[{"publisher":"Cell Press","type":"journal_article","oa_version":"None","publication_status":"published","external_id":{"pmid":["35058104"],"isi":["000795773900009"]},"_id":"10705","issue":"5","publication_identifier":{"eissn":["1879-3088"],"issn":["0962-8924"]},"isi":1,"month":"05","year":"2022","department":[{"_id":"EdHa"},{"_id":"CaHe"}],"article_type":"original","date_updated":"2023-08-02T14:03:53Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"abstract":[{"text":"Although rigidity and jamming transitions have been widely studied in physics and material science, their importance in a number of biological processes, including embryo development, tissue homeostasis, wound healing, and disease progression, has only begun to be recognized in the past few years. The hypothesis that biological systems can undergo rigidity/jamming transitions is attractive, as it would allow these systems to change their material properties rapidly and strongly. However, whether such transitions indeed occur in biological systems, how they are being regulated, and what their physiological relevance might be, is still being debated. Here, we review theoretical and experimental advances from the past few years, focusing on the regulation and role of potential tissue rigidity transitions in different biological processes.","lang":"eng"}],"scopus_import":"1","status":"public","author":[{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566"}],"date_created":"2022-01-30T23:01:34Z","citation":{"chicago":"Hannezo, Edouard B, and Carl-Philipp J Heisenberg. “Rigidity Transitions in Development and Disease.” <i>Trends in Cell Biology</i>. Cell Press, 2022. <a href=\"https://doi.org/10.1016/j.tcb.2021.12.006\">https://doi.org/10.1016/j.tcb.2021.12.006</a>.","apa":"Hannezo, E. B., &#38; Heisenberg, C.-P. J. (2022). Rigidity transitions in development and disease. <i>Trends in Cell Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tcb.2021.12.006\">https://doi.org/10.1016/j.tcb.2021.12.006</a>","mla":"Hannezo, Edouard B., and Carl-Philipp J. Heisenberg. “Rigidity Transitions in Development and Disease.” <i>Trends in Cell Biology</i>, vol. 32, no. 5, Cell Press, 2022, pp. P433-444, doi:<a href=\"https://doi.org/10.1016/j.tcb.2021.12.006\">10.1016/j.tcb.2021.12.006</a>.","short":"E.B. Hannezo, C.-P.J. Heisenberg, Trends in Cell Biology 32 (2022) P433-444.","ieee":"E. B. Hannezo and C.-P. J. Heisenberg, “Rigidity transitions in development and disease,” <i>Trends in Cell Biology</i>, vol. 32, no. 5. Cell Press, pp. P433-444, 2022.","ista":"Hannezo EB, Heisenberg C-PJ. 2022. Rigidity transitions in development and disease. Trends in Cell Biology. 32(5), P433-444.","ama":"Hannezo EB, Heisenberg C-PJ. Rigidity transitions in development and disease. <i>Trends in Cell Biology</i>. 2022;32(5):P433-444. doi:<a href=\"https://doi.org/10.1016/j.tcb.2021.12.006\">10.1016/j.tcb.2021.12.006</a>"},"quality_controlled":"1","page":"P433-444","title":"Rigidity transitions in development and disease","publication":"Trends in Cell Biology","acknowledgement":"We thank present and former members of the Heisenberg and Hannezo groups, in particular Bernat Corominas-Murtra and Nicoletta Petridou, for helpful discussions, and Claudia Flandoli for the artwork. We apologize for not being able to cite a number of highly relevant studies, to stay within the maximum allowed number of citations.","day":"01","volume":32,"pmid":1,"intvolume":"        32","date_published":"2022-05-01T00:00:00Z","doi":"10.1016/j.tcb.2021.12.006","article_processing_charge":"No"},{"publisher":"Springer Nature","type":"journal_article","oa_version":"Preprint","_id":"10706","publication_status":"published","external_id":{"arxiv":["2110.10750"]},"publication_identifier":{"issn":["2199-6792"],"eissn":["2199-6806"]},"month":"10","year":"2022","department":[{"_id":"VaKa"}],"article_type":"original","date_updated":"2023-02-27T07:34:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"abstract":[{"text":"This is a collection of problems composed by some participants of the workshop “Differential Geometry, Billiards, and Geometric Optics” that took place at CIRM on October 4–8, 2021.","lang":"eng"}],"related_material":{"link":[{"relation":"earlier_version","url":"https://conferences.cirm-math.fr/2383.html"}]},"main_file_link":[{"url":"https://arxiv.org/abs/2110.10750","open_access":"1"}],"scopus_import":"1","author":[{"first_name":"Misha","last_name":"Bialy","full_name":"Bialy, Misha"},{"full_name":"Fiorebe, Corentin","last_name":"Fiorebe","first_name":"Corentin","id":"06619f18-9070-11eb-847d-d1ee780bd88b"},{"full_name":"Glutsyuk, Alexey","last_name":"Glutsyuk","first_name":"Alexey"},{"last_name":"Levi","full_name":"Levi, Mark","first_name":"Mark"},{"first_name":"Alexander","full_name":"Plakhov, Alexander","last_name":"Plakhov"},{"full_name":"Tabachnikov, Serge","last_name":"Tabachnikov","first_name":"Serge"}],"status":"public","oa":1,"date_created":"2022-01-30T23:01:34Z","citation":{"short":"M. Bialy, C. Fiorebe, A. Glutsyuk, M. Levi, A. Plakhov, S. Tabachnikov, Arnold Mathematical Journal 8 (2022) 411–422.","ieee":"M. Bialy, C. Fiorebe, A. Glutsyuk, M. Levi, A. Plakhov, and S. Tabachnikov, “Open problems on billiards and geometric optics,” <i>Arnold Mathematical Journal</i>, vol. 8. Springer Nature, pp. 411–422, 2022.","ista":"Bialy M, Fiorebe C, Glutsyuk A, Levi M, Plakhov A, Tabachnikov S. 2022. Open problems on billiards and geometric optics. Arnold Mathematical Journal. 8, 411–422.","ama":"Bialy M, Fiorebe C, Glutsyuk A, Levi M, Plakhov A, Tabachnikov S. Open problems on billiards and geometric optics. <i>Arnold Mathematical Journal</i>. 2022;8:411-422. doi:<a href=\"https://doi.org/10.1007/s40598-022-00198-y\">10.1007/s40598-022-00198-y</a>","chicago":"Bialy, Misha, Corentin Fiorebe, Alexey Glutsyuk, Mark Levi, Alexander Plakhov, and Serge Tabachnikov. “Open Problems on Billiards and Geometric Optics.” <i>Arnold Mathematical Journal</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s40598-022-00198-y\">https://doi.org/10.1007/s40598-022-00198-y</a>.","apa":"Bialy, M., Fiorebe, C., Glutsyuk, A., Levi, M., Plakhov, A., &#38; Tabachnikov, S. (2022). Open problems on billiards and geometric optics. <i>Arnold Mathematical Journal</i>. Hybrid: Springer Nature. <a href=\"https://doi.org/10.1007/s40598-022-00198-y\">https://doi.org/10.1007/s40598-022-00198-y</a>","mla":"Bialy, Misha, et al. “Open Problems on Billiards and Geometric Optics.” <i>Arnold Mathematical Journal</i>, vol. 8, Springer Nature, 2022, pp. 411–22, doi:<a href=\"https://doi.org/10.1007/s40598-022-00198-y\">10.1007/s40598-022-00198-y</a>."},"conference":{"name":"CIRM: Centre International de Rencontres Mathématiques","start_date":"2021-10-04","end_date":"2021-10-08","location":"Hybrid"},"quality_controlled":"1","arxiv":1,"page":"411-422","title":"Open problems on billiards and geometric optics","volume":8,"day":"01","publication":"Arnold Mathematical Journal","intvolume":"         8","date_published":"2022-10-01T00:00:00Z","doi":"10.1007/s40598-022-00198-y","article_processing_charge":"No"},{"quality_controlled":"1","acknowledged_ssus":[{"_id":"Bio"}],"citation":{"mla":"Roblek, Marko, et al. “The Solute Carrier MFSD1 Decreases Β1 Integrin’s Activation Status and Thus Tumor Metastasis.” <i>Frontiers in Oncology</i>, vol. 12, 777634, Frontiers, 2022, doi:<a href=\"https://doi.org/10.3389/fonc.2022.777634\">10.3389/fonc.2022.777634</a>.","apa":"Roblek, M., Bicher, J., van Gogh, M., György, A., Seeböck, R., Szulc, B., … Siekhaus, D. E. (2022). The solute carrier MFSD1 decreases β1 integrin’s activation status and thus tumor metastasis. <i>Frontiers in Oncology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fonc.2022.777634\">https://doi.org/10.3389/fonc.2022.777634</a>","chicago":"Roblek, Marko, Julia Bicher, Merel van Gogh, Attila György, Rita Seeböck, Bozena Szulc, Markus Damme, Mariusz Olczak, Lubor Borsig, and Daria E Siekhaus. “The Solute Carrier MFSD1 Decreases Β1 Integrin’s Activation Status and Thus Tumor Metastasis.” <i>Frontiers in Oncology</i>. Frontiers, 2022. <a href=\"https://doi.org/10.3389/fonc.2022.777634\">https://doi.org/10.3389/fonc.2022.777634</a>.","ama":"Roblek M, Bicher J, van Gogh M, et al. The solute carrier MFSD1 decreases β1 integrin’s activation status and thus tumor metastasis. <i>Frontiers in Oncology</i>. 2022;12. doi:<a href=\"https://doi.org/10.3389/fonc.2022.777634\">10.3389/fonc.2022.777634</a>","ieee":"M. Roblek <i>et al.</i>, “The solute carrier MFSD1 decreases β1 integrin’s activation status and thus tumor metastasis,” <i>Frontiers in Oncology</i>, vol. 12. Frontiers, 2022.","short":"M. Roblek, J. Bicher, M. van Gogh, A. György, R. Seeböck, B. Szulc, M. Damme, M. Olczak, L. Borsig, D.E. Siekhaus, Frontiers in Oncology 12 (2022).","ista":"Roblek M, Bicher J, van Gogh M, György A, Seeböck R, Szulc B, Damme M, Olczak M, Borsig L, Siekhaus DE. 2022. The solute carrier MFSD1 decreases β1 integrin’s activation status and thus tumor metastasis. Frontiers in Oncology. 12, 777634."