[{"type":"journal_article","status":"public","author":[{"last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","full_name":"Erdös, László"},{"last_name":"McKenna","id":"b0cc634c-d549-11ee-96c8-87338c7ad808","orcid":"0000-0003-2625-495X","first_name":"Benjamin","full_name":"McKenna, Benjamin"}],"arxiv":1,"month":"02","publication_identifier":{"issn":["1050-5164"]},"oa_version":"Preprint","day":"01","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2208.12206","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication":"Annals of Applied Probability","oa":1,"date_updated":"2024-02-27T08:29:05Z","issue":"1B","article_processing_charge":"No","title":"Extremal statistics of quadratic forms of GOE/GUE eigenvectors","scopus_import":"1","intvolume":"        34","project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331","call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"publisher":"Institute of Mathematical Statistics","date_published":"2024-02-01T00:00:00Z","department":[{"_id":"LaEr"}],"page":"1623-1662","volume":34,"quality_controlled":"1","publication_status":"published","external_id":{"arxiv":["2208.12206"]},"abstract":[{"lang":"eng","text":"We consider quadratic forms of deterministic matrices A evaluated at the random eigenvectors of a large N×N GOE or GUE matrix, or equivalently evaluated at the columns of a Haar-orthogonal or Haar-unitary random matrix. We prove that, as long as the deterministic matrix has rank much smaller than √N, the distributions of the extrema of these quadratic forms are asymptotically the same as if the eigenvectors were independent Gaussians. This reduces the problem to Gaussian computations, which we carry out in several cases to illustrate our result, finding Gumbel or Weibull limiting distributions depending on the signature of A. Our result also naturally applies to the eigenvectors of any invariant ensemble."}],"article_type":"original","_id":"15025","doi":"10.1214/23-AAP2000","acknowledgement":"The first author was supported by the ERC Advanced Grant “RMTBeyond” No. 101020331. The second author was supported by Fulbright Austria and the Austrian Marshall Plan Foundation.","year":"2024","date_created":"2024-02-25T23:00:56Z","citation":{"ista":"Erdös L, McKenna B. 2024. Extremal statistics of quadratic forms of GOE/GUE eigenvectors. Annals of Applied Probability. 34(1B), 1623–1662.","chicago":"Erdös, László, and Benjamin McKenna. “Extremal Statistics of Quadratic Forms of GOE/GUE Eigenvectors.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2024. <a href=\"https://doi.org/10.1214/23-AAP2000\">https://doi.org/10.1214/23-AAP2000</a>.","mla":"Erdös, László, and Benjamin McKenna. “Extremal Statistics of Quadratic Forms of GOE/GUE Eigenvectors.” <i>Annals of Applied Probability</i>, vol. 34, no. 1B, Institute of Mathematical Statistics, 2024, pp. 1623–62, doi:<a href=\"https://doi.org/10.1214/23-AAP2000\">10.1214/23-AAP2000</a>.","short":"L. Erdös, B. McKenna, Annals of Applied Probability 34 (2024) 1623–1662.","ieee":"L. Erdös and B. McKenna, “Extremal statistics of quadratic forms of GOE/GUE eigenvectors,” <i>Annals of Applied Probability</i>, vol. 34, no. 1B. Institute of Mathematical Statistics, pp. 1623–1662, 2024.","ama":"Erdös L, McKenna B. Extremal statistics of quadratic forms of GOE/GUE eigenvectors. <i>Annals of Applied Probability</i>. 2024;34(1B):1623-1662. doi:<a href=\"https://doi.org/10.1214/23-AAP2000\">10.1214/23-AAP2000</a>","apa":"Erdös, L., &#38; McKenna, B. (2024). Extremal statistics of quadratic forms of GOE/GUE eigenvectors. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/23-AAP2000\">https://doi.org/10.1214/23-AAP2000</a>"},"ec_funded":1},{"abstract":[{"lang":"eng","text":"The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF) is among the best studied trafficking regulators in plants, playing crucial and unique developmental roles in patterning and polarity. The current models place GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis (CME). The mechanistic basis of the developmental function of GN, distinct from the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains elusive. Insights from this study largely extend the current notions of GN function. We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures distinct from clathrin-coated pits, while CME and secretion proceed normally in <jats:italic>gn</jats:italic> knockouts. The functional GN mutant variant GN<jats:sup>fewerroots</jats:sup>, absent from the GA, suggests that the cell periphery is the major site of GN action responsible for its developmental function. Following inhibition by Brefeldin A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting selective molecular associations en route to the cell periphery. A study of GN-GNL1 chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN function in a partially redundant manner. Together, this study offers significant steps toward the elucidation of the mechanism underlying unique cellular and development functions of GNOM."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["580"],"publication_status":"epub_ahead","quality_controlled":"1","volume":13,"department":[{"_id":"JiFr"}],"date_published":"2024-02-21T00:00:00Z","publisher":"eLife Sciences Publications","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"ec_funded":1,"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"date_created":"2024-02-27T07:10:11Z","citation":{"apa":"Adamowski, M., Matijevic, I., &#38; Friml, J. (2024). Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.68993\">https://doi.org/10.7554/elife.68993</a>","ista":"Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.","mla":"Adamowski, Maciek, et al. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” <i>ELife</i>, vol. 13, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.68993\">10.7554/elife.68993</a>.","chicago":"Adamowski, Maciek, Ivana Matijevic, and Jiří Friml. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.68993\">https://doi.org/10.7554/elife.68993</a>.","short":"M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024).","ieee":"M. Adamowski, I. Matijevic, and J. Friml, “Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery,” <i>eLife</i>, vol. 13. eLife Sciences Publications, 2024.","ama":"Adamowski M, Matijevic I, Friml J. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. <i>eLife</i>. 2024;13. doi:<a href=\"https://doi.org/10.7554/elife.68993\">10.7554/elife.68993</a>"},"year":"2024","acknowledgement":"The authors would like to gratefully acknowledge Dr Xixi Zhang for cloning the GNL1/pDONR221 construct and for useful discussions.H2020 European Research\r\nCouncil Advanced Grant ETAP742985 to Jiří Friml, Austrian Science Fund I 3630-B25 to Jiří Friml","doi":"10.7554/elife.68993","_id":"15033","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"21","main_file_link":[{"url":"https://doi.org/10.7554/eLife.68993","open_access":"1"}],"oa_version":"Published Version","month":"02","publication_identifier":{"issn":["2050-084X"]},"author":[{"full_name":"Adamowski, Maciek","first_name":"Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257"},{"first_name":"Ivana","full_name":"Matijevic, Ivana","last_name":"Matijevic","id":"83c17ce3-15b2-11ec-abd3-f486545870bd"},{"first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","status":"public","intvolume":"        13","has_accepted_license":"1","title":"Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery","article_processing_charge":"Yes","date_updated":"2024-02-28T12:29:43Z","oa":1,"publication":"eLife","language":[{"iso":"eng"}]},{"publication_identifier":{"issn":["1432-5411"]},"month":"02","oa_version":"Published Version","day":"17","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":436712,"creator":"dernst","date_updated":"2024-03-04T07:07:10Z","date_created":"2024-03-04T07:07:10Z","file_name":"2024_FewBodySys_Varshney.pdf","file_id":"15049","checksum":"c4e08cc7bc756da69b1b36fda7bb92fb","success":1}],"author":[{"last_name":"Varshney","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3072-5999","first_name":"Atul","full_name":"Varshney, Atul"},{"full_name":"Ghazaryan, Areg","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","orcid":"0000-0001-9666-3543"},{"orcid":"0000-0003-0393-5525","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem","first_name":"Artem"}],"arxiv":1,"status":"public","type":"journal_article","has_accepted_license":"1","intvolume":"        65","scopus_import":"1","oa":1,"date_updated":"2024-03-04T07:08:16Z","article_processing_charge":"Yes (via OA deal)","title":"Classical ‘spin’ filtering with two degrees of freedom and dissipation","publication":"Few-Body Systems","language":[{"iso":"eng"}],"ddc":["530"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"arxiv":["2401.08454"]},"abstract":[{"text":"Coupling of orbital motion to a spin degree of freedom gives rise to various transport phenomena in quantum systems that are beyond the standard paradigms of classical physics. Here, we discuss features of spin-orbit dynamics that can be visualized using a classical model with two coupled angular degrees of freedom. Specifically, we demonstrate classical ‘spin’ filtering through our model and show that the interplay between angular degrees of freedom and dissipation can lead to asymmetric ‘spin’ transport.","lang":"eng"}],"publication_status":"published","publisher":"Springer Nature","date_published":"2024-02-17T00:00:00Z","department":[{"_id":"MiLe"}],"quality_controlled":"1","volume":65,"article_number":"12","acknowledgement":"We thank Mikhail Lemeshko and members of his group for many inspiring discussions; Alberto Cappellaro for comments on the manuscript.