[{"oa":1,"day":"10","oa_version":"Published Version","doi":"10.1016/j.devcel.2021.11.024","external_id":{"pmid":["34919802"],"isi":["000768933800005"]},"issue":"1","scopus_import":"1","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"title":"WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues","article_processing_charge":"No","publication":"Developmental Cell","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.sciencedirect.com/science/article/pii/S1534580721009497","open_access":"1"}],"ddc":["570"],"status":"public","article_type":"original","date_published":"2022-01-10T00:00:00Z","acknowledgement":"We thank N. Darwish-Miranda, F. Leite, F.P. Assen, and A. Eichner for advice and help with experiments. We thank J. Renkawitz, E. Kiermaier, A. Juanes Garcia, and M. Avellaneda for critical reading of the manuscript. We thank M. Driscoll for advice on fluorescent labeling of collagen gels. This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Molecular Biology Services/Lab Support Facility (LSF)/Bioimaging Facility/Electron Microscopy Facility. This work was funded by grants from the European Research Council ( CoG 724373 ) and the Austrian Science Foundation (FWF) to M.S. F.G. received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 747687.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","date_updated":"2024-03-25T23:30:12Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"abstract":[{"text":"When crawling through the body, leukocytes often traverse tissues that are densely packed with extracellular matrix and other cells, and this raises the question: How do leukocytes overcome compressive mechanical loads? Here, we show that the actin cortex of leukocytes is mechanoresponsive and that this responsiveness requires neither force sensing via the nucleus nor adhesive interactions with a substrate. Upon global compression of the cell body as well as local indentation of the plasma membrane, Wiskott-Aldrich syndrome protein (WASp) assembles into dot-like structures, providing activation platforms for Arp2/3 nucleated actin patches. These patches locally push against the external load, which can be obstructing collagen fibers or other cells, and thereby create space to facilitate forward locomotion. We show in vitro and in vivo that this WASp function is rate limiting for ameboid leukocyte migration in dense but not in loose environments and is required for trafficking through diverse tissues such as skin and lymph nodes.","lang":"eng"}],"citation":{"apa":"Gaertner, F., Reis-Rodrigues, P., de Vries, I., Hons, M., Aguilera, J., Riedl, M., … Sixt, M. K. (2022). WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. Developmental Cell. Cell Press ; Elsevier. https://doi.org/10.1016/j.devcel.2021.11.024","mla":"Gaertner, Florian, et al. “WASp Triggers Mechanosensitive Actin Patches to Facilitate Immune Cell Migration in Dense Tissues.” Developmental Cell, vol. 57, no. 1, Cell Press ; Elsevier, 2022, p. 47–62.e9, doi:10.1016/j.devcel.2021.11.024.","ieee":"F. Gaertner et al., “WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues,” Developmental Cell, vol. 57, no. 1. Cell Press ; Elsevier, p. 47–62.e9, 2022.","short":"F. Gaertner, P. Reis-Rodrigues, I. de Vries, M. Hons, J. Aguilera, M. Riedl, A.F. Leithner, S. Tasciyan, A. Kopf, J. Merrin, V. Zheden, W. Kaufmann, R. Hauschild, M.K. Sixt, Developmental Cell 57 (2022) 47–62.e9.","ama":"Gaertner F, Reis-Rodrigues P, de Vries I, et al. WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. Developmental Cell. 2022;57(1):47-62.e9. doi:10.1016/j.devcel.2021.11.024","chicago":"Gaertner, Florian, Patricia Reis-Rodrigues, Ingrid de Vries, Miroslav Hons, Juan Aguilera, Michael Riedl, Alexander F Leithner, et al. “WASp Triggers Mechanosensitive Actin Patches to Facilitate Immune Cell Migration in Dense Tissues.” Developmental Cell. Cell Press ; Elsevier, 2022. https://doi.org/10.1016/j.devcel.2021.11.024.","ista":"Gaertner F, Reis-Rodrigues P, de Vries I, Hons M, Aguilera J, Riedl M, Leithner AF, Tasciyan S, Kopf A, Merrin J, Zheden V, Kaufmann W, Hauschild R, Sixt MK. 2022. WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. Developmental Cell. 57(1), 47–62.e9."},"volume":57,"page":"47-62.e9","publisher":"Cell Press ; Elsevier","pmid":1,"department":[{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"BjHo"}],"_id":"10703","year":"2022","type":"journal_article","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12726"},{"relation":"dissertation_contains","id":"14530","status":"public"},{"relation":"dissertation_contains","id":"12401","status":"public"}]},"date_created":"2022-01-30T23:01:33Z","intvolume":" 57","author":[{"last_name":"Gaertner","first_name":"Florian","full_name":"Gaertner, Florian"},{"full_name":"Reis-Rodrigues, Patricia","first_name":"Patricia","last_name":"Reis-Rodrigues"},{"full_name":"De Vries, Ingrid","first_name":"Ingrid","last_name":"De Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hons, Miroslav","first_name":"Miroslav","last_name":"Hons","orcid":"0000-0002-6625-3348","id":"4167FE56-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Aguilera, Juan","last_name":"Aguilera","first_name":"Juan"},{"full_name":"Riedl, Michael","last_name":"Riedl","first_name":"Michael","orcid":"0000-0003-4844-6311","id":"3BE60946-F248-11E8-B48F-1D18A9856A87"},{"id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1073-744X","first_name":"Alexander F","last_name":"Leithner","full_name":"Leithner, Alexander F"},{"last_name":"Tasciyan","first_name":"Saren","full_name":"Tasciyan, Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X"},{"full_name":"Kopf, Aglaja","last_name":"Kopf","first_name":"Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2187-6656"},{"full_name":"Merrin, Jack","first_name":"Jack","last_name":"Merrin","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9438-4783","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","full_name":"Zheden, Vanessa","last_name":"Zheden","first_name":"Vanessa"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","first_name":"Walter","full_name":"Kaufmann, Walter"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt"}],"project":[{"grant_number":"747687","call_identifier":"H2020","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"},{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular navigation along spatial gradients","call_identifier":"H2020","grant_number":"724373"}],"publication_status":"published","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"ec_funded":1,"month":"01","isi":1},{"department":[{"_id":"TaHa"}],"publisher":"Springer Nature","volume":228,"page":"893-989","citation":{"ista":"Hausel T, Hitchin N. 2022. Very stable Higgs bundles, equivariant multiplicity and mirror symmetry. Inventiones Mathematicae. 228, 893–989.","mla":"Hausel, Tamás, and Nigel Hitchin. “Very Stable Higgs Bundles, Equivariant Multiplicity and Mirror Symmetry.” Inventiones Mathematicae, vol. 228, Springer Nature, 2022, pp. 893–989, doi:10.1007/s00222-021-01093-7.","apa":"Hausel, T., & Hitchin, N. (2022). Very stable Higgs bundles, equivariant multiplicity and mirror symmetry. Inventiones Mathematicae. Springer Nature. https://doi.org/10.1007/s00222-021-01093-7","short":"T. Hausel, N. Hitchin, Inventiones Mathematicae 228 (2022) 893–989.","ieee":"T. Hausel and N. Hitchin, “Very stable Higgs bundles, equivariant multiplicity and mirror symmetry,” Inventiones Mathematicae, vol. 228. Springer Nature, pp. 893–989, 2022.","ama":"Hausel T, Hitchin N. Very stable Higgs bundles, equivariant multiplicity and mirror symmetry. Inventiones Mathematicae. 2022;228:893-989. doi:10.1007/s00222-021-01093-7","chicago":"Hausel, Tamás, and Nigel Hitchin. “Very Stable Higgs Bundles, Equivariant Multiplicity and Mirror Symmetry.” Inventiones Mathematicae. Springer Nature, 2022. https://doi.org/10.1007/s00222-021-01093-7."