[{"department":[{"_id":"KrCh"}],"month":"01","isi":1,"day":"27","intvolume":"        12","arxiv":1,"citation":{"ieee":"J. Svoboda, J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Infection dynamics of COVID-19 virus under lockdown and reopening,” <i>Scientific Reports</i>, 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. <i>Scientific Reports</i>. 2022;12(1). doi:<a href=\"https://doi.org/10.1038/s41598-022-05333-5\">10.1038/s41598-022-05333-5</a>","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.","chicago":"Svoboda, Jakub, Josef Tkadlec, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Infection Dynamics of COVID-19 Virus under Lockdown and Reopening.” <i>Scientific Reports</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41598-022-05333-5\">https://doi.org/10.1038/s41598-022-05333-5</a>.","short":"J. Svoboda, J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Scientific Reports 12 (2022).","mla":"Svoboda, Jakub, et al. “Infection Dynamics of COVID-19 Virus under Lockdown and Reopening.” <i>Scientific Reports</i>, vol. 12, no. 1, 1526, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41598-022-05333-5\">10.1038/s41598-022-05333-5</a>.","apa":"Svoboda, J., Tkadlec, J., Pavlogiannis, A., Chatterjee, K., &#38; Nowak, M. A. (2022). Infection dynamics of COVID-19 virus under lockdown and reopening. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-022-05333-5\">https://doi.org/10.1038/s41598-022-05333-5</a>"},"scopus_import":"1","project":[{"call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"external_id":{"arxiv":["2012.15155"],"isi":["000749198000039"]},"_id":"10731","date_created":"2022-02-06T23:01:30Z","file_date_updated":"2022-02-07T14:57:59Z","issue":"1","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.","date_updated":"2025-07-14T09:10:12Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","last_name":"Svoboda","first_name":"Jakub","full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267"},{"first_name":"Josef","last_name":"Tkadlec","full_name":"Tkadlec, Josef"},{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"license":"https://creativecommons.org/licenses/by/4.0/","article_type":"original","file":[{"relation":"main_file","date_created":"2022-02-07T14:57:59Z","access_level":"open_access","creator":"alisjak","content_type":"application/pdf","checksum":"247afd30c173390940f099ead35a28ed","file_id":"10744","success":1,"file_name":"2022_ScientificReports_Svoboda.pdf","date_updated":"2022-02-07T14:57:59Z","file_size":2971922}],"ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","title":"Infection dynamics of COVID-19 virus under lockdown and reopening","doi":"10.1038/s41598-022-05333-5","abstract":[{"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.","lang":"eng"}],"publication":"Scientific Reports","article_processing_charge":"No","article_number":"1526","ec_funded":1,"language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version","oa":1,"has_accepted_license":"1","year":"2022","publication_identifier":{"eissn":["2045-2322"]},"publication_status":"published","date_published":"2022-01-27T00:00:00Z","publisher":"Springer Nature","quality_controlled":"1"},{"doi":"10.1016/j.jfa.2022.109394","abstract":[{"lang":"eng","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."}],"publication":"Journal of Functional Analysis","file":[{"access_level":"open_access","creator":"dernst","content_type":"application/pdf","checksum":"b75fdad606ab507dc61109e0907d86c0","relation":"main_file","date_created":"2022-07-29T07:22:08Z","file_size":652573,"file_id":"11690","date_updated":"2022-07-29T07:22:08Z","file_name":"2022_JourFunctionalAnalysis_Cipolloni.pdf","success":1}],"ddc":["500"],"title":"Thermalisation for Wigner matrices","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2022","publication_status":"published","publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"date_published":"2022-04-15T00:00:00Z","quality_controlled":"1","publisher":"Elsevier","article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"article_number":"109394","oa_version":"Published Version","status":"public","has_accepted_license":"1","oa":1,"citation":{"short":"G. Cipolloni, L. Erdös, D.J. Schröder, Journal of Functional Analysis 282 (2022).","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2022). Thermalisation for Wigner matrices. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2022.109394\">https://doi.org/10.1016/j.jfa.2022.109394</a>","mla":"Cipolloni, Giorgio, et al. “Thermalisation for Wigner Matrices.” <i>Journal of Functional Analysis</i>, vol. 282, no. 8, 109394, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jfa.2022.109394\">10.1016/j.jfa.2022.109394</a>.","ama":"Cipolloni G, Erdös L, Schröder DJ. Thermalisation for Wigner matrices. <i>Journal of Functional Analysis</i>. 2022;282(8). doi:<a href=\"https://doi.org/10.1016/j.jfa.2022.109394\">10.1016/j.jfa.2022.109394</a>","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Thermalisation for Wigner Matrices.” <i>Journal of Functional Analysis</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jfa.2022.109394\">https://doi.org/10.1016/j.jfa.2022.109394</a>.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2022. Thermalisation for Wigner matrices. Journal of Functional Analysis. 282(8), 109394.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Thermalisation for Wigner matrices,” <i>Journal of Functional Analysis</i>, vol. 282, no. 8. Elsevier, 2022."},"scopus_import":"1","external_id":{"isi":["000781239100004"],"arxiv":["2102.09975"]},"isi":1,"month":"04","department":[{"_id":"LaEr"}],"intvolume":"       282","day":"15","arxiv":1,"date_updated":"2023-08-02T14:12:35Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni","first_name":"Giorgio","full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992"},{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dominik J","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J"}],"article_type":"original","date_created":"2022-02-06T23:01:30Z","_id":"10732","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.","issue":"8","file_date_updated":"2022-07-29T07:22:08Z"},{"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."}],"publication":"Granular Matter","doi":"10.1007/s10035-021-01200-8","title":"Intruders cooperatively interact with a wall into granular matter","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"url":"https://arxiv.org/abs/2110.15311","open_access":"1"}],"quality_controlled":"1","publisher":"Springer Nature","publication_status":"published","year":"2022","publication_identifier":{"eissn":["1434-7636"],"issn":["1434-5021"]},"date_published":"2022-01-24T00:00:00Z","oa_version":"Preprint","status":"public","oa":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"article_number":"39","external_id":{"isi":["000746623000001"],"arxiv":["2110.15311"]},"citation":{"apa":"Espinosa, M., Diaz Melian, V. L., Serrano-Muñoz, A., &#38; Altshuler, E. (2022). Intruders cooperatively interact with a wall into granular matter. <i>Granular Matter</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10035-021-01200-8\">https://doi.org/10.1007/s10035-021-01200-8</a>","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.” <i>Granular Matter</i>, vol. 24, no. 1, 39, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s10035-021-01200-8\">10.1007/s10035-021-01200-8</a>.","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. <i>Granular Matter</i>. 2022;24(1). doi:<a href=\"https://doi.org/10.1007/s10035-021-01200-8\">10.1007/s10035-021-01200-8</a>","chicago":"Espinosa, M., Vicente L Diaz Melian, A. Serrano-Muñoz, and E. Altshuler. “Intruders Cooperatively Interact with a Wall into Granular Matter.” <i>Granular Matter</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s10035-021-01200-8\">https://doi.org/10.1007/s10035-021-01200-8</a>.","ieee":"M. Espinosa, V. L. Diaz Melian, A. Serrano-Muñoz, and E. Altshuler, “Intruders cooperatively interact with a wall into granular matter,” <i>Granular Matter</i>, vol. 24, no. 1. Springer Nature, 2022."},"scopus_import":"1","intvolume":"        24","day":"24","arxiv":1,"isi":1,"month":"01","department":[{"_id":"ScWa"}],"keyword":["granular matter","boundary effects","intruder penetration","sedimentation"],"author":[{"last_name":"Espinosa","first_name":"M.","full_name":"Espinosa, M."},{"full_name":"Diaz Melian, Vicente L","first_name":"Vicente L","id":"b6798902-eea0-11ea-9cbc-a8e14286c631","last_name":"Diaz Melian"},{"first_name":"A.","last_name":"Serrano-Muñoz","full_name":"Serrano-Muñoz, A."