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","year":"2024","date_created":"2024-03-01T11:39:33Z","citation":{"chicago":"Varshney, Atul, Areg Ghazaryan, and Artem Volosniev. “Classical ‘Spin’ Filtering with Two Degrees of Freedom and Dissipation.” <i>Few-Body Systems</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s00601-024-01880-x\">https://doi.org/10.1007/s00601-024-01880-x</a>.","mla":"Varshney, Atul, et al. “Classical ‘Spin’ Filtering with Two Degrees of Freedom and Dissipation.” <i>Few-Body Systems</i>, vol. 65, 12, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1007/s00601-024-01880-x\">10.1007/s00601-024-01880-x</a>.","ista":"Varshney A, Ghazaryan A, Volosniev A. 2024. Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. 65, 12.","short":"A. Varshney, A. Ghazaryan, A. Volosniev, Few-Body Systems 65 (2024).","ama":"Varshney A, Ghazaryan A, Volosniev A. Classical ‘spin’ filtering with two degrees of freedom and dissipation. <i>Few-Body Systems</i>. 2024;65. doi:<a href=\"https://doi.org/10.1007/s00601-024-01880-x\">10.1007/s00601-024-01880-x</a>","ieee":"A. Varshney, A. Ghazaryan, and A. Volosniev, “Classical ‘spin’ filtering with two degrees of freedom and dissipation,” <i>Few-Body Systems</i>, vol. 65. Springer Nature, 2024.","apa":"Varshney, A., Ghazaryan, A., &#38; Volosniev, A. (2024). Classical ‘spin’ filtering with two degrees of freedom and dissipation. <i>Few-Body Systems</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00601-024-01880-x\">https://doi.org/10.1007/s00601-024-01880-x</a>"},"keyword":["Atomic and Molecular Physics","and Optics"],"doi":"10.1007/s00601-024-01880-x","file_date_updated":"2024-03-04T07:07:10Z","_id":"15045","article_type":"original"},{"doi":"10.1126/sciadv.adj6801","file_date_updated":"2024-03-04T07:34:00Z","article_type":"original","_id":"15047","ec_funded":1,"article_number":"eadj6801","related_material":{"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/cloud-clustering-causes-more-extreme-rain/","relation":"press_release"}]},"acknowledgement":"This work is supported by the Max-Planck-Gesellschaft (MPG). We greatly appreciate computational resources from Deutsches Klimarechenzentrum (DKRZ) and the Jülich Supercomputing Centre (JSC). ICONA/O simulations are funded through the NextGEMS project by the EU’s Horizon 2020 programme (grant agreement no. 101003470). ICONA simulations are funded through the MONSOON-2.0 project (grant agreement no. 01LP1927A) which is supported from German Federal Ministry of Education and Research (BMBF). J.B. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant (grant agreement no. 101034413). B.S. acknowledges funding from the EU’s Horizon 2020 programme (grant agreement no. 101003470). C.M. gratefully acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Project CLUSTER, grant agreement no. 805041).","year":"2024","date_created":"2024-03-03T23:00:50Z","citation":{"short":"J. Bao, B. Stevens, L. Kluft, C.J. Muller, Science Advances 10 (2024).","ieee":"J. Bao, B. Stevens, L. Kluft, and C. J. Muller, “Intensification of daily tropical precipitation extremes from more organized convection,” <i>Science Advances</i>, vol. 10, no. 8. American Association for the Advancement of Science, 2024.","ama":"Bao J, Stevens B, Kluft L, Muller CJ. Intensification of daily tropical precipitation extremes from more organized convection. <i>Science Advances</i>. 2024;10(8). doi:<a href=\"https://doi.org/10.1126/sciadv.adj6801\">10.1126/sciadv.adj6801</a>","mla":"Bao, Jiawei, et al. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” <i>Science Advances</i>, vol. 10, no. 8, eadj6801, American Association for the Advancement of Science, 2024, doi:<a href=\"https://doi.org/10.1126/sciadv.adj6801\">10.1126/sciadv.adj6801</a>.","ista":"Bao J, Stevens B, Kluft L, Muller CJ. 2024. Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. 10(8), eadj6801.","chicago":"Bao, Jiawei, Bjorn Stevens, Lukas Kluft, and Caroline J Muller. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” <i>Science Advances</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/sciadv.adj6801\">https://doi.org/10.1126/sciadv.adj6801</a>.","apa":"Bao, J., Stevens, B., Kluft, L., &#38; Muller, C. J. (2024). Intensification of daily tropical precipitation extremes from more organized convection. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.adj6801\">https://doi.org/10.1126/sciadv.adj6801</a>"},"publisher":"American Association for the Advancement of Science","date_published":"2024-02-23T00:00:00Z","department":[{"_id":"CaMu"}],"quality_controlled":"1","volume":10,"project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"name":"organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate","call_identifier":"H2020","grant_number":"805041","_id":"629205d8-2b32-11ec-9570-e1356ff73576"}],"ddc":["550"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["38394192"]},"abstract":[{"lang":"eng","text":"Tropical precipitation extremes and their changes with surface warming are investigated using global storm resolving simulations and high-resolution observations. The simulations demonstrate that the mesoscale organization of convection, a process that cannot be physically represented by conventional global climate models, is important for the variations of tropical daily accumulated precipitation extremes. In both the simulations and observations, daily precipitation extremes increase in a more organized state, in association with larger, but less frequent, storms. Repeating the simulations for a warmer climate results in a robust increase in monthly-mean daily precipitation extremes. Higher precipitation percentiles have a greater sensitivity to convective organization, which is predicted to increase with warming. Without changes in organization, the strongest daily precipitation extremes over the tropical oceans increase at a rate close to Clausius-Clapeyron (CC) scaling. Thus, in a future warmer state with increased organization, the strongest daily precipitation extremes over oceans increase at a faster rate than CC scaling."}],"publication_status":"published","publication":"Science Advances","language":[{"iso":"eng"}],"has_accepted_license":"1","scopus_import":"1","intvolume":"        10","oa":1,"date_updated":"2024-03-05T09:26:47Z","article_processing_charge":"Yes","issue":"8","title":"Intensification of daily tropical precipitation extremes from more organized convection","pmid":1,"type":"journal_article","status":"public","month":"02","publication_identifier":{"eissn":["2375-2548"]},"oa_version":"Published Version","day":"23","file":[{"checksum":"d4ec4f05a6d14745057e14d1b8bf45ae","file_name":"2024_ScienceAdv_Bao.pdf","file_id":"15051","success":1,"date_updated":"2024-03-04T07:34:00Z","date_created":"2024-03-04T07:34:00Z","creator":"dernst","file_size":800926,"access_level":"open_access","content_type":"application/pdf","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160","last_name":"Bao","first_name":"Jiawei","full_name":"Bao, Jiawei"},{"full_name":"Stevens, Bjorn","first_name":"Bjorn","last_name":"Stevens"},{"last_name":"Kluft","full_name":"Kluft, Lukas","first_name":"Lukas"},{"orcid":"0000-0001-5836-5350","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J","first_name":"Caroline J"}]},{"quality_controlled":"1","volume":151,"department":[{"_id":"CaHe"},{"_id":"Bio"}],"page":"1-18","date_published":"2024-02-01T00:00:00Z","publisher":"The Company of Biologists","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"},{"grant_number":"25239","_id":"26B1E39C-B435-11E9-9278-68D0E5697425","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues"}],"abstract":[{"lang":"eng","text":"Embryogenesis results from the coordinated activities of different signaling pathways controlling cell fate specification and morphogenesis. In vertebrate gastrulation, both Nodal and BMP signaling play key roles in germ layer specification and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis is still insufficiently understood. Here, we took a reductionist approach using zebrafish embryonic explants to study the coordination of Nodal and BMP signaling for embryo patterning and morphogenesis. We show that Nodal signaling triggers explant elongation by inducing mesendodermal progenitors but also suppressing BMP signaling activity at the site of mesendoderm induction. Consistent with this, ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm intercalations, key processes during explant elongation. Translating these ex vivo observations to the intact embryo showed that, similar to explants, Nodal signaling suppresses the effect of BMP signaling on cell intercalations in the dorsal domain, thus allowing robust embryonic axis elongation. These findings suggest a dual function of Nodal signaling in embryonic axis elongation by both inducing mesendoderm and suppressing BMP effects in the dorsal portion of the mesendoderm."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"publication_status":"published","doi":"10.1242/dev.202316","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"article_type":"original","_id":"15048","file_date_updated":"2024-03-04T07:24:43Z","related_material":{"record":[{"status":"public","id":"14926","relation":"research_data"}]},"ec_funded":1,"citation":{"ista":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. 2024. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 151(4), 1–18.","mla":"Schauer, Alexandra, et al. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” <i>Development</i>, vol. 151, no. 4, The Company of Biologists, 2024, pp. 1–18, doi:<a href=\"https://doi.org/10.1242/dev.202316\">10.1242/dev.202316</a>.","chicago":"Schauer, Alexandra, Kornelija Pranjic-Ferscha, Robert Hauschild, and Carl-Philipp J Heisenberg. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” <i>Development</i>. The Company of Biologists, 2024. <a href=\"https://doi.org/10.1242/dev.202316\">https://doi.org/10.1242/dev.202316</a>.","ieee":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, and C.-P. J. Heisenberg, “Robust axis elongation by Nodal-dependent restriction of BMP signaling,” <i>Development</i>, vol. 151, no. 4. The Company of Biologists, pp. 1–18, 2024.","ama":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. Robust axis elongation by Nodal-dependent restriction of BMP signaling. <i>Development</i>. 