},"date_created":"2022-02-01T10:33:50Z","oa":1,"article_number":"777634","title":"The solute carrier MFSD1 decreases β1 integrin’s activation status and thus tumor metastasis","date_published":"2022-02-08T00:00:00Z","has_accepted_license":"1","intvolume":"        12","acknowledgement":"We thank M. Sixt, A. Leithner, and J. Alanko for helpful advice and the BioImaging Facility at IST Austria for technical support and assistance. We thank the Siekhaus Lab for the careful review of the manuscript and their input. MR and DS were funded by the NO Forschungs- und Bildungsges.m.b.H. (LS16-021) and IST core funding. MD was funded by Deutsche Forschungsgemeinschaft (DA 1785-1).","publication":"Frontiers in Oncology","day":"08","volume":12,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","file_date_updated":"2022-02-08T13:26:40Z","doi":"10.3389/fonc.2022.777634","external_id":{"isi":["000760618800001"]},"publication_status":"published","_id":"10712","type":"journal_article","file":[{"file_name":"2022_FrontiersOncol_Roblek.pdf","relation":"main_file","file_id":"10751","creator":"cchlebak","date_updated":"2022-02-08T13:26:40Z","access_level":"open_access","content_type":"application/pdf","date_created":"2022-02-08T13:26:40Z","checksum":"63dfecf30c5bbf9408b3512bd603f78c","success":1,"file_size":6303227}],"ddc":["570"],"oa_version":"Published Version","publisher":"Frontiers","article_type":"original","department":[{"_id":"DaSi"}],"project":[{"_id":"2637E9C0-B435-11E9-9278-68D0E5697425","name":"Investigating the role of the novel major superfamily facilitator transporter family member MFSD1 in metastasis","grant_number":"LSC16-021 "}],"year":"2022","month":"02","publication_identifier":{"issn":["2234-943X"]},"isi":1,"scopus_import":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/suppressing-the-spread-of-tumors/","relation":"confirmation","description":"News on IST Homepage"}]},"abstract":[{"text":"Solute carriers are increasingly recognized as participating in a plethora of pathologies, including cancer. We describe here the involvement of the orphan solute carrier MFSD1 in the regulation of tumor cell migration. Loss of MFSD1 enabled higher levels of metastasis in a mouse model. We identified an increased migratory potential in MFSD1-/- tumor cells which was mediated by increased focal adhesion turn-over, reduced stability of mature inactive β1 integrin, and the resulting increased integrin activation index. We show that MFSD1 promoted recycling to the cell surface of endocytosed inactive β1 integrin and thereby protected β1 integrin from proteolytic degradation; this led to dampening of the integrin activation index. Furthermore, down-regulation of MFSD1 expression was observed during early steps of tumorigenesis and higher MFSD1 expression levels correlate with a better cancer patient prognosis. In sum, we describe a requirement for endolysosomal MFSD1 in efficient β1 integrin recycling to suppress tumor spread.","lang":"eng"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-02T14:05:44Z","status":"public","author":[{"id":"3047D808-F248-11E8-B48F-1D18A9856A87","first_name":"Marko","full_name":"Roblek, Marko","last_name":"Roblek","orcid":"0000-0001-9588-1389"},{"last_name":"Bicher","full_name":"Bicher, Julia","first_name":"Julia","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"van Gogh","full_name":"van Gogh, Merel","first_name":"Merel"},{"last_name":"György","full_name":"György, Attila","orcid":"0000-0002-1819-198X","first_name":"Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rita","full_name":"Seeböck, Rita","last_name":"Seeböck"},{"last_name":"Szulc","full_name":"Szulc, Bozena","first_name":"Bozena"},{"first_name":"Markus","full_name":"Damme, Markus","last_name":"Damme"},{"first_name":"Mariusz","full_name":"Olczak, Mariusz","last_name":"Olczak"},{"first_name":"Lubor","full_name":"Borsig, Lubor","last_name":"Borsig"},{"orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"}]},{"acknowledged_ssus":[{"_id":"Bio"}],"citation":{"short":"M. Akhmanova, S. Emtenani, D. Krueger, A. György, M. Pereira Guarda, M. Vlasov, F. Vlasov, A. Akopian, A. Ratheesh, S. De Renzis, D.E. Siekhaus, Science 376 (2022) 394–396.","ieee":"M. Akhmanova <i>et al.</i>, “Cell division in tissues enables macrophage infiltration,” <i>Science</i>, vol. 376, no. 6591. American Association for the Advancement of Science, pp. 394–396, 2022.","ista":"Akhmanova M, Emtenani S, Krueger D, György A, Pereira Guarda M, Vlasov M, Vlasov F, Akopian A, Ratheesh A, De Renzis S, Siekhaus DE. 2022. Cell division in tissues enables macrophage infiltration. Science. 376(6591), 394–396.","ama":"Akhmanova M, Emtenani S, Krueger D, et al. Cell division in tissues enables macrophage infiltration. <i>Science</i>. 2022;376(6591):394-396. doi:<a href=\"https://doi.org/10.1126/science.abj0425\">10.1126/science.abj0425</a>","chicago":"Akhmanova, Maria, Shamsi Emtenani, Daniel Krueger, Attila György, Mariana Pereira Guarda, Mikhail Vlasov, Fedor Vlasov, et al. “Cell Division in Tissues Enables Macrophage Infiltration.” <i>Science</i>. American Association for the Advancement of Science, 2022. <a href=\"https://doi.org/10.1126/science.abj0425\">https://doi.org/10.1126/science.abj0425</a>.","apa":"Akhmanova, M., Emtenani, S., Krueger, D., György, A., Pereira Guarda, M., Vlasov, M., … Siekhaus, D. E. (2022). Cell division in tissues enables macrophage infiltration. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.abj0425\">https://doi.org/10.1126/science.abj0425</a>","mla":"Akhmanova, Maria, et al. “Cell Division in Tissues Enables Macrophage Infiltration.” <i>Science</i>, vol. 376, no. 6591, American Association for the Advancement of Science, 2022, pp. 394–96, doi:<a href=\"https://doi.org/10.1126/science.abj0425\">10.1126/science.abj0425</a>."},"date_created":"2022-02-01T11:23:18Z","quality_controlled":"1","oa":1,"title":"Cell division in tissues enables macrophage infiltration","page":"394-396","intvolume":"       376","date_published":"2022-04-22T00:00:00Z","publication":"Science","day":"22","acknowledgement":"We thank J. Friml, C. Guet, T. Hurd, M. Fendrych and members of the laboratory for comments on the manuscript; the Bioimaging Facility of IST Austria for excellent support and T. Lecuit, E. Hafen, R. Levayer and A. Martin for fly strains. This work was supported by a grant from the Austrian Science Fund FWF: Lise Meitner Fellowship M2379-B28 to M.A and D.S., and internal funding from IST Austria to D.S. and EMBL to S.D.R.","volume":376,"pmid":1,"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"article_processing_charge":"No","doi":"10.1126/science.abj0425","type":"journal_article","oa_version":"Preprint","publication_status":"published","external_id":{"isi":["000788553700039"],"pmid":["35446632"]},"issue":"6591","_id":"10713","publisher":"American Association for the Advancement of Science","department":[{"_id":"DaSi"}],"article_type":"original","publication_identifier":{"issn":["0036-8075"]},"isi":1,"project":[{"grant_number":"M02379","_id":"264CBBAC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modeling epithelial tissue mechanics during cell invasion"}],"year":"2022","month":"04","main_file_link":[{"url":"https://doi.org/10.1101/2021.04.19.438995","open_access":"1"}],"abstract":[{"lang":"eng","text":"Cells migrate through crowded microenvironments within tissues during normal development, immune response, and cancer metastasis. Although migration through pores and tracks in the extracellular matrix (ECM) has been well studied, little is known about cellular traversal into confining cell-dense tissues. We find that embryonic tissue invasion by Drosophila macrophages requires division of an epithelial ectodermal cell at the site of entry. Dividing ectodermal cells disassemble ECM attachment formed by integrin-mediated focal adhesions next to mesodermal cells, allowing macrophages to move their nuclei ahead and invade between two immediately adjacent tissues. Invasion efficiency depends on division frequency, but reduction of adhesion strength allows macrophage entry independently of division. This work demonstrates that tissue dynamics can regulate cellular infiltration."