[{"publication_identifier":{"issn":["1672-9072"],"eissn":["1744-7909"]},"oa":1,"type":"journal_article","date_published":"2022-02-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jipb.13225"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","oa_version":"Published Version","month":"02","publication":"Journal of Integrative Plant Biology","language":[{"iso":"eng"}],"day":"01","doi":"10.1111/jipb.13225","abstract":[{"text":"Auxin, one of the first identified and most widely studied phytohormones, has been and will remain a hot topic in plant biology. After more than a century of passionate exploration, the mysteries of its synthesis, transport, signaling, and metabolism have largely been unlocked. Due to the rapid development of new technologies, new methods, and new genetic materials, the study of auxin has entered the fast lane over the past 30 years. Here, we highlight advances in understanding auxin signaling, including auxin perception, rapid auxin responses, TRANSPORT INHIBITOR RESPONSE 1 and AUXIN SIGNALING F-boxes (TIR1/AFBs)-mediated transcriptional and non-transcriptional branches, and the epigenetic regulation of auxin signaling. We also focus on feedback inhibition mechanisms that prevent the over-amplification of auxin signals. In addition, we cover the TRANSMEMBRANE KINASEs (TMKs)-mediated non-canonical signaling, which converges with TIR1/AFBs-mediated transcriptional regulation to coordinate plant growth and development. The identification of additional auxin signaling components and their regulation will continue to open new avenues of research in this field, leading to an increasingly deeper, more comprehensive understanding of how auxin signals are interpreted at the cellular level to regulate plant growth and development.","lang":"eng"}],"citation":{"short":"Z. Yu, F. Zhang, J. Friml, Z. Ding, Journal of Integrative Plant Biology 64 (2022) 371–392.","mla":"Yu, Z., et al. “Auxin Signaling: Research Advances over the Past 30 Years.” Journal of Integrative Plant Biology, vol. 64, no. 2, Wiley, 2022, pp. 371–92, doi:10.1111/jipb.13225.","ista":"Yu Z, Zhang F, Friml J, Ding Z. 2022. Auxin signaling: Research advances over the past 30 years. Journal of Integrative Plant Biology. 64(2), 371–392.","ama":"Yu Z, Zhang F, Friml J, Ding Z. Auxin signaling: Research advances over the past 30 years. Journal of Integrative Plant Biology. 2022;64(2):371-392. doi:10.1111/jipb.13225","apa":"Yu, Z., Zhang, F., Friml, J., & Ding, Z. (2022). Auxin signaling: Research advances over the past 30 years. Journal of Integrative Plant Biology. Wiley. https://doi.org/10.1111/jipb.13225","chicago":"Yu, Z, F Zhang, Jiří Friml, and Z Ding. “Auxin Signaling: Research Advances over the Past 30 Years.” Journal of Integrative Plant Biology. Wiley, 2022. https://doi.org/10.1111/jipb.13225.","ieee":"Z. Yu, F. Zhang, J. Friml, and Z. Ding, “Auxin signaling: Research advances over the past 30 years,” Journal of Integrative Plant Biology, vol. 64, no. 2. Wiley, pp. 371–392, 2022."},"year":"2022","date_updated":"2023-08-02T14:08:30Z","external_id":{"isi":["000761281200011"],"pmid":["35018726"]},"isi":1,"acknowledgement":"This research was financially supported by the National Natural Science Foundation of China and the Israel Science Foundation (NSFC-ISF; 32061143005), National Natural Science Foundation of China (32000225), Natural Science Foundation of Shandong Province (ZR2020QC036), and China Postdoctoral Science Foundation (2020M682165).\r\n","volume":64,"article_processing_charge":"No","date_created":"2022-02-03T09:52:59Z","department":[{"_id":"JiFr"}],"publication_status":"published","intvolume":" 64","title":"Auxin signaling: Research advances over the past 30 years","scopus_import":"1","pmid":1,"_id":"10719","issue":"2","author":[{"first_name":"Z","last_name":"Yu","full_name":"Yu, Z"},{"full_name":"Zhang, F","first_name":"F","last_name":"Zhang"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ding, Z","last_name":"Ding","first_name":"Z"}],"publisher":"Wiley","article_type":"review","quality_controlled":"1","page":"371-392"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","file":[{"embargo_to":"open_access","checksum":"47ba18bb270dd6cc266e0a3f7c69d0e4","file_size":6757886,"date_created":"2022-02-04T15:36:12Z","file_name":"Thesis_Sina_Metzler.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2023-02-03T23:30:03Z","access_level":"closed","relation":"source_file","creator":"smetzler","file_id":"10728"},{"embargo":"2023-02-02","date_created":"2022-02-04T15:36:43Z","file_size":6314921,"checksum":"f3ec07d5d6b20ae6e46bfeedebce9027","date_updated":"2023-02-03T23:30:03Z","content_type":"application/pdf","file_name":"Thesis_Sina_Metzler_A2.pdf","relation":"main_file","access_level":"open_access","file_id":"10730","creator":"smetzler"},{"embargo":"2023-02-02","date_created":"2022-02-07T10:35:02Z","checksum":"dedd14b7be7a75d63018dbfc68dd8113","file_size":6882557,"date_updated":"2023-02-04T23:30:03Z","file_name":"Thesis_Sina_Metzler_print.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"10742","creator":"smetzler"}],"supervisor":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"date_published":"2022-02-07T00:00:00Z","type":"dissertation","language":[{"iso":"eng"}],"month":"02","oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"}],"project":[{"call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","grant_number":"771402","name":"Epidemics in ant societies on a chip"}],"has_accepted_license":"1","ddc":["570"],"abstract":[{"lang":"eng","text":"Social insects are a common model to study disease dynamics in social animals. Even though pathogens should thrive in social insect colonies as the hosts engage in frequent social interactions, are closely related and live in a pathogen-rich environment, disease outbreaks are rare. This is because social insects have evolved mechanisms to keep pathogens at bay – and fight disease as a collective. Social insect colonies are often viewed as “superorganisms” with division of labor between reproductive “germ-like” queens and males and “somatic” workers, which together form an interdependent reproductive unit that parallels a multicellular body. Superorganisms possess a “social immune system” that comprises of collective disease defenses performed by the workers - summarized as “social immunity”. In social groups immunization (reduced susceptibility to a parasite upon secondary exposure to the same parasite) can e.g. be triggered by social interactions (“social immunization”). Social immunization can be caused by (i) asymptomatic low-level infections that are acquired during caregiving to a contagious individual that can give an immune boost, which can induce protection upon later encounter with the same pathogen (active immunization) or (ii) by transfer of immune effectors between individuals (passive immunization).\r\nIn the second chapter, I built up on a study that I co-authored that found that low-level infections can not only be protective, but also be costly and make the host more susceptible to detrimental superinfections after contact to a very dissimilar pathogen. I here now tested different degrees of phylogenetically-distant fungal strains of M. brunneum and M. robertsii in L. neglectus and can describe the occurrence of cross-protection of social immunization if the first and second pathogen are from the same level. Interestingly, low-level infections only provided protection when the first strain was less virulent than the second strain and elicited higher immune gene expression.\r\nIn the third and fourth chapters, I expanded on the role of social immunity in sexual selection, a so far unstudied field. I used the fungus Metarhizium robertsii and the ant Cardiocondyla obscurior as a model, as in this species mating occurs in the presence of workers and can be studied under laboratory conditions. Before males mate with virgin queens in the nest they engage in fierce combat over the access to their mating partners.\r\nFirst, I focused on male-male competition in the third chapter and found that fighting with a contagious male is costly as it can lead to contamination of the rival, but that workers can decrease the risk of disease contraction by performing sanitary care.\r\nIn the fourth chapter, I studied the effect of fungal infection on survival and mating success of sexuals (freshly emerged queens and males) and found that worker-performed sanitary care can buffer the negative effect that a pathogenic contagion would have on sexuals by spore removal from the exposed individuals. When social immunity was prevented and queens could contract spores from their mating partner, very low dosages led to negative consequences: their lifespan was reduced and they produced fewer offspring with poor immunocompetence compared to healthy queens. Interestingly, cohabitation with a late-stage infected male where no spore transfer was possible had a positive effect on offspring immunity – male offspring of mothers that apparently perceived an infected partner in their vicinity reacted more sensitively to fungal challenge than male offspring without paternal pathogen history."}],"doi":"10.15479/AT:ISTA:10727","degree_awarded":"PhD","day":"07","date_updated":"2023-09-07T13:43:23Z","year":"2022","citation":{"ama":"Metzler S. Pathogen-mediated sexual selection and immunization in ant colonies. 2022. doi:10.15479/AT:ISTA:10727","apa":"Metzler, S. (2022). Pathogen-mediated sexual selection and immunization in ant colonies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:10727","chicago":"Metzler, Sina. “Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:10727.","ieee":"S. Metzler, “Pathogen-mediated sexual selection and immunization in ant colonies,” Institute of Science and Technology Austria, 2022.","mla":"Metzler, Sina. Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies. Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:10727.","short":"S. Metzler, Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies, Institute of Science and Technology Austria, 2022.","ista":"Metzler S. 2022. Pathogen-mediated sexual selection and immunization in ant colonies. Institute of Science and Technology Austria."},"publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-02-04T23:30:03Z","ec_funded":1,"alternative_title":["ISTA Thesis"],"title":"Pathogen-mediated sexual selection and immunization in ant colonies","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"article_processing_charge":"No","date_created":"2022-02-04T15:45:12Z","author":[{"last_name":"Metzler","first_name":"Sina","full_name":"Metzler, Sina","orcid":"0000-0002-9547-2494","id":"48204546-F248-11E8-B48F-1D18A9856A87"}],"_id":"10727"},{"volume":12,"acknowledgement":"K.C. acknowledges support from ERC Consolidator Grant No. (863818: ForM-SMart). A.P. acknowledges support from FWF Grant No. J-4220. M.A.N. acknowledges support from Office of Naval Research grant N00014-16-1-2914 and from the John Templeton Foundation.","ddc":["570"],"date_updated":"2025-07-14T09:10:12Z","year":"2022","citation":{"ista":"Svoboda J, Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2022. Infection dynamics of COVID-19 virus under lockdown and reopening. Scientific Reports. 