},"date_updated":"2023-08-02T14:03:20Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"text":"We define and study the existence of very stable Higgs bundles on Riemann surfaces, how it implies a precise formula for the multiplicity of the very stable components of the global nilpotent cone and its relationship to mirror symmetry. The main ingredients are the Bialynicki-Birula theory of C∗-actions on semiprojective varieties, C∗ characters of indices of C∗-equivariant coherent sheaves, Hecke transformation for Higgs bundles, relative Fourier–Mukai transform along the Hitchin fibration, hyperholomorphic structures on universal bundles and cominuscule Higgs bundles.","lang":"eng"}],"has_accepted_license":"1","quality_controlled":"1","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"publication_status":"published","month":"05","isi":1,"author":[{"first_name":"Tamás","last_name":"Hausel","full_name":"Hausel, Tamás","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nigel","last_name":"Hitchin","full_name":"Hitchin, Nigel"}],"intvolume":" 228","date_created":"2022-01-30T23:01:34Z","type":"journal_article","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/the-tip-of-the-mathematical-iceberg/","description":"News on the ISTA Website"}]},"year":"2022","_id":"10704","file":[{"date_created":"2023-02-27T07:30:47Z","file_size":1069538,"creator":"dernst","success":1,"relation":"main_file","content_type":"application/pdf","file_id":"12687","checksum":"a382ba75acebc9adfb8fe56247cb410e","access_level":"open_access","date_updated":"2023-02-27T07:30:47Z","file_name":"2022_InventionesMahtematicae_Hausel.pdf"}],"publication_identifier":{"issn":["0020-9910"],"eissn":["1432-1297"]},"external_id":{"isi":["000745495400001"],"arxiv":["2101.08583"]},"scopus_import":"1","oa_version":"Published Version","doi":"10.1007/s00222-021-01093-7","oa":1,"day":"01","date_published":"2022-05-01T00:00:00Z","acknowledgement":"We would like to thank Brian Collier, Davide Gaiotto, Peter Gothen, Jochen Heinloth, Daniel Huybrechts, Quoc Ho, Joel Kamnitzer, Gérard Laumon, Luca Migliorini, Alexander Minets, Brent Pym, Peng Shan, Carlos Simpson, András Szenes, Fernando R. Villegas, Richard Wentworth, Edward Witten and Kōta Yoshioka for interesting comments and discussions. Most of all we are grateful for a long list of very helpful comments by the referee. We would also like to thank the organizers of the Summer School on Higgs bundles in Hamburg in September 2018, where the authors and Richard Wentworth were giving lectures and where the work in this paper started by considering the mirror of the Lagrangian upward flows W+E investigated in [17]. The second author wishes to thank EPSRC and ICMAT for support. Open access funding provided by Institute of Science and Technology (IST Austria).","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","status":"public","ddc":["510"],"file_date_updated":"2023-02-27T07:30:47Z","publication":"Inventiones Mathematicae","language":[{"iso":"eng"}],"title":"Very stable Higgs bundles, equivariant multiplicity and mirror symmetry","article_processing_charge":"Yes (via OA deal)","arxiv":1},{"quality_controlled":"1","abstract":[{"lang":"eng","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."}],"date_updated":"2023-02-27T07:34:08Z","volume":8,"page":"411-422","citation":{"mla":"Bialy, Misha, et al. “Open Problems on Billiards and Geometric Optics.” Arnold Mathematical Journal, vol. 8, Springer Nature, 2022, pp. 411–22, doi:10.1007/s40598-022-00198-y.","apa":"Bialy, M., Fiorebe, C., Glutsyuk, A., Levi, M., Plakhov, A., & Tabachnikov, S. (2022). Open problems on billiards and geometric optics. Arnold Mathematical Journal. Hybrid: Springer Nature. https://doi.org/10.1007/s40598-022-00198-y","ama":"Bialy M, Fiorebe C, Glutsyuk A, Levi M, Plakhov A, Tabachnikov S. Open problems on billiards and geometric optics. Arnold Mathematical Journal. 2022;8:411-422. doi:10.1007/s40598-022-00198-y","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,” Arnold Mathematical Journal, vol. 8. Springer Nature, pp. 411–422, 2022.","chicago":"Bialy, Misha, Corentin Fiorebe, Alexey Glutsyuk, Mark Levi, Alexander Plakhov, and Serge Tabachnikov. “Open Problems on Billiards and Geometric Optics.” Arnold Mathematical Journal. Springer Nature, 2022. https://doi.org/10.1007/s40598-022-00198-y.","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."},"publisher":"Springer Nature","conference":{"end_date":"2021-10-08","location":"Hybrid","start_date":"2021-10-04","name":"CIRM: Centre International de Rencontres Mathématiques"},"department":[{"_id":"VaKa"}],"_id":"10706","year":"2022","related_material":{"link":[{"url":"https://conferences.cirm-math.fr/2383.html","relation":"earlier_version"}]},"type":"journal_article","date_created":"2022-01-30T23:01:34Z","intvolume":" 8","author":[{"last_name":"Bialy","first_name":"Misha","full_name":"Bialy, Misha"},{"id":"06619f18-9070-11eb-847d-d1ee780bd88b","first_name":"Corentin","last_name":"Fiorebe","full_name":"Fiorebe, Corentin"},{"full_name":"Glutsyuk, Alexey","first_name":"Alexey","last_name":"Glutsyuk"},{"full_name":"Levi, Mark","last_name":"Levi","first_name":"Mark"},{"last_name":"Plakhov","first_name":"Alexander","full_name":"Plakhov, Alexander"},{"first_name":"Serge","last_name":"Tabachnikov","full_name":"Tabachnikov, Serge"}],"month":"10","publication_status":"published","day":"01","oa":1,"doi":"10.1007/s40598-022-00198-y","oa_version":"Preprint","scopus_import":"1","external_id":{"arxiv":["2110.10750"]},"publication_identifier":{"eissn":["2199-6806"],"issn":["2199-6792"]},"arxiv":1,"title":"Open problems on billiards and geometric optics","article_processing_charge":"No","language":[{"iso":"eng"}],"publication":"Arnold Mathematical Journal","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2110.10750"}],"status":"public","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-10-01T00:00:00Z"},{"oa":1,"day":"08","oa_version":"Published Version","doi":"10.3389/fonc.2022.777634","file":[{"file_name":"2022_FrontiersOncol_Roblek.pdf","content_type":"application/pdf","relation":"main_file","checksum":"63dfecf30c5bbf9408b3512bd603f78c","file_id":"10751","access_level":"open_access","date_updated":"2022-02-08T13:26:40Z","creator":"cchlebak","success":1,"date_created":"2022-02-08T13:26:40Z","file_size":6303227}],"publication_identifier":{"issn":["2234-943X"]},"external_id":{"isi":["000760618800001"]},"scopus_import":"1","publication":"Frontiers in Oncology","language":[{"iso":"eng"}],"title":"The solute carrier MFSD1 decreases β1 integrin’s activation status and thus tumor metastasis","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2022-02-08T13:26:40Z","status":"public","ddc":["570"],"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).","date_published":"2022-02-08T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-02T14:05:44Z","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"}],"quality_controlled":"1","has_accepted_license":"1","citation":{"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.” Frontiers in Oncology. Frontiers, 2022. https://doi.org/10.3389/fonc.2022.777634.","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).","ama":"Roblek M, Bicher J, van Gogh M, et al. The solute carrier MFSD1 decreases β1 integrin’s activation status and thus tumor metastasis. Frontiers in Oncology. 2022;12. doi:10.3389/fonc.2022.777634","ieee":"M. Roblek et al., “The solute carrier MFSD1 decreases β1 integrin’s activation status and thus tumor metastasis,” Frontiers in Oncology, vol. 12. Frontiers, 2022.","mla":"Roblek, Marko, et al. “The Solute Carrier MFSD1 Decreases Β1 Integrin’s Activation Status and Thus Tumor Metastasis.” Frontiers in Oncology, vol. 12, 777634, Frontiers, 2022, doi:10.3389/fonc.2022.777634.","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. Frontiers in Oncology. Frontiers. https://doi.org/10.3389/fonc.2022.777634","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."},"volume":12,"publisher":"Frontiers","department":[{"_id":"DaSi"}],"type":"journal_article","article_number":"777634","related_material":{"link":[{"relation":"confirmation","url":"https://ist.ac.at/en/news/suppressing-the-spread-of-tumors/","description":"News on IST Homepage"}]},"_id":"10712","year":"2022","intvolume":" 12","date_created":"2022-02-01T10:33:50Z","project":[{"grant_number":"LSC16-021 ","name":"Investigating the role of the novel major superfamily facilitator transporter family member MFSD1 in metastasis","_id":"2637E9C0-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","acknowledged_ssus":[{"_id":"Bio"}],"isi":1,"month":"02","author":[{"full_name":"Roblek, Marko","last_name":"Roblek","first_name":"Marko","orcid":"0000-0001-9588-1389","id":"3047D808-F248-11E8-B48F-1D18A9856A87"},{"id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","full_name":"Bicher, Julia","last_name":"Bicher","first_name":"Julia"},{"first_name":"Merel","last_name":"van Gogh","full_name":"van Gogh, Merel"},{"id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1819-198X","last_name":"György","first_name":"Attila","full_name":"György, Attila"},{"full_name":"Seeböck, Rita","first_name":"Rita","last_name":"Seeböck"},{"full_name":"Szulc, Bozena","first_name":"Bozena","last_name":"Szulc"},{"last_name":"Damme","first_name":"Markus","full_name":"Damme, Markus"},{"last_name":"Olczak","first_name":"Mariusz","full_name":"Olczak, Mariusz"},{"full_name":"Borsig, Lubor","first_name":"Lubor","last_name":"Borsig"},{"orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E","first_name":"Daria E","last_name":"Siekhaus"}]},{"abstract":[{"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.