}],"date_updated":"2023-08-02T14:06:15Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","author":[{"id":"3425EC26-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Akhmanova","full_name":"Akhmanova, Maria","orcid":"0000-0003-1522-3162"},{"last_name":"Emtenani","full_name":"Emtenani, Shamsi","orcid":"0000-0001-6981-6938","first_name":"Shamsi","id":"49D32318-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Krueger","full_name":"Krueger, Daniel","first_name":"Daniel"},{"last_name":"György","full_name":"György, Attila","orcid":"0000-0002-1819-198X","first_name":"Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pereira Guarda, Mariana","last_name":"Pereira Guarda","id":"6de81d9d-e2f2-11eb-945a-af8bc2a60b26","first_name":"Mariana"},{"first_name":"Mikhail","full_name":"Vlasov, Mikhail","last_name":"Vlasov"},{"first_name":"Fedor","last_name":"Vlasov","full_name":"Vlasov, Fedor"},{"first_name":"Andrei","last_name":"Akopian","full_name":"Akopian, Andrei"},{"full_name":"Ratheesh, Aparna","last_name":"Ratheesh","first_name":"Aparna","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"De Renzis, Stefano","last_name":"De Renzis","first_name":"Stefano"},{"orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/"},{"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"ec_funded":1,"article_processing_charge":"No","doi":"10.1016/j.devcel.2022.03.005","date_published":"2022-04-11T00:00:00Z","intvolume":"        57","day":"11","acknowledgement":"We are grateful to all members of the Rangan and Fuchs labs for their discussion and comments on the manuscript. We also thanks Dr. Sammons, Dr. Marlow, Life Science Editors, for their thoughts and comments the manuscript Additionally, we thank the Bloomington Stock Center, the Vienna Drosophila Resource Center, the BDGP Gene Disruption Project, and Flybase for fly stocks, reagents, and other resources. P.R. is funded by the NIH/NIGMS (R01GM111779-06 and RO1GM135628-01), G.F. is funded by NSF MCB-2047629 and NIH RO3 AI144839, D.E.S. was funded by Marie Curie CIG 334077/IRTIM and the Austrian Science Fund (FWF) grant ASI_FWF01_P29638S, and A.B is funded by NIH R01GM116889 and American Cancer Society RSG-17-197-01-RMC.","publication":"Developmental Cell","volume":57,"title":"A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis","page":"883-900.e10","quality_controlled":"1","date_created":"2022-02-01T13:15:05Z","citation":{"chicago":"Martin, Elliot T., Patrick Blatt, Elaine Ngyuen, Roni Lahr, Sangeetha Selvam, Hyun Ah M. Yoon, Tyler Pocchiari, et al. “A Translation Control Module Coordinates Germline Stem Cell Differentiation with Ribosome Biogenesis during Drosophila Oogenesis.” <i>Developmental Cell</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.devcel.2022.03.005\">https://doi.org/10.1016/j.devcel.2022.03.005</a>.","apa":"Martin, E. T., Blatt, P., Ngyuen, E., Lahr, R., Selvam, S., Yoon, H. A. M., … Rangan, P. (2022). A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2022.03.005\">https://doi.org/10.1016/j.devcel.2022.03.005</a>","mla":"Martin, Elliot T., et al. “A Translation Control Module Coordinates Germline Stem Cell Differentiation with Ribosome Biogenesis during Drosophila Oogenesis.” <i>Developmental Cell</i>, vol. 57, no. 7, Elsevier, 2022, p. 883–900.e10, doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.03.005\">10.1016/j.devcel.2022.03.005</a>.","ista":"Martin ET, Blatt P, Ngyuen E, Lahr R, Selvam S, Yoon HAM, Pocchiari T, Emtenani S, Siekhaus DE, Berman A, Fuchs G, Rangan P. 2022. A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis. Developmental Cell. 57(7), 883–900.e10.","short":"E.T. Martin, P. Blatt, E. Ngyuen, R. Lahr, S. Selvam, H.A.M. Yoon, T. Pocchiari, S. Emtenani, D.E. Siekhaus, A. Berman, G. Fuchs, P. Rangan, Developmental Cell 57 (2022) 883–900.e10.","ieee":"E. T. Martin <i>et al.</i>, “A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis,” <i>Developmental Cell</i>, vol. 57, no. 7. Elsevier, p. 883–900.e10, 2022.","ama":"Martin ET, Blatt P, Ngyuen E, et al. A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis. <i>Developmental Cell</i>. 2022;57(7):883-900.e10. doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.03.005\">10.1016/j.devcel.2022.03.005</a>"},"oa":1,"status":"public","author":[{"last_name":"Martin","full_name":"Martin, Elliot T.","first_name":"Elliot T."},{"last_name":"Blatt","full_name":"Blatt, Patrick","first_name":"Patrick"},{"last_name":"Ngyuen","full_name":"Ngyuen, Elaine","first_name":"Elaine"},{"first_name":"Roni","full_name":"Lahr, Roni","last_name":"Lahr"},{"first_name":"Sangeetha","last_name":"Selvam","full_name":"Selvam, Sangeetha"},{"last_name":"Yoon","full_name":"Yoon, Hyun Ah M.","first_name":"Hyun Ah M."},{"first_name":"Tyler","last_name":"Pocchiari","full_name":"Pocchiari, Tyler"},{"orcid":"0000-0001-6981-6938","full_name":"Emtenani, Shamsi","last_name":"Emtenani","id":"49D32318-F248-11E8-B48F-1D18A9856A87","first_name":"Shamsi"},{"orcid":"0000-0001-8323-8353","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"},{"first_name":"Andrea","last_name":"Berman","full_name":"Berman, Andrea"},{"full_name":"Fuchs, Gabriele","last_name":"Fuchs","first_name":"Gabriele"},{"full_name":"Rangan, Prashanth","last_name":"Rangan","first_name":"Prashanth"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1101/2021.04.04.438367","open_access":"1"}],"abstract":[{"text":"Ribosomal defects perturb stem cell differentiation, causing diseases called ribosomopathies. How ribosome levels control stem cell differentiation is not fully known. Here, we discovered three RNA helicases are required for ribosome biogenesis and for Drosophila oogenesis. Loss of these helicases, which we named Aramis, Athos and Porthos, lead to aberrant stabilization of p53, cell cycle arrest and stalled GSC differentiation. Unexpectedly, Aramis is required for efficient translation of a cohort of mRNAs containing a 5’-Terminal-Oligo-Pyrimidine (TOP)-motif, including mRNAs that encode ribosomal proteins and a conserved p53 inhibitor, Novel Nucleolar protein 1 (Non1). The TOP-motif co-regulates the translation of growth-related mRNAs in mammals. As in mammals, the La-related protein co-regulates the translation of TOP-motif containing RNAs during Drosophila oogenesis. Thus, a previously unappreciated TOP-motif in Drosophila responds to reduced ribosome biogenesis to co-regulate the translation of ribosomal proteins and a p53 repressor, thus coupling ribosome biogenesis to GSC differentiation.","lang":"eng"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-02T14:07:13Z","article_type":"original","department":[{"_id":"DaSi"}],"project":[{"call_identifier":"FP7","name":"Investigating the role of transporters in invasive migration through junctions","_id":"2536F660-B435-11E9-9278-68D0E5697425","grant_number":"334077"},{"call_identifier":"FWF","name":"Drosophila TNFa´s Funktion in Immunzellen","_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638"}],"year":"2022","month":"04","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"isi":1,"external_id":{"isi":["000789021800005"]},"publication_status":"published","issue":"7","_id":"10714","type":"journal_article","oa_version":"Preprint","publisher":"Elsevier"},{"project":[{"grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"year":"2022","month":"04","publication_identifier":{"eissn":["1460-2431"],"issn":["0022-0957"]},"isi":1,"article_type":"original","department":[{"_id":"JiFr"}],"publisher":"Oxford Academic","external_id":{"isi":["000764220900001"],"pmid":["35085386"]},"publication_status":"published","_id":"10717","issue":"8","type":"journal_article","oa_version":"Submitted Version","status":"public","author":[{"first_name":"R","last_name":"Wang","full_name":"Wang, R"},{"first_name":"E","last_name":"Himschoot","full_name":"Himschoot, E"},{"full_name":"Grenzi, M","last_name":"Grenzi","first_name":"M"},{"last_name":"Chen","full_name":"Chen, J","first_name":"J"},{"last_name":"Safi","full_name":"Safi, A","first_name":"A"},{"first_name":"M","last_name":"Krebs","full_name":"Krebs, M"},{"first_name":"K","last_name":"Schumacher","full_name":"Schumacher, K"},{"last_name":"Nowack","full_name":"Nowack, MK","first_name":"MK"},{"first_name":"W","last_name":"Moeder","full_name":"Moeder, W"},{"last_name":"Yoshioka","full_name":"Yoshioka, K","first_name":"K"},{"full_name":"Van Damme, D","last_name":"Van Damme","first_name":"D"},{"first_name":"I","last_name":"De Smet","full_name":"De Smet, I"},{"full_name":"Geelen, D","last_name":"Geelen","first_name":"D"},{"last_name":"Beeckman","full_name":"Beeckman, T","first_name":"T"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Costa, A","last_name":"Costa","first_name":"A"},{"first_name":"S","full_name":"Vanneste, S","last_name":"Vanneste"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-02T14:07:58Z","scopus_import":"1","main_file_link":[{"url":"https://biblio.ugent.be/publication/8738721","open_access":"1"}],"abstract":[{"text":"Much of what we know about the role of auxin in plant development derives from exogenous manipulations of auxin distribution and signaling, using inhibitors, auxins and auxin analogs. In this context, synthetic auxin analogs, such as 1-Naphtalene Acetic Acid (1-NAA), are often favored over the endogenous auxin indole-3-acetic acid (IAA), in part due to their higher stability. While such auxin analogs have proven to be instrumental to reveal the various faces of auxin, they display in some cases distinct bioactivities compared to IAA. Here, we focused on the effect of auxin analogs on the accumulation of PIN proteins in Brefeldin A-sensitive endosomal aggregations (BFA bodies), and the correlation with the ability to elicit Ca 2+ responses. For a set of commonly used auxin analogs, we evaluated if auxin-analog induced Ca 2+ signaling inhibits PIN accumulation. Not all auxin analogs elicited a Ca 2+ response, and their differential ability to elicit Ca 2+ responses correlated partially with their ability to inhibit BFA-body formation. However, in tir1/afb and cngc14, 1-NAA-induced Ca 2+ signaling was strongly impaired, yet 1-NAA still could inhibit PIN accumulation in BFA bodies. This demonstrates that TIR1/AFB-CNGC14-dependent Ca 2+ signaling does not inhibit BFA body formation in Arabidopsis roots.","lang":"eng"}],"title":"Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots","oa":1,"article_number":"erac019","quality_controlled":"1","date_created":"2022-02-03T09:19:01Z","citation":{"ista":"Wang R, Himschoot E, Grenzi M, Chen J, Safi A, Krebs M, Schumacher K, Nowack M, Moeder W, Yoshioka K, Van Damme D, De Smet I, Geelen D, Beeckman T, Friml J, Costa A, Vanneste S. 2022. Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots. Journal of Experimental Botany. 73(8), erac019.","ieee":"R. Wang <i>et al.</i>, “Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots,” <i>Journal of Experimental Botany</i>, vol. 73, no. 8. Oxford Academic, 2022.","short":"R. Wang, E. Himschoot, M. Grenzi, J. Chen, A. Safi, M. Krebs, K. Schumacher, M. Nowack, W. Moeder, K. Yoshioka, D. Van Damme, I. De Smet, D. Geelen, T. Beeckman, J. Friml, A. Costa, S. Vanneste, Journal of Experimental Botany 73 (2022).","ama":"Wang R, Himschoot E, Grenzi M, et al. Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots. <i>Journal of Experimental Botany</i>. 2022;73(8). doi:<a href=\"https://doi.org/10.1093/jxb/erac019\">10.1093/jxb/erac019</a>","chicago":"Wang, R, E Himschoot, M Grenzi, J Chen, A Safi, M Krebs, K Schumacher, et al. “Auxin Analog-Induced Ca2+ Signaling Is Independent of Inhibition of Endosomal Aggregation in Arabidopsis Roots.” <i>Journal of Experimental Botany</i>. Oxford Academic, 2022. <a href=\"https://doi.org/10.1093/jxb/erac019\">https://doi.org/10.1093/jxb/erac019</a>.","apa":"Wang, R., Himschoot, E., Grenzi, M., Chen, J., Safi, A., Krebs, M., … Vanneste, S. (2022). Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots. <i>Journal of Experimental Botany</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/jxb/erac019\">https://doi.org/10.1093/jxb/erac019</a>","mla":"Wang, R., et al. “Auxin Analog-Induced Ca2+ Signaling Is Independent of Inhibition of Endosomal Aggregation in Arabidopsis Roots.” <i>Journal of Experimental Botany</i>, vol. 73, no. 8, erac019, Oxford Academic, 2022, doi:<a href=\"https://doi.org/10.1093/jxb/erac019\">10.1093/jxb/erac019</a>."},"doi":"10.1093/jxb/erac019","article_processing_charge":"No","ec_funded":1,"pmid":1,"publication":"Journal of Experimental Botany","acknowledgement":"We thank Joerg Kudla (WWU Munster, Germany), Petra Dietrich (F.A. University of Erlangen-Nurnberg, Germany) for sharing published materials, and NASC for providing seeds. We thank Veronique Storme for help with the statistical analyses. Part of the imaging analysis was carried out at NOLIMITS, an advanced imaging facility established by the University of Milan.\r\nThis work was supported by grants of the China Scholarship Council (CSC) to RW and JC; Fonds Wetenschappelijk Onderzoek (FWO) to TB and (G002220N) SV; the special research fund of Ghent University to EH; the Deutsche Forschungsgemeinschaft (DFG) through Grants within FOR964 (MK and KS); Piano di Sviluppo di Ateneo 2019 (University of Milan) to AC; the European Research Council (ERC) T-Rex project 682436 to DVD; the ERC ETAP project 742985 to JF, and by a PhD fellowship from the University of Milan to MG.","day":"18","volume":73,"date_published":"2022-04-18T00:00:00Z","intvolume":"        73"},{"citation":{"ama":"Yu Z, Zhang F, Friml J, Ding Z. Auxin signaling: Research advances over the past 30 years. <i>Journal of Integrative Plant Biology</i>. 2022;64(2):371-392. doi:<a href=\"https://doi.org/10.1111/jipb.13225\">10.1111/jipb.13225</a>","short":"Z. Yu, F. Zhang, J. Friml, Z. Ding, Journal of Integrative Plant Biology 64 (2022) 371–392.","ieee":"Z. Yu, F. Zhang, J. Friml, and Z. Ding, “Auxin signaling: Research advances over the past 30 years,” <i>Journal of Integrative Plant Biology</i>, vol. 64, no. 2. Wiley, pp. 371–392, 2022.","ista":"Yu Z, Zhang F, Friml J, Ding Z. 2022. Auxin signaling: Research advances over the past 30 years. Journal of Integrative Plant Biology. 64(2), 371–392.","apa":"Yu, Z., Zhang, F., Friml, J., &#38; Ding, Z. (2022). Auxin signaling: Research advances over the past 30 years. <i>Journal of Integrative Plant Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jipb.13225\">https://doi.org/10.1111/jipb.13225</a>","chicago":"Yu, Z, F Zhang, Jiří Friml, and Z Ding. “Auxin Signaling: Research Advances over the Past 30 Years.” <i>Journal of Integrative Plant Biology</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/jipb.13225\">https://doi.org/10.1111/jipb.13225</a>.","mla":"Yu, Z., et al. “Auxin Signaling: Research Advances over the Past 30 Years.” <i>Journal of Integrative Plant Biology</i>, vol. 64, no. 2, Wiley, 2022, pp. 371–92, doi:<a href=\"https://doi.org/10.1111/jipb.13225\">10.1111/jipb.13225</a>."},"date_created":"2022-02-03T09:52:59Z","quality_controlled":"1","oa":1,"title":"Auxin signaling: Research advances over the past 30 years","page":"371-392","intvolume":"        64","date_published":"2022-02-01T00:00:00Z","acknowledgement":"This research was financially supported by the National Natural Science Foundation of China and the Israel Science Foundation (NSFC-ISF; 32061143005), National Natural Science Foundation of China (32000225), Natural Science Foundation of Shandong Province (ZR2020QC036), and China Postdoctoral Science Foundation (2020M682165).\r\n","publication":"Journal of Integrative Plant Biology","day":"01","volume":64,"pmid":1,"article_processing_charge":"No","doi":"10.1111/jipb.13225","oa_version":"Published Version","type":"journal_article","external_id":{"pmid":["35018726"],"isi":["000761281200011"]},"publication_status":"published","_id":"10719","issue":"2","publisher":"Wiley","department":[{"_id":"JiFr"}],"article_type":"review","publication_identifier":{"eissn":["1744-7909"],"issn":["1672-9072"]},"isi":1,"month":"02","year":"2022","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jipb.13225"}],"abstract":[{"lang":"eng","text":"Auxin, one of the first identified and most widely studied phytohormones, has been and will remain a hot topic in plant biology. After more than a century of passionate exploration, the mysteries of its synthesis, transport, signaling, and metabolism have largely been unlocked. Due to the rapid development of new technologies, new methods, and new genetic materials, the study of auxin has entered the fast lane over the past 30 years. Here, we highlight advances in understanding auxin signaling, including auxin perception, rapid auxin responses, TRANSPORT INHIBITOR RESPONSE 1 and AUXIN SIGNALING F-boxes (TIR1/AFBs)-mediated transcriptional and non-transcriptional branches, and the epigenetic regulation of auxin signaling. We also focus on feedback inhibition mechanisms that prevent the over-amplification of auxin signals. In addition, we cover the TRANSMEMBRANE KINASEs (TMKs)-mediated non-canonical signaling, which converges with TIR1/AFBs-mediated transcriptional regulation to coordinate plant growth and development. The identification of additional auxin signaling components and their regulation will continue to open new avenues of research in this field, leading to an increasingly deeper, more comprehensive understanding of how auxin signals are interpreted at the cellular level to regulate plant growth and development."}],"scopus_import":"1","date_updated":"2023-08-02T14:08:30Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","author":[{"full_name":"Yu, Z","last_name":"Yu","first_name":"Z"},{"first_name":"F","last_name":"Zhang","full_name":"Zhang, F"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"Z","last_name":"Ding","full_name":"Ding, Z"}]},{"_id":"10727","publication_status":"published","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","type":"dissertation","file":[{"date_updated":"2023-02-03T23:30:03Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_created":"2022-02-04T15:36:12Z","checksum":"47ba18bb270dd6cc266e0a3f7c69d0e4","file_size":6757886,"file_name":"Thesis_Sina_Metzler.docx","relation":"source_file","file_id":"10728","creator":"smetzler"},{"content_type":"application/pdf","embargo":"2023-02-02","access_level":"open_access","date_updated":"2023-02-03T23:30:03Z","checksum":"f3ec07d5d6b20ae6e46bfeedebce9027","file_size":6314921,"date_created":"2022-02-04T15:36:43Z","file_name":"Thesis_Sina_Metzler_A2.pdf","creator":"smetzler","file_id":"10730","relation":"main_file"},{"file_size":6882557,"checksum":"dedd14b7be7a75d63018dbfc68dd8113","date_created":"2022-02-07T10:35:02Z","content_type":"application/pdf","embargo":"2023-02-02","access_level":"open_access","date_updated":"2023-02-04T23:30:03Z","creator":"smetzler","file_id":"10742","relation":"main_file","file_name":"Thesis_Sina_Metzler_print.pdf"}],"ddc":["570"],"supervisor":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","full_name":"Cremer, Sylvia"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"month":"02","year":"2022","project":[{"grant_number":"771402","name":"Epidemics