2024;151(4):1-18. doi:<a href=\"https://doi.org/10.1242/dev.202316\">10.1242/dev.202316</a>","short":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, C.-P.J. Heisenberg, Development 151 (2024) 1–18.","apa":"Schauer, A., Pranjic-Ferscha, K., Hauschild, R., &#38; Heisenberg, C.-P. J. (2024). Robust axis elongation by Nodal-dependent restriction of BMP signaling. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.202316\">https://doi.org/10.1242/dev.202316</a>"},"date_created":"2024-03-03T23:00:50Z","year":"2024","acknowledgement":"We thank Patrick Müller for sharing the chordintt250 mutant zebrafish line as well as the plasmid for chrd-GFP, Katherine Rogers for sharing the bmp2b plasmid and Andrea Pauli for sharing the draculin plasmid. Diana Pinheiro generated the MZlefty1,2;Tg(sebox::EGFP) line. We are grateful to Patrick Müller, Diana Pinheiro and Katherine Rogers and members of the Heisenberg lab for discussions, technical advice and feedback on the manuscript. We also thank Anna Kicheva and Edouard Hannezo for discussions. We thank the Imaging and Optics Facility as well as the Life Science facility at IST Austria for support with microscopy and fish maintenance.\r\nThis work was supported by a European Research Council Advanced Grant\r\n(MECSPEC 742573 to C.-P.H.). A.S. is a recipient of a DOC Fellowship of the Austrian\r\nAcademy of Sciences at IST Austria. Open Access funding provided by Institute of\r\nScience and Technology Austria. ","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2024-03-04T07:24:43Z","date_created":"2024-03-04T07:24:43Z","file_name":"2024_Development_Schauer.pdf","file_id":"15050","checksum":"6961ea10012bf0d266681f9628bb8f13","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":14839986,"creator":"dernst"}],"oa_version":"Published Version","day":"01","month":"02","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"author":[{"full_name":"Schauer, Alexandra","first_name":"Alexandra","orcid":"0000-0001-7659-9142","last_name":"Schauer","id":"30A536BA-F248-11E8-B48F-1D18A9856A87"},{"id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","last_name":"Pranjic-Ferscha","full_name":"Pranjic-Ferscha, Kornelija","first_name":"Kornelija"},{"orcid":"0000-0001-9843-3522","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Hauschild, Robert"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"publication":"Development","language":[{"iso":"eng"}],"scopus_import":"1","intvolume":"       151","has_accepted_license":"1","title":"Robust axis elongation by Nodal-dependent restriction of BMP signaling","issue":"4","article_processing_charge":"Yes (via OA deal)","date_updated":"2024-03-04T07:28:25Z","oa":1},{"year":"2024","acknowledgement":"This work is supported by the Research Grants Council of Hong Kong (C7002-22Y and 17318122). The authors are grateful for the research computing facilities offered by\r\nITS, HKU. Z.Z. acknowledges the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","citation":{"ama":"Cheng R, Zeng Z, Wang C, Ouyang N, Chen Y. Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. <i>Physical Review B</i>. 2024;109(5). doi:<a href=\"https://doi.org/10.1103/physrevb.109.054305\">10.1103/physrevb.109.054305</a>","ieee":"R. Cheng, Z. Zeng, C. Wang, N. Ouyang, and Y. Chen, “Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites,” <i>Physical Review B</i>, vol. 109, no. 5. American Physical Society, 2024.","short":"R. Cheng, Z. Zeng, C. Wang, N. Ouyang, Y. Chen, Physical Review B 109 (2024).","chicago":"Cheng, Ruihuan, Zezhu Zeng, Chen Wang, Niuchang Ouyang, and Yue Chen. “Impact of Strain-Insensitive Low-Frequency Phonon Modes on Lattice Thermal Transport in AxXB6-Type Perovskites.” <i>Physical Review B</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/physrevb.109.054305\">https://doi.org/10.1103/physrevb.109.054305</a>.","mla":"Cheng, Ruihuan, et al. “Impact of Strain-Insensitive Low-Frequency Phonon Modes on Lattice Thermal Transport in AxXB6-Type Perovskites.” <i>Physical Review B</i>, vol. 109, no. 5, 054305, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/physrevb.109.054305\">10.1103/physrevb.109.054305</a>.","ista":"Cheng R, Zeng Z, Wang C, Ouyang N, Chen Y. 2024. Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. Physical Review B. 109(5), 054305.","apa":"Cheng, R., Zeng, Z., Wang, C., Ouyang, N., &#38; Chen, Y. (2024). Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.109.054305\">https://doi.org/10.1103/physrevb.109.054305</a>"},"date_created":"2024-03-04T07:41:23Z","article_number":"054305","ec_funded":1,"_id":"15052","article_type":"original","doi":"10.1103/physrevb.109.054305","publication_status":"published","abstract":[{"text":"Substrate induces mechanical strain on perovskite devices, which can result in alterations to its lattice dynamics and thermal transport. Herein, we have performed a theoretical investigation on the anharmonic lattice dynamics and thermal property of perovskite Rb2SnBr6 and Cs2SnBr6 under strains using perturbation theory up to the fourth-order terms and the unified thermal transport theory. We demonstrate a pronounced hardening of low-frequency optical phonons as temperature increases, indicating strong lattice anharmonicity and the necessity of adopting temperature-dependent interatomic force constants in the lattice thermal conductivity (\r\nκL) calculations. It is found that the low-lying optical phonon modes of Rb2SnBr6 are extremely soft and their phonon energies are almost strain independent, which ultimately lead to a lower \r\nκL and a weaker strain dependence than Cs2SnBr6. We further reveal that the strain dependence of these phonon modes in the A2XB6-type perovskites weakens as their ibrational frequency decreases. This study deepens the understanding of lattice thermal transport in perovskites A2XB6 and provides a perspective on the selection of materials that meet the expected thermal behaviors in practical applications.","lang":"eng"}],"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"date_published":"2024-02-14T00:00:00Z","publisher":"American Physical Society","volume":109,"quality_controlled":"1","department":[{"_id":"BiCh"}],"issue":"5","article_processing_charge":"No","date_updated":"2024-03-04T07:48:55Z","title":"Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites","scopus_import":"1","intvolume":"       109","language":[{"iso":"eng"}],"publication":"Physical Review B","author":[{"full_name":"Cheng, Ruihuan","first_name":"Ruihuan","last_name":"Cheng"},{"id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","last_name":"Zeng","full_name":"Zeng, Zezhu","first_name":"Zezhu"},{"full_name":"Wang, Chen","first_name":"Chen","last_name":"Wang"},{"last_name":"Ouyang","first_name":"Niuchang","full_name":"Ouyang, Niuchang"},{"last_name":"Chen","first_name":"Yue","full_name":"Chen, Yue"}],"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"14","oa_version":"None","status":"public","type":"journal_article"},{"has_accepted_license":"1","intvolume":"         6","scopus_import":"1","title":"Multipurpose platform for analog quantum simulation","article_processing_charge":"Yes","issue":"1","date_updated":"2024-03-04T07:55:29Z","oa":1,"publication":"Physical Review Research","language":[{"iso":"eng"}],"file":[{"creator":"dernst","content_type":"application/pdf","access_level":"open_access","file_size":4025988,"relation":"main_file","checksum":"ba2ae3e3a011f8897d3803c9366a67e2","file_id":"15054","file_name":"2024_PhysicalReviewResearch_Jin.pdf","success":1,"date_updated":"2024-03-04T07:53:08Z","date_created":"2024-03-04T07:53:08Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","day":"13","publication_identifier":{"issn":["2643-1564"]},"month":"02","arxiv":1,"author":[{"last_name":"Jin","full_name":"Jin, Shuwei","first_name":"Shuwei"},{"last_name":"Dai","first_name":"Kunlun","full_name":"Dai, Kunlun"},{"last_name":"Verstraten","first_name":"Joris","full_name":"Verstraten, Joris"},{"full_name":"Dixmerias, Maxime","first_name":"Maxime","last_name":"Dixmerias"},{"last_name":"Al Hyder","id":"d1c405be-ae15-11ed-8510-ccf53278162e","full_name":"Al Hyder, Ragheed","first_name":"Ragheed"},{"full_name":"Salomon, Christophe","first_name":"Christophe","last_name":"Salomon"},{"first_name":"Bruno","full_name":"Peaudecerf, Bruno","last_name":"Peaudecerf"},{"last_name":"de Jongh","first_name":"Tim","full_name":"de Jongh, Tim"},{"first_name":"Tarik","full_name":"Yefsah, Tarik","last_name":"Yefsah"}],"status":"public","type":"journal_article","article_number":"013158","keyword":["General Physics and Astronomy"],"citation":{"short":"S. Jin, K. Dai, J. Verstraten, M. Dixmerias, R. Al Hyder, C. Salomon, B. Peaudecerf, T. de Jongh, T. Yefsah, Physical Review Research 6 (2024).","ieee":"S. Jin <i>et al.</i>, “Multipurpose platform for analog quantum simulation,” <i>Physical Review Research</i>, vol. 6, no. 1. American Physical Society, 2024.","ama":"Jin S, Dai K, Verstraten J, et al. Multipurpose platform for analog quantum simulation. <i>Physical Review Research</i>. 2024;6(1). doi:<a href=\"https://doi.org/10.1103/physrevresearch.6.013158\">10.1103/physrevresearch.6.013158</a>","chicago":"Jin, Shuwei, Kunlun Dai, Joris Verstraten, Maxime Dixmerias, Ragheed Al Hyder, Christophe Salomon, Bruno Peaudecerf, Tim de Jongh, and Tarik Yefsah. “Multipurpose Platform for Analog Quantum Simulation.” <i>Physical Review Research</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/physrevresearch.6.013158\">https://doi.org/10.1103/physrevresearch.6.013158</a>.","ista":"Jin S, Dai K, Verstraten J, Dixmerias M, Al Hyder R, Salomon C, Peaudecerf B, de Jongh T, Yefsah T. 2024. Multipurpose platform for analog quantum simulation. Physical Review Research. 6(1), 013158.","mla":"Jin, Shuwei, et al. “Multipurpose Platform for Analog Quantum Simulation.” <i>Physical Review Research</i>, vol. 6, no. 1, 013158, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/physrevresearch.6.013158\">10.1103/physrevresearch.6.013158</a>.","apa":"Jin, S., Dai, K., Verstraten, J., Dixmerias, M., Al Hyder, R., Salomon, C., … Yefsah, T. (2024). Multipurpose platform for analog quantum simulation. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevresearch.6.013158\">https://doi.org/10.1103/physrevresearch.6.013158</a>"},"date_created":"2024-03-04T07:42:52Z","year":"2024","acknowledgement":"We thank Clara Bachorz, Darby Bates, Markus Bohlen, Valentin Crépel, Yann Kiefer, Joanna Lis, Mihail Rabinovic, and Julian Struck for experimental assistance in the early stages of this project, and Sebastian Will for a critical reading of the manuscript. This work has been supported by Agence Nationale de la Recherche (Grant No. ANR-21-CE30-0021), the European Research Council (Grant No. ERC-2016-ADG-743159), CNRS (Tremplin@INP 2020), and Région Ile-de-France in the framework of DIM SIRTEQ (Super2D and SISCo) and DIM QuanTiP.","doi":"10.1103/physrevresearch.6.013158","article_type":"original","_id":"15053","file_date_updated":"2024-03-04T07:53:08Z","abstract":[{"lang":"eng","text":"Atom-based quantum simulators have had many successes in tackling challenging quantum many-body problems, owing to the precise and dynamical control that they provide over the systems' parameters. They are, however, often optimized to address a specific type of problem. Here, we present the design and implementation of a 6Li-based quantum gas platform that provides wide-ranging capabilities and is able to address a variety of quantum many-body problems. Our two-chamber architecture relies on a robust combination of gray molasses and optical transport from a laser-cooling chamber to a glass cell with excellent optical access. There, we first create unitary Fermi superfluids in a three-dimensional axially symmetric harmonic trap and characterize them using in situ thermometry, reaching temperatures below 20 nK. This allows us to enter the deep superfluid regime with samples of extreme diluteness, where the interparticle spacing is sufficiently large for direct single-atom imaging. Second, we generate optical lattice potentials with triangular and honeycomb geometry in which we study diffraction of molecular Bose-Einstein condensates, and show how going beyond the Kapitza-Dirac regime allows us to unambiguously distinguish between the two geometries. With the ability to probe quantum many-body physics in both discrete and continuous space, and its suitability for bulk and single-atom imaging, our setup represents an important step towards achieving a wide-scope quantum simulator."}],"external_id":{"arxiv":["2304.08433"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["530"],"publication_status":"published","quality_controlled":"1","volume":6,"department":[{"_id":"MiLe"}],"date_published":"2024-02-13T00:00:00Z","publisher":"American Physical Society"},{"_id":"15177","date_updated":"2024-06-11T10:05:06Z","year":"2024","article_processing_charge":"No","title":"RD Ref","date_created":"2024-06-11T10:04:54Z","publisher":"ISTA","status":"public","type":"research_data_reference","date_published":"2024-01-01T00:00:00Z","department":[{"_id":"E-Lib"}],"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Doris","full_name":"Ernst, Doris","orcid":"0000-0002-2354-0195","id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","last_name":"Ernst"}]},{"project":[{"name":"A Test Grant","_id":"42f76822-911d-11ef-982b-ce758d810b28","grant_number":"AB123"},{"_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"name":"Aagain a test","_id":"4b739304-2d65-11ef-919e-fdbedb4a0279","grant_number":"345"}],"type":"journal_article","date_published":"2024-11-18T00:00:00Z","status":"public","department":[{"_id":"E-Lib"}],"author":[{"full_name":"Ernst, Doris","first_name":"Doris","last_name":"Ernst","id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2354-0195"}],"month":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","day":"18","language":[{"iso":"eng"}],"_id":"15262","publication":"Today","article_processing_charge":"No","year":"2024","date_updated":"2024-11-19T09:19:59Z","title":"Doris Test 18.11.","date_created":"2024-11-18T14:11:31Z","ec_funded":1},{"has_accepted_license":"1","date_created":"2023-08-22T14:19:59Z","title":"Divided attention: Unsupervised multi-object discovery with contextually separated slots","oa":1,"date_updated":"2025-02-13T08:10:28Z","year":"2024","article_processing_charge":"No","publication":"1st Conference on Parsimony and Learning","file_date_updated":"2024-02-12T08:40:36Z","language":[{"iso":"eng"}],"_id":"14213","oa_version":"Published Version","external_id":{"arxiv":["2304.01430"]},"day":"03","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":8038511,"creator":"dernst","date_updated":"2024-02-12T08:40:36Z","date_created":"2024-02-12T08:40:36Z","file_name":"2024_CPAL_Lao.pdf","checksum":"8fad894c34f1b3d5a14fb8ffb12f7277","file_id":"14978","success":1}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We introduce a method to segment the visual field into independently moving regions, trained with no ground truth or supervision. It consists of an adversarial conditional encoder-decoder architecture based on Slot Attention, modified to use the image as context to decode optical flow without attempting to reconstruct the image itself. In the resulting multi-modal representation, one modality (flow) feeds the encoder to produce separate latent codes (slots), whereas the other modality (image) conditions the decoder to generate the first (flow) from the slots. This design frees the representation from having to encode complex nuisance variability in the image due to, for instance, illumination and reflectance properties of the scene. Since customary autoencoding based on minimizing the reconstruction error does not preclude the entire flow from being encoded into a single slot, we modify the loss to an adversarial criterion based on Contextual Information Separation. The resulting min-max optimization fosters the separation of objects and their assignment to different attention slots, leading to Divided Attention, or DivA. DivA outperforms recent unsupervised multi-object motion segmentation methods while tripling run-time speed up to 104FPS and reducing the performance gap from supervised methods to 12% or less. DivA can handle different numbers of objects and different image sizes at training and test time, is invariant to permutation of object labels, and does not require explicit regularization.","lang":"eng"}],"ddc":["000"],"conference":{"location":"Hong Kong, China","end_date":"2024-01-03","name":"CPAL: Conference on Parsimony and Learning","start_date":"2024-01-03"},"publication_identifier":{"issnl":["1234-4321"]},"month":"01","publication_status":"published","author":[{"full_name":"Lao, Dong","first_name":"Dong","last_name":"Lao"},{"full_name":"Hu, Zhengyang","first_name":"Zhengyang","last_name":"Hu"},{"orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","full_name":"Locatello, Francesco","first_name":"Francesco"},{"full_name":"Yang, Yanchao","first_name":"Yanchao","last_name":"Yang"},{"last_name":"Soatto","full_name":"Soatto, Stefano","first_name":"Stefano"}],"arxiv":1,"department":[{"_id":"FrLo"}],"quality_controlled":"1","date_published":"2024-01-03T00:00:00Z","type":"conference","status":"public"},{"status":"public","type":"journal_article","pmid":1,"file":[{"creator":"dernst","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":2825565,"success":1,"file_name":"2023_PlantCommunications_Tang.pdf","checksum":"edbc44c6d4a394d2bf70f92fdbb08f0a","file_id":"14911","date_created":"2024-01-30T12:59:57Z","date_updated":"2024-01-30T12:59:57Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"08","oa_version":"Published Version","publication_identifier":{"issnl":["1234-4567"],"issn":["2590-3462"]},"month":"01","author":[{"first_name":"Han","full_name":"Tang, Han","id":"19BDF720-25A0-11EA-AC6E-928F3DDC885E","last_name":"Tang","orcid":"0000-0001-6152-6637"},{"last_name":"Lu","full_name":"Lu, KJ","first_name":"KJ"},{"first_name":"Y","full_name":"Zhang, Y","last_name":"Zhang"},{"full_name":"Cheng, YL","first_name":"YL","last_name":"Cheng"},{"last_name":"Tu","first_name":"SL","full_name":"Tu, SL"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"publication":"Plant Communications","language":[{"iso":"eng"}],"intvolume":"         5","has_accepted_license":"1","scopus_import":"1","title":"Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution","article_processing_charge":"Yes","issue":"1","date_updated":"2025-07-02T12:51:02Z","oa":1,"quality_controlled":"1","volume":5,"department":[{"_id":"JiFr"}],"date_published":"2024-01-08T00:00:00Z","publisher":"Elsevier","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"abstract":[{"lang":"eng","text":"The phytohormone auxin and its directional transport through tissues play a fundamental role in development of higher plants. This polar auxin transport predominantly relies on PIN-FORMED (PIN) auxin exporters. Hence, PIN polarization is crucial for development, but its evolution during the rise of morphological complexity in land plants remains unclear. Here, we performed a cross-species investigation by observing the trafficking and localization of endogenous and exogenous PINs in two bryophytes, Physcomitrium patens and Marchantia polymorpha, and in the flowering plant Arabidopsis thaliana. We confirmed that the GFP fusion did not compromise the auxin export function of all examined PINs by using radioactive auxin export assay and by observing the phenotypic changes in transgenic bryophytes. Endogenous PINs polarize to filamentous apices, while exogenous Arabidopsis PINs distribute symmetrically on the membrane in both bryophytes. In Arabidopsis root epidermis, bryophytic PINs show no defined polarity. Pharmacological interference revealed a strong cytoskeleton dependence of bryophytic but not Arabidopsis PIN polarization. The divergence of PIN polarization and trafficking is also observed within the bryophyte clade and between tissues of individual species. These results collectively reveal a divergence of PIN trafficking and polarity mechanisms throughout land plant evolution and a co-evolution of PIN sequence-based and cell-based polarity mechanisms."