},{"last_name":"Altshuler","first_name":"E.","full_name":"Altshuler, E."}],"article_type":"original","date_updated":"2023-08-02T14:10:13Z","volume":24,"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.","issue":"1","date_created":"2022-02-06T23:01:30Z","_id":"10733"},{"department":[{"_id":"KiMo"}],"month":"01","isi":1,"pmid":1,"day":"20","intvolume":"        34","citation":{"apa":"Nauman, M., Hussain, T., Choi, J., Lee, N., Choi, Y. J., Kang, W., &#38; Jo, Y. (2022). Low-field magnetic anisotropy of Sr2IrO4. <i>Journal of Physics: Condensed Matter</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-648X/ac484d\">https://doi.org/10.1088/1361-648X/ac484d</a>","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.” <i>Journal of Physics: Condensed Matter</i>, vol. 34, no. 13, 135802, IOP Publishing, 2022, doi:<a href=\"https://doi.org/10.1088/1361-648X/ac484d\">10.1088/1361-648X/ac484d</a>.","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.","chicago":"Nauman, Muhammad, Tayyaba Hussain, Joonyoung Choi, Nara Lee, Young Jai Choi, Woun Kang, and Younjung Jo. “Low-Field Magnetic Anisotropy of Sr2IrO4.” <i>Journal of Physics: Condensed Matter</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.1088/1361-648X/ac484d\">https://doi.org/10.1088/1361-648X/ac484d</a>.","ama":"Nauman M, Hussain T, Choi J, et al. Low-field magnetic anisotropy of Sr2IrO4. <i>Journal of physics: Condensed matter</i>. 2022;34(13). doi:<a href=\"https://doi.org/10.1088/1361-648X/ac484d\">10.1088/1361-648X/ac484d</a>","ieee":"M. Nauman <i>et al.</i>, “Low-field magnetic anisotropy of Sr2IrO4,” <i>Journal of physics: Condensed matter</i>, vol. 34, no. 13. IOP Publishing, 2022."},"scopus_import":"1","external_id":{"isi":["000775191800001"],"pmid":["34986467"]},"_id":"10735","date_created":"2022-02-06T23:01:31Z","file_date_updated":"2022-02-07T10:35:28Z","issue":"13","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).","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-02T14:12:01Z","article_type":"original","author":[{"full_name":"Nauman, Muhammad","orcid":"0000-0002-2111-4846","first_name":"Muhammad","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","last_name":"Nauman"},{"full_name":"Hussain, Tayyaba","first_name":"Tayyaba","last_name":"Hussain"},{"full_name":"Choi, Joonyoung","first_name":"Joonyoung","last_name":"Choi"},{"full_name":"Lee, Nara","last_name":"Lee","first_name":"Nara"},{"full_name":"Choi, Young Jai","first_name":"Young Jai","last_name":"Choi"},{"full_name":"Kang, Woun","last_name":"Kang","first_name":"Woun"},{"full_name":"Jo, Younjung","last_name":"Jo","first_name":"Younjung"}],"file":[{"file_size":1742414,"success":1,"file_name":"2022_JPhysCondensMatter_Nauman.pdf","date_updated":"2022-02-07T10:35:28Z","file_id":"10741","checksum":"b6c705c7f03dcb1dbcb06b1b4d4938d6","content_type":"application/pdf","access_level":"open_access","creator":"cchlebak","date_created":"2022-02-07T10:35:28Z","relation":"main_file"}],"ddc":["530"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","title":"Low-field magnetic anisotropy of Sr2IrO4","doi":"10.1088/1361-648X/ac484d","abstract":[{"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.","lang":"eng"}],"publication":"Journal of physics: Condensed matter","article_processing_charge":"No","article_number":"135802","language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version","oa":1,"has_accepted_license":"1","publication_identifier":{"eissn":["1361-648X"]},"publication_status":"published","year":"2022","date_published":"2022-01-20T00:00:00Z","publisher":"IOP Publishing","quality_controlled":"1"},{"doi":"10.7554/eLife.64543","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."}],"publication":"eLife","file":[{"relation":"main_file","date_created":"2022-02-07T07:14:09Z","checksum":"decdcdf600ff51e9a9703b49ca114170","creator":"cchlebak","access_level":"open_access","content_type":"application/pdf","date_updated":"2022-02-07T07:14:09Z","success":1,"file_name":"2022_ELife_Lagator.pdf","file_id":"10739","file_size":5604343}],"ddc":["576"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","title":"Predicting bacterial promoter function and evolution from random sequences","publication_status":"published","year":"2022","publication_identifier":{"eissn":["2050-084X"]},"date_published":"2022-01-26T00:00:00Z","publisher":"eLife Sciences Publications","quality_controlled":"1","article_processing_charge":"No","ec_funded":1,"article_number":"e64543","language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version","oa":1,"has_accepted_license":"1","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.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.64543\">https://doi.org/10.7554/eLife.64543</a>.","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.","ama":"Lagator M, Sarikas S, Steinrueck M, et al. Predicting bacterial promoter function and evolution from random sequences. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.64543\">10.7554/eLife.64543</a>","short":"M. Lagator, S. Sarikas, M. Steinrueck, D. Toledo-Aparicio, J.P. Bollback, C.C. Guet, G. Tkačik, ELife 11 (2022).","apa":"Lagator, M., Sarikas, S., Steinrueck, M., Toledo-Aparicio, D., Bollback, J. P., Guet, C. C., &#38; Tkačik, G. (2022). Predicting bacterial promoter function and evolution from random sequences. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.64543\">https://doi.org/10.7554/eLife.64543</a>","mla":"Lagator, Mato, et al. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” <i>ELife</i>, vol. 11, e64543, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.64543\">10.7554/eLife.64543</a>.","ieee":"M. Lagator <i>et al.</i>, “Predicting bacterial promoter function and evolution from random sequences,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022."},"scopus_import":"1","project":[{"name":"Selective Barriers to Horizontal Gene Transfer","_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","call_identifier":"H2020"}],"external_id":{"pmid":["35080492"],"isi":["000751104400001"]},"month":"01","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"NiBa"}],"isi":1,"pmid":1,"day":"26","intvolume":"        11","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-02T14:09:02Z","author":[{"full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato"},{"last_name":"Sarikas","id":"35F0286E-F248-11E8-B48F-1D18A9856A87","first_name":"Srdjan","full_name":"Sarikas, Srdjan"},{"first_name":"Magdalena","last_name":"Steinrueck","full_name":"Steinrueck, Magdalena"},{"first_name":"David","last_name":"Toledo-Aparicio","full_name":"Toledo-Aparicio, David"},{"last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C"},{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"article_type":"original","_id":"10736","date_created":"2022-02-06T23:01:32Z","file_date_updated":"2022-02-07T07:14:09Z","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.","volume":11},{"quality_controlled":"1","publisher":"IOS Press","page":"257-272","publication_identifier":{"eissn":["1571-4128"],"issn":["1088-467X"]},"year":"2022","publication_status":"published","date_published":"2022-01-14T00:00:00Z","oa_version":"Preprint","status":"public","oa":1,"article_processing_charge":"No","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."}],"publication":"Intelligent Data Analysis","doi":"10.3233/IDA-205623","title":"Combining pattern-based CRFs and weighted context-free grammars","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1404.5475"}],"author":[{"id":"2CCAC26C-F248-11E8-B48F-1D18A9856A87","last_name":"Takhanov","first_name":"Rustem","full_name":"Takhanov, Rustem"},{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","date_updated":"2023-08-02T14:09:41Z","volume":26,"issue":"1","date_created":"2022-02-06T23:01:32Z","_id":"10737","external_id":{"isi":["000749997700015"],"arxiv":["1404.5475"]},"citation":{"chicago":"Takhanov, Rustem, and Vladimir Kolmogorov. “Combining Pattern-Based CRFs and Weighted Context-Free Grammars.” <i>Intelligent Data Analysis</i>. IOS Press, 2022. <a href=\"https://doi.org/10.3233/IDA-205623\">https://doi.org/10.3233/IDA-205623</a>.","ista":"Takhanov R, Kolmogorov V. 2022. Combining pattern-based CRFs and weighted context-free grammars. Intelligent Data Analysis. 26(1), 257–272.","ama":"Takhanov R, Kolmogorov V. Combining pattern-based CRFs and weighted context-free grammars. <i>Intelligent Data Analysis</i>. 