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"date_updated":"2023-08-02T14:06:15Z","quality_controlled":"1","page":"394-396","citation":{"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.","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.","ama":"Akhmanova M, Emtenani S, Krueger D, et al. Cell division in tissues enables macrophage infiltration. Science. 2022;376(6591):394-396. doi:10.1126/science.abj0425","ieee":"M. Akhmanova et al., “Cell division in tissues enables macrophage infiltration,” Science, vol. 376, no. 6591. American Association for the Advancement of Science, pp. 394–396, 2022.","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.” Science. American Association for the Advancement of Science, 2022. https://doi.org/10.1126/science.abj0425.","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. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abj0425","mla":"Akhmanova, Maria, et al. “Cell Division in Tissues Enables Macrophage Infiltration.” Science, vol. 376, no. 6591, American Association for the Advancement of Science, 2022, pp. 394–96, doi:10.1126/science.abj0425."},"volume":376,"pmid":1,"publisher":"American Association for the Advancement of Science","department":[{"_id":"DaSi"}],"type":"journal_article","_id":"10713","year":"2022","intvolume":" 376","date_created":"2022-02-01T11:23:18Z","isi":1,"month":"04","project":[{"_id":"264CBBAC-B435-11E9-9278-68D0E5697425","name":"Modeling epithelial tissue mechanics during cell invasion","call_identifier":"FWF","grant_number":"M02379"}],"acknowledged_ssus":[{"_id":"Bio"}],"publication_status":"published","author":[{"last_name":"Akhmanova","first_name":"Maria","full_name":"Akhmanova, Maria","orcid":"0000-0003-1522-3162","id":"3425EC26-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Shamsi","last_name":"Emtenani","full_name":"Emtenani, Shamsi","orcid":"0000-0001-6981-6938","id":"49D32318-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Krueger","first_name":"Daniel","full_name":"Krueger, Daniel"},{"first_name":"Attila","last_name":"György","full_name":"György, Attila","orcid":"0000-0002-1819-198X","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87"},{"id":"6de81d9d-e2f2-11eb-945a-af8bc2a60b26","first_name":"Mariana","last_name":"Pereira Guarda","full_name":"Pereira Guarda, Mariana"},{"last_name":"Vlasov","first_name":"Mikhail","full_name":"Vlasov, Mikhail"},{"full_name":"Vlasov, Fedor","last_name":"Vlasov","first_name":"Fedor"},{"first_name":"Andrei","last_name":"Akopian","full_name":"Akopian, Andrei"},{"full_name":"Ratheesh, Aparna","first_name":"Aparna","last_name":"Ratheesh","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"De Renzis","first_name":"Stefano","full_name":"De Renzis, Stefano"},{"full_name":"Siekhaus, Daria E","last_name":"Siekhaus","first_name":"Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"}],"day":"22","oa":1,"doi":"10.1126/science.abj0425","oa_version":"Preprint","publication_identifier":{"issn":["0036-8075"]},"issue":"6591","external_id":{"pmid":["35446632"],"isi":["000788553700039"]},"language":[{"iso":"eng"}],"publication":"Science","title":"Cell division in tissues enables macrophage infiltration","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1101/2021.04.19.438995","open_access":"1"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-04-22T00:00:00Z","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.","article_type":"original"},{"publisher":"Elsevier","department":[{"_id":"DaSi"}],"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"}],"date_updated":"2023-08-02T14:07:13Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"quality_controlled":"1","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.” Developmental Cell. Elsevier, 2022. https://doi.org/10.1016/j.devcel.2022.03.005.","ama":"Martin ET, Blatt P, Ngyuen E, et al. A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis. Developmental Cell. 2022;57(7):883-900.e10. doi:10.1016/j.devcel.2022.03.005","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 et al., “A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis,” Developmental Cell, vol. 57, no. 7. Elsevier, p. 883–900.e10, 2022.","mla":"Martin, Elliot T., et al. “A Translation Control Module Coordinates Germline Stem Cell Differentiation with Ribosome Biogenesis during Drosophila Oogenesis.” Developmental Cell, vol. 57, no. 7, Elsevier, 2022, p. 883–900.e10, doi:10.1016/j.devcel.2022.03.005.","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. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2022.03.005","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."},"volume":57,"page":"883-900.e10","intvolume":" 57","date_created":"2022-02-01T13:15:05Z","isi":1,"month":"04","ec_funded":1,"publication_status":"published","project":[{"grant_number":"334077","call_identifier":"FP7","_id":"2536F660-B435-11E9-9278-68D0E5697425","name":"Investigating the role of transporters in invasive migration through junctions"},{"grant_number":"P29638","call_identifier":"FWF","name":"Drosophila TNFa´s Funktion in Immunzellen","_id":"253B6E48-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Martin, Elliot T.","first_name":"Elliot T.","last_name":"Martin"},{"full_name":"Blatt, Patrick","first_name":"Patrick","last_name":"Blatt"},{"first_name":"Elaine","last_name":"Ngyuen","full_name":"Ngyuen, Elaine"},{"last_name":"Lahr","first_name":"Roni","full_name":"Lahr, Roni"},{"full_name":"Selvam, Sangeetha","first_name":"Sangeetha","last_name":"Selvam"},{"first_name":"Hyun Ah M.","last_name":"Yoon","full_name":"Yoon, Hyun Ah M."},{"full_name":"Pocchiari, Tyler","last_name":"Pocchiari","first_name":"Tyler"},{"full_name":"Emtenani, Shamsi","last_name":"Emtenani","first_name":"Shamsi","orcid":"0000-0001-6981-6938","id":"49D32318-F248-11E8-B48F-1D18A9856A87"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","last_name":"Siekhaus","first_name":"Daria E","full_name":"Siekhaus, Daria E"},{"full_name":"Berman, Andrea","last_name":"Berman","first_name":"Andrea"},{"full_name":"Fuchs, Gabriele","first_name":"Gabriele","last_name":"Fuchs"},{"full_name":"Rangan, Prashanth","first_name":"Prashanth","last_name":"Rangan"}],"type":"journal_article","_id":"10714","year":"2022","doi":"10.1016/j.devcel.2022.03.005","oa_version":"Preprint","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"issue":"7","scopus_import":"1","external_id":{"isi":["000789021800005"]},"day":"11","oa":1,"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","date_published":"2022-04-11T00:00:00Z","article_type":"original","language":[{"iso":"eng"}],"publication":"Developmental Cell","article_processing_charge":"No","title":"A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2021.04.04.438367"}]},{"oa":1,"day":"18","publication_identifier":{"eissn":["1460-2431"],"issn":["0022-0957"]},"external_id":{"pmid":["35085386"],"isi":["000764220900001"]},"issue":"8","scopus_import":"1","oa_version":"Submitted Version","doi":"10.1093/jxb/erac019","main_file_link":[{"url":"https://biblio.ugent.be/publication/8738721","open_access":"1"}],"publication":"Journal of Experimental Botany","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots","date_published":"2022-04-18T00:00:00Z","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.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","status":"public","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.","mla":"Wang, R., et al. “Auxin Analog-Induced Ca2+ Signaling Is Independent of Inhibition of Endosomal Aggregation in Arabidopsis Roots.” Journal of Experimental Botany, vol. 73, no. 8, erac019, Oxford Academic, 2022, doi:10.1093/jxb/erac019.","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. Journal of Experimental Botany. Oxford Academic. https://doi.org/10.1093/jxb/erac019","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).","ieee":"R. Wang et al., “Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots,” Journal of Experimental Botany, vol. 73, no. 8. Oxford Academic, 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. Journal of Experimental Botany. 2022;73(8). doi:10.1093/jxb/erac019","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.” Journal of Experimental Botany. Oxford Academic, 2022. https://doi.org/10.1093/jxb/erac019."