12(1), 1526.","mla":"Svoboda, Jakub, et al. “Infection Dynamics of COVID-19 Virus under Lockdown and Reopening.” Scientific Reports, vol. 12, no. 1, 1526, Springer Nature, 2022, doi:10.1038/s41598-022-05333-5.","short":"J. Svoboda, J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Scientific Reports 12 (2022).","chicago":"Svoboda, Jakub, Josef Tkadlec, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Infection Dynamics of COVID-19 Virus under Lockdown and Reopening.” Scientific Reports. Springer Nature, 2022. https://doi.org/10.1038/s41598-022-05333-5.","ieee":"J. Svoboda, J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Infection dynamics of COVID-19 virus under lockdown and reopening,” Scientific Reports, vol. 12, no. 1. Springer Nature, 2022.","ama":"Svoboda J, Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Infection dynamics of COVID-19 virus under lockdown and reopening. Scientific Reports. 2022;12(1). doi:10.1038/s41598-022-05333-5","apa":"Svoboda, J., Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2022). Infection dynamics of COVID-19 virus under lockdown and reopening. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-05333-5"},"isi":1,"external_id":{"isi":["000749198000039"],"arxiv":["2012.15155"]},"arxiv":1,"doi":"10.1038/s41598-022-05333-5","day":"27","abstract":[{"lang":"eng","text":"Motivated by COVID-19, we develop and analyze a simple stochastic model for the spread of disease in human population. We track how the number of infected and critically ill people develops over time in order to estimate the demand that is imposed on the hospital system. To keep this demand under control, we consider a class of simple policies for slowing down and reopening society and we compare their efficiency in mitigating the spread of the virus from several different points of view. We find that in order to avoid overwhelming of the hospital system, a policy must impose a harsh lockdown or it must react swiftly (or both). While reacting swiftly is universally beneficial, being harsh pays off only when the country is patient about reopening and when the neighboring countries coordinate their mitigation efforts. Our work highlights the importance of acting decisively when closing down and the importance of patience and coordination between neighboring countries when reopening."}],"quality_controlled":"1","ec_funded":1,"file_date_updated":"2022-02-07T14:57:59Z","publisher":"Springer Nature","article_type":"original","_id":"10731","scopus_import":"1","author":[{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","last_name":"Svoboda","first_name":"Jakub","full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267"},{"last_name":"Tkadlec","first_name":"Josef","full_name":"Tkadlec, Josef"},{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Nowak, Martin A.","first_name":"Martin A.","last_name":"Nowak"}],"issue":"1","publication_status":"published","department":[{"_id":"KrCh"}],"article_processing_charge":"No","date_created":"2022-02-06T23:01:30Z","title":"Infection dynamics of COVID-19 virus under lockdown and reopening","intvolume":" 12","file":[{"file_size":2971922,"checksum":"247afd30c173390940f099ead35a28ed","date_created":"2022-02-07T14:57:59Z","file_name":"2022_ScientificReports_Svoboda.pdf","content_type":"application/pdf","date_updated":"2022-02-07T14:57:59Z","relation":"main_file","success":1,"access_level":"open_access","creator":"alisjak","file_id":"10744"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-01-27T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["2045-2322"]},"oa":1,"language":[{"iso":"eng"}],"publication":"Scientific Reports","has_accepted_license":"1","oa_version":"Published Version","project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"}],"month":"01","article_number":"1526"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","file":[{"date_created":"2022-07-29T07:22:08Z","file_size":652573,"checksum":"b75fdad606ab507dc61109e0907d86c0","date_updated":"2022-07-29T07:22:08Z","file_name":"2022_JourFunctionalAnalysis_Cipolloni.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","success":1,"file_id":"11690","creator":"dernst"}],"date_published":"2022-04-15T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"language":[{"iso":"eng"}],"publication":"Journal of Functional Analysis","has_accepted_license":"1","month":"04","article_number":"109394","oa_version":"Published Version","ddc":["500"],"volume":282,"acknowledgement":"We compute the deterministic approximation of products of Sobolev functions of large Wigner matrices W and provide an optimal error bound on their fluctuation with very high probability. This generalizes Voiculescu's seminal theorem from polynomials to general Sobolev functions, as well as from tracial quantities to individual matrix elements. Applying the result to for large t, we obtain a precise decay rate for the overlaps of several deterministic matrices with temporally well separated Heisenberg time evolutions; thus we demonstrate the thermalisation effect of the unitary group generated by Wigner matrices.","isi":1,"external_id":{"arxiv":["2102.09975"],"isi":["000781239100004"]},"date_updated":"2023-08-02T14:12:35Z","citation":{"ista":"Cipolloni G, Erdös L, Schröder DJ. 2022. Thermalisation for Wigner matrices. Journal of Functional Analysis. 282(8), 109394.","mla":"Cipolloni, Giorgio, et al. “Thermalisation for Wigner Matrices.” Journal of Functional Analysis, vol. 282, no. 8, 109394, Elsevier, 2022, doi:10.1016/j.jfa.2022.109394.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Journal of Functional Analysis 282 (2022).","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Thermalisation for Wigner matrices,” Journal of Functional Analysis, vol. 282, no. 8. Elsevier, 2022.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Thermalisation for Wigner Matrices.” Journal of Functional Analysis. Elsevier, 2022. https://doi.org/10.1016/j.jfa.2022.109394.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2022). Thermalisation for Wigner matrices. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2022.109394","ama":"Cipolloni G, Erdös L, Schröder DJ. Thermalisation for Wigner matrices. Journal of Functional Analysis. 2022;282(8). doi:10.1016/j.jfa.2022.109394"},"year":"2022","abstract":[{"text":"We compute the deterministic approximation of products of Sobolev functions of large Wigner matrices W and provide an optimal error bound on their fluctuation with very high probability. This generalizes Voiculescu's seminal theorem from polynomials to general Sobolev functions, as well as from tracial quantities to individual matrix elements. Applying the result to eitW for large t, we obtain a precise decay rate for the overlaps of several deterministic matrices with temporally well separated Heisenberg time evolutions; thus we demonstrate the thermalisation effect of the unitary group generated by Wigner matrices.","lang":"eng"}],"arxiv":1,"doi":"10.1016/j.jfa.2022.109394","day":"15","file_date_updated":"2022-07-29T07:22:08Z","quality_controlled":"1","article_type":"original","publisher":"Elsevier","author":[{"first_name":"Giorgio","last_name":"Cipolloni","orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László","last_name":"Erdös"},{"last_name":"Schröder","first_name":"Dominik J","full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87"}],"issue":"8","_id":"10732","scopus_import":"1","title":"Thermalisation for Wigner matrices","intvolume":" 282","publication_status":"published","date_created":"2022-02-06T23:01:30Z","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"LaEr"}]},{"article_type":"original","publisher":"Springer Nature","quality_controlled":"1","intvolume":" 24","title":"Intruders cooperatively interact with a wall into granular matter","date_created":"2022-02-06T23:01:30Z","department":[{"_id":"ScWa"}],"article_processing_charge":"No","publication_status":"published","issue":"1","author":[{"last_name":"Espinosa","first_name":"M.","full_name":"Espinosa, M."},{"id":"b6798902-eea0-11ea-9cbc-a8e14286c631","full_name":"Diaz Melian, Vicente L","first_name":"Vicente L","last_name":"Diaz Melian"},{"full_name":"Serrano-Muñoz, A.","last_name":"Serrano-Muñoz","first_name":"A."},{"full_name":"Altshuler, E.","first_name":"E.","last_name":"Altshuler"}],"scopus_import":"1","_id":"10733","acknowledgement":"We acknowledge the University of Havana’s institutional project “Granular media: creating tools for the prevention of catastrophes”. The Institute “Pedro Kourí” is thanked for allowing us using their computing cluster. E. Altshuler found inspiration in the late M. Álvarez-Ponte.","volume":24,"abstract":[{"lang":"eng","text":"When a cylindrical object penetrates granular matter near a vertical boundary, it experiences two effects: its center of mass moves horizontally away from the wall, and it rotates around its symmetry axis. Here we show experimentally that, if two identical intruders instead of one are released side-by-side near the wall, both effects are also detected. However, unexpected phenomena appear due to a cooperative dynamics between the intruders. The net horizontal distance traveled by the common center of mass of the twin intruders is much larger than that traveled by one intruder released at the same initial distance from the wall, and the rotation is also larger. The experimental results are well described by the Discrete Element Method (DEM), which reveals that, as the number of intruders horizontally released side-by-side increases, the total energy dissipation per intruder decreases. Finally, DEM simulations demonstrate that the horizontal repulsion is substantially enhanced if groups of intruders are released forming a column near the wall."}],"day":"24","doi":"10.1007/s10035-021-01200-8","arxiv":1,"external_id":{"arxiv":["2110.15311"],"isi":["000746623000001"]},"isi":1,"year":"2022","citation":{"short":"M. Espinosa, V.L. Diaz Melian, A. Serrano-Muñoz, E. Altshuler, Granular Matter 24 (2022).","mla":"Espinosa, M., et al. “Intruders Cooperatively Interact with a Wall into Granular Matter.” Granular Matter, vol. 24, no. 1, 39, Springer Nature, 2022, doi:10.1007/s10035-021-01200-8.","ista":"Espinosa M, Diaz Melian VL, Serrano-Muñoz A, Altshuler E. 2022. Intruders cooperatively interact with a wall into granular matter. Granular Matter. 24(1), 39.","ama":"Espinosa M, Diaz Melian VL, Serrano-Muñoz A, Altshuler E. Intruders cooperatively interact with a wall into granular matter. Granular Matter. 2022;24(1). doi:10.1007/s10035-021-01200-8","apa":"Espinosa, M., Diaz Melian, V. L., Serrano-Muñoz, A., & Altshuler, E. (2022). Intruders cooperatively interact with a wall into granular matter. Granular Matter. Springer Nature. https://doi.org/10.1007/s10035-021-01200-8","chicago":"Espinosa, M., Vicente L Diaz Melian, A. Serrano-Muñoz, and E. Altshuler. “Intruders Cooperatively Interact with a Wall into Granular Matter.” Granular Matter. Springer Nature, 2022. https://doi.org/10.1007/s10035-021-01200-8.","ieee":"M. Espinosa, V. L. Diaz Melian, A. Serrano-Muñoz, and E. Altshuler, “Intruders cooperatively interact with a wall into granular matter,” Granular Matter, vol. 24, no. 1. Springer Nature, 2022."