in ant societies on a chip","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["2663-337X"]},"abstract":[{"text":"Social insects are a common model to study disease dynamics in social animals. Even though pathogens should thrive in social insect colonies as the hosts engage in frequent social interactions, are closely related and live in a pathogen-rich environment, disease outbreaks are rare. This is because social insects have evolved mechanisms to keep pathogens at bay – and fight disease as a collective. Social insect colonies are often viewed as “superorganisms” with division of labor between reproductive “germ-like” queens and males and “somatic” workers, which together form an interdependent reproductive unit that parallels a multicellular body. Superorganisms possess a “social immune system” that comprises of collective disease defenses performed by the workers - summarized as “social immunity”. In social groups immunization (reduced susceptibility to a parasite upon secondary exposure to the same parasite) can e.g. be triggered by social interactions (“social immunization”). Social immunization can be caused by (i) asymptomatic low-level infections that are acquired during caregiving to a contagious individual that can give an immune boost, which can induce protection upon later encounter with the same pathogen (active immunization) or (ii) by transfer of immune effectors between individuals (passive immunization).\r\nIn the second chapter, I built up on a study that I co-authored that found that low-level infections can not only be protective, but also be costly and make the host more susceptible to detrimental superinfections after contact to a very dissimilar pathogen. I here now tested different degrees of phylogenetically-distant fungal strains of M. brunneum and M. robertsii in L. neglectus and can describe the occurrence of cross-protection of social immunization if the first and second pathogen are from the same level. Interestingly, low-level infections only provided protection when the first strain was less virulent than the second strain and elicited higher immune gene expression.\r\nIn the third and fourth chapters, I expanded on the role of social immunity in sexual selection, a so far unstudied field. I used the fungus Metarhizium robertsii and the ant Cardiocondyla obscurior as a model, as in this species mating occurs in the presence of workers and can be studied under laboratory conditions. Before males mate with virgin queens in the nest they engage in fierce combat over the access to their mating partners.\r\nFirst, I focused on male-male competition in the third chapter and found that fighting with a contagious male is costly as it can lead to contamination of the rival, but that workers can decrease the risk of disease contraction by performing sanitary care.\r\nIn the fourth chapter, I studied the effect of fungal infection on survival and mating success of sexuals (freshly emerged queens and males) and found that worker-performed sanitary care can buffer the negative effect that a pathogenic contagion would have on sexuals by spore removal from the exposed individuals. When social immunity was prevented and queens could contract spores from their mating partner, very low dosages led to negative consequences: their lifespan was reduced and they produced fewer offspring with poor immunocompetence compared to healthy queens. Interestingly, cohabitation with a late-stage infected male where no spore transfer was possible had a positive effect on offspring immunity – male offspring of mothers that apparently perceived an infected partner in their vicinity reacted more sensitively to fungal challenge than male offspring without paternal pathogen history.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"date_updated":"2023-09-07T13:43:23Z","author":[{"full_name":"Metzler, Sina","last_name":"Metzler","orcid":"0000-0002-9547-2494","first_name":"Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87"}],"status":"public","citation":{"ama":"Metzler S. Pathogen-mediated sexual selection and immunization in ant colonies. 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10727\">10.15479/AT:ISTA:10727</a>","short":"S. Metzler, Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies, Institute of Science and Technology Austria, 2022.","ieee":"S. Metzler, “Pathogen-mediated sexual selection and immunization in ant colonies,” Institute of Science and Technology Austria, 2022.","ista":"Metzler S. 2022. Pathogen-mediated sexual selection and immunization in ant colonies. Institute of Science and Technology Austria.","apa":"Metzler, S. (2022). <i>Pathogen-mediated sexual selection and immunization in ant colonies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:10727\">https://doi.org/10.15479/AT:ISTA:10727</a>","chicago":"Metzler, Sina. “Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:10727\">https://doi.org/10.15479/AT:ISTA:10727</a>.","mla":"Metzler, Sina. <i>Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10727\">10.15479/AT:ISTA:10727</a>."},"date_created":"2022-02-04T15:45:12Z","acknowledged_ssus":[{"_id":"LifeSc"}],"oa":1,"title":"Pathogen-mediated sexual selection and immunization in ant colonies","date_published":"2022-02-07T00:00:00Z","has_accepted_license":"1","degree_awarded":"PhD","day":"07","ec_funded":1,"article_processing_charge":"No","file_date_updated":"2023-02-04T23:30:03Z","doi":"10.15479/AT:ISTA:10727"},{"date_created":"2022-02-06T23:01:30Z","citation":{"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>","short":"J. Svoboda, J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Scientific Reports 12 (2022).","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.","ista":"Svoboda J, Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2022. Infection dynamics of COVID-19 virus under lockdown and reopening. Scientific Reports. 12(1), 1526.","mla":"Svoboda, Jakub, et al. “Infection Dynamics of COVID-19 Virus under Lockdown and Reopening.” <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>","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>."},"quality_controlled":"1","arxiv":1,"oa":1,"article_number":"1526","title":"Infection dynamics of COVID-19 virus under lockdown and reopening","intvolume":"        12","has_accepted_license":"1","date_published":"2022-01-27T00:00:00Z","publication":"Scientific Reports","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.","day":"27","volume":12,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","ec_funded":1,"doi":"10.1038/s41598-022-05333-5","file_date_updated":"2022-02-07T14:57:59Z","oa_version":"Published Version","file":[{"file_id":"10744","creator":"alisjak","relation":"main_file","file_name":"2022_ScientificReports_Svoboda.pdf","success":1,"file_size":2971922,"checksum":"247afd30c173390940f099ead35a28ed","date_created":"2022-02-07T14:57:59Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2022-02-07T14:57:59Z"}],"ddc":["570"],"type":"journal_article","publication_status":"published","external_id":{"arxiv":["2012.15155"],"isi":["000749198000039"]},"issue":"1","_id":"10731","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"article_type":"original","publication_identifier":{"eissn":["2045-2322"]},"isi":1,"project":[{"grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"year":"2022","month":"01","abstract":[{"lang":"eng","text":"Motivated by COVID-19, we develop and analyze a simple stochastic model for the spread of disease in human population. We track how the number of infected and critically ill people develops over time in order to estimate the demand that is imposed on the hospital system. To keep this demand under control, we consider a class of simple policies for slowing down and reopening society and we compare their efficiency in mitigating the spread of the virus from several different points of view. We find that in order to avoid overwhelming of the hospital system, a policy must impose a harsh lockdown or it must react swiftly (or both). While reacting swiftly is universally beneficial, being harsh pays off only when the country is patient about reopening and when the neighboring countries coordinate their mitigation efforts. Our work highlights the importance of acting decisively when closing down and the importance of patience and coordination between neighboring countries when reopening."}],"scopus_import":"1","date_updated":"2025-07-14T09:10:12Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","author":[{"orcid":"0000-0002-1419-3267","full_name":"Svoboda, Jakub","last_name":"Svoboda","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub"},{"first_name":"Josef","full_name":"Tkadlec, Josef","last_name":"Tkadlec"},{"last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Martin A.","full_name":"Nowak, Martin A.","last_name":"Nowak"}]},{"scopus_import":"1","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."