},"volume":73,"date_updated":"2023-08-02T14:07:58Z","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"}],"quality_controlled":"1","department":[{"_id":"JiFr"}],"pmid":1,"publisher":"Oxford Academic","type":"journal_article","article_number":"erac019","_id":"10717","year":"2022","project":[{"call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"publication_status":"published","month":"04","ec_funded":1,"isi":1,"author":[{"last_name":"Wang","first_name":"R","full_name":"Wang, R"},{"last_name":"Himschoot","first_name":"E","full_name":"Himschoot, E"},{"first_name":"M","last_name":"Grenzi","full_name":"Grenzi, M"},{"first_name":"J","last_name":"Chen","full_name":"Chen, J"},{"full_name":"Safi, A","last_name":"Safi","first_name":"A"},{"full_name":"Krebs, M","first_name":"M","last_name":"Krebs"},{"last_name":"Schumacher","first_name":"K","full_name":"Schumacher, K"},{"full_name":"Nowack, MK","last_name":"Nowack","first_name":"MK"},{"full_name":"Moeder, W","last_name":"Moeder","first_name":"W"},{"first_name":"K","last_name":"Yoshioka","full_name":"Yoshioka, K"},{"full_name":"Van Damme, D","first_name":"D","last_name":"Van Damme"},{"first_name":"I","last_name":"De Smet","full_name":"De Smet, I"},{"full_name":"Geelen, D","last_name":"Geelen","first_name":"D"},{"first_name":"T","last_name":"Beeckman","full_name":"Beeckman, T"},{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Costa, A","first_name":"A","last_name":"Costa"},{"first_name":"S","last_name":"Vanneste","full_name":"Vanneste, S"}],"intvolume":" 73","date_created":"2022-02-03T09:19:01Z"},{"doi":"10.1111/jipb.13225","oa_version":"Published Version","issue":"2","scopus_import":"1","external_id":{"pmid":["35018726"],"isi":["000761281200011"]},"publication_identifier":{"issn":["1672-9072"],"eissn":["1744-7909"]},"day":"01","oa":1,"status":"public","article_type":"review","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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","title":"Auxin signaling: Research advances over the past 30 years","article_processing_charge":"No","language":[{"iso":"eng"}],"publication":"Journal of Integrative Plant Biology","main_file_link":[{"url":"https://doi.org/10.1111/jipb.13225","open_access":"1"}],"publisher":"Wiley","pmid":1,"department":[{"_id":"JiFr"}],"quality_controlled":"1","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."}],"date_updated":"2023-08-02T14:08:30Z","page":"371-392","volume":64,"citation":{"apa":"Yu, Z., Zhang, F., Friml, J., & Ding, Z. (2022). Auxin signaling: Research advances over the past 30 years. Journal of Integrative Plant Biology. Wiley. https://doi.org/10.1111/jipb.13225","mla":"Yu, Z., et al. “Auxin Signaling: Research Advances over the Past 30 Years.” Journal of Integrative Plant Biology, vol. 64, no. 2, Wiley, 2022, pp. 371–92, doi:10.1111/jipb.13225.","chicago":"Yu, Z, F Zhang, Jiří Friml, and Z Ding. “Auxin Signaling: Research Advances over the Past 30 Years.” Journal of Integrative Plant Biology. Wiley, 2022. https://doi.org/10.1111/jipb.13225.","ama":"Yu Z, Zhang F, Friml J, Ding Z. Auxin signaling: Research advances over the past 30 years. Journal of Integrative Plant Biology. 2022;64(2):371-392. doi:10.1111/jipb.13225","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,” Journal of Integrative Plant Biology, 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."},"date_created":"2022-02-03T09:52:59Z","intvolume":" 64","author":[{"first_name":"Z","last_name":"Yu","full_name":"Yu, Z"},{"first_name":"F","last_name":"Zhang","full_name":"Zhang, F"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Z","last_name":"Ding","full_name":"Ding, Z"}],"isi":1,"month":"02","publication_status":"published","year":"2022","_id":"10719","type":"journal_article"},{"degree_awarded":"PhD","oa":1,"day":"07","oa_version":"Published Version","doi":"10.15479/AT:ISTA:10727","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_id":"10728","checksum":"47ba18bb270dd6cc266e0a3f7c69d0e4","access_level":"closed","date_updated":"2023-02-03T23:30:03Z","embargo_to":"open_access","file_name":"Thesis_Sina_Metzler.docx","date_created":"2022-02-04T15:36:12Z","file_size":6757886,"creator":"smetzler"},{"file_name":"Thesis_Sina_Metzler_A2.pdf","embargo":"2023-02-02","content_type":"application/pdf","relation":"main_file","checksum":"f3ec07d5d6b20ae6e46bfeedebce9027","file_id":"10730","access_level":"open_access","date_updated":"2023-02-03T23:30:03Z","creator":"smetzler","date_created":"2022-02-04T15:36:43Z","file_size":6314921},{"embargo":"2023-02-02","file_name":"Thesis_Sina_Metzler_print.pdf","content_type":"application/pdf","relation":"main_file","file_id":"10742","checksum":"dedd14b7be7a75d63018dbfc68dd8113","access_level":"open_access","date_updated":"2023-02-04T23:30:03Z","creator":"smetzler","date_created":"2022-02-07T10:35:02Z","file_size":6882557}],"publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"title":"Pathogen-mediated sexual selection and immunization in ant colonies","article_processing_charge":"No","file_date_updated":"2023-02-04T23:30:03Z","status":"public","ddc":["570"],"date_published":"2022-02-07T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"supervisor":[{"full_name":"Cremer, Sylvia","last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"date_updated":"2023-09-07T13:43:23Z","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"}],"has_accepted_license":"1","citation":{"ieee":"S. Metzler, “Pathogen-mediated sexual selection and immunization in ant colonies,” Institute of Science and Technology Austria, 2022.","chicago":"Metzler, Sina. “Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:10727.","short":"S. Metzler, Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies, Institute of Science and Technology Austria, 2022.","ama":"Metzler S. Pathogen-mediated sexual selection and immunization in ant colonies. 2022. doi:10.15479/AT:ISTA:10727","mla":"Metzler, Sina. Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies. Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:10727.","apa":"Metzler, S. (2022). Pathogen-mediated sexual selection and immunization in ant colonies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:10727","ista":"Metzler S. 2022. Pathogen-mediated sexual selection and immunization in ant colonies. Institute of Science and Technology Austria."},"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"type":"dissertation","year":"2022","_id":"10727","date_created":"2022-02-04T15:45:12Z","publication_status":"published","project":[{"call_identifier":"H2020","grant_number":"771402","name":"Epidemics in ant societies on a chip","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"month":"02","ec_funded":1,"author":[{"last_name":"Metzler","first_name":"Sina","full_name":"Metzler, Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9547-2494"}]},{"quality_controlled":"1","has_accepted_license":"1","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."}],"date_updated":"2025-07-14T09:10:12Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":12,"citation":{"ista":"Svoboda J, Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2022. Infection dynamics of COVID-19 virus under lockdown and reopening. Scientific Reports. 12(1), 1526.","ieee":"J. Svoboda, J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Infection dynamics of COVID-19 virus under lockdown and reopening,” Scientific Reports, vol. 12, no. 1. Springer Nature, 2022.","short":"J. Svoboda, J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Scientific Reports 12 (2022).","chicago":"Svoboda, Jakub, Josef Tkadlec, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Infection Dynamics of COVID-19 Virus under Lockdown and Reopening.” Scientific Reports. Springer Nature, 2022. https://doi.org/10.1038/s41598-022-05333-5.","ama":"Svoboda J, Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Infection dynamics of COVID-19 virus under lockdown and reopening. Scientific Reports. 2022;12(1). doi:10.1038/s41598-022-05333-5","mla":"Svoboda, Jakub, et al. “Infection Dynamics of COVID-19 Virus under Lockdown and Reopening.” Scientific Reports, vol. 12, no. 1, 1526, Springer Nature, 2022, doi:10.1038/s41598-022-05333-5.","apa":"Svoboda, J., Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2022). Infection dynamics of COVID-19 virus under lockdown and reopening. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-05333-5"},"publisher":"Springer Nature","department":[{"_id":"KrCh"}],"_id":"10731","year":"2022","article_number":"1526","type":"journal_article","date_created":"2022-02-06T23:01:30Z","intvolume":" 12","author":[{"last_name":"Svoboda","first_name":"Jakub","full_name":"Svoboda, Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","orcid":"0000-0002-1419-3267"},{"last_name":"Tkadlec","first_name":"Josef","full_name":"Tkadlec, Josef"},{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"},{"first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"ec_funded":1,"isi":1,"month":"01","publication_status":"published","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020"}],"day":"27","oa":1,"doi":"10.1038/s41598-022-05333-5","oa_version":"Published Version","scopus_import":"1","issue":"1","external_id":{"isi":["000749198000039"],"arxiv":["2012.15155"]},"publication_identifier":{"eissn":["2045-2322"]},"file":[{"success":1,"creator":"alisjak","date_created":"2022-02-07T14:57:59Z","file_size":2971922,"file_name":"2022_ScientificReports_Svoboda.pdf","content_type":"application/pdf","relation":"main_file","date_updated":"2022-02-07T14:57:59Z","access_level":"open_access","checksum":"247afd30c173390940f099ead35a28ed","file_id":"10744"}],"arxiv":1,"title":"Infection dynamics of COVID-19 virus under lockdown and reopening","article_processing_charge":"No","language":[{"iso":"eng"}],"publication":"Scientific Reports","file_date_updated":"2022-02-07T14:57:59Z","ddc":["570"],"status":"public","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-01-27T00:00:00Z","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."},{"_id":"10732","year":"2022","article_number":"109394","type":"journal_article","author":[{"full_name":"Cipolloni, Giorgio","last_name":"Cipolloni","first_name":"Giorgio","orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Erdös, László","first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","first_name":"Dominik J","last_name":"Schröder"}],"isi":1,"month":"04","publication_status":"published","date_created":"2022-02-06T23:01:30Z","intvolume":" 282","citation":{"apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2022). Thermalisation for Wigner matrices. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2022.109394","mla":"Cipolloni, Giorgio, et al. “Thermalisation for Wigner Matrices.” Journal of Functional Analysis, vol. 282, no. 8, 109394, Elsevier, 2022, doi:10.1016/j.jfa.2022.109394.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Thermalisation for Wigner Matrices.” Journal of Functional Analysis. Elsevier, 2022. https://doi.org/10.1016/j.jfa.2022.109394.","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. Journal of Functional Analysis. 2022;282(8). doi:10.1016/j.jfa.2022.109394","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Thermalisation for Wigner matrices,” Journal of Functional Analysis, vol. 282, no. 8. Elsevier, 2022.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2022. Thermalisation for Wigner matrices. Journal of Functional Analysis. 282(8), 109394."},"volume":282,"has_accepted_license":"1","quality_controlled":"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."}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-02T14:12:35Z","department":[{"_id":"LaEr"}],"publisher":"Elsevier","file_date_updated":"2022-07-29T07:22:08Z","arxiv":1,"title":"Thermalisation for Wigner matrices","article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"publication":"Journal of Functional Analysis","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-04-15T00:00:00Z","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.","ddc":["500"],"status":"public","day":"15","oa":1,"issue":"8","scopus_import":"1","external_id":{"arxiv":["2102.09975"],"isi":["000781239100004"]},"file":[{"creator":"dernst","success":1,"file_size":652573,"date_created":"2022-07-29T07:22:08Z","file_name":"2022_JourFunctionalAnalysis_Cipolloni.pdf","file_id":"11690","checksum":"b75fdad606ab507dc61109e0907d86c0","date_updated":"2022-07-29T07:22:08Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"doi":"10.1016/j.jfa.2022.109394","oa_version":"Published Version"},{"_id":"10733","year":"2022","article_number":"39","type":"journal_article","date_created":"2022-02-06T23:01:30Z","intvolume":" 24","author":[{"full_name":"Espinosa, M.","first_name":"M.","last_name":"Espinosa"},{"last_name":"Diaz Melian","first_name":"Vicente L","full_name":"Diaz Melian, Vicente L","id":"b6798902-eea0-11ea-9cbc-a8e14286c631"},{"last_name":"Serrano-Muñoz","first_name":"A.","full_name":"Serrano-Muñoz, A."},{"full_name":"Altshuler, E.","last_name":"Altshuler","first_name":"E."}],"month":"01","isi":1,"publication_status":"published","quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"date_updated":"2023-08-02T14:10:13Z","volume":24,"citation":{"apa":"Espinosa, M., Diaz Melian, V. L., Serrano-Muñoz, A., & Altshuler, E. (2022). Intruders cooperatively interact with a wall into granular matter. Granular Matter. Springer Nature. https://doi.org/10.1007/s10035-021-01200-8","mla":"Espinosa, M., et al. “Intruders Cooperatively Interact with a Wall into Granular Matter.” Granular Matter, vol. 24, no. 1, 39, Springer Nature, 2022, doi:10.1007/s10035-021-01200-8.","ieee":"M. Espinosa, V. L. Diaz Melian, A. Serrano-Muñoz, and E. Altshuler, “Intruders cooperatively interact with a wall into granular matter,” Granular Matter, vol. 24, no. 1. Springer Nature, 2022.","ama":"Espinosa M, Diaz Melian VL, Serrano-Muñoz A, Altshuler E. Intruders cooperatively interact with a wall into granular matter. Granular Matter. 2022;24(1). doi:10.1007/s10035-021-01200-8","chicago":"Espinosa, M., Vicente L Diaz Melian, A. Serrano-Muñoz, and E. Altshuler. “Intruders Cooperatively Interact with a Wall into Granular Matter.” Granular Matter. Springer Nature, 2022. https://doi.org/10.1007/s10035-021-01200-8.","short":"M. Espinosa, V.L. Diaz Melian, A. Serrano-Muñoz, E. Altshuler, Granular Matter 24 (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."},"publisher":"Springer Nature","department":[{"_id":"ScWa"}],"keyword":["granular matter","boundary effects","intruder penetration","sedimentation"],"arxiv":1,"title":"Intruders cooperatively interact with a wall into granular matter","article_processing_charge":"No","language":[{"iso":"eng"}],"publication":"Granular Matter","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2110.15311"}],"status":"public","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","date_published":"2022-01-24T00:00:00Z","day":"24","oa":1,"doi":"10.1007/s10035-021-01200-8","oa_version":"Preprint","scopus_import":"1","issue":"1","external_id":{"isi":["000746623000001"],"arxiv":["2110.15311"]},"publication_identifier":{"issn":["1434-5021"],"eissn":["1434-7636"]}},{"pmid":1,"publisher":"IOP Publishing","department":[{"_id":"KiMo"}],"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."}],"date_updated":"2023-08-02T14:12:01Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","quality_controlled":"1","citation":{"chicago":"Nauman, Muhammad, Tayyaba Hussain, Joonyoung Choi, Nara Lee, Young Jai Choi, Woun Kang, and Younjung Jo. “Low-Field Magnetic Anisotropy of Sr2IrO4.” Journal of Physics: Condensed Matter. IOP Publishing, 2022. https://doi.org/10.1088/1361-648X/ac484d.","ama":"Nauman M, Hussain T, Choi J, et al. Low-field magnetic anisotropy of Sr2IrO4. Journal of physics: Condensed matter. 2022;34(13). doi:10.1088/1361-648X/ac484d","ieee":"M. Nauman et al., “Low-field magnetic anisotropy of Sr2IrO4,” Journal of physics: Condensed matter, vol. 34, no. 13. IOP Publishing, 2022.","short":"M. Nauman, T. Hussain, J. Choi, N. Lee, Y.J. Choi, W. Kang, Y. Jo, Journal of Physics: Condensed Matter 34 (2022).","mla":"Nauman, Muhammad, et al. “Low-Field Magnetic Anisotropy of Sr2IrO4.” Journal of Physics: Condensed Matter, vol. 34, no. 13, 135802, IOP Publishing, 2022, doi:10.1088/1361-648X/ac484d.","apa":"Nauman, M., Hussain, T., Choi, J., Lee, N., Choi, Y. J., Kang, W., & Jo, Y. (2022). Low-field magnetic anisotropy of Sr2IrO4. Journal of Physics: Condensed Matter. IOP Publishing. https://doi.org/10.1088/1361-648X/ac484d","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."