2022;26(1):257-272. doi:<a href=\"https://doi.org/10.3233/IDA-205623\">10.3233/IDA-205623</a>","mla":"Takhanov, Rustem, and Vladimir Kolmogorov. “Combining Pattern-Based CRFs and Weighted Context-Free Grammars.” <i>Intelligent Data Analysis</i>, vol. 26, no. 1, IOS Press, 2022, pp. 257–72, doi:<a href=\"https://doi.org/10.3233/IDA-205623\">10.3233/IDA-205623</a>.","short":"R. Takhanov, V. Kolmogorov, Intelligent Data Analysis 26 (2022) 257–272.","apa":"Takhanov, R., &#38; Kolmogorov, V. (2022). Combining pattern-based CRFs and weighted context-free grammars. <i>Intelligent Data Analysis</i>. IOS Press. <a href=\"https://doi.org/10.3233/IDA-205623\">https://doi.org/10.3233/IDA-205623</a>","ieee":"R. Takhanov and V. Kolmogorov, “Combining pattern-based CRFs and weighted context-free grammars,” <i>Intelligent Data Analysis</i>, vol. 26, no. 1. IOS Press, pp. 257–272, 2022."},"scopus_import":"1","intvolume":"        26","day":"14","arxiv":1,"isi":1,"department":[{"_id":"VlKo"}],"month":"01"},{"date_updated":"2023-08-02T14:27:50Z","publication_identifier":{"isbn":["9781665439022"]},"publication_status":"published","year":"2022","date_published":"2022-01-13T00:00:00Z","publisher":"IEEE","author":[{"first_name":"Jasmin","last_name":"Lampert","full_name":"Lampert, Jasmin"},{"orcid":"0000-0002-4561-241X","full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"quality_controlled":"1","page":"5185-5192","article_processing_charge":"No","_id":"10752","language":[{"iso":"eng"}],"date_created":"2022-02-10T14:08:23Z","status":"public","oa_version":"None","citation":{"mla":"Lampert, Jasmin, and Christoph Lampert. “Overcoming Rare-Language Discrimination in Multi-Lingual Sentiment Analysis.” <i>2021 IEEE International Conference on Big Data</i>, IEEE, 2022, pp. 5185–92, doi:<a href=\"https://doi.org/10.1109/bigdata52589.2021.9672003\">10.1109/bigdata52589.2021.9672003</a>.","apa":"Lampert, J., &#38; Lampert, C. (2022). Overcoming rare-language discrimination in multi-lingual sentiment analysis. In <i>2021 IEEE International Conference on Big Data</i> (pp. 5185–5192). Orlando, FL, United States: IEEE. <a href=\"https://doi.org/10.1109/bigdata52589.2021.9672003\">https://doi.org/10.1109/bigdata52589.2021.9672003</a>","short":"J. Lampert, C. Lampert, in:, 2021 IEEE International Conference on Big Data, IEEE, 2022, pp. 5185–5192.","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.","ama":"Lampert J, Lampert C. Overcoming rare-language discrimination in multi-lingual sentiment analysis. In: <i>2021 IEEE International Conference on Big Data</i>. IEEE; 2022:5185-5192. doi:<a href=\"https://doi.org/10.1109/bigdata52589.2021.9672003\">10.1109/bigdata52589.2021.9672003</a>","chicago":"Lampert, Jasmin, and Christoph Lampert. “Overcoming Rare-Language Discrimination in Multi-Lingual Sentiment Analysis.” In <i>2021 IEEE International Conference on Big Data</i>, 5185–92. IEEE, 2022. <a href=\"https://doi.org/10.1109/bigdata52589.2021.9672003\">https://doi.org/10.1109/bigdata52589.2021.9672003</a>.","ieee":"J. Lampert and C. Lampert, “Overcoming rare-language discrimination in multi-lingual sentiment analysis,” in <i>2021 IEEE International Conference on Big Data</i>, Orlando, FL, United States, 2022, pp. 5185–5192."},"conference":{"location":"Orlando, FL, United States","start_date":"2021-12-15","name":"Big Data: International Conference on Big Data","end_date":"2021-12-18"},"doi":"10.1109/bigdata52589.2021.9672003","abstract":[{"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. ","lang":"eng"}],"external_id":{"isi":["000800559505036"]},"publication":"2021 IEEE International Conference on Big Data","department":[{"_id":"ChLa"}],"month":"01","isi":1,"day":"13","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"conference","title":"Overcoming rare-language discrimination in multi-lingual sentiment analysis"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2022.01.014"}],"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A familiar thought: Machines that replace us?","publication":"Neuron","abstract":[{"lang":"eng","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."}],"doi":"10.1016/j.neuron.2022.01.014","oa":1,"status":"public","oa_version":"Published Version","language":[{"iso":"eng"}],"article_processing_charge":"No","page":"361-362","publisher":"Elsevier","quality_controlled":"1","date_published":"2022-02-02T00:00:00Z","year":"2022","publication_status":"published","publication_identifier":{"eissn":["1097-4199"]},"day":"02","intvolume":"       110","month":"02","department":[{"_id":"TiVo"}],"pmid":1,"isi":1,"external_id":{"pmid":["35114107"],"isi":["000751819100005"]},"scopus_import":"1","citation":{"ieee":"B. J. Confavreux and T. P. Vogels, “A familiar thought: Machines that replace us?,” <i>Neuron</i>, vol. 110, no. 3. Elsevier, pp. 361–362, 2022.","chicago":"Confavreux, Basile J, and Tim P Vogels. “A Familiar Thought: Machines That Replace Us?” <i>Neuron</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.neuron.2022.01.014\">https://doi.org/10.1016/j.neuron.2022.01.014</a>.","ista":"Confavreux BJ, Vogels TP. 2022. A familiar thought: Machines that replace us? Neuron. 110(3), 361–362.","ama":"Confavreux BJ, Vogels TP. A familiar thought: Machines that replace us? <i>Neuron</i>. 2022;110(3):361-362. doi:<a href=\"https://doi.org/10.1016/j.neuron.2022.01.014\">10.1016/j.neuron.2022.01.014</a>","mla":"Confavreux, Basile J., and Tim P. Vogels. “A Familiar Thought: Machines That Replace Us?” <i>Neuron</i>, vol. 110, no. 3, Elsevier, 2022, pp. 361–62, doi:<a href=\"https://doi.org/10.1016/j.neuron.2022.01.014\">10.1016/j.neuron.2022.01.014</a>.","apa":"Confavreux, B. J., &#38; Vogels, T. P. (2022). A familiar thought: Machines that replace us? <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2022.01.014\">https://doi.org/10.1016/j.neuron.2022.01.014</a>","short":"B.J. Confavreux, T.P. Vogels, Neuron 110 (2022) 361–362."},"issue":"3","volume":110,"_id":"10753","date_created":"2022-02-13T23:01:34Z","article_type":"letter_note","author":[{"full_name":"Confavreux, Basile J","first_name":"Basile J","id":"C7610134-B532-11EA-BD9F-F5753DDC885E","last_name":"Confavreux"},{"first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181"}],"date_updated":"2023-10-03T10:53:17Z"},{"_id":"10754","date_created":"2022-02-13T23:01:35Z","file_date_updated":"2022-02-14T07:46:30Z","issue":"3","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.). ","volume":23,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-09T10:17:07Z","article_type":"original","author":[{"first_name":"Yan","last_name":"Chang","full_name":"Chang, Yan"},{"first_name":"Marah","last_name":"Funk","full_name":"Funk, Marah"},{"full_name":"Roy, Souvik","last_name":"Roy","first_name":"Souvik"},{"id":"2D04F932-F248-11E8-B48F-1D18A9856A87","last_name":"Stephenson","first_name":"Elizabeth R","full_name":"Stephenson, Elizabeth R","orcid":"0000-0002-6862-208X"},{"last_name":"Choi","first_name":"Sangyong","full_name":"Choi, Sangyong"},{"full_name":"Kojouharov, Hristo V.","first_name":"Hristo V.","last_name":"Kojouharov"},{"full_name":"Chen, Benito","last_name":"Chen","first_name":"Benito"},{"last_name":"Pan","first_name":"Zui","full_name":"Pan, Zui"}],"department":[{"_id":"HeEd"}],"month":"02","isi":1,"day":"01","intvolume":"        23","scopus_import":"1","citation":{"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.” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 3, 1763, MDPI, 2022, doi:<a href=\"https://doi.org/10.3390/ijms23031763\">10.3390/ijms23031763</a>.","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).","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. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms23031763\">https://doi.org/10.3390/ijms23031763</a>","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.","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.” <i>International Journal of Molecular Sciences</i>. MDPI, 2022. <a href=\"https://doi.org/10.3390/ijms23031763\">https://doi.org/10.3390/ijms23031763</a>.","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. <i>International Journal of Molecular Sciences</i>. 2022;23(3). doi:<a href=\"https://doi.org/10.3390/ijms23031763\">10.3390/ijms23031763</a>","ieee":"Y. Chang <i>et al.</i>, “Developing a mathematical model of intracellular Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer,” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 3. MDPI, 2022."