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-02T14:12:35Z","author":[{"first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio","last_name":"Cipolloni","orcid":"0000-0002-4901-7992"},{"full_name":"Erdös, László","last_name":"Erdös","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","full_name":"Schröder, Dominik J","last_name":"Schröder","orcid":"0000-0002-2904-1856"}],"status":"public","_id":"10732","issue":"8","publication_status":"published","external_id":{"arxiv":["2102.09975"],"isi":["000781239100004"]},"oa_version":"Published Version","file":[{"relation":"main_file","creator":"dernst","file_id":"11690","file_name":"2022_JourFunctionalAnalysis_Cipolloni.pdf","date_created":"2022-07-29T07:22:08Z","success":1,"file_size":652573,"checksum":"b75fdad606ab507dc61109e0907d86c0","date_updated":"2022-07-29T07:22:08Z","content_type":"application/pdf","access_level":"open_access"}],"ddc":["500"],"type":"journal_article","publisher":"Elsevier","article_type":"original","department":[{"_id":"LaEr"}],"month":"04","year":"2022","isi":1,"publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"date_published":"2022-04-15T00:00:00Z","has_accepted_license":"1","intvolume":"       282","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.","day":"15","publication":"Journal of Functional Analysis","article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2022-07-29T07:22:08Z","doi":"10.1016/j.jfa.2022.109394","quality_controlled":"1","arxiv":1,"date_created":"2022-02-06T23:01:30Z","citation":{"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>.","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>.","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>","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.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Journal of Functional Analysis 282 (2022).","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>"},"article_number":"109394","oa":1,"title":"Thermalisation for Wigner matrices"},{"title":"Intruders cooperatively interact with a wall into granular matter","oa":1,"article_number":"39","date_created":"2022-02-06T23:01:30Z","citation":{"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>.","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>.","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).","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.","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>"},"quality_controlled":"1","arxiv":1,"doi":"10.1007/s10035-021-01200-8","article_processing_charge":"No","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.","publication":"Granular Matter","day":"24","volume":24,"intvolume":"        24","date_published":"2022-01-24T00:00:00Z","publication_identifier":{"issn":["1434-5021"],"eissn":["1434-7636"]},"isi":1,"month":"01","year":"2022","department":[{"_id":"ScWa"}],"article_type":"original","publisher":"Springer Nature","type":"journal_article","oa_version":"Preprint","publication_status":"published","external_id":{"arxiv":["2110.15311"],"isi":["000746623000001"]},"issue":"1","_id":"10733","status":"public","author":[{"full_name":"Espinosa, M.","last_name":"Espinosa","first_name":"M."},{"id":"b6798902-eea0-11ea-9cbc-a8e14286c631","first_name":"Vicente L","last_name":"Diaz Melian","full_name":"Diaz Melian, Vicente L"},{"first_name":"A.","full_name":"Serrano-Muñoz, A.","last_name":"Serrano-Muñoz"},{"last_name":"Altshuler","full_name":"Altshuler, E.","first_name":"E."}],"date_updated":"2023-08-02T14:10:13Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","keyword":["granular matter","boundary effects","intruder penetration","sedimentation"],"main_file_link":[{"url":"https://arxiv.org/abs/2110.15311","open_access":"1"}],"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."}],"scopus_import":"1"},{"oa":1,"article_number":"135802","citation":{"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>.","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>","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.","short":"M. Nauman, T. Hussain, J. Choi, N. Lee, Y.J. Choi, W. Kang, Y. Jo, Journal of Physics: Condensed Matter 34 (2022).","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.","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>"},"date_created":"2022-02-06T23:01:31Z","quality_controlled":"1","title":"Low-field magnetic anisotropy of Sr2IrO4","day":"20","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).","publication":"Journal of physics: Condensed matter","volume":34,"pmid":1,"intvolume":"        34","has_accepted_license":"1","date_published":"2022-01-20T00:00:00Z","doi":"10.1088/1361-648X/ac484d","file_date_updated":"2022-02-07T10:35:28Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","publisher":"IOP Publishing","file":[{"file_name":"2022_JPhysCondensMatter_Nauman.pdf","relation":"main_file","creator":"cchlebak","file_id":"10741","date_updated":"2022-02-07T10:35:28Z","content_type":"application/pdf","access_level":"open_access","date_created":"2022-02-07T10:35:28Z","file_size":1742414,"checksum":"b6c705c7f03dcb1dbcb06b1b4d4938d6","success":1}],"type":"journal_article","ddc":["530"],"oa_version":"Published Version","publication_status":"published","external_id":{"pmid":["34986467"],"isi":["000775191800001"]},"issue":"13","_id":"10735","publication_identifier":{"eissn":["1361-648X"]},"isi":1,"month":"01","year":"2022","department":[{"_id":"KiMo"}],"article_type":"original","date_updated":"2023-08-02T14:12:01Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Magnetic anisotropy in strontium iridate (Sr2IrO4) is essential because of its strong spin–orbit coupling and crystal field effect. In this paper, we present a detailed mapping of the out-of-plane (OOP) magnetic anisotropy in Sr2IrO4 for different sample orientations using torque magnetometry measurements in the low-magnetic-field region before the isospins are completely ordered. Dominant in-plane anisotropy was identified at low fields, confirming the b axis as an easy magnetization axis. Based on the fitting analysis of the strong uniaxial magnetic anisotropy, we observed that the main anisotropic effect arises from a spin–orbit-coupled magnetic exchange interaction affecting the OOP interaction. The effect of interlayer exchange interaction results in additional anisotropic terms owing to the tilting of the isospins. The results are relevant for understanding OOP magnetic anisotropy and provide a new way to analyze the effects of spin–orbit-coupling and interlayer magnetic exchange interactions. This study provides insight into the understanding of bulk magnetic, magnetotransport, and spintronic behavior on Sr2IrO4 for future studies."}],"scopus_import":"1","status":"public","author":[{"full_name":"Nauman, Muhammad","last_name":"Nauman","orcid":"0000-0002-2111-4846","first_name":"Muhammad","id":"32c21954-2022-11eb-9d5f-af9f93c24e71"},{"full_name":"Hussain, Tayyaba","last_name":"Hussain","first_name":"Tayyaba"},{"full_name":"Choi, Joonyoung","last_name":"Choi","first_name":"Joonyoung"},{"first_name":"Nara","last_name":"Lee","full_name":"Lee, Nara"},{"full_name":"Choi, Young Jai","last_name":"Choi","first_name":"Young Jai"},{"full_name":"Kang, Woun","last_name":"Kang","first_name":"Woun"},{"first_name":"Younjung","last_name":"Jo","full_name":"Jo, Younjung"}]},{"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","ec_funded":1,"file_date_updated":"2022-02-07T07:14:09Z","doi":"10.7554/eLife.64543","date_published":"2022-01-26T00:00:00Z","intvolume":"        11","has_accepted_license":"1","pmid":1,"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.","day":"26","publication":"eLife","volume":11,"title":"Predicting bacterial promoter function and evolution from random sequences","quality_controlled":"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>.","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>.","short":"M. Lagator, S. Sarikas, M. Steinrueck, D. Toledo-Aparicio, J.P. Bollback, C.C. Guet, G. Tkačik, ELife 11 (2022).","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.","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.","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>"},"date_created":"2022-02-06T23:01:32Z","oa":1,"article_number":"e64543","status":"public","author":[{"last_name":"Lagator","full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato"},{"first_name":"Srdjan","id":"35F0286E-F248-11E8-B48F-1D18A9856A87","last_name":"Sarikas","full_name":"Sarikas, Srdjan"},{"first_name":"Magdalena","full_name":"Steinrueck, Magdalena","last_name":"Steinrueck"},{"first_name":"David","full_name":"Toledo-Aparicio, David","last_name":"Toledo-Aparicio"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612"},{"orcid":"0000-0001-6220-2052","last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","full_name":"Tkačik, Gašper"}],"scopus_import":"1","abstract":[{"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.","lang":"eng"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-02T14:09:02Z","article_type":"original","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"NiBa"}],"project":[{"call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer","_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440"}],"year":"2022","month":"01","publication_identifier":{"eissn":["2050-084X"]},"isi":1,"publication_status":"published","external_id":{"pmid":["35080492"],"isi":["000751104400001"]},"_id":"10736","type":"journal_article","ddc":["576"],"oa_version":"Published Version","file":[{"file_id":"10739","creator":"cchlebak","relation":"main_file","file_name":"2022_ELife_Lagator.pdf","checksum":"decdcdf600ff51e9a9703b49ca114170","success":1,"file_size":5604343,"date_created":"2022-02-07T07:14:09Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2022-02-07T07:14:09Z"}],"publisher":"eLife Sciences Publications"},{"oa_version":"Preprint","type":"journal_article","external_id":{"isi":["000749997700015"],"arxiv":["1404.5475"]},"publication_status":"published","issue":"1","_id":"10737","publisher":"IOS Press","department":[{"_id":"VlKo"}],"article_type":"original","publication_identifier":{"eissn":["1571-4128"],"issn":["1088-467X"]},"isi":1,"month":"01","year":"2022","main_file_link":[{"url":"https://arxiv.org/abs/1404.5475","open_access":"1"}],"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."