},"volume":34,"intvolume":" 34","date_created":"2022-02-06T23:01:31Z","isi":1,"month":"01","publication_status":"published","author":[{"orcid":"0000-0002-2111-4846","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","last_name":"Nauman","first_name":"Muhammad","full_name":"Nauman, Muhammad"},{"full_name":"Hussain, Tayyaba","first_name":"Tayyaba","last_name":"Hussain"},{"first_name":"Joonyoung","last_name":"Choi","full_name":"Choi, Joonyoung"},{"last_name":"Lee","first_name":"Nara","full_name":"Lee, Nara"},{"full_name":"Choi, Young Jai","last_name":"Choi","first_name":"Young Jai"},{"first_name":"Woun","last_name":"Kang","full_name":"Kang, Woun"},{"full_name":"Jo, Younjung","last_name":"Jo","first_name":"Younjung"}],"article_number":"135802","type":"journal_article","_id":"10735","year":"2022","doi":"10.1088/1361-648X/ac484d","oa_version":"Published Version","file":[{"date_created":"2022-02-07T10:35:28Z","file_size":1742414,"success":1,"creator":"cchlebak","content_type":"application/pdf","relation":"main_file","date_updated":"2022-02-07T10:35:28Z","access_level":"open_access","file_id":"10741","checksum":"b6c705c7f03dcb1dbcb06b1b4d4938d6","file_name":"2022_JPhysCondensMatter_Nauman.pdf"}],"publication_identifier":{"eissn":["1361-648X"]},"scopus_import":"1","issue":"13","external_id":{"pmid":["34986467"],"isi":["000775191800001"]},"day":"20","oa":1,"status":"public","ddc":["530"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-01-20T00:00:00Z","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).","article_type":"original","language":[{"iso":"eng"}],"publication":"Journal of physics: Condensed matter","title":"Low-field magnetic anisotropy of Sr2IrO4","article_processing_charge":"No","file_date_updated":"2022-02-07T10:35:28Z"},{"publication_identifier":{"eissn":["2050-084X"]},"file":[{"file_name":"2022_ELife_Lagator.pdf","access_level":"open_access","date_updated":"2022-02-07T07:14:09Z","checksum":"decdcdf600ff51e9a9703b49ca114170","file_id":"10739","content_type":"application/pdf","relation":"main_file","creator":"cchlebak","success":1,"file_size":5604343,"date_created":"2022-02-07T07:14:09Z"}],"scopus_import":"1","external_id":{"isi":["000751104400001"],"pmid":["35080492"]},"doi":"10.7554/eLife.64543","oa_version":"Published Version","day":"26","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","date_published":"2022-01-26T00:00:00Z","article_type":"original","status":"public","ddc":["576"],"file_date_updated":"2022-02-07T07:14:09Z","language":[{"iso":"eng"}],"publication":"eLife","title":"Predicting bacterial promoter function and evolution from random sequences","article_processing_charge":"No","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"NiBa"}],"pmid":1,"publisher":"eLife Sciences Publications","volume":11,"citation":{"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.","chicago":"Lagator, Mato, Srdjan Sarikas, Magdalena Steinrueck, David Toledo-Aparicio, Jonathan P Bollback, Calin C Guet, and Gašper Tkačik. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/eLife.64543.","short":"M. Lagator, S. Sarikas, M. Steinrueck, D. Toledo-Aparicio, J.P. Bollback, C.C. Guet, G. Tkačik, ELife 11 (2022).","ama":"Lagator M, Sarikas S, Steinrueck M, et al. Predicting bacterial promoter function and evolution from random sequences. eLife. 2022;11. doi:10.7554/eLife.64543","ieee":"M. Lagator et al., “Predicting bacterial promoter function and evolution from random sequences,” eLife, vol. 11. eLife Sciences Publications, 2022.","mla":"Lagator, Mato, et al. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” ELife, vol. 11, e64543, eLife Sciences Publications, 2022, doi:10.7554/eLife.64543.","apa":"Lagator, M., Sarikas, S., Steinrueck, M., Toledo-Aparicio, D., Bollback, J. P., Guet, C. C., & Tkačik, G. (2022). Predicting bacterial promoter function and evolution from random sequences. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.64543"},"abstract":[{"lang":"eng","text":"Predicting function from sequence is a central problem of biology. Currently, this is possible only locally in a narrow mutational neighborhood around a wildtype sequence rather than globally from any sequence. Using random mutant libraries, we developed a biophysical model that accounts for multiple features of σ70 binding bacterial promoters to predict constitutive gene expression levels from any sequence. We experimentally and theoretically estimated that 10–20% of random sequences lead to expression and ~80% of non-expressing sequences are one mutation away from a functional promoter. The potential for generating expression from random sequences is so pervasive that selection acts against σ70-RNA polymerase binding sites even within inter-genic, promoter-containing regions. This pervasiveness of σ70-binding sites implies that emergence of promoters is not the limiting step in gene regulatory evolution. Ultimately, the inclusion of novel features of promoter function into a mechanistic model enabled not only more accurate predictions of gene expression levels, but also identified that promoters evolve more rapidly than previously thought."}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-02T14:09:02Z","has_accepted_license":"1","quality_controlled":"1","month":"01","ec_funded":1,"isi":1,"project":[{"grant_number":"648440","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato","full_name":"Lagator, Mato"},{"id":"35F0286E-F248-11E8-B48F-1D18A9856A87","full_name":"Sarikas, Srdjan","last_name":"Sarikas","first_name":"Srdjan"},{"last_name":"Steinrueck","first_name":"Magdalena","full_name":"Steinrueck, Magdalena"},{"full_name":"Toledo-Aparicio, David","last_name":"Toledo-Aparicio","first_name":"David"},{"orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P","full_name":"Bollback, Jonathan P"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper"}],"intvolume":" 11","date_created":"2022-02-06T23:01:32Z","article_number":"e64543","type":"journal_article","_id":"10736","year":"2022"},{"intvolume":" 26","date_created":"2022-02-06T23:01:32Z","month":"01","isi":1,"publication_status":"published","author":[{"full_name":"Takhanov, Rustem","last_name":"Takhanov","first_name":"Rustem","id":"2CCAC26C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","year":"2022","_id":"10737","publisher":"IOS Press","department":[{"_id":"VlKo"}],"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."}],"date_updated":"2023-08-02T14:09:41Z","quality_controlled":"1","page":"257-272","volume":26,"citation":{"apa":"Takhanov, R., & Kolmogorov, V. (2022). Combining pattern-based CRFs and weighted context-free grammars. Intelligent Data Analysis. IOS Press. https://doi.org/10.3233/IDA-205623","mla":"Takhanov, Rustem, and Vladimir Kolmogorov. “Combining Pattern-Based CRFs and Weighted Context-Free Grammars.” Intelligent Data Analysis, vol. 26, no. 1, IOS Press, 2022, pp. 257–72, doi:10.3233/IDA-205623.","ieee":"R. Takhanov and V. Kolmogorov, “Combining pattern-based CRFs and weighted context-free grammars,” Intelligent Data Analysis, vol. 26, no. 1. IOS Press, pp. 257–272, 2022.","short":"R. Takhanov, V. Kolmogorov, Intelligent Data Analysis 26 (2022) 257–272.","chicago":"Takhanov, Rustem, and Vladimir Kolmogorov. “Combining Pattern-Based CRFs and Weighted Context-Free Grammars.” Intelligent Data Analysis. IOS Press, 2022. https://doi.org/10.3233/IDA-205623.","ama":"Takhanov R, Kolmogorov V. Combining pattern-based CRFs and weighted context-free grammars. Intelligent Data Analysis. 2022;26(1):257-272. doi:10.3233/IDA-205623","ista":"Takhanov R, Kolmogorov V. 2022. Combining pattern-based CRFs and weighted context-free grammars. Intelligent Data Analysis. 26(1), 257–272."},"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-01-14T00:00:00Z","article_type":"original","language":[{"iso":"eng"}],"publication":"Intelligent Data Analysis","arxiv":1,"article_processing_charge":"No","title":"Combining pattern-based CRFs and weighted context-free grammars","main_file_link":[{"url":"https://arxiv.org/abs/1404.5475","open_access":"1"}],"doi":"10.3233/IDA-205623","oa_version":"Preprint","publication_identifier":{"eissn":["1571-4128"],"issn":["1088-467X"]},"scopus_import":"1","issue":"1","external_id":{"isi":["000749997700015"],"arxiv":["1404.5475"]},"day":"14","oa":1},{"year":"2022","_id":"10753","type":"journal_article","date_created":"2022-02-13T23:01:34Z","intvolume":" 110","author":[{"id":"C7610134-B532-11EA-BD9F-F5753DDC885E","first_name":"Basile J","last_name":"Confavreux","full_name":"Confavreux, Basile J"},{"orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","full_name":"Vogels, Tim P","first_name":"Tim P","last_name":"Vogels"}],"publication_status":"published","month":"02","isi":1,"quality_controlled":"1","date_updated":"2023-10-03T10:53:17Z","abstract":[{"lang":"eng","text":"This is a comment on \"Meta-learning synaptic plasticity and memory addressing for continual familiarity detection.\" Neuron. 2022 Feb 2;110(3):544-557.e8."}],"volume":110,"citation":{"ista":"Confavreux BJ, Vogels TP. 2022. A familiar thought: Machines that replace us? Neuron. 110(3), 361–362.","short":"B.J. Confavreux, T.P. Vogels, Neuron 110 (2022) 361–362.","ama":"Confavreux BJ, Vogels TP. A familiar thought: Machines that replace us? Neuron. 2022;110(3):361-362. doi:10.1016/j.neuron.2022.01.014","ieee":"B. J. Confavreux and T. P. Vogels, “A familiar thought: Machines that replace us?,” Neuron, vol. 110, no. 3. Elsevier, pp. 361–362, 2022.","chicago":"Confavreux, Basile J, and Tim P Vogels. “A Familiar Thought: Machines That Replace Us?” Neuron. Elsevier, 2022. https://doi.org/10.1016/j.neuron.2022.01.014.","apa":"Confavreux, B. J., & Vogels, T. P. (2022). A familiar thought: Machines that replace us? Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2022.01.014","mla":"Confavreux, Basile J., and Tim P. Vogels. “A Familiar Thought: Machines That Replace Us?” Neuron, vol. 110, no. 3, Elsevier, 2022, pp. 361–62, doi:10.1016/j.neuron.2022.01.014."