},"date_updated":"2023-08-02T14:10:13Z","keyword":["granular matter","boundary effects","intruder penetration","sedimentation"],"language":[{"iso":"eng"}],"article_number":"39","month":"01","oa_version":"Preprint","publication":"Granular Matter","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2110.15311"}],"oa":1,"publication_identifier":{"eissn":["1434-7636"],"issn":["1434-5021"]},"type":"journal_article","date_published":"2022-01-24T00:00:00Z"},{"quality_controlled":"1","file_date_updated":"2022-02-07T10:35:28Z","publisher":"IOP Publishing","article_type":"original","pmid":1,"_id":"10735","scopus_import":"1","author":[{"last_name":"Nauman","first_name":"Muhammad","full_name":"Nauman, Muhammad","orcid":"0000-0002-2111-4846","id":"32c21954-2022-11eb-9d5f-af9f93c24e71"},{"full_name":"Hussain, Tayyaba","last_name":"Hussain","first_name":"Tayyaba"},{"full_name":"Choi, Joonyoung","last_name":"Choi","first_name":"Joonyoung"},{"first_name":"Nara","last_name":"Lee","full_name":"Lee, Nara"},{"last_name":"Choi","first_name":"Young Jai","full_name":"Choi, Young Jai"},{"full_name":"Kang, Woun","first_name":"Woun","last_name":"Kang"},{"last_name":"Jo","first_name":"Younjung","full_name":"Jo, Younjung"}],"issue":"13","publication_status":"published","date_created":"2022-02-06T23:01:31Z","article_processing_charge":"No","department":[{"_id":"KiMo"}],"title":"Low-field magnetic anisotropy of Sr2IrO4","intvolume":" 34","volume":34,"acknowledgement":"YJ was supported by the National Research Foundation of Korea (NRF) (Grant Nos. NRF-2018K2A9A1A06069211 and NRF-2019R1A2C1089017). The work at Yonsei was supported by the NRF (Grant Nos. NRF-2017R1A5A-1014862 (SRC program: vdWMRC center), NRF-2019R1A2C2002601, and NRF-2021R1A2C1006375). WK acknowledges the support by the NRF (Grant Nos. 2018R1D1A1B07050087, 2018R1A6A1A03025340).","ddc":["530"],"date_updated":"2023-08-02T14:12:01Z","year":"2022","citation":{"apa":"Nauman, M., Hussain, T., Choi, J., Lee, N., Choi, Y. J., Kang, W., & Jo, Y. (2022). Low-field magnetic anisotropy of Sr2IrO4. Journal of Physics: Condensed Matter. IOP Publishing. https://doi.org/10.1088/1361-648X/ac484d","ama":"Nauman M, Hussain T, Choi J, et al. Low-field magnetic anisotropy of Sr2IrO4. Journal of physics: Condensed matter. 2022;34(13). doi:10.1088/1361-648X/ac484d","ieee":"M. Nauman et al., “Low-field magnetic anisotropy of Sr2IrO4,” Journal of physics: Condensed matter, vol. 34, no. 13. IOP Publishing, 2022.","chicago":"Nauman, Muhammad, Tayyaba Hussain, Joonyoung Choi, Nara Lee, Young Jai Choi, Woun Kang, and Younjung Jo. “Low-Field Magnetic Anisotropy of Sr2IrO4.” Journal of Physics: Condensed Matter. IOP Publishing, 2022. https://doi.org/10.1088/1361-648X/ac484d.","short":"M. Nauman, T. Hussain, J. Choi, N. Lee, Y.J. Choi, W. Kang, Y. Jo, Journal of Physics: Condensed Matter 34 (2022).","mla":"Nauman, Muhammad, et al. “Low-Field Magnetic Anisotropy of Sr2IrO4.” Journal of Physics: Condensed Matter, vol. 34, no. 13, 135802, IOP Publishing, 2022, doi:10.1088/1361-648X/ac484d.","ista":"Nauman M, Hussain T, Choi J, Lee N, Choi YJ, Kang W, Jo Y. 2022. Low-field magnetic anisotropy of Sr2IrO4. Journal of physics: Condensed matter. 34(13), 135802."},"isi":1,"external_id":{"pmid":["34986467"],"isi":["000775191800001"]},"doi":"10.1088/1361-648X/ac484d","day":"20","abstract":[{"lang":"eng","text":"Magnetic anisotropy in strontium iridate (Sr2IrO4) is essential because of its strong spin–orbit coupling and crystal field effect. In this paper, we present a detailed mapping of the out-of-plane (OOP) magnetic anisotropy in Sr2IrO4 for different sample orientations using torque magnetometry measurements in the low-magnetic-field region before the isospins are completely ordered. Dominant in-plane anisotropy was identified at low fields, confirming the b axis as an easy magnetization axis. Based on the fitting analysis of the strong uniaxial magnetic anisotropy, we observed that the main anisotropic effect arises from a spin–orbit-coupled magnetic exchange interaction affecting the OOP interaction. The effect of interlayer exchange interaction results in additional anisotropic terms owing to the tilting of the isospins. The results are relevant for understanding OOP magnetic anisotropy and provide a new way to analyze the effects of spin–orbit-coupling and interlayer magnetic exchange interactions. This study provides insight into the understanding of bulk magnetic, magnetotransport, and spintronic behavior on Sr2IrO4 for future studies."}],"language":[{"iso":"eng"}],"publication":"Journal of physics: Condensed matter","has_accepted_license":"1","oa_version":"Published Version","month":"01","article_number":"135802","file":[{"creator":"cchlebak","file_id":"10741","relation":"main_file","access_level":"open_access","success":1,"file_name":"2022_JPhysCondensMatter_Nauman.pdf","content_type":"application/pdf","date_updated":"2022-02-07T10:35:28Z","checksum":"b6c705c7f03dcb1dbcb06b1b4d4938d6","file_size":1742414,"date_created":"2022-02-07T10:35:28Z"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-01-20T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["1361-648X"]},"oa":1},{"isi":1,"external_id":{"isi":["000751104400001"],"pmid":["35080492"]},"date_updated":"2023-08-02T14:09:02Z","citation":{"chicago":"Lagator, Mato, Srdjan Sarikas, Magdalena Steinrueck, David Toledo-Aparicio, Jonathan P Bollback, Calin C Guet, and Gašper Tkačik. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/eLife.64543.","ieee":"M. Lagator et al., “Predicting bacterial promoter function and evolution from random sequences,” eLife, vol. 11. eLife Sciences Publications, 2022.","ama":"Lagator M, Sarikas S, Steinrueck M, et al. Predicting bacterial promoter function and evolution from random sequences. eLife. 2022;11. doi:10.7554/eLife.64543","apa":"Lagator, M., Sarikas, S., Steinrueck, M., Toledo-Aparicio, D., Bollback, J. P., Guet, C. C., & Tkačik, G. (2022). Predicting bacterial promoter function and evolution from random sequences. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.64543","ista":"Lagator M, Sarikas S, Steinrueck M, Toledo-Aparicio D, Bollback JP, Guet CC, Tkačik G. 2022. Predicting bacterial promoter function and evolution from random sequences. eLife. 11, e64543.","short":"M. Lagator, S. Sarikas, M. Steinrueck, D. Toledo-Aparicio, J.P. Bollback, C.C. Guet, G. Tkačik, ELife 11 (2022).","mla":"Lagator, Mato, et al. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” ELife, vol. 11, e64543, eLife Sciences Publications, 2022, doi:10.7554/eLife.64543."},"year":"2022","abstract":[{"lang":"eng","text":"Predicting function from sequence is a central problem of biology. Currently, this is possible only locally in a narrow mutational neighborhood around a wildtype sequence rather than globally from any sequence. Using random mutant libraries, we developed a biophysical model that accounts for multiple features of σ70 binding bacterial promoters to predict constitutive gene expression levels from any sequence. We experimentally and theoretically estimated that 10–20% of random sequences lead to expression and ~80% of non-expressing sequences are one mutation away from a functional promoter. The potential for generating expression from random sequences is so pervasive that selection acts against σ70-RNA polymerase binding sites even within inter-genic, promoter-containing regions. This pervasiveness of σ70-binding sites implies that emergence of promoters is not the limiting step in gene regulatory evolution. Ultimately, the inclusion of novel features of promoter function into a mechanistic model enabled not only more accurate predictions of gene expression levels, but also identified that promoters evolve more rapidly than previously thought."}],"doi":"10.7554/eLife.64543","day":"26","ddc":["576"],"volume":11,"acknowledgement":"We thank Hande Acar, Nicholas H Barton, Rok Grah, Tiago Paixao, Maros Pleska, Anna Staron, and Murat Tugrul for insightful comments and input on the manuscript. This work was supported by: Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (grant number 216779/Z/19/Z) to ML; IPC Grant from IST Austria to ML and SS; European Research Council Funding Programme 7 (2007–2013, grant agreement number 648440) to JPB.","author":[{"full_name":"Lagator, Mato","first_name":"Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"id":"35F0286E-F248-11E8-B48F-1D18A9856A87","last_name":"Sarikas","first_name":"Srdjan","full_name":"Sarikas, Srdjan"},{"full_name":"Steinrueck, Magdalena","first_name":"Magdalena","last_name":"Steinrueck"},{"last_name":"Toledo-Aparicio","first_name":"David","full_name":"Toledo-Aparicio, David"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper"}],"pmid":1,"_id":"10736","scopus_import":"1","title":"Predicting bacterial promoter function and evolution from random sequences","intvolume":" 11","publication_status":"published","date_created":"2022-02-06T23:01:32Z","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"NiBa"}],"article_processing_charge":"No","file_date_updated":"2022-02-07T07:14:09Z","quality_controlled":"1","ec_funded":1,"article_type":"original","publisher":"eLife Sciences Publications","date_published":"2022-01-26T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["2050-084X"]},"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_size":5604343,"checksum":"decdcdf600ff51e9a9703b49ca114170","date_created":"2022-02-07T07:14:09Z","file_name":"2022_ELife_Lagator.pdf","content_type":"application/pdf","date_updated":"2022-02-07T07:14:09Z","success":1,"relation":"main_file","access_level":"open_access","creator":"cchlebak","file_id":"10739"}],"publication":"eLife","has_accepted_license":"1","month":"01","article_number":"e64543","oa_version":"Published Version","project":[{"name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","text":"We consider two models for the sequence labeling (tagging) problem. The first one is a Pattern-Based Conditional Random Field (PB), in which the energy of a string (chain labeling) x=x1⁢…⁢xn∈Dn is a sum of terms over intervals [i,j] where each term is non-zero only if the substring xi⁢…⁢xj equals a prespecified word w∈Λ. The second model is a Weighted Context-Free Grammar (WCFG) frequently used for natural language processing. PB and WCFG encode local and non-local interactions respectively, and thus can be viewed as complementary. We propose a Grammatical Pattern-Based CRF model (GPB) that combines the two in a natural way. We argue that it has certain advantages over existing approaches such as the Hybrid model of Benedí and Sanchez that combines N-grams and WCFGs. The focus of this paper is to analyze the complexity of inference tasks in a GPB such as computing MAP. We present a polynomial-time algorithm for general GPBs and a faster version for a special case that we call Interaction Grammars."}],"doi":"10.3233/IDA-205623","arxiv":1,"day":"14","isi":1,"external_id":{"arxiv":["1404.5475"],"isi":["000749997700015"]},"date_updated":"2023-08-02T14:09:41Z","year":"2022","citation":{"apa":"Takhanov, R., & Kolmogorov, V. (2022). Combining pattern-based CRFs and weighted context-free grammars. Intelligent Data Analysis. IOS Press. https://doi.org/10.3233/IDA-205623","ama":"Takhanov R, Kolmogorov V. Combining pattern-based CRFs and weighted context-free grammars. Intelligent Data Analysis. 