}],"scopus_import":"1","date_updated":"2023-08-02T14:09:41Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","author":[{"full_name":"Takhanov, Rustem","last_name":"Takhanov","first_name":"Rustem","id":"2CCAC26C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"}],"date_created":"2022-02-06T23:01:32Z","citation":{"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>","short":"R. Takhanov, V. Kolmogorov, Intelligent Data Analysis 26 (2022) 257–272.","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.","ista":"Takhanov R, Kolmogorov V. 2022. Combining pattern-based CRFs and weighted context-free grammars. Intelligent Data Analysis. 26(1), 257–272.","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>.","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>","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>."},"arxiv":1,"quality_controlled":"1","oa":1,"title":"Combining pattern-based CRFs and weighted context-free grammars","page":"257-272","intvolume":"        26","date_published":"2022-01-14T00:00:00Z","publication":"Intelligent Data Analysis","day":"14","volume":26,"article_processing_charge":"No","doi":"10.3233/IDA-205623"},{"status":"public","article_processing_charge":"No","author":[{"last_name":"Lampert","full_name":"Lampert, Jasmin","first_name":"Jasmin"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Lampert","full_name":"Lampert, Christoph"}],"doi":"10.1109/bigdata52589.2021.9672003","date_published":"2022-01-13T00:00:00Z","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"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"2021 IEEE International Conference on Big Data","day":"13","date_updated":"2023-08-02T14:27:50Z","department":[{"_id":"ChLa"}],"title":"Overcoming rare-language discrimination in multi-lingual sentiment analysis","page":"5185-5192","year":"2022","month":"01","publication_identifier":{"isbn":["9781665439022"]},"isi":1,"publication_status":"published","quality_controlled":"1","external_id":{"isi":["000800559505036"]},"_id":"10752","conference":{"end_date":"2021-12-18","location":"Orlando, FL, United States","name":"Big Data: International Conference on Big Data","start_date":"2021-12-15"},"type":"conference","oa_version":"None","date_created":"2022-02-10T14:08:23Z","citation":{"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>.","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>","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>.","ista":"Lampert J, Lampert C. 2022. Overcoming rare-language discrimination in multi-lingual sentiment analysis. 2021 IEEE International Conference on Big Data. Big Data: International Conference on Big Data, 5185–5192.","short":"J. Lampert, C. Lampert, in:, 2021 IEEE International Conference on Big Data, IEEE, 2022, pp. 5185–5192.","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.","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>"},"publisher":"IEEE"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2023-10-03T10:53:17Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2022.01.014"}],"abstract":[{"text":"This is a comment on \"Meta-learning synaptic plasticity and memory addressing for continual familiarity detection.\" Neuron. 2022 Feb 2;110(3):544-557.e8.","lang":"eng"}],"status":"public","author":[{"first_name":"Basile J","id":"C7610134-B532-11EA-BD9F-F5753DDC885E","full_name":"Confavreux, Basile J","last_name":"Confavreux"},{"orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P"}],"publisher":"Elsevier","publication_status":"published","external_id":{"isi":["000751819100005"],"pmid":["35114107"]},"issue":"3","_id":"10753","type":"journal_article","oa_version":"Published Version","month":"02","year":"2022","publication_identifier":{"eissn":["1097-4199"]},"isi":1,"article_type":"letter_note","department":[{"_id":"TiVo"}],"pmid":1,"publication":"Neuron","day":"02","volume":110,"date_published":"2022-02-02T00:00:00Z","intvolume":"       110","doi":"10.1016/j.neuron.2022.01.014","article_processing_charge":"No","oa":1,"quality_controlled":"1","citation":{"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>","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>.","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>.","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>","short":"B.J. Confavreux, T.P. Vogels, Neuron 110 (2022) 361–362.","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.","ista":"Confavreux BJ, Vogels TP. 2022. A familiar thought: Machines that replace us? Neuron. 110(3), 361–362."},"date_created":"2022-02-13T23:01:34Z","page":"361-362","title":"A familiar thought: Machines that replace us?"},{"title":"Developing a mathematical model of intracellular Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer","date_created":"2022-02-13T23:01:35Z","citation":{"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>","ista":"Chang Y, Funk M, Roy S, Stephenson ER, Choi S, Kojouharov HV, Chen B, Pan Z. 2022. Developing a mathematical model of intracellular Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer. International Journal of Molecular Sciences. 23(3), 1763.","short":"Y. Chang, M. Funk, S. Roy, E.R. Stephenson, S. Choi, H.V. Kojouharov, B. Chen, Z. Pan, International Journal of Molecular Sciences 23 (2022).","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.","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>","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>.","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>."},"quality_controlled":"1","oa":1,"article_number":"1763","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes","doi":"10.3390/ijms23031763","file_date_updated":"2022-02-14T07:46:30Z","intvolume":"        23","has_accepted_license":"1","date_published":"2022-02-01T00:00:00Z","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.). ","publication":"International Journal of Molecular Sciences","day":"01","volume":23,"department":[{"_id":"HeEd"}],"article_type":"original","publication_identifier":{"issn":["16616596"],"eissn":["14220067"]},"isi":1,"year":"2022","month":"02","ddc":["510","576"],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2022_IJMS_Chang.pdf","relation":"main_file","file_id":"10756","creator":"dernst","date_updated":"2022-02-14T07:46:30Z","access_level":"open_access","content_type":"application/pdf","date_created":"2022-02-14T07:46:30Z","success":1,"file_size":24416183,"checksum":"8890ad20c54e90dc58ad5ea97c902998"}],"external_id":{"isi":["000754773500001"]},"publication_status":"published","_id":"10754","issue":"3","publisher":"MDPI","status":"public","author":[{"last_name":"Chang","full_name":"Chang, Yan","first_name":"Yan"},{"first_name":"Marah","full_name":"Funk, Marah","last_name":"Funk"},{"last_name":"Roy","full_name":"Roy, Souvik","first_name":"Souvik"},{"first_name":"Elizabeth R","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-208X","last_name":"Stephenson","full_name":"Stephenson, Elizabeth R"},{"first_name":"Sangyong","full_name":"Choi, Sangyong","last_name":"Choi"},{"first_name":"Hristo V.","full_name":"Kojouharov, Hristo V.","last_name":"Kojouharov"},{"first_name":"Benito","last_name":"Chen","full_name":"Chen, Benito"},{"first_name":"Zui","full_name":"Pan, Zui","last_name":"Pan"}],"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."