},"page":"361-362","publisher":"Elsevier","pmid":1,"department":[{"_id":"TiVo"}],"article_processing_charge":"No","title":"A familiar thought: Machines that replace us?","publication":"Neuron","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2022.01.014","open_access":"1"}],"status":"public","article_type":"letter_note","date_published":"2022-02-02T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"day":"02","oa_version":"Published Version","doi":"10.1016/j.neuron.2022.01.014","external_id":{"pmid":["35114107"],"isi":["000751819100005"]},"scopus_import":"1","issue":"3","publication_identifier":{"eissn":["1097-4199"]}},{"file":[{"file_name":"2022_IJMS_Chang.pdf","access_level":"open_access","date_updated":"2022-02-14T07:46:30Z","file_id":"10756","checksum":"8890ad20c54e90dc58ad5ea97c902998","relation":"main_file","content_type":"application/pdf","success":1,"creator":"dernst","file_size":24416183,"date_created":"2022-02-14T07:46:30Z"}],"publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"issue":"3","scopus_import":"1","external_id":{"isi":["000754773500001"]},"doi":"10.3390/ijms23031763","oa_version":"Published Version","day":"01","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","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.). ","date_published":"2022-02-01T00:00:00Z","article_type":"original","status":"public","ddc":["510","576"],"file_date_updated":"2022-02-14T07:46:30Z","language":[{"iso":"eng"}],"publication":"International Journal of Molecular Sciences","article_processing_charge":"Yes","title":"Developing a mathematical model of intracellular Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer","department":[{"_id":"HeEd"}],"publisher":"MDPI","citation":{"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.","ama":"Chang Y, Funk M, Roy S, et al. Developing a mathematical model of intracellular Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer. International Journal of Molecular Sciences. 2022;23(3). doi:10.3390/ijms23031763","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 et al., “Developing a mathematical model of intracellular Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer,” International Journal of Molecular Sciences, vol. 23, no. 3. MDPI, 2022.","chicago":"Chang, Yan, Marah Funk, Souvik Roy, Elizabeth R Stephenson, Sangyong Choi, Hristo V. Kojouharov, Benito Chen, and Zui Pan. “Developing a Mathematical Model of Intracellular Calcium Dynamics for Evaluating Combined Anticancer Effects of Afatinib and RP4010 in Esophageal Cancer.” International Journal of Molecular Sciences. MDPI, 2022. https://doi.org/10.3390/ijms23031763.","mla":"Chang, Yan, et al. “Developing a Mathematical Model of Intracellular Calcium Dynamics for Evaluating Combined Anticancer Effects of Afatinib and RP4010 in Esophageal Cancer.” International Journal of Molecular Sciences, vol. 23, no. 3, 1763, MDPI, 2022, doi:10.3390/ijms23031763.","apa":"Chang, Y., Funk, M., Roy, S., Stephenson, E. R., Choi, S., Kojouharov, H. V., … Pan, Z. (2022). Developing a mathematical model of intracellular Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms23031763"},"volume":23,"abstract":[{"text":"Targeting dysregulated Ca2+ signaling in cancer cells is an emerging chemotherapy approach. We previously reported that store-operated Ca2+ entry (SOCE) blockers, such as RP4010, are promising antitumor drugs for esophageal cancer. As a tyrosine kinase inhibitor (TKI), afatinib received FDA approval to be used in targeted therapy for patients with EGFR mutation-positive cancers. While preclinical studies and clinical trials have shown that afatinib has benefits for esophageal cancer patients, it is not known whether a combination of afatinib and RP4010 could achieve better anticancer effects. Since TKI can alter intracellular Ca2+ dynamics through EGFR/phospholipase C-γ pathway, in this study, we evaluated the inhibitory effect of afatinib and RP4010 on intracellular Ca2+ oscillations in KYSE-150, a human esophageal squamous cell carcinoma cell line, using both experimental and mathematical simulations. Our mathematical simulation of Ca2+ oscillations could fit well with experimental data responding to afatinib or RP4010, both separately or in combination. Guided by simulation, we were able to identify a proper ratio of afatinib and RP4010 for combined treatment, and such a combination presented synergistic anticancer-effect evidence by experimental measurement of intracellular Ca2+ and cell proliferation. This intracellular Ca2+ dynamic-based mathematical simulation approach could be useful for a rapid and cost-effective evaluation of combined targeting therapy drugs.","lang":"eng"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-09T10:17:07Z","quality_controlled":"1","has_accepted_license":"1","month":"02","isi":1,"publication_status":"published","author":[{"last_name":"Chang","first_name":"Yan","full_name":"Chang, Yan"},{"full_name":"Funk, Marah","last_name":"Funk","first_name":"Marah"},{"first_name":"Souvik","last_name":"Roy","full_name":"Roy, Souvik"},{"id":"2D04F932-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-208X","full_name":"Stephenson, Elizabeth R","last_name":"Stephenson","first_name":"Elizabeth R"},{"full_name":"Choi, Sangyong","last_name":"Choi","first_name":"Sangyong"},{"first_name":"Hristo V.","last_name":"Kojouharov","full_name":"Kojouharov, Hristo V."},{"first_name":"Benito","last_name":"Chen","full_name":"Chen, Benito"},{"full_name":"Pan, Zui","last_name":"Pan","first_name":"Zui"}],"intvolume":" 23","date_created":"2022-02-13T23:01:35Z","article_number":"1763","type":"journal_article","year":"2022","_id":"10754"},{"month":"01","ec_funded":1,"publication_status":"published","project":[{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227"},{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Feliciangeli, Dario","first_name":"Dario","last_name":"Feliciangeli","orcid":"0000-0003-0754-8530","id":"41A639AA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5059-4466","id":"856966FE-A408-11E9-977E-802DE6697425","first_name":"Simone Anna Elvira","last_name":"Rademacher","full_name":"Rademacher, Simone Anna Elvira"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert"}],"intvolume":" 55","date_created":"2022-02-13T23:01:35Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"9791"}]},"article_number":"015201","type":"journal_article","year":"2022","_id":"10755","department":[{"_id":"RoSe"}],"publisher":"IOP Publishing","citation":{"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.","mla":"Feliciangeli, Dario, et al. “The Effective Mass Problem for the Landau-Pekar Equations.” Journal of Physics A: Mathematical and Theoretical, vol. 55, no. 1, 015201, IOP Publishing, 2022, doi:10.1088/1751-8121/ac3947.","apa":"Feliciangeli, D., Rademacher, S. A. E., & Seiringer, R. (2022). The effective mass problem for the Landau-Pekar equations. Journal of Physics A: Mathematical and Theoretical. IOP Publishing. https://doi.org/10.1088/1751-8121/ac3947","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,” Journal of Physics A: Mathematical and Theoretical, vol. 55, no. 1. IOP Publishing, 2022.","chicago":"Feliciangeli, Dario, Simone Anna Elvira Rademacher, and Robert Seiringer. “The Effective Mass Problem for the Landau-Pekar Equations.” Journal of Physics A: Mathematical and Theoretical. IOP Publishing, 2022. https://doi.org/10.1088/1751-8121/ac3947.","ama":"Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for the Landau-Pekar equations. Journal of Physics A: Mathematical and Theoretical. 2022;55(1). doi:10.1088/1751-8121/ac3947"},"volume":55,"abstract":[{"lang":"eng","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)."