}],"external_id":{"pmid":["37528584"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["580"],"publication_status":"published","doi":"10.1016/j.xplc.2023.100669","article_type":"original","_id":"14251","file_date_updated":"2024-01-30T12:59:57Z","article_number":"100669","ec_funded":1,"citation":{"apa":"Tang, H., Lu, K., Zhang, Y., Cheng, Y., Tu, S., &#38; Friml, J. (2024). Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution. <i>Plant Communications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xplc.2023.100669\">https://doi.org/10.1016/j.xplc.2023.100669</a>","short":"H. Tang, K. Lu, Y. Zhang, Y. Cheng, S. Tu, J. Friml, Plant Communications 5 (2024).","ama":"Tang H, Lu K, Zhang Y, Cheng Y, Tu S, Friml J. Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution. <i>Plant Communications</i>. 2024;5(1). doi:<a href=\"https://doi.org/10.1016/j.xplc.2023.100669\">10.1016/j.xplc.2023.100669</a>","ieee":"H. Tang, K. Lu, Y. Zhang, Y. Cheng, S. Tu, and J. Friml, “Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution,” <i>Plant Communications</i>, vol. 5, no. 1. Elsevier, 2024.","ista":"Tang H, Lu K, Zhang Y, Cheng Y, Tu S, Friml J. 2024. Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution. Plant Communications. 5(1), 100669.","mla":"Tang, Han, et al. “Divergence of Trafficking and Polarization Mechanisms for PIN Auxin Transporters during Land Plant Evolution.” <i>Plant Communications</i>, vol. 5, no. 1, 100669, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xplc.2023.100669\">10.1016/j.xplc.2023.100669</a>.","chicago":"Tang, Han, KJ Lu, Y Zhang, YL Cheng, SL Tu, and Jiří Friml. “Divergence of Trafficking and Polarization Mechanisms for PIN Auxin Transporters during Land Plant Evolution.” <i>Plant Communications</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xplc.2023.100669\">https://doi.org/10.1016/j.xplc.2023.100669</a>."},"date_created":"2023-09-01T11:32:02Z","year":"2024","acknowledgement":"This work was supported by the ERC grant (PR1023ERC02) to H. T. and J. F., and by the ministry of science and technology (grant number 110-2636-B-005-001) to K. J. L."},{"abstract":[{"text":"In animals, parasitic infections impose significant fitness costs.1,2,3,4,5,6 Infected animals can alter their feeding behavior to resist infection,7,8,9,10,11,12 but parasites can manipulate animal foraging behavior to their own benefits.13,14,15,16 How nutrition influences host-parasite interactions is not well understood, as studies have mainly focused on the host and less on the parasite.9,12,17,18,19,20,21,22,23 We used the nutritional geometry framework24 to investigate the role of amino acids (AA) and carbohydrates (C) in a host-parasite system: the Argentine ant, Linepithema humile, and the entomopathogenic fungus, Metarhizium brunneum. First, using 18 diets varying in AA:C composition, we established that the fungus performed best on the high-amino-acid diet 1:4. Second, we found that the fungus reached this optimal diet when given various diet pairings, revealing its ability to cope with nutritional challenges. Third, we showed that the optimal fungal diet reduced the lifespan of healthy ants when compared with a high-carbohydrate diet but had no effect on infected ants. Fourth, we revealed that infected ant colonies, given a choice between the optimal fungal diet and a high-carbohydrate diet, chose the optimal fungal diet, whereas healthy colonies avoided it. Lastly, by disentangling fungal infection from host immune response, we demonstrated that infected ants foraged on the optimal fungal diet in response to immune activation and not as a result of parasite manipulation. Therefore, we revealed that infected ant colonies chose a diet that is costly for survival in the long term but beneficial in the short term—a form of collective self-medication.","lang":"eng"}],"external_id":{"pmid":["38307022"]},"publication_status":"published","date_published":"2024-02-26T00:00:00Z","publisher":"Elsevier","quality_controlled":"1","volume":34,"page":"902-909.e6","department":[{"_id":"SyCr"}],"dataavailabilitystatement":"no DAS","year":"2024","acknowledgement":"We are sincerely grateful to the referees for their valuable comments and suggestions, which helped us to improve the paper. We are thankful to Jorgen Eilenberg and Nicolai V. Meyling for the fungal strain, to Simon Tragust, Abel Bernadou, and Brian Lazarro for insightful discussions, to Iago Sanmartín-Villar, Léa Briard, Céline Maitrel, and Nolwenn Rissen for their help with the experiments. Furthermore, we thank Anna V. Grasse for help with the immune gene expression analyses. We thank Sergio Ibarra for creating the graphical abstract. E.C. was supported by a Fyssen Foundation grant and the Alexander von Humboldt Foundation. A.D. was supported by the CNRS.","supplementarymaterial":"yes","citation":{"apa":"Csata, E., Perez-Escudero, A., Laury, E., Leitner, H., Latil, G., Heinze, J., … Dussutour, A. (2024). Fungal infection alters collective nutritional intake of ant colonies. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2024.01.017\">https://doi.org/10.1016/j.cub.2024.01.017</a>","ista":"Csata E, Perez-Escudero A, Laury E, Leitner H, Latil G, Heinze J, Simpson S, Cremer S, Dussutour A. 2024. Fungal infection alters collective nutritional intake of ant colonies. Current Biology. 34(4), 902–909.e6.","chicago":"Csata, Eniko, Alfonso Perez-Escudero, Emmanuel Laury, Hanna Leitner, Gerard Latil, Juerge Heinze, Stephen Simpson, Sylvia Cremer, and Audrey Dussutour. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” <i>Current Biology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cub.2024.01.017\">https://doi.org/10.1016/j.cub.2024.01.017</a>.","mla":"Csata, Eniko, et al. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” <i>Current Biology</i>, vol. 34, no. 4, Elsevier, 2024, p. 902–909.e6, doi:<a href=\"https://doi.org/10.1016/j.cub.2024.01.017\">10.1016/j.cub.2024.01.017</a>.","short":"E. Csata, A. Perez-Escudero, E. Laury, H. Leitner, G. Latil, J. Heinze, S. Simpson, S. Cremer, A. Dussutour, Current Biology 34 (2024) 902–909.e6.","ama":"Csata E, Perez-Escudero A, Laury E, et al. Fungal infection alters collective nutritional intake of ant colonies. <i>Current Biology</i>. 2024;34(4):902-909.e6. doi:<a href=\"https://doi.org/10.1016/j.cub.2024.01.017\">10.1016/j.cub.2024.01.017</a>","ieee":"E. Csata <i>et al.</i>, “Fungal infection alters collective nutritional intake of ant colonies,” <i>Current Biology</i>, vol. 34, no. 4. Elsevier, p. 902–909.e6, 2024."},"date_created":"2023-10-31T13:30:20Z","doi":"10.1016/j.cub.2024.01.017","_id":"14479","article_type":"original","publication_identifier":{"issnl":["1234-5678"],"issn":["0960-9822"],"eissn":["1879-0445"]},"month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"26","oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.1101/2023.10.26.564092","open_access":"1"}],"author":[{"last_name":"Csata","first_name":"Eniko","full_name":"Csata, Eniko"},{"last_name":"Perez-Escudero","full_name":"Perez-Escudero, Alfonso","first_name":"Alfonso"},{"last_name":"Laury","full_name":"Laury, Emmanuel","first_name":"Emmanuel"},{"first_name":"Hanna","full_name":"Leitner, Hanna","last_name":"Leitner","id":"8fc5c6f6-5903-11ec-abad-c83f046253e7"},{"first_name":"Gerard","full_name":"Latil, Gerard","last_name":"Latil"},{"last_name":"Heinze","full_name":"Heinze, Juerge","first_name":"Juerge"},{"last_name":"Simpson","full_name":"Simpson, Stephen","first_name":"Stephen"},{"orcid":"0000-0002-2193-3868","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","full_name":"Cremer, Sylvia"},{"first_name":"Audrey","full_name":"Dussutour, Audrey","last_name":"Dussutour"}],"status":"public","type":"journal_article","pmid":1,"scopus_import":"1","intvolume":"        34","article_processing_charge":"No","issue":"4","oa":1,"date_updated":"2026-03-18T11:15:21Z","title":"Fungal infection alters collective nutritional intake of ant colonies","researchdata_availability":"unclear","publication":"Current Biology","language":[{"iso":"eng"}]},{"citation":{"apa":"Elkrewi, M. N. (2024). Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14705\">https://doi.org/10.15479/AT:ISTA:14705</a>","ieee":"M. N. Elkrewi, “Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.’” Institute of Science and Technology Austria, 2024.","ama":"Elkrewi MN. Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14705\">10.15479/AT:ISTA:14705</a>","short":"M.N. Elkrewi, (2024).","ista":"Elkrewi MN. 2024. Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14705\">10.15479/AT:ISTA:14705</a>.","mla":"Elkrewi, Marwan N. <i>Data from “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.”</i> Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14705\">10.15479/AT:ISTA:14705</a>.","chicago":"Elkrewi, Marwan N. “Data from ‘Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.’” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:14705\">https://doi.org/10.15479/AT:ISTA:14705</a>."