2022;26(1):257-272. doi:10.3233/IDA-205623","ieee":"R. Takhanov and V. Kolmogorov, “Combining pattern-based CRFs and weighted context-free grammars,” Intelligent Data Analysis, vol. 26, no. 1. IOS Press, pp. 257–272, 2022.","chicago":"Takhanov, Rustem, and Vladimir Kolmogorov. “Combining Pattern-Based CRFs and Weighted Context-Free Grammars.” Intelligent Data Analysis. IOS Press, 2022. https://doi.org/10.3233/IDA-205623.","mla":"Takhanov, Rustem, and Vladimir Kolmogorov. “Combining Pattern-Based CRFs and Weighted Context-Free Grammars.” Intelligent Data Analysis, vol. 26, no. 1, IOS Press, 2022, pp. 257–72, doi:10.3233/IDA-205623.","short":"R. Takhanov, V. Kolmogorov, Intelligent Data Analysis 26 (2022) 257–272.","ista":"Takhanov R, Kolmogorov V. 2022. Combining pattern-based CRFs and weighted context-free grammars. Intelligent Data Analysis. 26(1), 257–272."},"volume":26,"title":"Combining pattern-based CRFs and weighted context-free grammars","intvolume":" 26","publication_status":"published","department":[{"_id":"VlKo"}],"date_created":"2022-02-06T23:01:32Z","article_processing_charge":"No","author":[{"id":"2CCAC26C-F248-11E8-B48F-1D18A9856A87","last_name":"Takhanov","first_name":"Rustem","full_name":"Takhanov, Rustem"},{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"issue":"1","_id":"10737","scopus_import":"1","article_type":"original","publisher":"IOS Press","page":"257-272","quality_controlled":"1","oa":1,"publication_identifier":{"issn":["1088-467X"],"eissn":["1571-4128"]},"date_published":"2022-01-14T00:00:00Z","type":"journal_article","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1404.5475"}],"month":"01","oa_version":"Preprint","publication":"Intelligent Data Analysis","language":[{"iso":"eng"}]},{"publication":"2021 IEEE International Conference on Big Data","_id":"10752","author":[{"last_name":"Lampert","first_name":"Jasmin","full_name":"Lampert, Jasmin"},{"full_name":"Lampert, Christoph","orcid":"0000-0002-4561-241X","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","oa_version":"None","date_created":"2022-02-10T14:08:23Z","department":[{"_id":"ChLa"}],"article_processing_charge":"No","month":"01","title":"Overcoming rare-language discrimination in multi-lingual sentiment analysis","page":"5185-5192","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"IEEE","conference":{"location":"Orlando, FL, United States","end_date":"2021-12-18","start_date":"2021-12-15","name":"Big Data: International Conference on Big Data"},"date_updated":"2023-08-02T14:27:50Z","year":"2022","citation":{"ista":"Lampert J, Lampert C. 2022. Overcoming rare-language discrimination in multi-lingual sentiment analysis. 2021 IEEE International Conference on Big Data. Big Data: International Conference on Big Data, 5185–5192.","short":"J. Lampert, C. Lampert, in:, 2021 IEEE International Conference on Big Data, IEEE, 2022, pp. 5185–5192.","mla":"Lampert, Jasmin, and Christoph Lampert. “Overcoming Rare-Language Discrimination in Multi-Lingual Sentiment Analysis.” 2021 IEEE International Conference on Big Data, IEEE, 2022, pp. 5185–92, doi:10.1109/bigdata52589.2021.9672003.","ieee":"J. Lampert and C. Lampert, “Overcoming rare-language discrimination in multi-lingual sentiment analysis,” in 2021 IEEE International Conference on Big Data, Orlando, FL, United States, 2022, pp. 5185–5192.","chicago":"Lampert, Jasmin, and Christoph Lampert. “Overcoming Rare-Language Discrimination in Multi-Lingual Sentiment Analysis.” In 2021 IEEE International Conference on Big Data, 5185–92. IEEE, 2022. https://doi.org/10.1109/bigdata52589.2021.9672003.","apa":"Lampert, J., & Lampert, C. (2022). Overcoming rare-language discrimination in multi-lingual sentiment analysis. In 2021 IEEE International Conference on Big Data (pp. 5185–5192). Orlando, FL, United States: IEEE. https://doi.org/10.1109/bigdata52589.2021.9672003","ama":"Lampert J, Lampert C. Overcoming rare-language discrimination in multi-lingual sentiment analysis. In: 2021 IEEE International Conference on Big Data. IEEE; 2022:5185-5192. doi:10.1109/bigdata52589.2021.9672003"},"date_published":"2022-01-13T00:00:00Z","isi":1,"type":"conference","external_id":{"isi":["000800559505036"]},"doi":"10.1109/bigdata52589.2021.9672003","day":"13","publication_identifier":{"isbn":["9781665439022"]},"abstract":[{"lang":"eng","text":"The digitalization of almost all aspects of our everyday lives has led to unprecedented amounts of data being freely available on the Internet. In particular social media platforms provide rich sources of user-generated data, though typically in unstructured form, and with high diversity, such as written in many different languages. Automatically identifying meaningful information in such big data resources and extracting it efficiently is one of the ongoing challenges of our time. A common step for this is sentiment analysis, which forms the foundation for tasks such as opinion mining or trend prediction. Unfortunately, publicly available tools for this task are almost exclusively available for English-language texts. Consequently, a large fraction of the Internet users, who do not communicate in English, are ignored in automatized studies, a phenomenon called rare-language discrimination.In this work we propose a technique to overcome this problem by a truly multi-lingual model, which can be trained automatically without linguistic knowledge or even the ability to read the many target languages. The main step is to combine self-annotation, specifically the use of emoticons as a proxy for labels, with multi-lingual sentence representations.To evaluate our method we curated several large datasets from data obtained via the free Twitter streaming API. The results show that our proposed multi-lingual training is able to achieve sentiment predictions at the same quality level for rare languages as for frequent ones, and in particular clearly better than what mono-lingual training achieves on the same data. "}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public"},{"oa_version":"Published Version","month":"02","publication":"Neuron","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1097-4199"]},"oa":1,"date_published":"2022-02-02T00:00:00Z","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2022.01.014"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","article_processing_charge":"No","date_created":"2022-02-13T23:01:34Z","department":[{"_id":"TiVo"}],"title":"A familiar thought: Machines that replace us?","intvolume":" 110","pmid":1,"_id":"10753","scopus_import":"1","author":[{"full_name":"Confavreux, Basile J","last_name":"Confavreux","first_name":"Basile J","id":"C7610134-B532-11EA-BD9F-F5753DDC885E"},{"last_name":"Vogels","first_name":"Tim P","full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"}],"issue":"3","publisher":"Elsevier","article_type":"letter_note","page":"361-362","quality_controlled":"1","doi":"10.1016/j.neuron.2022.01.014","day":"02","abstract":[{"text":"This is a comment on \"Meta-learning synaptic plasticity and memory addressing for continual familiarity detection.\" Neuron. 2022 Feb 2;110(3):544-557.e8.","lang":"eng"}],"date_updated":"2023-10-03T10:53:17Z","citation":{"ista":"Confavreux BJ, Vogels TP. 2022. A familiar thought: Machines that replace us? Neuron. 110(3), 361–362.","short":"B.J. Confavreux, T.P. Vogels, Neuron 110 (2022) 361–362.","mla":"Confavreux, Basile J., and Tim P. Vogels. “A Familiar Thought: Machines That Replace Us?” Neuron, vol. 110, no. 3, Elsevier, 2022, pp. 361–62, doi:10.1016/j.neuron.2022.01.014.","ieee":"B. J. Confavreux and T. P. Vogels, “A familiar thought: Machines that replace us?,” Neuron, vol. 110, no. 3. Elsevier, pp. 361–362, 2022.","chicago":"Confavreux, Basile J, and Tim P Vogels. “A Familiar Thought: Machines That Replace Us?” Neuron. Elsevier, 2022. https://doi.org/10.1016/j.neuron.2022.01.014.","ama":"Confavreux BJ, Vogels TP. A familiar thought: Machines that replace us? Neuron. 2022;110(3):361-362. doi:10.1016/j.neuron.2022.01.014","apa":"Confavreux, B. J., & Vogels, T. P. (2022). A familiar thought: Machines that replace us? Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2022.01.014"},"year":"2022","isi":1,"external_id":{"isi":["000751819100005"],"pmid":["35114107"]},"volume":110},{"date_updated":"2023-08-09T10:17:07Z","citation":{"ieee":"Y. Chang et al., “Developing a mathematical model of intracellular Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer,” International Journal of Molecular Sciences, vol. 23, no. 3. MDPI, 2022.","chicago":"Chang, Yan, Marah Funk, Souvik Roy, Elizabeth R Stephenson, Sangyong Choi, Hristo V. Kojouharov, Benito Chen, and Zui Pan. “Developing a Mathematical Model of Intracellular Calcium Dynamics for Evaluating Combined Anticancer Effects of Afatinib and RP4010 in Esophageal Cancer.” International Journal of Molecular Sciences. MDPI, 2022. https://doi.org/10.3390/ijms23031763.","apa":"Chang, Y., Funk, M., Roy, S., Stephenson, E. R., Choi, S., Kojouharov, H. V., … Pan, Z. (2022). Developing a mathematical model of intracellular Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms23031763","ama":"Chang Y, Funk M, Roy S, et al. Developing a mathematical model of intracellular Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer. International Journal of Molecular Sciences. 2022;23(3). doi:10.3390/ijms23031763","ista":"Chang Y, Funk M, Roy S, Stephenson ER, Choi S, Kojouharov HV, Chen B, Pan Z. 2022. Developing a mathematical model of intracellular Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer. International Journal of Molecular Sciences. 23(3), 1763.","short":"Y. Chang, M. Funk, S. Roy, E.R. Stephenson, S. Choi, H.V. Kojouharov, B. Chen, Z. Pan, International Journal of Molecular Sciences 23 (2022).","mla":"Chang, Yan, et al. “Developing a Mathematical Model of Intracellular Calcium Dynamics for Evaluating Combined Anticancer Effects of Afatinib and RP4010 in Esophageal Cancer.” International Journal of Molecular Sciences, vol. 23, no. 3, 1763, MDPI, 2022, doi:10.3390/ijms23031763."