}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2024-03-06T12:30:44Z","has_accepted_license":"1","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-01-19T00:00:00Z","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.","article_type":"original","status":"public","ddc":["510"],"file_date_updated":"2022-02-14T08:20:19Z","language":[{"iso":"eng"}],"publication":"Journal of Physics A: Mathematical and Theoretical","arxiv":1,"title":"The effective mass problem for the Landau-Pekar equations","article_processing_charge":"Yes (via OA deal)","file":[{"file_size":1132380,"date_created":"2022-02-14T08:20:19Z","success":1,"creator":"dernst","date_updated":"2022-02-14T08:20:19Z","access_level":"open_access","file_id":"10757","checksum":"0875e562705563053d6dd98fba4d8578","relation":"main_file","content_type":"application/pdf","file_name":"2022_JournalPhysicsA_Feliciangeli.pdf"}],"publication_identifier":{"eissn":["1751-8121"],"issn":["1751-8113"]},"issue":"1","scopus_import":"1","external_id":{"arxiv":["2107.03720"]},"doi":"10.1088/1751-8121/ac3947","oa_version":"Published Version","day":"19","oa":1},{"oa":1,"day":"11","external_id":{"pmid":["35637781"]},"scopus_import":"1","issue":"3","publication_identifier":{"eissn":["2694-2445"]},"file":[{"content_type":"application/pdf","relation":"main_file","file_id":"11692","checksum":"5ce3f907848f5c7caf77f1adfe5826c6","access_level":"open_access","date_updated":"2022-07-29T07:53:20Z","file_name":"2022_ACSPhysChemAU_Dubini.pdf","date_created":"2022-07-29T07:53:20Z","file_size":2351220,"creator":"dernst","success":1}],"oa_version":"Published Version","doi":"10.1021/acsphyschemau.1c00050","file_date_updated":"2022-07-29T07:53:20Z","title":"1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives","article_processing_charge":"Yes (via OA deal)","publication":"ACS Physical Chemistry Au","language":[{"iso":"eng"}],"article_type":"original","date_published":"2022-02-11T00:00:00Z","acknowledgement":"We thank Markus Müller for valued discussions and Felix Xu for assistance in the measurement of UV/vis melting profiles. This work was supported in part by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – SFB 1309-325871075, EU-ITN LightDyNAmics (ID: 765266), the ERC-AG EpiR (ID: 741912), the Center for NanoScience, the Excellence Clusters CIPSM, and the Fonds der Chemischen Industrie. Open access funding provided by Institute of Science and Technology Austria (ISTA).\r\n\r\n","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["540"],"status":"public","volume":2,"citation":{"ieee":"R. C. A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, and P. Rovo, “1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives,” ACS Physical Chemistry Au, vol. 2, no. 3. American Chemical Society, pp. 237–246, 2022.","short":"R.C.A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, P. Rovo, ACS Physical Chemistry Au 2 (2022) 237–246.","chicago":"Dubini, Romeo C. A., Eva Korytiaková, Thea Schinkel, Pia Heinrichs, Thomas Carell, and Petra Rovo. “1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives.” ACS Physical Chemistry Au. American Chemical Society, 2022. https://doi.org/10.1021/acsphyschemau.1c00050.","ama":"Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. 2022;2(3):237-246. doi:10.1021/acsphyschemau.1c00050","mla":"Dubini, Romeo C. A., et al. “1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives.” ACS Physical Chemistry Au, vol. 2, no. 3, American Chemical Society, 2022, pp. 237–46, doi:10.1021/acsphyschemau.1c00050.","apa":"Dubini, R. C. A., Korytiaková, E., Schinkel, T., Heinrichs, P., Carell, T., & Rovo, P. (2022). 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. American Chemical Society. https://doi.org/10.1021/acsphyschemau.1c00050","ista":"Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 2022. 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. 2(3), 237–246."},"page":"237-246","has_accepted_license":"1","quality_controlled":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-01-31T07:33:07Z","abstract":[{"text":"5-Carboxycytosine (5caC) is a rare epigenetic modification found in nucleic acids of all domains of life. Despite its sparse genomic abundance, 5caC is presumed to play essential regulatory roles in transcription, maintenance and base-excision processes in DNA. In this work, we utilize nuclear magnetic resonance (NMR) spectroscopy to address the effects of 5caC incorporation into canonical DNA strands at multiple pH and temperature conditions. Our results demonstrate that 5caC has a pH-dependent global destabilizing and a base-pair mobility enhancing local impact on dsDNA, albeit without any detectable influence on the ground-state B-DNA structure. Measurement of hybridization thermodynamics and kinetics of 5caC-bearing DNA duplexes highlighted how acidic environment (pH 5.8 and 4.7) destabilizes the double-stranded structure by ∼10–20 kJ mol–1 at 37 °C when compared to the same sample at neutral pH. Protonation of 5caC results in a lower activation energy for the dissociation process and a higher barrier for annealing. Studies on conformational exchange on the microsecond time scale regime revealed a sharply localized base-pair motion involving exclusively the modified site and its immediate surroundings. By direct comparison with canonical and 5-formylcytosine (5fC)-edited strands, we were able to address the impact of the two most oxidized naturally occurring cytosine derivatives in the genome. These insights on 5caC’s subtle sensitivity to acidic pH contribute to the long-standing questions of its capacity as a substrate in base excision repair processes and its purpose as an independent, stable epigenetic mark.","lang":"eng"}],"department":[{"_id":"NMR"}],"publisher":"American Chemical Society","pmid":1,"year":"2022","_id":"10758","type":"journal_article","related_material":{"link":[{"relation":"earlier_version","url":"https://www.biorxiv.org/content/10.1101/2021.12.14.472563"}]},"author":[{"last_name":"Dubini","first_name":"Romeo C. A.","full_name":"Dubini, Romeo C. A."},{"full_name":"Korytiaková, Eva","first_name":"Eva","last_name":"Korytiaková"},{"last_name":"Schinkel","first_name":"Thea","full_name":"Schinkel, Thea"},{"full_name":"Heinrichs, Pia","first_name":"Pia","last_name":"Heinrichs"},{"full_name":"Carell, Thomas","last_name":"Carell","first_name":"Thomas"},{"full_name":"Rovo, Petra","last_name":"Rovo","first_name":"Petra","orcid":"0000-0001-8729-7326","id":"c316e53f-b965-11eb-b128-bb26acc59c00"}],"publication_status":"published","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"month":"02","date_created":"2022-02-16T11:18:21Z","intvolume":" 2"},{"page":"120","citation":{"mla":"Rzadkowski, Wojciech. Analytic and Machine Learning Approaches to Composite Quantum Impurities. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:10759.","apa":"Rzadkowski, W. (2022). Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10759","ieee":"W. Rzadkowski, “Analytic and machine learning approaches to composite quantum impurities,” Institute of Science and Technology Austria, 2022.","short":"W. Rzadkowski, Analytic and Machine Learning Approaches to Composite Quantum Impurities, Institute of Science and Technology Austria, 2022.","chicago":"Rzadkowski, Wojciech. “Analytic and Machine Learning Approaches to Composite Quantum Impurities.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:10759.","ama":"Rzadkowski W. Analytic and machine learning approaches to composite quantum impurities. 2022. doi:10.15479/at:ista:10759","ista":"Rzadkowski W. 2022. Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria."},"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."}],"supervisor":[{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail"}],"date_updated":"2024-08-07T07:16:53Z","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"MiLe"}],"publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"status":"public","id":"10762","relation":"part_of_dissertation"},{"id":"7956","status":"public","relation":"part_of_dissertation"},{"id":"415","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"8644","relation":"part_of_dissertation"}]},"type":"dissertation","year":"2022","_id":"10759","month":"02","ec_funded":1,"project":[{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","author":[{"full_name":"Rzadkowski, Wojciech","first_name":"Wojciech","last_name":"Rzadkowski","id":"48C55298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1106-4419"}],"date_created":"2022-02-16T13:27:37Z","day":"21","oa":1,"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"file":[{"date_created":"2022-02-21T13:58:16Z","file_size":17668233,"creator":"wrzadkow","relation":"source_file","content_type":"application/zip","checksum":"0fc54ad1eaede879c665ac9b53c93e22","file_id":"10785","date_updated":"2022-02-22T07:20:12Z","access_level":"closed","file_name":"Rzadkowski_thesis_final_source.zip"},{"file_id":"10786","checksum":"22d2d7af37ca31f6b1730c26cac7bced","access_level":"open_access","date_updated":"2022-02-21T14:02:54Z","relation":"main_file","content_type":"application/pdf","file_name":"Rzadkowski_thesis_final.pdf","file_size":13307331,"date_created":"2022-02-21T14:02:54Z","creator":"wrzadkow","success":1}],"doi":"10.15479/at:ista:10759","oa_version":"Published Version","file_date_updated":"2022-02-22T07:20:12Z","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"Analytic and machine learning approaches to composite quantum impurities","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"date_published":"2022-02-21T00:00:00Z","status":"public","ddc":["530"]}]