},"date_created":"2023-12-22T13:40:48Z","title":"Data from \"Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation\"","keyword":["sex chromosome evolution","genome assembly","dosage compensation"],"date_updated":"2026-05-18T12:46:40Z","year":"2024","article_processing_charge":"No","retracted":"1","has_accepted_license":"1","related_material":{"record":[{"relation":"used_in_publication","id":"15009","status":"public"}]},"_id":"14705","doi":"10.15479/AT:ISTA:14705","author":[{"full_name":"Elkrewi, Marwan N","first_name":"Marwan N","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231"}],"oa_version":"Published Version","day":"02","contributor":[{"id":"57854184-AAE0-11E9-8D04-98D6E5697425","contributor_type":"researcher","last_name":"Bett","first_name":"Vincent K"},{"first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Macon"},{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","contributor_type":"supervisor","orcid":"0000-0002-4579-8306","first_name":"Beatriz"},{"first_name":"Marwan N","last_name":"Elkrewi","contributor_type":"researcher","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake, USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.","lang":"eng"}],"ddc":["576"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"01","project":[{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"publisher":"Institute of Science and Technology Austria","type":"research_data","date_published":"2024-01-02T00:00:00Z","status":"public"},{"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"name":"Causes and consequences of population fragmentation","grant_number":"P32896","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"},{"_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6","grant_number":"26380","name":"Polygenic Adaptation in a Metapopulation"}],"page":"183","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"supervisor":[{"orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H"},{"full_name":"Polechova, Jitka","first_name":"Jitka","last_name":"Polechova"},{"last_name":"Sachdeva","first_name":"Himani","full_name":"Sachdeva, Himani"}],"date_published":"2024-01-19T00:00:00Z","publisher":"Institute of Science and Technology Austria","publication_status":"published","abstract":[{"lang":"eng","text":"In nature, different species find their niche in a range of environments, each with its unique characteristics. While some thrive in uniform (homogeneous) landscapes where environmental conditions stay relatively consistent across space, others traverse the complexities of spatially heterogeneous terrains. Comprehending how species are distributed and how they interact within these landscapes holds the key to gaining insights into their evolutionary dynamics while also informing conservation and management strategies.\r\n\r\nFor species inhabiting heterogeneous landscapes, when the rate of dispersal is low compared to spatial fluctuations in selection pressure, localized adaptations may emerge. Such adaptation in response to varying selection strengths plays an important role in the persistence of populations in our rapidly changing world. Hence, species in nature are continuously in a struggle to adapt to local environmental conditions, to ensure their continued survival. Natural populations can often adapt in time scales short enough for evolutionary changes to influence ecological dynamics and vice versa, thereby creating a feedback between evolution and demography. The analysis of this feedback and the relative contributions of gene flow, demography, drift, and natural selection to genetic variation and differentiation has remained a recurring theme in evolutionary biology. Nevertheless, the effective role of these forces in maintaining variation and shaping patterns of diversity is not fully understood. Even in homogeneous environments devoid of local adaptations, such understanding remains elusive. Understanding this feedback is crucial, for example in determining the conditions under which extinction risk can be mitigated in peripheral populations subject to deleterious mutation accumulation at the edges of species’ ranges\r\nas well as in highly fragmented populations.\r\n\r\nIn this thesis we explore both uniform and spatially heterogeneous metapopulations, investigating and providing theoretical insights into the dynamics of local adaptation in the latter and examining the dynamics of load and extinction as well as the impact of joint ecological and evolutionary (eco-evolutionary) dynamics in the former. The thesis is divided into 5 chapters.\r\n\r\nChapter 1 provides a general introduction into the subject matter, clarifying concepts and ideas used throughout the thesis. In chapter 2, we explore how fast a species distributed across a heterogeneous landscape adapts to changing conditions marked by alterations in carrying capacity, selection pressure, and migration rate.\r\n\r\nIn chapter 3, we investigate how migration selection and drift influences adaptation and the maintenance of variation in a metapopulation with three habitats, an extension of previous models of adaptation in two habitats. We further develop analytical approximations for the critical threshold required for polymorphism to persist.\r\n\r\nThe focus of chapter 4 of the thesis is on understanding the interplay between ecology and evolution as coupled processes. We investigate how eco-evolutionary feedback between migration, selection, drift, and demography influences eco-evolutionary outcomes in marginal populations subject to deleterious mutation accumulation. Using simulations as well as theoretical approximations of the coupled dynamics of population size and allele frequency, we analyze how gene flow from a large mainland source influences genetic load and population size on an island (i.e., in a marginal population) under genetically realistic assumptions. Analyses of this sort are important because small isolated populations, are repeatedly affected by complex interactions between ecological and evolutionary processes, which can lead to their death. Understanding these interactions can therefore provide an insight into the conditions under which extinction risk can be mitigated in peripheral populations thus, contributing to conservation and restoration efforts.\r\n\r\nChapter 5 extends the analysis in chapter 4 to consider the dynamics of load (due to deleterious mutation accumulation) and extinction risk in a metapopulation. We explore the role of gene flow, selection, and dominance on load and extinction risk and further pinpoint critical thresholds required for metapopulation persistence.\r\n\r\nOverall this research contributes to our understanding of ecological and evolutionary mechanisms that shape species’ persistence in fragmented landscapes, a crucial foundation for successful conservation efforts and biodiversity management."}],"tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"ddc":["576"],"acknowledged_ssus":[{"_id":"SSU"}],"_id":"14711","file_date_updated":"2024-01-03T18:31:34Z","doi":"10.15479/at:ista:14711","date_created":"2023-12-26T22:49:53Z","year":"2024","degree_awarded":"MS","related_material":{"record":[{"relation":"part_of_dissertation","id":"10658","status":"public"},{"id":"10787","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"14732","status":"public"}]},"ec_funded":1,"status":"public","type":"dissertation","alternative_title":["ISTA Thesis"],"author":[{"orcid":"0000-0003-1971-8314","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","last_name":"Olusanya","full_name":"Olusanya, Oluwafunmilola O","first_name":"Oluwafunmilola O"}],"file":[{"date_updated":"2024-01-03T18:30:13Z","date_created":"2024-01-03T18:30:13Z","checksum":"de179b1c6758f182ff0c70d8b38c1501","file_name":"FinalSubmission_Thesis_OLUSANYA.zip","file_id":"14730","access_level":"closed","content_type":"application/zip","relation":"source_file","file_size":16986244,"creator":"oolusany"},{"date_updated":"2024-01-03T18:31:34Z","date_created":"2024-01-03T18:31:34Z","file_id":"14731","checksum":"0e331585e3cd4823320aab4e69e64ccf","file_name":"FinalSubmission2_Thesis_OLUSANYA.pdf","success":1,"relation":"main_file","access_level":"open_access","file_size":6460403,"content_type":"application/pdf","creator":"oolusany"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","day":"19","publication_identifier":{"issn":["2663 - 337X"]},"month":"01","language":[{"iso":"eng"}],"title":"Local adaptation, genetic load and extinction in metapopulations","article_processing_charge":"No","date_updated":"2025-05-26T09:05:10Z","oa":1,"has_accepted_license":"1"},{"language":[{"iso":"eng"}],"publication":"2024 Proceedings of the Symposium on Algorithm Engineering and Experiments","article_processing_charge":"No","date_updated":"2025-07-15T12:51:52Z","oa":1,"title":"Experimental evaluation of fully dynamic k-means via coresets","scopus_import":"1","status":"public","type":"conference","arxiv":1,"author":[{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","full_name":"Henzinger, Monika H","first_name":"Monika H"},{"id":"f8e48cf0-b0ff-11ed-b0e9-b4c35598f964","last_name":"Saulpic","full_name":"Saulpic, David","first_name":"David"},{"id":"8b563fd0-b441-11ee-9101-a3891c61efa6","last_name":"Sidl","full_name":"Sidl, Leonhard","first_name":"Leonhard"}],"month":"01","publication_identifier":{"eisbn":["9781611977929"]},"conference":{"end_date":"2024-01-08","location":"Alexandria, VA, United States","start_date":"2024-01-07","name":"ALENEX: Workshop on Algorithm Engineering and Experiments"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2310.18034","open_access":"1"}],"oa_version":"Preprint","day":"04","_id":"14769","doi":"10.1137/1.9781611977929.17","year":"2024","acknowledgement":"This   project   has   received   funding   from   the   Euro-pean  Research  Council  (ERC)  under  the  EuropeanUnion’s  Horizon  2020  research  and  innovation  programme  (Grant  agreement  No.   101019564  “The  De-sign  of  Modern  Fully  Dynamic  Data  Structures  (Mo-DynStruct)”  and  the  Austrian  Science  Fund  (FWF)project Z 422-N, project “Static and Dynamic Hierar-chical  Graph  Decompositions”,  I  5982-N,  and  project“Fast  Algorithms  for  a  Reactive  Network  Layer  (Re-actNet)”, P 33775-N, with additional funding from thenetidee SCIENCE Stiftung, 2020–2024.D.  