},"year":"2022","isi":1,"external_id":{"isi":["000754773500001"]},"doi":"10.3390/ijms23031763","day":"01","abstract":[{"text":"Targeting dysregulated Ca2+ signaling in cancer cells is an emerging chemotherapy approach. We previously reported that store-operated Ca2+ entry (SOCE) blockers, such as RP4010, are promising antitumor drugs for esophageal cancer. As a tyrosine kinase inhibitor (TKI), afatinib received FDA approval to be used in targeted therapy for patients with EGFR mutation-positive cancers. While preclinical studies and clinical trials have shown that afatinib has benefits for esophageal cancer patients, it is not known whether a combination of afatinib and RP4010 could achieve better anticancer effects. Since TKI can alter intracellular Ca2+ dynamics through EGFR/phospholipase C-γ pathway, in this study, we evaluated the inhibitory effect of afatinib and RP4010 on intracellular Ca2+ oscillations in KYSE-150, a human esophageal squamous cell carcinoma cell line, using both experimental and mathematical simulations. Our mathematical simulation of Ca2+ oscillations could fit well with experimental data responding to afatinib or RP4010, both separately or in combination. Guided by simulation, we were able to identify a proper ratio of afatinib and RP4010 for combined treatment, and such a combination presented synergistic anticancer-effect evidence by experimental measurement of intracellular Ca2+ and cell proliferation. This intracellular Ca2+ dynamic-based mathematical simulation approach could be useful for a rapid and cost-effective evaluation of combined targeting therapy drugs.","lang":"eng"}],"volume":23,"acknowledgement":"This work was partially supported by grants from National Institutes of Health (NIH) (R01 CA185055, S10OD0252300) and The University of Texas System STARs Award (to Z.P.),\r\nThe University of Texas at Arlington Interdisciplinary Research Program (to B.C., H.V.K. and Z.P.). ","ddc":["510","576"],"_id":"10754","scopus_import":"1","author":[{"last_name":"Chang","first_name":"Yan","full_name":"Chang, Yan"},{"last_name":"Funk","first_name":"Marah","full_name":"Funk, Marah"},{"full_name":"Roy, Souvik","first_name":"Souvik","last_name":"Roy"},{"last_name":"Stephenson","first_name":"Elizabeth R","full_name":"Stephenson, Elizabeth R","orcid":"0000-0002-6862-208X","id":"2D04F932-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sangyong","last_name":"Choi","full_name":"Choi, Sangyong"},{"first_name":"Hristo V.","last_name":"Kojouharov","full_name":"Kojouharov, Hristo V."},{"full_name":"Chen, Benito","last_name":"Chen","first_name":"Benito"},{"first_name":"Zui","last_name":"Pan","full_name":"Pan, Zui"}],"issue":"3","publication_status":"published","date_created":"2022-02-13T23:01:35Z","department":[{"_id":"HeEd"}],"article_processing_charge":"Yes","title":"Developing a mathematical model of intracellular Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer","intvolume":" 23","quality_controlled":"1","file_date_updated":"2022-02-14T07:46:30Z","publisher":"MDPI","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-02-01T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"oa":1,"file":[{"file_id":"10756","creator":"dernst","access_level":"open_access","relation":"main_file","success":1,"date_updated":"2022-02-14T07:46:30Z","content_type":"application/pdf","file_name":"2022_IJMS_Chang.pdf","date_created":"2022-02-14T07:46:30Z","file_size":24416183,"checksum":"8890ad20c54e90dc58ad5ea97c902998"}],"status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication":"International Journal of Molecular Sciences","has_accepted_license":"1","oa_version":"Published Version","month":"02","article_number":"1763","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"publication":"Journal of Physics A: Mathematical and Theoretical","has_accepted_license":"1","month":"01","article_number":"015201","oa_version":"Published Version","project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"9791"}]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"10757","creator":"dernst","relation":"main_file","access_level":"open_access","success":1,"date_updated":"2022-02-14T08:20:19Z","content_type":"application/pdf","file_name":"2022_JournalPhysicsA_Feliciangeli.pdf","date_created":"2022-02-14T08:20:19Z","file_size":1132380,"checksum":"0875e562705563053d6dd98fba4d8578"}],"date_published":"2022-01-19T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"issn":["1751-8113"],"eissn":["1751-8121"]},"file_date_updated":"2022-02-14T08:20:19Z","ec_funded":1,"quality_controlled":"1","article_type":"original","publisher":"IOP Publishing","author":[{"orcid":"0000-0003-0754-8530","full_name":"Feliciangeli, Dario","first_name":"Dario","last_name":"Feliciangeli","id":"41A639AA-F248-11E8-B48F-1D18A9856A87"},{"id":"856966FE-A408-11E9-977E-802DE6697425","last_name":"Rademacher","first_name":"Simone Anna Elvira","full_name":"Rademacher, Simone Anna Elvira","orcid":"0000-0001-5059-4466"},{"first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"issue":"1","_id":"10755","scopus_import":"1","title":"The effective mass problem for the Landau-Pekar equations","intvolume":" 55","publication_status":"published","date_created":"2022-02-13T23:01:35Z","department":[{"_id":"RoSe"}],"article_processing_charge":"Yes (via OA deal)","ddc":["510"],"volume":55,"acknowledgement":"We thank Herbert Spohn for helpful comments. Funding from the European Union’s Horizon\r\n2020 research and innovation programme under the ERC Grant Agreement No. 694227\r\n(DF and RS) and under the Marie Skłodowska-Curie Grant Agreement No. 754411 (SR) is\r\ngratefully acknowledged.","external_id":{"arxiv":["2107.03720"]},"date_updated":"2024-03-06T12:30:44Z","year":"2022","citation":{"short":"D. Feliciangeli, S.A.E. Rademacher, R. Seiringer, Journal of Physics A: Mathematical and Theoretical 55 (2022).","mla":"Feliciangeli, Dario, et al. “The Effective Mass Problem for the Landau-Pekar Equations.” Journal of Physics A: Mathematical and Theoretical, vol. 55, no. 1, 015201, IOP Publishing, 2022, doi:10.1088/1751-8121/ac3947.","ista":"Feliciangeli D, Rademacher SAE, Seiringer R. 2022. The effective mass problem for the Landau-Pekar equations. Journal of Physics A: Mathematical and Theoretical. 55(1), 015201.","ama":"Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for the Landau-Pekar equations. Journal of Physics A: Mathematical and Theoretical. 2022;55(1). doi:10.1088/1751-8121/ac3947","apa":"Feliciangeli, D., Rademacher, S. A. E., & Seiringer, R. (2022). The effective mass problem for the Landau-Pekar equations. Journal of Physics A: Mathematical and Theoretical. IOP Publishing. https://doi.org/10.1088/1751-8121/ac3947","chicago":"Feliciangeli, Dario, Simone Anna Elvira Rademacher, and Robert Seiringer. “The Effective Mass Problem for the Landau-Pekar Equations.” Journal of Physics A: Mathematical and Theoretical. IOP Publishing, 2022. https://doi.org/10.1088/1751-8121/ac3947.","ieee":"D. Feliciangeli, S. A. E. Rademacher, and R. Seiringer, “The effective mass problem for the Landau-Pekar equations,” Journal of Physics A: Mathematical and Theoretical, vol. 55, no. 1. IOP Publishing, 2022."},"abstract":[{"text":"We provide a definition of the effective mass for the classical polaron described by the Landau–Pekar (LP) equations. It is based on a novel variational principle, minimizing the energy functional over states with given (initial) velocity. The resulting formula for the polaron's effective mass agrees with the prediction by LP (1948 J. Exp. Theor. Phys. 18 419–423).","lang":"eng"}],"arxiv":1,"doi":"10.1088/1751-8121/ac3947","day":"19"},{"has_accepted_license":"1","publication":"ACS Physical Chemistry Au","month":"02","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"type":"journal_article","date_published":"2022-02-11T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["2694-2445"]},"related_material":{"link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.12.14.472563","relation":"earlier_version"}]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2022-07-29T07:53:20Z","file_name":"2022_ACSPhysChemAU_Dubini.pdf","content_type":"application/pdf","date_created":"2022-07-29T07:53:20Z","file_size":2351220,"checksum":"5ce3f907848f5c7caf77f1adfe5826c6","file_id":"11692","creator":"dernst","access_level":"open_access","success":1,"relation":"main_file"}],"issue":"3","author":[{"first_name":"Romeo C. A.","last_name":"Dubini","full_name":"Dubini, Romeo C. A."},{"last_name":"Korytiaková","first_name":"Eva","full_name":"Korytiaková, Eva"},{"full_name":"Schinkel, Thea","last_name":"Schinkel","first_name":"Thea"},{"full_name":"Heinrichs, Pia","last_name":"Heinrichs","first_name":"Pia"},{"full_name":"Carell, Thomas","first_name":"Thomas","last_name":"Carell"},{"full_name":"Rovo, Petra","orcid":"0000-0001-8729-7326","last_name":"Rovo","first_name":"Petra","id":"c316e53f-b965-11eb-b128-bb26acc59c00"}],"scopus_import":"1","pmid":1,"_id":"10758","intvolume":" 2","title":"1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives","date_created":"2022-02-16T11:18:21Z","department":[{"_id":"NMR"}],"article_processing_charge":"Yes (via OA deal)","publication_status":"published","file_date_updated":"2022-07-29T07:53:20Z","quality_controlled":"1","page":"237-246","article_type":"original","publisher":"American Chemical Society","external_id":{"pmid":["35637781"]},"year":"2022","citation":{"ieee":"R. C. A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, and P. Rovo, “1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives,” ACS Physical Chemistry Au, vol. 2, no. 3. American Chemical Society, pp. 237–246, 2022.","chicago":"Dubini, Romeo C. A., Eva Korytiaková, Thea Schinkel, Pia Heinrichs, Thomas Carell, and Petra Rovo. “1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives.” ACS Physical Chemistry Au. American Chemical Society, 2022. https://doi.org/10.1021/acsphyschemau.1c00050.","apa":"Dubini, R. C. A., Korytiaková, E., Schinkel, T., Heinrichs, P., Carell, T., & Rovo, P. (2022). 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. American Chemical Society. https://doi.org/10.1021/acsphyschemau.1c00050","ama":"Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. 2022;2(3):237-246. doi:10.1021/acsphyschemau.1c00050","ista":"Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 2022. 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. 2(3), 237–246.","short":"R.C.A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, P. Rovo, ACS Physical Chemistry Au 2 (2022) 237–246.","mla":"Dubini, Romeo C. A., et al. “1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives.” ACS Physical Chemistry Au, vol. 2, no. 3, American Chemical Society, 2022, pp. 237–46, doi:10.1021/acsphyschemau.1c00050."},"date_updated":"2023-01-31T07:33:07Z","abstract":[{"lang":"eng","text":"5-Carboxycytosine (5caC) is a rare epigenetic modification found in nucleic acids of all domains of life. Despite its sparse genomic abundance, 5caC is presumed to play essential regulatory roles in transcription, maintenance and base-excision processes in DNA. In this work, we utilize nuclear magnetic resonance (NMR) spectroscopy to address the effects of 5caC incorporation into canonical DNA strands at multiple pH and temperature conditions. Our results demonstrate that 5caC has a pH-dependent global destabilizing and a base-pair mobility enhancing local impact on dsDNA, albeit without any detectable influence on the ground-state B-DNA structure. Measurement of hybridization thermodynamics and kinetics of 5caC-bearing DNA duplexes highlighted how acidic environment (pH 5.8 and 4.7) destabilizes the double-stranded structure by ∼10–20 kJ mol–1 at 37 °C when compared to the same sample at neutral pH. Protonation of 5caC results in a lower activation energy for the dissociation process and a higher barrier for annealing. Studies on conformational exchange on the microsecond time scale regime revealed a sharply localized base-pair motion involving exclusively the modified site and its immediate surroundings. By direct comparison with canonical and 5-formylcytosine (5fC)-edited strands, we were able to address the impact of the two most oxidized naturally occurring cytosine derivatives in the genome. These insights on 5caC’s subtle sensitivity to acidic pH contribute to the long-standing questions of its capacity as a substrate in base excision repair processes and its purpose as an independent, stable epigenetic mark."