},"external_id":{"isi":["000754773500001"]},"article_number":"1763","language":[{"iso":"eng"}],"article_processing_charge":"Yes","oa":1,"has_accepted_license":"1","status":"public","oa_version":"Published Version","date_published":"2022-02-01T00:00:00Z","publication_identifier":{"issn":["16616596"],"eissn":["14220067"]},"year":"2022","publication_status":"published","publisher":"MDPI","quality_controlled":"1","file":[{"file_id":"10756","success":1,"file_name":"2022_IJMS_Chang.pdf","date_updated":"2022-02-14T07:46:30Z","file_size":24416183,"relation":"main_file","date_created":"2022-02-14T07:46:30Z","access_level":"open_access","content_type":"application/pdf","creator":"dernst","checksum":"8890ad20c54e90dc58ad5ea97c902998"}],"ddc":["510","576"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","title":"Developing a mathematical model of intracellular Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer","doi":"10.3390/ijms23031763","publication":"International Journal of Molecular Sciences","abstract":[{"lang":"eng","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."}]},{"ddc":["510"],"file":[{"success":1,"file_name":"2022_JournalPhysicsA_Feliciangeli.pdf","date_updated":"2022-02-14T08:20:19Z","file_id":"10757","file_size":1132380,"relation":"main_file","date_created":"2022-02-14T08:20:19Z","checksum":"0875e562705563053d6dd98fba4d8578","access_level":"open_access","content_type":"application/pdf","creator":"dernst"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","title":"The effective mass problem for the Landau-Pekar equations","doi":"10.1088/1751-8121/ac3947","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"}],"publication":"Journal of Physics A: Mathematical and Theoretical","article_processing_charge":"Yes (via OA deal)","ec_funded":1,"article_number":"015201","related_material":{"record":[{"status":"public","id":"9791","relation":"earlier_version"}]},"language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version","oa":1,"has_accepted_license":"1","publication_status":"published","year":"2022","publication_identifier":{"issn":["1751-8113"],"eissn":["1751-8121"]},"date_published":"2022-01-19T00:00:00Z","publisher":"IOP Publishing","quality_controlled":"1","department":[{"_id":"RoSe"}],"month":"01","day":"19","intvolume":"        55","arxiv":1,"citation":{"ieee":"D. Feliciangeli, S. A. E. Rademacher, and R. Seiringer, “The effective mass problem for the Landau-Pekar equations,” <i>Journal of Physics A: Mathematical and Theoretical</i>, vol. 55, no. 1. IOP Publishing, 2022.","ama":"Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for the Landau-Pekar equations. <i>Journal of Physics A: Mathematical and Theoretical</i>. 2022;55(1). doi:<a href=\"https://doi.org/10.1088/1751-8121/ac3947\">10.1088/1751-8121/ac3947</a>","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.","chicago":"Feliciangeli, Dario, Simone Anna Elvira Rademacher, and Robert Seiringer. “The Effective Mass Problem for the Landau-Pekar Equations.” <i>Journal of Physics A: Mathematical and Theoretical</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.1088/1751-8121/ac3947\">https://doi.org/10.1088/1751-8121/ac3947</a>.","apa":"Feliciangeli, D., Rademacher, S. A. E., &#38; Seiringer, R. (2022). The effective mass problem for the Landau-Pekar equations. <i>Journal of Physics A: Mathematical and Theoretical</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1751-8121/ac3947\">https://doi.org/10.1088/1751-8121/ac3947</a>","mla":"Feliciangeli, Dario, et al. “The Effective Mass Problem for the Landau-Pekar Equations.” <i>Journal of Physics A: Mathematical and Theoretical</i>, vol. 55, no. 1, 015201, IOP Publishing, 2022, doi:<a href=\"https://doi.org/10.1088/1751-8121/ac3947\">10.1088/1751-8121/ac3947</a>.","short":"D. Feliciangeli, S.A.E. Rademacher, R. Seiringer, Journal of Physics A: Mathematical and Theoretical 55 (2022)."},"scopus_import":"1","project":[{"grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems"},{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"external_id":{"arxiv":["2107.03720"]},"_id":"10755","date_created":"2022-02-13T23:01:35Z","issue":"1","file_date_updated":"2022-02-14T08:20:19Z","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.","volume":55,"date_updated":"2024-03-06T12:30:44Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"first_name":"Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","last_name":"Feliciangeli","full_name":"Feliciangeli, Dario","orcid":"0000-0003-0754-8530"},{"full_name":"Rademacher, Simone Anna Elvira","orcid":"0000-0001-5059-4466","id":"856966FE-A408-11E9-977E-802DE6697425","last_name":"Rademacher","first_name":"Simone Anna Elvira"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"article_type":"original"},{"date_updated":"2023-01-31T07:33:07Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Dubini, Romeo C. A.","last_name":"Dubini","first_name":"Romeo C. A."},{"full_name":"Korytiaková, Eva","last_name":"Korytiaková","first_name":"Eva"},{"last_name":"Schinkel","first_name":"Thea","full_name":"Schinkel, Thea"},{"first_name":"Pia","last_name":"Heinrichs","full_name":"Heinrichs, Pia"},{"full_name":"Carell, Thomas","first_name":"Thomas","last_name":"Carell"},{"last_name":"Rovo","id":"c316e53f-b965-11eb-b128-bb26acc59c00","first_name":"Petra","orcid":"0000-0001-8729-7326","full_name":"Rovo, Petra"}],"article_type":"original","_id":"10758","date_created":"2022-02-16T11:18:21Z","file_date_updated":"2022-07-29T07:53:20Z","issue":"3","volume":2,"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","citation":{"apa":"Dubini, R. C. A., Korytiaková, E., Schinkel, T., Heinrichs, P., Carell, T., &#38; Rovo, P. (2022). 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. <i>ACS Physical Chemistry Au</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsphyschemau.1c00050\">https://doi.org/10.1021/acsphyschemau.1c00050</a>","mla":"Dubini, Romeo C. A., et al. “1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives.” <i>ACS Physical Chemistry Au</i>, vol. 2, no. 3, American Chemical Society, 2022, pp. 237–46, doi:<a href=\"https://doi.org/10.1021/acsphyschemau.1c00050\">10.1021/acsphyschemau.1c00050</a>.","short":"R.C.A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, P. Rovo, ACS Physical Chemistry Au 2 (2022) 237–246.","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.","ama":"Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. <i>ACS Physical Chemistry Au</i>. 2022;2(3):237-246. doi:<a href=\"https://doi.org/10.1021/acsphyschemau.1c00050\">10.1021/acsphyschemau.1c00050</a>","chicago":"Dubini, Romeo C. A., Eva Korytiaková, Thea Schinkel, Pia Heinrichs, Thomas Carell, and Petra Rovo. “1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives.” <i>ACS Physical Chemistry Au</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acsphyschemau.1c00050\">https://doi.org/10.1021/acsphyschemau.1c00050</a>.","ieee":"R. C. A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, and P. Rovo, “1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives,” <i>ACS Physical Chemistry Au</i>, vol. 2, no. 3. American Chemical Society, pp. 237–246, 2022."},"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"scopus_import":"1","external_id":{"pmid":["35637781"]},"month":"02","department":[{"_id":"NMR"}],"pmid":1,"day":"11","intvolume":"         2","publication_status":"published","year":"2022","publication_identifier":{"eissn":["2694-2445"]},"date_published":"2022-02-11T00:00:00Z","publisher":"American Chemical Society","quality_controlled":"1","page":"237-246","article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"related_material":{"link":[{"relation":"earlier_version","url":"https://www.biorxiv.org/content/10.1101/2021.12.14.472563"}]},"status":"public","oa_version":"Published Version","oa":1,"has_accepted_license":"1","doi":"10.1021/acsphyschemau.1c00050","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."}],"publication":"ACS Physical Chemistry Au","file":[{"relation":"main_file","date_created":"2022-07-29T07:53:20Z","content_type":"application/pdf","creator":"dernst","access_level":"open_access","checksum":"5ce3f907848f5c7caf77f1adfe5826c6","file_id":"11692","date_updated":"2022-07-29T07:53:20Z","file_name":"2022_ACSPhysChemAU_Dubini.pdf","success":1,"file_size":2351220}],"ddc":["540"],"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives"},{"department":[{"_id":"GradSch"},{"_id":"MiLe"}],"month":"02","day":"21","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"}],"citation":{"short":"W. Rzadkowski, Analytic and Machine Learning Approaches to Composite Quantum Impurities, Institute of Science and Technology Austria, 2022.","mla":"Rzadkowski, Wojciech. <i>Analytic and Machine Learning Approaches to Composite Quantum Impurities</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:10759\">10.15479/at:ista:10759</a>.","apa":"Rzadkowski, W. (2022). <i>Analytic and machine learning approaches to composite quantum impurities</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10759\">https://doi.org/10.15479/at:ista:10759</a>","ista":"Rzadkowski W. 2022. Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria.","ama":"Rzadkowski W. Analytic and machine learning approaches to composite quantum impurities. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:10759\">10.15479/at:ista:10759</a>","chicago":"Rzadkowski, Wojciech. “Analytic and Machine Learning Approaches to Composite Quantum Impurities.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:10759\">https://doi.org/10.15479/at:ista:10759</a>.","ieee":"W. Rzadkowski, “Analytic and machine learning approaches to composite quantum impurities,” Institute of Science and Technology Austria, 2022."},"date_created":"2022-02-16T13:27:37Z","_id":"10759","file_date_updated":"2022-02-22T07:20:12Z","date_updated":"2024-08-07T07:16:53Z","author":[{"orcid":"0000-0002-1106-4419","full_name":"Rzadkowski, Wojciech","first_name":"Wojciech","last_name":"Rzadkowski","id":"48C55298-F248-11E8-B48F-1D18A9856A87"}],"file":[{"date_created":"2022-02-21T13:58:16Z","relation":"source_file","access_level":"closed","creator":"wrzadkow","content_type":"application/zip","checksum":"0fc54ad1eaede879c665ac9b53c93e22","file_id":"10785","date_updated":"2022-02-22T07:20:12Z","file_name":"Rzadkowski_thesis_final_source.zip","file_size":17668233},{"relation":"main_file","date_created":"2022-02-21T14:02:54Z","access_level":"open_access","content_type":"application/pdf","creator":"wrzadkow","checksum":"22d2d7af37ca31f6b1730c26cac7bced","file_id":"10786","file_name":"Rzadkowski_thesis_final.pdf","success":1,"date_updated":"2022-02-21T14:02:54Z","file_size":13307331}],"ddc":["530"],"title":"Analytic and machine learning approaches to composite quantum impurities","degree_awarded":"PhD","type":"dissertation","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.15479/at:ista:10759","abstract":[{"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.","lang":"eng"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"related_material":{"record":[{"id":"10762","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7956"},{"relation":"part_of_dissertation","status":"public","id":"415"},{"relation":"part_of_dissertation","id":"8644","status":"public"}]},"ec_funded":1,"supervisor":[{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","has_accepted_license":"1","oa":1,"oa_version":"Published Version","status":"public","date_published":"2022-02-21T00:00:00Z","year":"2022","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","page":"120","publisher":"Institute of Science and Technology Austria"},{"file":[{"date_created":"2022-02-21T07:59:32Z","relation":"main_file","checksum":"d86ee8eabe8b794730729ffbb1a8832e","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_updated":"2022-02-21T07:59:32Z","success":1,"file_name":"2022_NatureCommunications_Herguedas.pdf","file_id":"10778","file_size":2625540}],"ddc":["570"],"title":"Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1038/s41467-022-28404-7","publication":"Nature Communications","abstract":[{"lang":"eng","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."}],"language":[{"iso":"eng"}],"article_number":"734","article_processing_charge":"No","has_accepted_license":"1","oa":1,"oa_version":"Published Version","status":"public","date_published":"2022-02-08T00:00:00Z","year":"2022","publication_identifier":{"eissn":["20411723"]},"publication_status":"published","quality_controlled":"1","publisher":"Springer Nature","isi":1,"pmid":1,"department":[{"_id":"PeJo"}],"month":"02","intvolume":"        13","day":"08","scopus_import":"1","citation":{"ieee":"B. Herguedas <i>et al.</i>, “Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","ista":"Herguedas B, Kohegyi BK, Dohrke JN, Watson J, Zhang D, Ho H, Shaikh SA, Lape R, Krieger JM, Greger IH. 2022. Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor. Nature Communications. 13, 734.","ama":"Herguedas B, Kohegyi BK, Dohrke JN, et al. Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-28404-7\">10.1038/s41467-022-28404-7</a>","chicago":"Herguedas, Beatriz, Bianka K. Kohegyi, Jan Niklas Dohrke, Jake Watson, Danyang Zhang, Hinze Ho, Saher A. Shaikh, Remigijus Lape, James M. Krieger, and Ingo H. Greger. “Mechanisms Underlying TARP Modulation of the GluA1/2-Γ8 AMPA Receptor.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-28404-7\">https://doi.org/10.1038/s41467-022-28404-7</a>.","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.” <i>Nature Communications</i>, vol. 13, 734, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-28404-7\">10.1038/s41467-022-28404-7</a>.","apa":"Herguedas, B., Kohegyi, B. K., Dohrke, J. N., Watson, J., Zhang, D., Ho, H., … Greger, I. H. (2022). Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-28404-7\">https://doi.org/10.1038/s41467-022-28404-7</a>"},"external_id":{"isi":["000757297200008"],"pmid":["35136046"]},"date_created":"2022-02-20T23:01:30Z","_id":"10763","volume":13,"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).","file_date_updated":"2022-02-21T07:59:32Z","date_updated":"2023-08-02T14:25:33Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Herguedas, Beatriz","first_name":"Beatriz","last_name":"Herguedas"},{"full_name":"Kohegyi, Bianka K.","last_name":"Kohegyi","first_name":"Bianka K."},{"first_name":"Jan Niklas","last_name":"Dohrke","full_name":"Dohrke, Jan Niklas"},{"full_name":"Watson, Jake","orcid":"0000-0002-8698-3823","first_name":"Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson"},{"last_name":"Zhang","first_name":"Danyang","full_name":"Zhang, Danyang"},{"first_name":"Hinze","last_name":"Ho","full_name":"Ho, Hinze"},{"full_name":"Shaikh, Saher A.","first_name":"Saher A.","last_name":"Shaikh"},{"full_name":"Lape, Remigijus","first_name":"Remigijus","last_name":"Lape"},{"last_name":"Krieger","first_name":"James M.","full_name":"Krieger, James M."},{"last_name":"Greger","first_name":"Ingo H.","full_name":"Greger, Ingo H."}],"article_type":"original"},{"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."}],"publication":"Nature Communications","doi":"10.1038/s41467-022-28331-7","title":"Physiological synaptic activity and recognition memory require astroglial glutamine","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"file":[{"file_id":"10777","date_updated":"2022-02-21T07:51:33Z","success":1,"file_name":"2022_NatureCommunications_Cheung.pdf","file_size":7910519,"relation":"main_file","date_created":"2022-02-21T07:51:33Z","access_level":"open_access","content_type":"application/pdf","creator":"dernst","checksum":"51d580aff2327dd957946208a9749e1a"}],"quality_controlled":"1","publisher":"Springer Nature","publication_status":"published","year":"2022","publication_identifier":{"eissn":["20411723"]},"date_published":"2022-02-08T00:00:00Z","oa_version":"Published Version","status":"public","has_accepted_license":"1","oa":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"article_number":"753","external_id":{"pmid":["35136061"],"isi":["000757297200017"]},"citation":{"mla":"Cheung, Giselle T., et al. “Physiological Synaptic Activity and Recognition Memory Require Astroglial Glutamine.” <i>Nature Communications</i>, vol. 13, 753, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-28331-7\">10.1038/s41467-022-28331-7</a>.","apa":"Cheung, G. T., Bataveljic, D., Visser, J., Kumar, N., Moulard, J., Dallérac, G., … Rouach, N. (2022). Physiological synaptic activity and recognition memory require astroglial glutamine. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-28331-7\">https://doi.org/10.1038/s41467-022-28331-7</a>","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).","ista":"Cheung GT, Bataveljic D, Visser J, Kumar N, Moulard J, Dallérac G, Mozheiko D, Rollenhagen A, Ezan P, Mongin C, Chever O, Bemelmans AP, Lübke J, Leray I, Rouach N. 2022. Physiological synaptic activity and recognition memory require astroglial glutamine. Nature Communications. 13, 753.","ama":"Cheung GT, Bataveljic D, Visser J, et al. Physiological synaptic activity and recognition memory require astroglial glutamine. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-28331-7\">10.1038/s41467-022-28331-7</a>","chicago":"Cheung, Giselle T, Danijela Bataveljic, Josien Visser, Naresh Kumar, Julien Moulard, Glenn Dallérac, Daria Mozheiko, et al. “Physiological Synaptic Activity and Recognition Memory Require Astroglial Glutamine.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-28331-7\">https://doi.org/10.1038/s41467-022-28331-7</a>.","ieee":"G. T. Cheung <i>et al.