}],"scopus_import":"1","date_updated":"2023-08-09T10:17:07Z","language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"status":"public","author":[{"first_name":"Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","full_name":"Feliciangeli, Dario","last_name":"Feliciangeli","orcid":"0000-0003-0754-8530"},{"id":"856966FE-A408-11E9-977E-802DE6697425","first_name":"Simone Anna Elvira","orcid":"0000-0001-5059-4466","full_name":"Rademacher, Simone Anna Elvira","last_name":"Rademacher"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"scopus_import":"1","related_material":{"record":[{"id":"9791","status":"public","relation":"earlier_version"}]},"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"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-03-06T12:30:44Z","article_type":"original","department":[{"_id":"RoSe"}],"project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"year":"2022","month":"01","publication_identifier":{"eissn":["1751-8121"],"issn":["1751-8113"]},"external_id":{"arxiv":["2107.03720"]},"publication_status":"published","issue":"1","_id":"10755","file":[{"date_updated":"2022-02-14T08:20:19Z","content_type":"application/pdf","access_level":"open_access","date_created":"2022-02-14T08:20:19Z","checksum":"0875e562705563053d6dd98fba4d8578","success":1,"file_size":1132380,"file_name":"2022_JournalPhysicsA_Feliciangeli.pdf","relation":"main_file","creator":"dernst","file_id":"10757"}],"type":"journal_article","oa_version":"Published Version","ddc":["510"],"publisher":"IOP Publishing","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","ec_funded":1,"file_date_updated":"2022-02-14T08:20:19Z","doi":"10.1088/1751-8121/ac3947","date_published":"2022-01-19T00:00:00Z","has_accepted_license":"1","intvolume":"        55","publication":"Journal of Physics A: Mathematical and Theoretical","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.","day":"19","volume":55,"title":"The effective mass problem for the Landau-Pekar equations","arxiv":1,"quality_controlled":"1","date_created":"2022-02-13T23:01:35Z","citation":{"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.","short":"D. Feliciangeli, S.A.E. Rademacher, R. Seiringer, Journal of Physics A: Mathematical and Theoretical 55 (2022).","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.","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>.","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>","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>."},"oa":1,"article_number":"015201"},{"day":"21","degree_awarded":"PhD","has_accepted_license":"1","date_published":"2022-02-21T00:00:00Z","doi":"10.15479/at:ista:10759","file_date_updated":"2022-02-22T07:20:12Z","article_processing_charge":"No","ec_funded":1,"oa":1,"date_created":"2022-02-16T13:27:37Z","citation":{"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>","short":"W. Rzadkowski, Analytic and Machine Learning Approaches to Composite Quantum Impurities, Institute of Science and Technology Austria, 2022.","ieee":"W. Rzadkowski, “Analytic and machine learning approaches to composite quantum impurities,” Institute of Science and Technology Austria, 2022.","ista":"Rzadkowski W. 2022. Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria.","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>","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>.","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>."},"page":"120","title":"Analytic and machine learning approaches to composite quantum impurities","date_updated":"2024-08-07T07:16:53Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10762"},{"status":"public","relation":"part_of_dissertation","id":"7956"},{"id":"415","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8644"}]},"abstract":[{"lang":"eng","text":"In this Thesis, I study composite quantum impurities with variational techniques, both inspired by machine learning as well as fully analytic. I supplement this with exploration of other applications of machine learning, in particular artificial neural networks, in many-body physics. In Chapters 3 and 4, I study quasiparticle systems with variational approach. I derive a Hamiltonian describing the angulon quasiparticle in the presence of a magnetic field. I apply analytic variational treatment to this Hamiltonian. Then, I introduce a variational approach for non-additive systems, based on artificial neural networks. I exemplify this approach on the example of the polaron quasiparticle (Fröhlich Hamiltonian). In Chapter 5, I continue using artificial neural networks, albeit in a different setting. I apply artificial neural networks to detect phases from snapshots of two types physical systems. Namely, I study Monte Carlo snapshots of multilayer classical spin models as well as molecular dynamics maps of colloidal systems. The main type of networks that I use here are convolutional neural networks, known for their applicability to image data."}],"status":"public","author":[{"id":"48C55298-F248-11E8-B48F-1D18A9856A87","first_name":"Wojciech","last_name":"Rzadkowski","full_name":"Rzadkowski, Wojciech","orcid":"0000-0002-1106-4419"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"ddc":["530"],"file":[{"file_name":"Rzadkowski_thesis_final_source.zip","relation":"source_file","file_id":"10785","creator":"wrzadkow","date_updated":"2022-02-22T07:20:12Z","access_level":"closed","content_type":"application/zip","date_created":"2022-02-21T13:58:16Z","checksum":"0fc54ad1eaede879c665ac9b53c93e22","file_size":17668233},{"file_name":"Rzadkowski_thesis_final.pdf","file_id":"10786","creator":"wrzadkow","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2022-02-21T14:02:54Z","file_size":13307331,"success":1,"checksum":"22d2d7af37ca31f6b1730c26cac7bced","date_created":"2022-02-21T14:02:54Z"}],"oa_version":"Published Version","type":"dissertation","publication_status":"published","alternative_title":["ISTA Thesis"],"_id":"10759","publication_identifier":{"issn":["2663-337X"]},"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"year":"2022","month":"02","department":[{"_id":"GradSch"},{"_id":"MiLe"}]},{"department":[{"_id":"PeJo"}],"article_type":"original","isi":1,"publication_identifier":{"eissn":["20411723"]},"year":"2022","month":"02","ddc":["570"],"file":[{"checksum":"d86ee8eabe8b794730729ffbb1a8832e","success":1,"file_size":2625540,"date_created":"2022-02-21T07:59:32Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2022-02-21T07:59:32Z","file_id":"10778","creator":"dernst","relation":"main_file","file_name":"2022_NatureCommunications_Herguedas.pdf"}],"oa_version":"Published Version","type":"journal_article","_id":"10763","external_id":{"isi":["000757297200008"],"pmid":["35136046"]},"publication_status":"published","publisher":"Springer Nature","author":[{"first_name":"Beatriz","full_name":"Herguedas, 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"},{"first_name":"Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","orcid":"0000-0002-8698-3823","last_name":"Watson","full_name":"Watson, Jake"},{"first_name":"Danyang","full_name":"Zhang, Danyang","last_name":"Zhang"},{"first_name":"Hinze","last_name":"Ho","full_name":"Ho, Hinze"},{"full_name":"Shaikh, Saher A.","last_name":"Shaikh","first_name":"Saher A."},{"last_name":"Lape","full_name":"Lape, Remigijus","first_name":"Remigijus"},{"first_name":"James M.","full_name":"Krieger, James M.","last_name":"Krieger"},{"full_name":"Greger, Ingo H.","last_name":"Greger","first_name":"Ingo H."}],"status":"public","abstract":[{"text":"AMPA-type glutamate receptors (AMPARs) mediate rapid signal transmission at excitatory\r\nsynapses in the brain. Glutamate binding to the receptor’s ligand-binding domains (LBDs)\r\nleads to ion channel activation and desensitization. Gating kinetics shape synaptic transmission\r\nand are strongly modulated by transmembrane AMPAR regulatory proteins (TARPs)\r\nthrough currently incompletely resolved mechanisms. Here, electron cryo-microscopy\r\nstructures of the GluA1/2 TARP-γ8 complex, in both open and desensitized states\r\n(at 3.5 Å), reveal state-selective engagement of the LBDs by the large TARP-γ8 loop (‘β1’),\r\nelucidating how this TARP stabilizes specific gating states. We further show how TARPs alter\r\nchannel rectification, by interacting with the pore helix of the selectivity filter. Lastly, we\r\nreveal that the Q/R-editing site couples the channel constriction at the filter entrance to the\r\ngate, and forms the major cation binding site in the conduction path. Our results provide a\r\nmechanistic framework of how TARPs modulate AMPAR gating and conductance.","lang":"eng"}],"scopus_import":"1","date_updated":"2023-08-02T14:25:33Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor","citation":{"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>","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>.","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>","ista":"Herguedas B, Kohegyi BK, Dohrke JN, Watson J, Zhang D, Ho H, Shaikh SA, Lape R, Krieger JM, Greger IH. 2022. Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor. Nature Communications. 13, 734.","short":"B. Herguedas, B.K. Kohegyi, J.N. Dohrke, J. Watson, D. Zhang, H. Ho, S.A. Shaikh, R. Lape, J.M. Krieger, I.H. Greger, Nature Communications 13 (2022).","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."},"date_created":"2022-02-20T23:01:30Z","quality_controlled":"1","article_number":"734","oa":1,"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41467-022-28404-7","file_date_updated":"2022-02-21T07:59:32Z","has_accepted_license":"1","intvolume":"        13","date_published":"2022-02-08T00:00:00Z","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).","day":"08","publication":"Nature Communications","pmid":1}]