}],"day":"11","doi":"10.1021/acsphyschemau.1c00050","ddc":["540"],"acknowledgement":"We thank Markus Müller for valued discussions and Felix Xu for assistance in the measurement of UV/vis melting profiles. This work was supported in part by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – SFB 1309-325871075, EU-ITN LightDyNAmics (ID: 765266), the ERC-AG EpiR (ID: 741912), the Center for NanoScience, the Excellence Clusters CIPSM, and the Fonds der Chemischen Industrie. Open access funding provided by Institute of Science and Technology Austria (ISTA).\r\n\r\n","volume":2},{"has_accepted_license":"1","oa_version":"Published Version","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"month":"02","language":[{"iso":"eng"}],"date_published":"2022-02-21T00:00:00Z","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","first_name":"Mikhail"}],"oa":1,"file":[{"file_size":17668233,"checksum":"0fc54ad1eaede879c665ac9b53c93e22","date_created":"2022-02-21T13:58:16Z","file_name":"Rzadkowski_thesis_final_source.zip","content_type":"application/zip","date_updated":"2022-02-22T07:20:12Z","relation":"source_file","access_level":"closed","creator":"wrzadkow","file_id":"10785"},{"content_type":"application/pdf","file_name":"Rzadkowski_thesis_final.pdf","date_updated":"2022-02-21T14:02:54Z","checksum":"22d2d7af37ca31f6b1730c26cac7bced","file_size":13307331,"date_created":"2022-02-21T14:02:54Z","creator":"wrzadkow","file_id":"10786","access_level":"open_access","relation":"main_file","success":1}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"id":"10762","relation":"part_of_dissertation","status":"public"},{"id":"7956","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"415"},{"id":"8644","relation":"part_of_dissertation","status":"public"}]},"status":"public","_id":"10759","author":[{"id":"48C55298-F248-11E8-B48F-1D18A9856A87","last_name":"Rzadkowski","first_name":"Wojciech","full_name":"Rzadkowski, Wojciech","orcid":"0000-0002-1106-4419"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MiLe"}],"article_processing_charge":"No","date_created":"2022-02-16T13:27:37Z","title":"Analytic and machine learning approaches to composite quantum impurities","alternative_title":["ISTA Thesis"],"page":"120","ec_funded":1,"file_date_updated":"2022-02-22T07:20:12Z","publisher":"Institute of Science and Technology Austria","date_updated":"2024-08-07T07:16:53Z","year":"2022","citation":{"ama":"Rzadkowski W. Analytic and machine learning approaches to composite quantum impurities. 2022. doi:10.15479/at:ista:10759","apa":"Rzadkowski, W. (2022). Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10759","chicago":"Rzadkowski, Wojciech. “Analytic and Machine Learning Approaches to Composite Quantum Impurities.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:10759.","ieee":"W. Rzadkowski, “Analytic and machine learning approaches to composite quantum impurities,” Institute of Science and Technology Austria, 2022.","mla":"Rzadkowski, Wojciech. Analytic and Machine Learning Approaches to Composite Quantum Impurities. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:10759.","short":"W. Rzadkowski, Analytic and Machine Learning Approaches to Composite Quantum Impurities, Institute of Science and Technology Austria, 2022.","ista":"Rzadkowski W. 2022. Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria."},"doi":"10.15479/at:ista:10759","degree_awarded":"PhD","day":"21","abstract":[{"lang":"eng","text":"In this Thesis, I study composite quantum impurities with variational techniques, both inspired by machine learning as well as fully analytic. I supplement this with exploration of other applications of machine learning, in particular artificial neural networks, in many-body physics. In Chapters 3 and 4, I study quasiparticle systems with variational approach. I derive a Hamiltonian describing the angulon quasiparticle in the presence of a magnetic field. I apply analytic variational treatment to this Hamiltonian. Then, I introduce a variational approach for non-additive systems, based on artificial neural networks. I exemplify this approach on the example of the polaron quasiparticle (Fröhlich Hamiltonian). In Chapter 5, I continue using artificial neural networks, albeit in a different setting. I apply artificial neural networks to detect phases from snapshots of two types physical systems. Namely, I study Monte Carlo snapshots of multilayer classical spin models as well as molecular dynamics maps of colloidal systems. The main type of networks that I use here are convolutional neural networks, known for their applicability to image data."}],"ddc":["530"]},{"pmid":1,"_id":"10763","scopus_import":"1","author":[{"full_name":"Herguedas, Beatriz","first_name":"Beatriz","last_name":"Herguedas"},{"first_name":"Bianka K.","last_name":"Kohegyi","full_name":"Kohegyi, Bianka K."},{"first_name":"Jan Niklas","last_name":"Dohrke","full_name":"Dohrke, Jan Niklas"},{"first_name":"Jake","last_name":"Watson","orcid":"0000-0002-8698-3823","full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"full_name":"Zhang, Danyang","first_name":"Danyang","last_name":"Zhang"},{"first_name":"Hinze","last_name":"Ho","full_name":"Ho, Hinze"},{"full_name":"Shaikh, Saher A.","last_name":"Shaikh","first_name":"Saher A."},{"first_name":"Remigijus","last_name":"Lape","full_name":"Lape, Remigijus"},{"last_name":"Krieger","first_name":"James M.","full_name":"Krieger, James M."},{"full_name":"Greger, Ingo H.","first_name":"Ingo H.","last_name":"Greger"}],"publication_status":"published","date_created":"2022-02-20T23:01:30Z","article_processing_charge":"No","department":[{"_id":"PeJo"}],"title":"Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor","intvolume":" 13","quality_controlled":"1","file_date_updated":"2022-02-21T07:59:32Z","publisher":"Springer Nature","article_type":"original","date_updated":"2023-08-02T14:25:33Z","year":"2022","citation":{"ista":"Herguedas B, Kohegyi BK, Dohrke JN, Watson J, Zhang D, Ho H, Shaikh SA, Lape R, Krieger JM, Greger IH. 2022. Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor. Nature Communications. 13, 734.","short":"B. Herguedas, B.K. Kohegyi, J.N. Dohrke, J. Watson, D. Zhang, H. Ho, S.A. Shaikh, R. Lape, J.M. Krieger, I.H. Greger, Nature Communications 13 (2022).","mla":"Herguedas, Beatriz, et al. “Mechanisms Underlying TARP Modulation of the GluA1/2-Γ8 AMPA Receptor.” Nature Communications, vol. 13, 734, Springer Nature, 2022, doi:10.1038/s41467-022-28404-7.","ieee":"B. Herguedas et al., “Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor,” Nature Communications, vol. 13. Springer Nature, 2022.","chicago":"Herguedas, Beatriz, Bianka K. Kohegyi, Jan Niklas Dohrke, Jake Watson, Danyang Zhang, Hinze Ho, Saher A. Shaikh, Remigijus Lape, James M. Krieger, and Ingo H. Greger. “Mechanisms Underlying TARP Modulation of the GluA1/2-Γ8 AMPA Receptor.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-28404-7.","ama":"Herguedas B, Kohegyi BK, Dohrke JN, et al. Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor. Nature Communications. 2022;13. doi:10.1038/s41467-022-28404-7","apa":"Herguedas, B., Kohegyi, B. K., Dohrke, J. N., Watson, J., Zhang, D., Ho, H., … Greger, I. H. (2022). Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-28404-7"},"isi":1,"external_id":{"pmid":["35136046"],"isi":["000757297200008"]},"doi":"10.1038/s41467-022-28404-7","day":"08","abstract":[{"text":"AMPA-type glutamate receptors (AMPARs) mediate rapid signal transmission at excitatory\r\nsynapses in the brain. Glutamate binding to the receptor’s ligand-binding domains (LBDs)\r\nleads to ion channel activation and desensitization. Gating kinetics shape synaptic transmission\r\nand are strongly modulated by transmembrane AMPAR regulatory proteins (TARPs)\r\nthrough currently incompletely resolved mechanisms. Here, electron cryo-microscopy\r\nstructures of the GluA1/2 TARP-γ8 complex, in both open and desensitized states\r\n(at 3.5 Å), reveal state-selective engagement of the LBDs by the large TARP-γ8 loop (‘β1’),\r\nelucidating how this TARP stabilizes specific gating states. We further show how TARPs alter\r\nchannel rectification, by interacting with the pore helix of the selectivity filter. Lastly, we\r\nreveal that the Q/R-editing site couples the channel constriction at the filter entrance to the\r\ngate, and forms the major cation binding site in the conduction path. Our results provide a\r\nmechanistic framework of how TARPs modulate AMPAR gating and conductance.","lang":"eng"}],"acknowledgement":"We thank Ondrej Cais for critical reading of the manuscript. We are grateful to LMB\r\nscientific computing and the EM facility for support, Paul Emsley for help with model\r\nbuilding and Takanori Nakane for helpful comments with Relion 3.1. This work was\r\nsupported by grants from the Medical Research Council (MC_U105174197) and BBSRC\r\n(BB/N002113/1) to I.H.G, and grants from the MCIN/AEI/ 10.13039/501100011033 and\r\n“ESF Investing in your future” to B.H (PID2019-106284GA-I00 and RYC2018-025720-I).","volume":13,"ddc":["570"],"publication":"Nature Communications","has_accepted_license":"1","oa_version":"Published Version","month":"02","article_number":"734","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-02-08T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["20411723"]},"oa":1,"file":[{"file_id":"10778","creator":"dernst","access_level":"open_access","success":1,"relation":"main_file","date_updated":"2022-02-21T07:59:32Z","file_name":"2022_NatureCommunications_Herguedas.pdf","content_type":"application/pdf","date_created":"2022-02-21T07:59:32Z","file_size":2625540,"checksum":"d86ee8eabe8b794730729ffbb1a8832e"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public"},{"quality_controlled":"1","file_date_updated":"2022-02-21T07:51:33Z","publisher":"Springer Nature","article_type":"original","scopus_import":"1","pmid":1,"_id":"10764","author":[{"full_name":"Cheung, Giselle T","last_name":"Cheung","first_name":"Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bataveljic, Danijela","last_name":"Bataveljic","first_name":"Danijela"},{"last_name":"Visser","first_name":"Josien","full_name":"Visser, Josien"},{"full_name":"Kumar, Naresh","last_name":"Kumar","first_name":"Naresh"},{"first_name":"Julien","last_name":"Moulard","full_name":"Moulard, Julien"},{"full_name":"Dallérac, Glenn","last_name":"Dallérac","first_name":"Glenn"},{"first_name":"Daria","last_name":"Mozheiko","full_name":"Mozheiko, Daria"},{"first_name":"Astrid","last_name":"Rollenhagen","full_name":"Rollenhagen, Astrid"},{"full_name":"Ezan, Pascal","first_name":"Pascal","last_name":"Ezan"},{"full_name":"Mongin, Cédric","last_name":"Mongin","first_name":"Cédric"},{"full_name":"Chever, Oana","last_name":"Chever","first_name":"Oana"},{"full_name":"Bemelmans, Alexis Pierre","last_name":"Bemelmans","first_name":"Alexis Pierre"},{"last_name":"Lübke","first_name":"Joachim","full_name":"Lübke, Joachim"},{"full_name":"Leray, Isabelle","first_name":"Isabelle","last_name":"Leray"},{"full_name":"Rouach, Nathalie","first_name":"Nathalie","last_name":"Rouach"}],"date_created":"2022-02-20T23:01:30Z","department":[{"_id":"SiHi"}],"article_processing_charge":"No","publication_status":"published","intvolume":" 13","title":"Physiological synaptic activity and recognition memory require astroglial glutamine","volume":13,"acknowledgement":"We thank D. Mazaud and. J. Cazères for technical assistance. This work was supported by grants from the European Research Council (Consolidator grant #683154) and European Union’s Horizon 2020 research and innovation program (Marie Sklodowska-Curie Innovative Training Networks, grant #722053, EU-GliaPhD) to N.R. and from FP7-PEOPLE Marie Curie Intra-European Fellowship for career development (grant #622289) to G.C.","ddc":["570"],"year":"2022","citation":{"short":"G.T. Cheung, D. Bataveljic, J. Visser, N. Kumar, J. Moulard, G. Dallérac, D. Mozheiko, A. Rollenhagen, P. Ezan, C. Mongin, O. Chever, A.P. Bemelmans, J. Lübke, I. Leray, N. Rouach, Nature Communications 13 (2022).","mla":"Cheung, Giselle T., et al. “Physiological Synaptic Activity and Recognition Memory Require Astroglial Glutamine.” Nature Communications, vol. 13, 753, Springer Nature, 2022, doi:10.1038/s41467-022-28331-7.","ista":"Cheung GT, Bataveljic D, Visser J, Kumar N, Moulard J, Dallérac G, Mozheiko D, Rollenhagen A, Ezan P, Mongin C, Chever O, Bemelmans AP, Lübke J, Leray I, Rouach N. 2022. Physiological synaptic activity and recognition memory require astroglial glutamine. Nature Communications. 