Environment. 2021;44(6):1846-1857. doi:10.1111/pce.14029","apa":"Zhao, Y., Wu, L., Fu, Q., Wang, D., Li, J., Yao, B., … Du, Y. (2021). INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant, Cell & Environment. Wiley. https://doi.org/10.1111/pce.14029","mla":"Zhao, Y., et al. “INDITTO2 Transposon Conveys Auxin-Mediated DRO1 Transcription for Rice Drought Avoidance.” Plant, Cell & Environment, vol. 44, no. 6, Wiley, 2021, pp. 1846–57, doi:10.1111/pce.14029.","ista":"Zhao Y, Wu L, Fu Q, Wang D, Li J, Yao B, Yu S, Jiang L, Qian J, Zhou X, Han L, Zhao S, Ma C, Zhang Y, Luo C, Dong Q, Li S, Zhang L, Jiang X, Li Y, Luo H, Li K, Yang J, Luo Q, Li L, Peng S, Huang H, Zuo Z, Liu C, Wang L, Li C, He X, Friml J, Du Y. 2021. INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant, Cell & Environment. 44(6), 1846–1857.","chicago":"Zhao, Y, L Wu, Q Fu, D Wang, J Li, B Yao, S Yu, et al. “INDITTO2 Transposon Conveys Auxin-Mediated DRO1 Transcription for Rice Drought Avoidance.” Plant, Cell & Environment. Wiley, 2021. https://doi.org/10.1111/pce.14029."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"acknowledgement":"This work started when A.G. was visiting the Erwin Schrödinger Institute and then continued when D.F. and L.P visited the Theoretical Chemistry Department of the Vrije Universiteit Amsterdam. The authors thanks the hospitality of both places and, especially, P. Gori-Giorgi and K. Giesbertz for fruitful discussions and literature suggestions in the early state of the project. Finally, the authors also thanks J. Maas and R. Seiringer for their feedback and useful comments to a first draft of the article. L.P. acknowledges support by the Austrian Science Fund (FWF), grants No W1245 and NoF65. D.F acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 716117 and No 694227). A.G. acknowledges funding by the European Research Council under H2020/MSCA-IF “OTmeetsDFT” [grant ID: 795942].","oa":1,"year":"2021","has_accepted_license":"1","publication":"arXiv","day":"21","date_created":"2021-08-06T09:07:12Z","date_published":"2021-07-21T00:00:00Z","doi":"10.48550/arXiv.2106.11217","article_number":"2106.11217","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems"},{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"citation":{"chicago":"Feliciangeli, Dario, Augusto Gerolin, and Lorenzo Portinale. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2106.11217.","ista":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. arXiv, 2106.11217.","mla":"Feliciangeli, Dario, et al. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” ArXiv, 2106.11217, doi:10.48550/arXiv.2106.11217.","ama":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. arXiv. doi:10.48550/arXiv.2106.11217","apa":"Feliciangeli, D., Gerolin, A., & Portinale, L. (n.d.). A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. arXiv. https://doi.org/10.48550/arXiv.2106.11217","ieee":"D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature,” arXiv. .","short":"D. Feliciangeli, A. Gerolin, L. Portinale, ArXiv (n.d.)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2106.11217"]},"article_processing_charge":"No","author":[{"orcid":"0000-0003-0754-8530","full_name":"Feliciangeli, Dario","last_name":"Feliciangeli","first_name":"Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gerolin, Augusto","last_name":"Gerolin","first_name":"Augusto"},{"first_name":"Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","full_name":"Portinale, Lorenzo","last_name":"Portinale"}],"title":"A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature","abstract":[{"text":"This paper establishes new connections between many-body quantum systems, One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport (OT), by interpreting the problem of computing the ground-state energy of a finite dimensional composite quantum system at positive temperature as a non-commutative entropy regularized Optimal Transport problem. We develop a new approach to fully characterize the dual-primal solutions in such non-commutative setting. The mathematical formalism is particularly relevant in quantum chemistry: numerical realizations of the many-electron ground state energy can be computed via a non-commutative version of Sinkhorn algorithm. Our approach allows to prove convergence and robustness of this algorithm, which, to our best knowledge, were unknown even in the two marginal case. Our methods are based on careful a priori estimates in the dual problem, which we believe to be of independent interest. Finally, the above results are extended in 1RDMFT setting, where bosonic or fermionic symmetry conditions are enforced on the problem.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.11217","open_access":"1"}],"month":"07","publication_status":"submitted","language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"status":"public","id":"9733","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"10030"},{"status":"public","id":"12911","relation":"later_version"}]},"_id":"9792","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"preprint","status":"public","date_updated":"2023-11-14T13:21:01Z","ddc":["510"],"department":[{"_id":"RoSe"},{"_id":"JaMa"}]}]