</i>, “Physiological synaptic activity and recognition memory require astroglial glutamine,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022."},"scopus_import":"1","intvolume":"        13","day":"08","isi":1,"pmid":1,"department":[{"_id":"SiHi"}],"month":"02","author":[{"full_name":"Cheung, Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung","first_name":"Giselle T"},{"full_name":"Bataveljic, Danijela","first_name":"Danijela","last_name":"Bataveljic"},{"full_name":"Visser, Josien","first_name":"Josien","last_name":"Visser"},{"full_name":"Kumar, Naresh","first_name":"Naresh","last_name":"Kumar"},{"full_name":"Moulard, Julien","last_name":"Moulard","first_name":"Julien"},{"first_name":"Glenn","last_name":"Dallérac","full_name":"Dallérac, Glenn"},{"full_name":"Mozheiko, Daria","first_name":"Daria","last_name":"Mozheiko"},{"last_name":"Rollenhagen","first_name":"Astrid","full_name":"Rollenhagen, Astrid"},{"first_name":"Pascal","last_name":"Ezan","full_name":"Ezan, Pascal"},{"full_name":"Mongin, Cédric","first_name":"Cédric","last_name":"Mongin"},{"last_name":"Chever","first_name":"Oana","full_name":"Chever, Oana"},{"full_name":"Bemelmans, Alexis Pierre","first_name":"Alexis Pierre","last_name":"Bemelmans"},{"full_name":"Lübke, Joachim","first_name":"Joachim","last_name":"Lübke"},{"full_name":"Leray, Isabelle","last_name":"Leray","first_name":"Isabelle"},{"last_name":"Rouach","first_name":"Nathalie","full_name":"Rouach, Nathalie"}],"article_type":"original","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-02T14:25:01Z","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.","volume":13,"file_date_updated":"2022-02-21T07:51:33Z","date_created":"2022-02-20T23:01:30Z","_id":"10764"},{"publication_identifier":{"eissn":["1090-2082"],"issn":["0001-8708"]},"year":"2022","publication_status":"published","date_published":"2022-03-26T00:00:00Z","publisher":"Elsevier","quality_controlled":"1","article_processing_charge":"No","article_number":"108236","language":[{"iso":"eng"}],"status":"public","oa_version":"Preprint","oa":1,"doi":"10.1016/j.aim.2022.108236","abstract":[{"lang":"eng","text":"We establish the Hardy-Littlewood property (à la Borovoi-Rudnick) for Zariski open subsets in affine quadrics of the form q(x1,...,xn)=m, where q is a non-degenerate integral quadratic form in  n>3 variables and m is a non-zero integer. This gives asymptotic formulas for the density of integral points taking coprime polynomial values, which is a quantitative version of the arithmetic purity of strong approximation property off infinity for affine quadrics."}],"publication":"Advances in Mathematics","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","title":"Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics","main_file_link":[{"url":"https://arxiv.org/abs/2003.07287","open_access":"1"}],"date_updated":"2023-08-02T14:24:18Z","article_type":"original","author":[{"full_name":"Cao, Yang","first_name":"Yang","last_name":"Cao"},{"last_name":"Huang","id":"21f1b52f-2fd1-11eb-a347-a4cdb9b18a51","first_name":"Zhizhong","full_name":"Huang, Zhizhong"}],"_id":"10765","date_created":"2022-02-20T23:01:30Z","issue":"3","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.","volume":398,"citation":{"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.” <i>Advances in Mathematics</i>, vol. 398, no. 3, 108236, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.aim.2022.108236\">10.1016/j.aim.2022.108236</a>.","apa":"Cao, Y., &#38; Huang, Z. (2022). Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2022.108236\">https://doi.org/10.1016/j.aim.2022.108236</a>","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.","chicago":"Cao, Yang, and Zhizhong Huang. “Arithmetic Purity of the Hardy-Littlewood Property and Geometric Sieve for Affine Quadrics.” <i>Advances in Mathematics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.aim.2022.108236\">https://doi.org/10.1016/j.aim.2022.108236</a>.","ama":"Cao Y, Huang Z. Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics. <i>Advances in Mathematics</i>. 2022;398(3). doi:<a href=\"https://doi.org/10.1016/j.aim.2022.108236\">10.1016/j.aim.2022.108236</a>","ieee":"Y. Cao and Z. Huang, “Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics,” <i>Advances in Mathematics</i>, vol. 398, no. 3. Elsevier, 2022."},"scopus_import":"1","external_id":{"arxiv":["2003.07287"],"isi":["000792517300014"]},"month":"03","department":[{"_id":"TiBr"}],"isi":1,"day":"26","intvolume":"       398","arxiv":1},{"quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","date_published":"2022-02-14T00:00:00Z","publication_status":"published","year":"2022","publication_identifier":{"eissn":["10916490"]},"has_accepted_license":"1","oa":1,"oa_version":"Published Version","status":"public","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"earlier_version","id":"9750","status":"public"}]},"article_number":"e2122030119","ec_funded":1,"article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences of the United States of America","abstract":[{"text":"Tension of the actomyosin cell cortex plays a key role in determining cell–cell contact growth and size. The level of cortical tension outside of the cell–cell contact, when pulling at the contact edge, scales with the total size to which a cell–cell contact can grow [J.-L. Maître et al., Science 338, 253–256 (2012)]. Here, we show in zebrafish primary germ-layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell–cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. After tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell–cell contact size is limited by tension-stabilizing E-cadherin–actin complexes at the contact.","lang":"eng"}],"doi":"10.1073/pnas.2122030119","title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"ddc":["570"],"file":[{"file_id":"10780","date_updated":"2022-02-21T08:45:11Z","success":1,"file_name":"2022_PNAS_Slovakova.pdf","file_size":1609678,"relation":"main_file","date_created":"2022-02-21T08:45:11Z","creator":"dernst","access_level":"open_access","content_type":"application/pdf","checksum":"d49f83c3580613966f71768ddb9a55a5"}],"article_type":"original","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","author":[{"full_name":"Slovakova, Jana","first_name":"Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","last_name":"Slovakova"},{"full_name":"Sikora, Mateusz K","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora"},{"first_name":"Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","last_name":"Arslan","full_name":"Arslan, Feyza N","orcid":"0000-0001-5809-9566"},{"full_name":"Caballero Mancebo, Silvia","orcid":"0000-0002-5223-3346","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","last_name":"Caballero Mancebo","first_name":"Silvia"},{"orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel","last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel"},{"last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"date_updated":"2023-08-02T14:26:51Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"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.).","file_date_updated":"2022-02-21T08:45:11Z","issue":"8","date_created":"2022-02-20T23:01:31Z","_id":"10766","external_id":{"isi":["000766926900009"]},"scopus_import":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"},{"grant_number":"742573","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"_id":"2521E28E-B435-11E9-9278-68D0E5697425","name":"Modulation of adhesion function in cell-cell contact formation by cortical tension","grant_number":"187-2013"}],"citation":{"ieee":"J. Slovakova <i>et al.</i>, “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 8. Proceedings of the National Academy of Sciences, 2022.","chicago":"Slovakova, Jana, Mateusz K Sikora, Feyza N Arslan, Silvia Caballero Mancebo, Gabriel Krens, Walter Kaufmann, Jack Merrin, and Carl-Philipp J Heisenberg. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122030119\">https://doi.org/10.1073/pnas.2122030119</a>.","ista":"Slovakova J, Sikora MK, Arslan FN, Caballero Mancebo S, Krens G, Kaufmann W, Merrin J, Heisenberg C-PJ. 2022. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America. 119(8), e2122030119.","ama":"Slovakova J, Sikora MK, Arslan FN, et al. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(8). doi:<a href=\"https://doi.org/10.1073/pnas.2122030119\">10.1073/pnas.2122030119</a>","apa":"Slovakova, J., Sikora, M. K., Arslan, F. N., Caballero Mancebo, S., Krens, G., Kaufmann, W., … Heisenberg, C.-P. J. (2022). Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122030119\">https://doi.org/10.1073/pnas.2122030119</a>","short":"J. Slovakova, M.K. Sikora, F.N. Arslan, S. Caballero Mancebo, G. Krens, W. Kaufmann, J. Merrin, C.-P.J. Heisenberg, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","mla":"Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 8, e2122030119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122030119\">10.1073/pnas.2122030119</a>."},"intvolume":"       119","day":"14","isi":1,"month":"02","department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}]},{"publication_identifier":{"eissn":["14712954"]},"year":"2022","publication_status":"published","date_published":"2022-02-09T00:00:00Z","publisher":"The Royal Society","quality_controlled":"1","page":"20211985","article_processing_charge":"No","ec_funded":1,"language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version","oa":1,"has_accepted_license":"1","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."}],"publication":"Proceedings of the Royal Society B: Biological Sciences","ddc":["570"],"file":[{"date_updated":"2022-02-21T08:17:38Z","success":1,"file_name":"2022_ProceedingsRoyalSocB_Kelemen.pdf","file_id":"10779","file_size":2366976,"date_created":"2022-02-21T08:17:38Z","relation":"main_file","checksum":"27042a3706ae52a919fed1ac114bf7bb","creator":"dernst","access_level":"open_access","content_type":"application/pdf"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","title":"Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome","date_updated":"2023-08-02T14:26:07Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_type":"original","author":[{"full_name":"Kelemen, Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","last_name":"Kelemen","first_name":"Réka K"},{"full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi"},{"full_name":"Lindholm, Anna K.","first_name":"Anna K.","last_name":"Lindholm"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"_id":"10767","date_created":"2022-02-20T23:01:31Z","issue":"1968","file_date_updated":"2022-02-21T08:17:38Z","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. ","citation":{"chicago":"Kelemen, Réka K, Marwan N Elkrewi, Anna K. Lindholm, and Beatriz Vicoso. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society, 2022. <a href=\"https://doi.org/10.1098/rspb.2021.1985\">https://doi.org/10.1098/rspb.2021.1985</a>.","ama":"Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. <i>Proceedings of the Royal Society B: Biological Sciences</i>. 2022;289(1968):20211985. doi:<a href=\"https://doi.org/10.1098/rspb.2021.1985\">10.1098/rspb.2021.1985</a>","ista":"Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. 2022. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. Proceedings of the Royal Society B: Biological Sciences. 289(1968), 20211985.","mla":"Kelemen, Réka K., et al. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 289, no. 1968, The Royal Society, 2022, p. 20211985, doi:<a href=\"https://doi.org/10.1098/rspb.2021.1985\">10.1098/rspb.2021.1985</a>.","apa":"Kelemen, R. K., Elkrewi, M. N., Lindholm, A. K., &#38; Vicoso, B. (2022). Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2021.1985\">https://doi.org/10.1098/rspb.2021.1985</a>","short":"R.K. Kelemen, M.N. Elkrewi, A.K. Lindholm, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 289 (2022) 20211985.","ieee":"R. K. Kelemen, M. N. Elkrewi, A. K. Lindholm, and B. Vicoso, “Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome,” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 289, no. 1968. The Royal Society, p. 20211985, 2022."},"scopus_import":"1","project":[{"grant_number":"715257","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"external_id":{"pmid":["35135349"],"isi":["000752812800012"]},"month":"02","department":[{"_id":"BeVi"}],"isi":1,"pmid":1,"day":"09","intvolume":"       289"},{"publisher":"Elsevier","quality_controlled":"1","year":"2022","publication_status":"published","publication_identifier":{"issn":["1369-5266"]},"date_published":"2022-02-01T00:00:00Z","status":"public","oa_version":"Published Version","oa":1,"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","article_number":"102174","language":[{"iso":"eng"}],"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."}],"publication":"Current Opinion in Plant Biology","doi":"10.1016/j.pbi.2022.102174","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Auxin canalization: From speculative models toward molecular players","ddc":["580"],"file":[{"relation":"main_file","date_created":"2022-03-10T13:34:09Z","creator":"dernst","content_type":"application/pdf","access_level":"open_access","checksum":"f1ee02b6fb4200934eeb31fa69120885","file_id":"10844","file_name":"2022_CurrentOpPlantBiology_Hajny.pdf","success":1,"date_updated":"2022-03-10T13:34:09Z","file_size":820322}],"author":[{"orcid":"0000-0003-2140-7195","full_name":"Hajny, Jakub","first_name":"Jakub","last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"article_type":"original","date_updated":"2023-08-02T14:29:12Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"2","file_date_updated":"2022-03-10T13:34:09Z","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,"_id":"10768","date_created":"2022-02-20T23:01:32Z","external_id":{"pmid":["35123880"],"isi":["000758724700004"]},"citation":{"ieee":"J. Hajny, S. Tan, and J. Friml, “Auxin canalization: From speculative models toward molecular players,” <i>Current Opinion in Plant Biology</i>, vol. 65, no. 2. Elsevier, 2022.","mla":"Hajny, Jakub, et al. “Auxin Canalization: From Speculative Models toward Molecular Players.” <i>Current Opinion in Plant Biology</i>, vol. 65, no. 2, 102174, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.pbi.2022.102174\">10.1016/j.pbi.2022.102174</a>.","short":"J. Hajny, S. Tan, J. Friml, Current Opinion in Plant Biology 65 (2022).","apa":"Hajny, J., Tan, S., &#38; Friml, J. (2022). Auxin canalization: From speculative models toward molecular players. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2022.102174\">https://doi.org/10.1016/j.pbi.2022.102174</a>","ama":"Hajny J, Tan S, Friml J. Auxin canalization: From speculative models toward molecular players. <i>Current Opinion in Plant Biology</i>. 2022;65(2). doi:<a href=\"https://doi.org/10.1016/j.pbi.2022.102174\">10.1016/j.pbi.2022.102174</a>","ista":"Hajny J, Tan S, Friml J. 2022. Auxin canalization: From speculative models toward molecular players. Current Opinion in Plant Biology. 65(2), 102174.","chicago":"Hajny, Jakub, Shutang Tan, and Jiří Friml. “Auxin Canalization: From Speculative Models toward Molecular Players.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.pbi.2022.102174\">https://doi.org/10.1016/j.pbi.2022.102174</a>."},"scopus_import":"1","day":"01","intvolume":"        65","department":[{"_id":"JiFr"}],"month":"02","pmid":1,"isi":1},{"intvolume":"        32","day":"13","department":[{"_id":"MaSe"}],"month":"01","scopus_import":"1","citation":{"apa":"Daguerre, L., Torroba, G., Medina Ramos, R. A., &#38; Solís, M. (2022). Non relativistic quantum field theory: Dynamics and irreversibility. <i>Anales de la Asociacion Fisica Argentina</i>. Asociación Física Argentina. <a href=\"https://doi.org/10.31527/analesafa.2021.32.4.93\">https://doi.org/10.31527/analesafa.2021.32.4.93</a>","mla":"Daguerre, L., et al. “Non relativistic quantum field theory: Dynamics and irreversibility.” <i>Anales de la Asociacion Fisica Argentina</i>, vol. 32, no. 4, Asociación Física Argentina, 2022, pp. 93–98, doi:<a href=\"https://doi.org/10.31527/analesafa.2021.32.4.93\">10.31527/analesafa.2021.32.4.93</a>.","short":"L. Daguerre, G. Torroba, R.A. Medina Ramos, M. Solís, Anales de la Asociacion Fisica Argentina 32 (2022) 93–98.","chicago":"Daguerre, L., G. Torroba, Raimel A Medina Ramos, and M. Solís. “Non relativistic quantum field theory: Dynamics and irreversibility.” <i>Anales de la Asociacion Fisica Argentina</i>. Asociación Física Argentina, 2022. <a href=\"https://doi.org/10.31527/analesafa.2021.32.4.93\">https://doi.org/10.31527/analesafa.2021.32.4.93</a>.","ista":"Daguerre L, Torroba G, Medina Ramos RA, Solís M. 2022. Non relativistic quantum field theory: Dynamics and irreversibility. Anales de la Asociacion Fisica Argentina. 32(4), 93–98.","ama":"Daguerre L, Torroba G, Medina Ramos RA, Solís M. Non relativistic quantum field theory: Dynamics and irreversibility. <i>Anales de la Asociacion Fisica Argentina</i>. 2022;32(4):93-98. doi:<a href=\"https://doi.org/10.31527/analesafa.2021.32.4.93\">10.31527/analesafa.2021.32.4.93</a>","ieee":"L. Daguerre, G. Torroba, R. A. Medina Ramos, and M. Solís, “Non relativistic quantum field theory: Dynamics and irreversibility,” <i>Anales de la Asociacion Fisica Argentina</i>, vol. 32, no. 4. Asociación Física Argentina, pp. 93–98, 2022."