13, 753.","apa":"Cheung, G. T., Bataveljic, D., Visser, J., Kumar, N., Moulard, J., Dallérac, G., … Rouach, N. (2022). Physiological synaptic activity and recognition memory require astroglial glutamine. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-28331-7","ama":"Cheung GT, Bataveljic D, Visser J, et al. Physiological synaptic activity and recognition memory require astroglial glutamine. Nature Communications. 2022;13. doi:10.1038/s41467-022-28331-7","ieee":"G. T. Cheung et al., “Physiological synaptic activity and recognition memory require astroglial glutamine,” Nature Communications, vol. 13. Springer Nature, 2022.","chicago":"Cheung, Giselle T, Danijela Bataveljic, Josien Visser, Naresh Kumar, Julien Moulard, Glenn Dallérac, Daria Mozheiko, et al. “Physiological Synaptic Activity and Recognition Memory Require Astroglial Glutamine.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-28331-7."},"date_updated":"2023-08-02T14:25:01Z","external_id":{"pmid":["35136061"],"isi":["000757297200017"]},"isi":1,"day":"08","doi":"10.1038/s41467-022-28331-7","abstract":[{"lang":"eng","text":"Presynaptic glutamate replenishment is fundamental to brain function. In high activity regimes, such as epileptic episodes, this process is thought to rely on the glutamate-glutamine cycle between neurons and astrocytes. However the presence of an astroglial glutamine supply, as well as its functional relevance in vivo in the healthy brain remain controversial, partly due to a lack of tools that can directly examine glutamine transfer. Here, we generated a fluorescent probe that tracks glutamine in live cells, which provides direct visual evidence of an activity-dependent glutamine supply from astroglial networks to presynaptic structures under physiological conditions. This mobilization is mediated by connexin43, an astroglial protein with both gap-junction and hemichannel functions, and is essential for synaptic transmission and object recognition memory. Our findings uncover an indispensable recruitment of astroglial glutamine in physiological synaptic activity and memory via an unconventional pathway, thus providing an astrocyte basis for cognitive processes."}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Nature Communications","oa_version":"Published Version","article_number":"753","month":"02","file":[{"file_size":7910519,"checksum":"51d580aff2327dd957946208a9749e1a","date_created":"2022-02-21T07:51:33Z","content_type":"application/pdf","file_name":"2022_NatureCommunications_Cheung.pdf","date_updated":"2022-02-21T07:51:33Z","access_level":"open_access","success":1,"relation":"main_file","creator":"dernst","file_id":"10777"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-02-08T00:00:00Z","publication_identifier":{"eissn":["20411723"]},"oa":1},{"scopus_import":"1","_id":"10765","issue":"3","author":[{"full_name":"Cao, Yang","first_name":"Yang","last_name":"Cao"},{"id":"21f1b52f-2fd1-11eb-a347-a4cdb9b18a51","first_name":"Zhizhong","last_name":"Huang","full_name":"Huang, Zhizhong"}],"department":[{"_id":"TiBr"}],"date_created":"2022-02-20T23:01:30Z","article_processing_charge":"No","publication_status":"published","intvolume":" 398","title":"Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics","quality_controlled":"1","publisher":"Elsevier","article_type":"original","citation":{"ieee":"Y. Cao and Z. Huang, “Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics,” Advances in Mathematics, vol. 398, no. 3. Elsevier, 2022.","chicago":"Cao, Yang, and Zhizhong Huang. “Arithmetic Purity of the Hardy-Littlewood Property and Geometric Sieve for Affine Quadrics.” Advances in Mathematics. Elsevier, 2022. https://doi.org/10.1016/j.aim.2022.108236.","ama":"Cao Y, Huang Z. Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics. Advances in Mathematics. 2022;398(3). doi:10.1016/j.aim.2022.108236","apa":"Cao, Y., & Huang, Z. (2022). Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2022.108236","ista":"Cao Y, Huang Z. 2022. Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics. Advances in Mathematics. 398(3), 108236.","short":"Y. Cao, Z. Huang, Advances in Mathematics 398 (2022).","mla":"Cao, Yang, and Zhizhong Huang. “Arithmetic Purity of the Hardy-Littlewood Property and Geometric Sieve for Affine Quadrics.” Advances in Mathematics, vol. 398, no. 3, 108236, Elsevier, 2022, doi:10.1016/j.aim.2022.108236."},"year":"2022","date_updated":"2023-08-02T14:24:18Z","external_id":{"arxiv":["2003.07287"],"isi":["000792517300014"]},"isi":1,"day":"26","doi":"10.1016/j.aim.2022.108236","arxiv":1,"abstract":[{"text":"We establish the Hardy-Littlewood property (à la Borovoi-Rudnick) for Zariski open subsets in affine quadrics of the form q(x1,...,xn)=m, where q is a non-degenerate integral quadratic form in n>3 variables and m is a non-zero integer. This gives asymptotic formulas for the density of integral points taking coprime polynomial values, which is a quantitative version of the arithmetic purity of strong approximation property off infinity for affine quadrics.","lang":"eng"}],"volume":398,"acknowledgement":"We are grateful to Mikhail Borovoi, Zeev Rudnick and Olivier Wienberg for their interest in our\r\nwork. We would like to address our gratitude to Ulrich Derenthal for his generous support at Leibniz Universitat Hannover. We are in debt to Tim Browning for an enlightening discussion and to the anonymous referees for critical comments, which lead to overall improvements of various preliminary versions of this paper. Part of this work was carried out and reported during a visit to the University of Science and Technology of China. We thank Yongqi Liang for offering warm hospitality. The first author was supported by a Humboldt-Forschungsstipendium. The second author was supported by grant DE 1646/4-2 of the Deutsche Forschungsgemeinschaft.","publication":"Advances in Mathematics","oa_version":"Preprint","article_number":"108236","month":"03","language":[{"iso":"eng"}],"type":"journal_article","date_published":"2022-03-26T00:00:00Z","publication_identifier":{"issn":["0001-8708"],"eissn":["1090-2082"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2003.07287","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public"},{"author":[{"id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","full_name":"Slovakova, Jana","last_name":"Slovakova","first_name":"Jana"},{"id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora","first_name":"Mateusz K","full_name":"Sikora, Mateusz K"},{"orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N","first_name":"Feyza N","last_name":"Arslan","id":"49DA7910-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Caballero Mancebo","first_name":"Silvia","full_name":"Caballero Mancebo, Silvia","orcid":"0000-0002-5223-3346","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel","first_name":"Gabriel","last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","first_name":"Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","first_name":"Jack","last_name":"Merrin"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"issue":"8","_id":"10766","scopus_import":"1","title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells","intvolume":" 119","publication_status":"published","department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}],"date_created":"2022-02-20T23:01:31Z","article_processing_charge":"No","file_date_updated":"2022-02-21T08:45:11Z","ec_funded":1,"quality_controlled":"1","article_type":"original","publisher":"Proceedings of the National Academy of Sciences","isi":1,"external_id":{"isi":["000766926900009"]},"date_updated":"2023-08-02T14:26:51Z","year":"2022","citation":{"chicago":"Slovakova, Jana, Mateusz K Sikora, Feyza N Arslan, Silvia Caballero Mancebo, Gabriel Krens, Walter Kaufmann, Jack Merrin, and Carl-Philipp J Heisenberg. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2122030119.","ieee":"J. Slovakova et al., “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells,” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 8. Proceedings of the National Academy of Sciences, 2022.","apa":"Slovakova, J., Sikora, M. K., Arslan, F. N., Caballero Mancebo, S., Krens, G., Kaufmann, W., … Heisenberg, C.-P. J. (2022). Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2122030119","ama":"Slovakova J, Sikora MK, Arslan FN, et al. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America. 2022;119(8). doi:10.1073/pnas.2122030119","ista":"Slovakova J, Sikora MK, Arslan FN, Caballero Mancebo S, Krens G, Kaufmann W, Merrin J, Heisenberg C-PJ. 2022. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America. 119(8), e2122030119.","mla":"Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 8, e2122030119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2122030119.","short":"J. Slovakova, M.K. Sikora, F.N. Arslan, S. Caballero Mancebo, G. Krens, W. Kaufmann, J. Merrin, C.-P.J. Heisenberg, Proceedings of the National Academy of Sciences of the United States of America 119 (2022)."},"abstract":[{"lang":"eng","text":"Tension of the actomyosin cell cortex plays a key role in determining cell–cell contact growth and size. The level of cortical tension outside of the cell–cell contact, when pulling at the contact edge, scales with the total size to which a cell–cell contact can grow [J.-L. Maître et al., Science 338, 253–256 (2012)]. Here, we show in zebrafish primary germ-layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell–cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. After tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell–cell contact size is limited by tension-stabilizing E-cadherin–actin complexes at the contact."}],"doi":"10.1073/pnas.2122030119","day":"14","ddc":["570"],"volume":119,"acknowledgement":"We thank Guillaume Salbreaux, Silvia Grigolon, Edouard Hannezo, and Vanessa Barone for discussions and comments on the manuscript and Shayan Shamipour and Daniel Capek for help with data analysis. We also thank the Imaging & Optics, Electron Microscopy, and Zebrafish Facility Scientific Service Units at the Institute of Science and Technology Austria (ISTA)Nasser Darwish-Miranda for continuous support. We acknowledge Hitoshi Morita for the gift of VinculinB-GFP plasmid. This research was supported by an ISTA Fellow Marie-Curie Co-funding of regional, national, and international programmes Grant P_IST_EU01 (to J.S.), European Molecular Biology Organization Long-Term Fellowship Grant, ALTF reference number: 187-2013 (to M.S.), Schroedinger Fellowship J4332-B28 (to M.S.), and European Research Council Advanced Grant (MECSPEC; to C.-P.H.).","publication":"Proceedings of the National Academy of Sciences of the United States of America","has_accepted_license":"1","month":"02","article_number":"e2122030119","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"oa_version":"Published Version","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"_id":"2521E28E-B435-11E9-9278-68D0E5697425","grant_number":"187-2013","name":"Modulation of adhesion function in cell-cell contact formation by cortical tension"}],"language":[{"iso":"eng"}],"date_published":"2022-02-14T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"publication_identifier":{"eissn":["10916490"]},"related_material":{"record":[{"status":"public","id":"9750","relation":"earlier_version"}]},"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_created":"2022-02-21T08:45:11Z","checksum":"d49f83c3580613966f71768ddb9a55a5","file_size":1609678,"date_updated":"2022-02-21T08:45:11Z","content_type":"application/pdf","file_name":"2022_PNAS_Slovakova.pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"10780","creator":"dernst"}]},{"publication_identifier":{"eissn":["14712954"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-02-09T00:00:00Z","file":[{"success":1,"access_level":"open_access","relation":"main_file","file_id":"10779","creator":"dernst","date_created":"2022-02-21T08:17:38Z","checksum":"27042a3706ae52a919fed1ac114bf7bb","file_size":2366976,"date_updated":"2022-02-21T08:17:38Z","content_type":"application/pdf","file_name":"2022_ProceedingsRoyalSocB_Kelemen.pdf"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","month":"02","has_accepted_license":"1","publication":"Proceedings of the Royal Society B: Biological Sciences","language":[{"iso":"eng"}],"day":"09","doi":"10.1098/rspb.2021.1985","abstract":[{"lang":"eng","text":"The t-haplotype of mice is a classical model for autosomal transmission distortion. A largely non-recombining variant of the proximal region of chromosome 17, it is transmitted to more than 90% of the progeny of heterozygous males through the disabling of sperm carrying a standard chromosome. While extensive genetic and functional work has shed light on individual genes involved in drive, much less is known about the evolution and function of the rest of its hundreds of genes. Here, we characterize the sequence and expression of dozens of t-specific transcripts and of their chromosome 17 homologues. Many genes showed reduced expression of the t-allele, but an equal number of genes showed increased expression of their t-copy, consistent with increased activity or a newly evolved function. Genes on the t-haplotype had a significantly higher non-synonymous substitution rate than their homologues on the standard chromosome, with several genes harbouring dN/dS ratios above 1. Finally, the t-haplotype has acquired at least two genes from other chromosomes, which show high and tissue-specific expression. These results provide a first overview of the gene content of this selfish element, and support a more dynamic evolutionary scenario than expected of a large genomic region with almost no recombination."}],"citation":{"ama":"Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. Proceedings of the Royal Society B: Biological Sciences. 2022;289(1968):20211985. doi:10.1098/rspb.2021.1985","apa":"Kelemen, R. K., Elkrewi, M. N., Lindholm, A. K., & Vicoso, B. (2022). Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. Proceedings of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2021.1985","chicago":"Kelemen, Réka K, Marwan N Elkrewi, Anna K. Lindholm, and Beatriz Vicoso. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” Proceedings of the Royal Society B: Biological Sciences. The Royal Society, 2022. https://doi.org/10.1098/rspb.2021.1985.","ieee":"R. K. Kelemen, M. N. Elkrewi, A. K. Lindholm, and B. Vicoso, “Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome,” Proceedings of the Royal Society B: Biological Sciences, vol. 289, no. 1968. The Royal Society, p. 20211985, 2022.","short":"R.K. Kelemen, M.N. Elkrewi, A.K. Lindholm, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 289 (2022) 20211985.","mla":"Kelemen, Réka K., et al. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” Proceedings of the Royal Society B: Biological Sciences, vol. 289, no. 1968, The Royal Society, 2022, p. 20211985, doi:10.1098/rspb.2021.1985.","ista":"Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. 2022. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. Proceedings of the Royal Society B: Biological Sciences. 289(1968), 20211985."},"year":"2022","date_updated":"2023-08-02T14:26:07Z","external_id":{"pmid":["35135349"],"isi":["000752812800012"]},"isi":1,"volume":289,"acknowledgement":"This project has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 715257) and from the Swiss National Science Foundation (grant no. 310030_189145).\r\nWe thank Jari Garbely of the Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland, for conducting the PCR verification. Barbara\r\nKonig, Gabi Stichel and A.K.L. collected mouse tissue samples, from the field study led by R.K.K. ","ddc":["570"],"department":[{"_id":"BeVi"}],"article_processing_charge":"No","date_created":"2022-02-20T23:01:31Z","publication_status":"published","intvolume":" 289","title":"Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome","scopus_import":"1","pmid":1,"_id":"10767","issue":"1968","author":[{"full_name":"Kelemen, Réka K","last_name":"Kelemen","first_name":"Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"full_name":"Lindholm, Anna K.","first_name":"Anna K.","last_name":"Lindholm"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso"}],"publisher":"The Royal Society","article_type":"original","quality_controlled":"1","ec_funded":1,"page":"20211985","file_date_updated":"2022-02-21T08:17:38Z"},{"publisher":"Elsevier","article_type":"original","quality_controlled":"1","file_date_updated":"2022-03-10T13:34:09Z","publication_status":"published","article_processing_charge":"Yes (via OA deal)","date_created":"2022-02-20T23:01:32Z","department":[{"_id":"JiFr"}],"title":"Auxin canalization: From speculative models toward molecular players","intvolume":" 65","pmid":1,"_id":"10768","scopus_import":"1","author":[{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2140-7195","full_name":"Hajny, Jakub","first_name":"Jakub","last_name":"Hajny"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","first_name":"Shutang","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"issue":"2","acknowledgement":"The authors apologize to those researchers whose work was not cited. In addition, exciting topics such as PIN polarization in context of phyllotaxis, shoot branching and termination of gravitropic bending, or role of additional auxin transporters could not have been included owing to lack of space. This work was supported by the Czech Science Foundation GAČR (GA18-26981S). The authors also acknowledge the EMBO for supporting J.H. with a long-term fellowship (ALTF217-2021).","volume":65,"ddc":["580"],"doi":"10.1016/j.pbi.2022.102174","day":"01","abstract":[{"lang":"eng","text":"Among the most fascinated properties of the plant hormone auxin is its ability to promote formation of its own directional transport routes. These gradually narrowing auxin channels form from the auxin source toward the sink and involve coordinated, collective polarization of individual cells. Once established, the channels provide positional information, along which new vascular strands form, for example, during organogenesis, regeneration, or leave venation. The main prerequisite of this still mysterious auxin canalization mechanism is a feedback between auxin signaling and its directional transport. This is manifested by auxin-induced re-arrangements of polar, subcellular localization of PIN-FORMED (PIN) auxin exporters. Immanent open questions relate to how position of auxin source and sink as well as tissue context are sensed and translated into tissue polarization and how cells communicate to polarize coordinately. Recently, identification of the first molecular players opens new avenues into molecular studies of this intriguing example of self-organizing plant development."}],"date_updated":"2023-08-02T14:29:12Z","citation":{"ista":"Hajny J, Tan S, Friml J. 2022. Auxin canalization: From speculative models toward molecular players. Current Opinion in Plant Biology. 65(2), 102174.","short":"J. Hajny, S. Tan, J. Friml, Current Opinion in Plant Biology 65 (2022).","mla":"Hajny, Jakub, et al. “Auxin Canalization: From Speculative Models toward Molecular Players.” Current Opinion in Plant Biology, vol. 65, no. 2, 102174, Elsevier, 2022, doi:10.1016/j.pbi.2022.102174.","chicago":"Hajny, Jakub, Shutang Tan, and Jiří Friml. “Auxin Canalization: From Speculative Models toward Molecular Players.” Current Opinion in Plant Biology. Elsevier, 2022. https://doi.org/10.1016/j.pbi.2022.102174.","ieee":"J. Hajny, S. Tan, and J. Friml, “Auxin canalization: From speculative models toward molecular players,” Current Opinion in Plant Biology, vol. 65, no. 2. Elsevier, 2022.","ama":"Hajny J, Tan S, Friml J. Auxin canalization: From speculative models toward molecular players. Current Opinion in Plant Biology. 2022;65(2). doi:10.1016/j.pbi.2022.102174","apa":"Hajny, J., Tan, S., & Friml, J. (2022). Auxin canalization: From speculative models toward molecular players. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2022.102174"},"year":"2022","isi":1,"external_id":{"pmid":["35123880"],"isi":["000758724700004"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","month":"02","article_number":"102174","publication":"Current Opinion in Plant Biology","has_accepted_license":"1","file":[{"file_name":"2022_CurrentOpPlantBiology_Hajny.pdf","content_type":"application/pdf","date_updated":"2022-03-10T13:34:09Z","file_size":820322,"checksum":"f1ee02b6fb4200934eeb31fa69120885","date_created":"2022-03-10T13:34:09Z","creator":"dernst","file_id":"10844","relation":"main_file","access_level":"open_access","success":1}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication_identifier":{"issn":["1369-5266"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-02-01T00:00:00Z","type":"journal_article"}]