},"volume":32,"acknowledgement":"Se agradece a Horacio Casini por distintas discusiones y comentarios a lo largo del trabajo. LD cuenta con el apoyo de CNEA y UNCuyo, Inst. GT cuenta con el apoyo de CONICET,\r\nANPCyT, CNEA, y UNCuyo, Inst. Balseiro. RM cuenta con el apoyo de IST Austria. MS cuenta con el apoyode CONICET y UNCuyo, Inst. Balseiro. También se agradece a la Asociación Argentina de Física por la posibilidad de presentar este artículo en el marco de una Mención Especial por el Premio Luis Másperi 2020.","issue":"4","file_date_updated":"2022-02-21T09:32:44Z","date_created":"2022-02-20T23:01:32Z","_id":"10769","author":[{"last_name":"Daguerre","first_name":"L.","full_name":"Daguerre, L."},{"first_name":"G.","last_name":"Torroba","full_name":"Torroba, G."},{"full_name":"Medina Ramos, Raimel A","first_name":"Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425","last_name":"Medina Ramos"},{"full_name":"Solís, M.","last_name":"Solís","first_name":"M."}],"article_type":"original","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2022-02-21T09:36:01Z","title":"Non relativistic quantum field theory: Dynamics and irreversibility","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"10782","date_updated":"2022-02-21T09:32:44Z","success":1,"file_name":"2022_AnalesAFA_Daguerre.pdf","file_size":4505751,"relation":"main_file","date_created":"2022-02-21T09:32:44Z","access_level":"open_access","content_type":"application/pdf","creator":"dernst","checksum":"ca66a3017205677c5b4d22b3bb74fb0b"}],"ddc":["530"],"publication":"Anales de la Asociacion Fisica Argentina","abstract":[{"lang":"eng","text":"studiamos aspectos de Teoría Cuántica de Campos a densidad finita usando técnicas y conceptos de información cuántica. Nos enfocamos en fermiones de Dirac masivos con potencial químico en 1+1 dimensiones espacio-temporales. Usando la entropía de entrelazamiento en un intervalo, construimos la función c entrópica que es finita. Esta función c no es monótona, e incorpora el entrelazamiento de largo alcance proveniente de la superficie de Fermi. Motivados por trabajos previos de modelos en la red, calculamos numéricamente las entropías de Renyi y encontramos oscilaciones de Friedel. Seguidamente, analizamos la información mutua como una medida de correlación entre diferentes regiones. Usando una expansión de distancia grande desarrollada por Cardy, argumentamos que la información mutua detecta las correlaciones inducidas por la superficie de Fermi todavía al orden dominante en la expansión. Finalmente, analizamos la entropía relativa y sus generalizaciones de Renyi para distinguir estados con diferente carga. Encontramos que estados en diferentes sectores de superselección dan origen a un comportamiento super-extensivo en la entropía relativa."}],"doi":"10.31527/analesafa.2021.32.4.93","has_accepted_license":"1","oa":1,"oa_version":"Published Version","status":"public","language":[{"iso":"spa"}],"article_processing_charge":"No","page":"93-98","quality_controlled":"1","publisher":"Asociación Física Argentina","date_published":"2022-01-13T00:00:00Z","publication_identifier":{"eissn":["18501168"]},"year":"2022","publication_status":"published"},{"status":"public","oa_version":"Preprint","oa":1,"article_processing_charge":"No","article_number":"2106629","language":[{"iso":"eng"}],"publisher":"Wiley","quality_controlled":"1","publication_status":"published","publication_identifier":{"eissn":["15214095"],"issn":["09359648"]},"year":"2022","date_published":"2022-04-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","title":"Theory of chirality induced spin selectivity: Progress and challenges","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2108.09998"}],"abstract":[{"text":"A critical overview of the theory of the chirality-induced spin selectivity (CISS) effect, that is, phenomena in which the chirality of molecular species imparts significant spin selectivity to various electron processes, is provided. Based on discussions in a recently held workshop, and further work published since, the status of CISS effects—in electron transmission, electron transport, and chemical reactions—is reviewed. For each, a detailed discussion of the state-of-the-art in theoretical understanding is provided and remaining challenges and research opportunities are identified.","lang":"eng"}],"publication":"Advanced Materials","doi":"10.1002/adma.202106629","issue":"13","volume":34,"_id":"10771","date_created":"2022-02-20T23:01:33Z","author":[{"full_name":"Evers, Ferdinand","last_name":"Evers","first_name":"Ferdinand"},{"first_name":"Amnon","last_name":"Aharony","full_name":"Aharony, Amnon"},{"full_name":"Bar-Gill, Nir","last_name":"Bar-Gill","first_name":"Nir"},{"full_name":"Entin-Wohlman, Ora","last_name":"Entin-Wohlman","first_name":"Ora"},{"last_name":"Hedegård","first_name":"Per","full_name":"Hedegård, Per"},{"full_name":"Hod, Oded","first_name":"Oded","last_name":"Hod"},{"full_name":"Jelinek, Pavel","last_name":"Jelinek","first_name":"Pavel"},{"first_name":"Grzegorz","last_name":"Kamieniarz","full_name":"Kamieniarz, Grzegorz"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail"},{"first_name":"Karen","last_name":"Michaeli","full_name":"Michaeli, Karen"},{"full_name":"Mujica, Vladimiro","last_name":"Mujica","first_name":"Vladimiro"},{"first_name":"Ron","last_name":"Naaman","full_name":"Naaman, Ron"},{"first_name":"Yossi","last_name":"Paltiel","full_name":"Paltiel, Yossi"},{"last_name":"Refaely-Abramson","first_name":"Sivan","full_name":"Refaely-Abramson, Sivan"},{"last_name":"Tal","first_name":"Oren","full_name":"Tal, Oren"},{"full_name":"Thijssen, Jos","first_name":"Jos","last_name":"Thijssen"},{"last_name":"Thoss","first_name":"Michael","full_name":"Thoss, Michael"},{"full_name":"Van Ruitenbeek, Jan M.","first_name":"Jan M.","last_name":"Van Ruitenbeek"},{"first_name":"Latha","last_name":"Venkataraman","full_name":"Venkataraman, Latha"},{"full_name":"Waldeck, David H.","first_name":"David H.","last_name":"Waldeck"},{"full_name":"Yan, Binghai","last_name":"Yan","first_name":"Binghai"},{"full_name":"Kronik, Leeor","last_name":"Kronik","first_name":"Leeor"}],"article_type":"review","date_updated":"2023-08-02T14:30:22Z","day":"01","intvolume":"        34","arxiv":1,"month":"04","department":[{"_id":"MiLe"}],"isi":1,"external_id":{"arxiv":["2108.09998"],"isi":["000753795900001"]},"citation":{"ieee":"F. Evers <i>et al.</i>, “Theory of chirality induced spin selectivity: Progress and challenges,” <i>Advanced Materials</i>, vol. 34, no. 13. Wiley, 2022.","ama":"Evers F, Aharony A, Bar-Gill N, et al. Theory of chirality induced spin selectivity: Progress and challenges. <i>Advanced Materials</i>. 2022;34(13). doi:<a href=\"https://doi.org/10.1002/adma.202106629\">10.1002/adma.202106629</a>","chicago":"Evers, Ferdinand, Amnon Aharony, Nir Bar-Gill, Ora Entin-Wohlman, Per Hedegård, Oded Hod, Pavel Jelinek, et al. “Theory of Chirality Induced Spin Selectivity: Progress and Challenges.” <i>Advanced Materials</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/adma.202106629\">https://doi.org/10.1002/adma.202106629</a>.","ista":"Evers F, Aharony A, Bar-Gill N, Entin-Wohlman O, Hedegård P, Hod O, Jelinek P, Kamieniarz G, Lemeshko M, Michaeli K, Mujica V, Naaman R, Paltiel Y, Refaely-Abramson S, Tal O, Thijssen J, Thoss M, Van Ruitenbeek JM, Venkataraman L, Waldeck DH, Yan B, Kronik L. 2022. Theory of chirality induced spin selectivity: Progress and challenges. Advanced Materials. 34(13), 2106629.","mla":"Evers, Ferdinand, et al. “Theory of Chirality Induced Spin Selectivity: Progress and Challenges.” <i>Advanced Materials</i>, vol. 34, no. 13, 2106629, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/adma.202106629\">10.1002/adma.202106629</a>.","apa":"Evers, F., Aharony, A., Bar-Gill, N., Entin-Wohlman, O., Hedegård, P., Hod, O., … Kronik, L. (2022). Theory of chirality induced spin selectivity: Progress and challenges. <i>Advanced Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adma.202106629\">https://doi.org/10.1002/adma.202106629</a>","short":"F. Evers, A. Aharony, N. Bar-Gill, O. Entin-Wohlman, P. Hedegård, O. Hod, P. Jelinek, G. Kamieniarz, M. Lemeshko, K. Michaeli, V. Mujica, R. Naaman, Y. Paltiel, S. Refaely-Abramson, O. Tal, J. Thijssen, M. Thoss, J.M. Van Ruitenbeek, L. Venkataraman, D.H. Waldeck, B. Yan, L. Kronik, Advanced Materials 34 (2022)."},"scopus_import":"1"}]