Sauplic  has  received  funding  from  the  Euro-pean  Union’s  Horizon  2020  research  and  innovation programme under the Marie Sklodowska-Curie    grant    agreementNo 101034413.","date_created":"2024-01-09T16:22:47Z","citation":{"ieee":"M. H. Henzinger, D. Saulpic, and L. Sidl, “Experimental evaluation of fully dynamic k-means via coresets,” in <i>2024 Proceedings of the Symposium on Algorithm Engineering and Experiments</i>, Alexandria, VA, United States, 2024, pp. 220–233.","ama":"Henzinger MH, Saulpic D, Sidl L. Experimental evaluation of fully dynamic k-means via coresets. In: <i>2024 Proceedings of the Symposium on Algorithm Engineering and Experiments</i>. Society for Industrial &#38; Applied Mathematics; 2024:220-233. doi:<a href=\"https://doi.org/10.1137/1.9781611977929.17\">10.1137/1.9781611977929.17</a>","short":"M.H. Henzinger, D. Saulpic, L. Sidl, in:, 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, Society for Industrial &#38; Applied Mathematics, 2024, pp. 220–233.","chicago":"Henzinger, Monika H, David Saulpic, and Leonhard Sidl. “Experimental Evaluation of Fully Dynamic K-Means via Coresets.” In <i>2024 Proceedings of the Symposium on Algorithm Engineering and Experiments</i>, 220–33. Society for Industrial &#38; Applied Mathematics, 2024. <a href=\"https://doi.org/10.1137/1.9781611977929.17\">https://doi.org/10.1137/1.9781611977929.17</a>.","ista":"Henzinger MH, Saulpic D, Sidl L. 2024. Experimental evaluation of fully dynamic k-means via coresets. 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments. ALENEX: Workshop on Algorithm Engineering and Experiments, 220–233.","mla":"Henzinger, Monika H., et al. “Experimental Evaluation of Fully Dynamic K-Means via Coresets.” <i>2024 Proceedings of the Symposium on Algorithm Engineering and Experiments</i>, Society for Industrial &#38; Applied Mathematics, 2024, pp. 220–33, doi:<a href=\"https://doi.org/10.1137/1.9781611977929.17\">10.1137/1.9781611977929.17</a>.","apa":"Henzinger, M. H., Saulpic, D., &#38; Sidl, L. (2024). Experimental evaluation of fully dynamic k-means via coresets. In <i>2024 Proceedings of the Symposium on Algorithm Engineering and Experiments</i> (pp. 220–233). Alexandria, VA, United States: Society for Industrial &#38; Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611977929.17\">https://doi.org/10.1137/1.9781611977929.17</a>"},"ec_funded":1,"project":[{"grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020"},{"name":"Wittgenstein Award - Monika Henzinger","grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775 ","name":"Fast Algorithms for a Reactive Network Layer"},{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"date_published":"2024-01-04T00:00:00Z","publisher":"Society for Industrial & Applied Mathematics","quality_controlled":"1","page":"220-233","department":[{"_id":"MoHe"}],"publication_status":"published","abstract":[{"text":"For a set of points in Rd, the Euclidean k-means problems consists of finding k centers such that the sum of distances squared from each data point to its closest center is minimized. Coresets are one the main tools developed recently to solve this problem in a big data context. They allow to compress the initial dataset while preserving its structure: running any algorithm on the coreset provides a guarantee almost equivalent to running it on the full data. In this work, we study coresets in a fully-dynamic setting: points are added and deleted with the goal to efficiently maintain a coreset with which a k-means solution can be computed. Based on an algorithm from Henzinger and Kale [ESA'20], we present an efficient and practical implementation of a fully dynamic coreset algorithm, that improves the running time by up to a factor of 20 compared to our non-optimized implementation of the algorithm by Henzinger and Kale, without sacrificing more than 7% on the quality of the k-means solution.","lang":"eng"}],"external_id":{"arxiv":["2310.18034"]}},{"status":"public","type":"journal_article","month":"02","publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"file":[{"access_level":"open_access","file_size":21484855,"relation":"main_file","content_type":"application/pdf","creator":"dernst","date_created":"2023-02-27T07:46:45Z","date_updated":"2023-02-27T07:46:45Z","success":1,"file_name":"2023_NatureGenetics_Zeller.pdf","file_id":"12688","checksum":"6fdb8e34fbeea63edd0f2c6c2cc5823e"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Published Version","author":[{"last_name":"Zeller","first_name":"Peter","full_name":"Zeller, Peter"},{"orcid":"0000-0003-1732-1559","id":"123012b2-db30-11eb-b4d8-a35840c0551b","last_name":"Yeung","full_name":"Yeung, Jake","first_name":"Jake"},{"last_name":"Viñas Gaza","first_name":"Helena","full_name":"Viñas Gaza, Helena"},{"last_name":"de Barbanson","first_name":"Buys Anton","full_name":"de Barbanson, Buys Anton"},{"first_name":"Vivek","full_name":"Bhardwaj, Vivek","last_name":"Bhardwaj"},{"last_name":"Florescu","full_name":"Florescu, Maria","first_name":"Maria"},{"last_name":"van der Linden","full_name":"van der Linden, Reinier","first_name":"Reinier"},{"last_name":"van Oudenaarden","first_name":"Alexander","full_name":"van Oudenaarden, Alexander"}],"publication":"Nature Genetics","language":[{"iso":"eng"}],"has_accepted_license":"1","scopus_import":"1","intvolume":"        55","article_processing_charge":"No","date_updated":"2023-02-27T07:48:24Z","oa":1,"title":"Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis","date_published":"2023-02-01T00:00:00Z","publisher":"Springer Nature","volume":55,"quality_controlled":"1","department":[{"_id":"ScienComp"}],"page":"333-345","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570","000"],"abstract":[{"text":"Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages.","lang":"eng"}],"publication_status":"published","doi":"10.1038/s41588-022-01260-3","article_type":"review","_id":"12158","file_date_updated":"2023-02-27T07:46:45Z","year":"2023","acknowledgement":"We thank A. Giladi for sharing mRNA abundance tables of cell types together with J. van den Berg for critical reading of the manuscript. We thank M. Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973). Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström under CC-BY-SA 3.0 license. This work was supported by European Research Council Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991), HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z. The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF (ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","keyword":["Genetics"],"date_created":"2023-01-12T12:09:09Z","citation":{"apa":"Zeller, P., Yeung, J., Viñas Gaza, H., de Barbanson, B. A., Bhardwaj, V., Florescu, M., … van Oudenaarden, A. (2023). Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. <i>Nature Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41588-022-01260-3\">https://doi.org/10.1038/s41588-022-01260-3</a>","mla":"Zeller, Peter, et al. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” <i>Nature Genetics</i>, vol. 55, Springer Nature, 2023, pp. 333–45, doi:<a href=\"https://doi.org/10.1038/s41588-022-01260-3\">10.1038/s41588-022-01260-3</a>.","ista":"Zeller P, Yeung J, Viñas Gaza H, de Barbanson BA, Bhardwaj V, Florescu M, van der Linden R, van Oudenaarden A. 2023. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 55, 333–345.","chicago":"Zeller, Peter, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, and Alexander van Oudenaarden. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” <i>Nature Genetics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41588-022-01260-3\">https://doi.org/10.1038/s41588-022-01260-3</a>.","short":"P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu, R. van der Linden, A. van Oudenaarden, Nature Genetics 55 (2023) 333–345.","ama":"Zeller P, Yeung J, Viñas Gaza H, et al. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. <i>Nature Genetics</i>. 2023;55:333-345. doi:<a href=\"https://doi.org/10.1038/s41588-022-01260-3\">10.1038/s41588-022-01260-3</a>","ieee":"P. Zeller <i>et al.</i>, “Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis,” <i>Nature Genetics</i>, vol. 55. Springer Nature, pp. 333–345, 2023."}},{"date_published":"2023-03-01T00:00:00Z","publisher":"Wiley","quality_controlled":"1","volume":32,"page":"1441-1457","department":[{"_id":"NiBa"}],"project":[{"name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"abstract":[{"text":"The term “haplotype block” is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies.","lang":"eng"}],"external_id":{"pmid":["36433653"],"isi":["000900762000001"]},"publication_status":"published","doi":"10.1111/mec.16793","_id":"12159","article_type":"original","file_date_updated":"2023-08-16T08:15:41Z","year":"2023","acknowledgement":"We thank the Barton group for useful discussion and feedback during the writing of this article. Comments from Roger Butlin, Molly Schumer's Group, the tskit development team, editors and three reviewers greatly improved the manuscript. Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"date_created":"2023-01-12T12:09:17Z","citation":{"ista":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.","mla":"Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.” <i>Molecular Ecology</i>, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:<a href=\"https://doi.org/10.1111/mec.16793\">10.1111/mec.16793</a>.","chicago":"Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” <i>Molecular Ecology</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/mec.16793\">https://doi.org/10.1111/mec.16793</a>.","ama":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. <i>Molecular Ecology</i>. 2023;32(6):1441-1457. doi:<a href=\"https://doi.org/10.1111/mec.16793\">10.1111/mec.16793</a>","ieee":"D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the origin and structure of haplotype blocks,” <i>Molecular Ecology</i>, vol. 32, no. 6. Wiley, pp. 1441–1457, 2023.","short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457.","apa":"Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., &#38; Barton, N. H. (2023). On the origin and structure of haplotype blocks. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.16793\">https://doi.org/10.1111/mec.16793</a>"},"type":"journal_article","status":"public","pmid":1,"publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"dernst","file_size":7144607,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2023_MolecularEcology_Shipilina.pdf","file_id":"14062","checksum":"b10e0f8fa3dc4d72aaf77a557200978a","success":1,"date_updated":"2023-08-16T08:15:41Z","date_created":"2023-08-16T08:15:41Z"}],"oa_version":"Published Version","day":"01","author":[{"orcid":"0000-0002-1145-9226","last_name":"Shipilina","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","first_name":"Daria","full_name":"Shipilina, Daria"},{"full_name":"Pal, Arka","first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal","orcid":"0000-0002-4530-8469"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean","full_name":"Stankowski, Sean"},{"last_name":"Chan","full_name":"Chan, Yingguang Frank","first_name":"Yingguang Frank"},{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"publication":"Molecular Ecology","language":[{"iso":"eng"}],"isi":1,"intvolume":"        32","has_accepted_license":"1","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","issue":"6","date_updated":"2023-08-16T08:18:47Z","oa":1,"title":"On the origin and structure of haplotype blocks"},{"pmid":1,"type":"journal_article","status":"public","day":"02","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":1343750,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"dernst","date_updated":"2024-01-08T10:16:04Z","date_created":"2024-01-08T10:16:04Z","checksum":"c619887cf130f4649bf3035417186004","file_name":"2023_SeminarsCellDevBiology_CorominasMurtra.pdf","file_id":"14741","success":1}],"publication_identifier":{"issn":["1084-9521"]},"month":"12","author":[{"full_name":"Corominas-Murtra, Bernat","first_name":"Bernat","last_name":"Corominas-Murtra","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9806-5643"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B"}],"publication":"Seminars in Cell & Developmental Biology","language":[{"iso":"eng"}],"scopus_import":"1","has_accepted_license":"1","isi":1,"title":"Modelling the dynamics of mammalian gut homeostasis","oa":1,"date_updated":"2024-01-16T13:22:32Z","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"EdHa"}],"page":"58-65","volume":"150-151","quality_controlled":"1","publisher":"Elsevier","date_published":"2023-12-02T00:00:00Z","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"}],"external_id":{"pmid":["36470715"],"isi":["001053522200001"]},"abstract":[{"lang":"eng","text":"Homeostatic balance in the intestinal epithelium relies on a fast cellular turnover, which is coordinated by an intricate interplay between biochemical signalling, mechanical forces and organ geometry. We review recent modelling approaches that have been developed to understand different facets of this remarkable homeostatic equilibrium. Existing models offer different, albeit complementary, perspectives on the problem. First, biomechanical models aim to explain the local and global mechanical stresses driving cell renewal as well as tissue shape maintenance. Second, compartmental models provide insights into the conditions necessary to keep a constant flow of cells with well-defined ratios of cell types, and how perturbations can lead to an unbalance of relative compartment sizes. A third family of models address, at the cellular level, the nature and regulation of stem fate choices that are necessary to fuel cellular turnover. We also review how these different approaches are starting to be integrated together across scales, to provide quantitative predictions and new conceptual frameworks to think about the dynamics of cell renewal in complex tissues."}],"ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published","doi":"10.1016/j.semcdb.2022.11.005","file_date_updated":"2024-01-08T10:16:04Z","_id":"12162","article_type":"review","ec_funded":1,"date_created":"2023-01-12T12:09:47Z","citation":{"chicago":"Corominas-Murtra, Bernat, and Edouard B Hannezo. “Modelling the Dynamics of Mammalian Gut Homeostasis.” <i>Seminars in Cell &#38; Developmental Biology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.semcdb.2022.11.005\">https://doi.org/10.1016/j.semcdb.2022.11.005</a>.","ista":"Corominas-Murtra B, Hannezo EB. 2023. Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell &#38; Developmental Biology. 150–151, 58–65.","mla":"Corominas-Murtra, Bernat, and Edouard B. Hannezo. “Modelling the Dynamics of Mammalian Gut Homeostasis.” <i>Seminars in Cell &#38; Developmental Biology</i>, vol. 150–151, Elsevier, 2023, pp. 58–65, doi:<a href=\"https://doi.org/10.1016/j.semcdb.2022.11.005\">10.1016/j.semcdb.2022.11.005</a>.","ieee":"B. Corominas-Murtra and E. B. Hannezo, “Modelling the dynamics of mammalian gut homeostasis,” <i>Seminars in Cell &#38; Developmental Biology</i>, vol. 150–151. Elsevier, pp. 58–65, 2023.","ama":"Corominas-Murtra B, Hannezo EB. Modelling the dynamics of mammalian gut homeostasis. <i>Seminars in Cell &#38; Developmental Biology</i>. 2023;150-151:58-65. doi:<a href=\"https://doi.org/10.1016/j.semcdb.2022.11.005\">10.1016/j.semcdb.2022.11.005</a>","short":"B. Corominas-Murtra, E.B. Hannezo, Seminars in Cell &#38; Developmental Biology 150–151 (2023) 58–65.","apa":"Corominas-Murtra, B., &#38; Hannezo, E. B. (2023). Modelling the dynamics of mammalian gut homeostasis. <i>Seminars in Cell &#38; Developmental Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.semcdb.2022.11.005\">https://doi.org/10.1016/j.semcdb.2022.11.005</a>"},"keyword":["Cell Biology","Developmental Biology"],"acknowledgement":"This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.).\r\nB. C-M wants to acknowledge the support of the field of excellence Complexity of Life, in Basic Research and Innovation of the University of Graz.","year":"2023"},{"pmid":1,"type":"journal_article","status":"public","oa_version":"Published Version","day":"01","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":3148143,"creator":"dernst","date_updated":"2023-08-16T08:31:04Z","date_created":"2023-08-16T08:31:04Z","file_name":"2023_FEBSLetters_Loose.pdf","checksum":"7492244d3f9c5faa1347ef03f6e5bc84","file_id":"14063","success":1}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","publication_identifier":{"issn":["0014-5793"],"eissn":["1873-3468"]},"author":[{"full_name":"Loose, Martin","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose"},{"first_name":"Albert","full_name":"Auer, Albert","orcid":"0000-0002-3580-2906","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","last_name":"Auer"},{"last_name":"Brognara","id":"D96FFDA0-A884-11E9-9968-DC26E6697425","first_name":"Gabriel","full_name":"Brognara, Gabriel"},{"full_name":"Budiman, Hanifatul R","first_name":"Hanifatul R","id":"55380f95-15b2-11ec-abd3-aff8e230696b","last_name":"Budiman"},{"first_name":"Lukasz M","full_name":"Kowalski, Lukasz M","last_name":"Kowalski","id":"e3a512e2-4bbe-11eb-a68a-e3857a7844c2"},{"id":"83c17ce3-15b2-11ec-abd3-f486545870bd","last_name":"Matijevic","full_name":"Matijevic, Ivana","first_name":"Ivana"}],"publication":"FEBS Letters","language":[{"iso":"eng"}],"intvolume":"       597","has_accepted_license":"1","scopus_import":"1","isi":1,"title":"In vitro reconstitution of small GTPase regulation","oa":1,"date_updated":"2023-08-16T08:32:29Z","issue":"6","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"MaLo"}],"page":"762-777","quality_controlled":"1","volume":597,"publisher":"Wiley","date_published":"2023-03-01T00:00:00Z","external_id":{"pmid":["36448231"],"isi":["000891573000001"]},"abstract":[{"lang":"eng","text":"Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time."}],"ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"publication_status":"published","doi":"10.1002/1873-3468.14540","file_date_updated":"2023-08-16T08:31:04Z","_id":"12163","article_type":"review","date_created":"2023-01-12T12:09:58Z","citation":{"apa":"Loose, M., Auer, A., Brognara, G., Budiman, H. R., Kowalski, L. M., &#38; Matijevic, I. (2023). In vitro reconstitution of small GTPase regulation. <i>FEBS Letters</i>. Wiley. <a href=\"https://doi.org/10.1002/1873-3468.14540\">https://doi.org/10.1002/1873-3468.14540</a>","chicago":"Loose, Martin, Albert Auer, Gabriel Brognara, Hanifatul R Budiman, Lukasz M Kowalski, and Ivana Matijevic. “In Vitro Reconstitution of Small GTPase Regulation.” <i>FEBS Letters</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/1873-3468.14540\">https://doi.org/10.1002/1873-3468.14540</a>.","mla":"Loose, Martin, et al. “In Vitro Reconstitution of Small GTPase Regulation.” <i>FEBS Letters</i>, vol. 597, no. 6, Wiley, 2023, pp. 762–77, doi:<a href=\"https://doi.org/10.1002/1873-3468.14540\">10.1002/1873-3468.14540</a>.","ista":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. 2023. In vitro reconstitution of small GTPase regulation. FEBS Letters. 597(6), 762–777.","ieee":"M. Loose, A. Auer, G. Brognara, H. R. Budiman, L. M. Kowalski, and I. Matijevic, “In vitro reconstitution of small GTPase regulation,” <i>FEBS Letters</i>, vol. 597, no. 6. Wiley, pp. 762–777, 2023.","ama":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. In vitro reconstitution of small GTPase regulation. <i>FEBS Letters</i>. 2023;597(6):762-777. doi:<a href=\"https://doi.org/10.1002/1873-3468.14540\">10.1002/1873-3468.14540</a>","short":"M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic, FEBS Letters 597 (2023) 762–777."},"keyword":["Cell Biology","Genetics","Molecular Biology","Biochemistry","Structural Biology","Biophysics"],"acknowledgement":"The authors acknowledge support from IST Austria and helpful comments from the anonymous reviewers that helped to improve this manuscript. We apologize to the authors of primary literature and outstanding research not cited here due to space restraints.","year":"2023"},{"publication":"Distributed Computing","language":[{"iso":"eng"}],"intvolume":"        36","scopus_import":"1","isi":1,"title":"Long-lived counters with polylogarithmic amortized step complexity","date_updated":"2023-08-16T08:39:36Z","oa":1,"article_processing_charge":"No","type":"journal_article","status":"public","day":"01","main_file_link":[{"open_access":"1","url":"https://drops.dagstuhl.de/opus/volltexte/2019/11310/"}],"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","publication_identifier":{"eissn":["1432-0452"],"issn":["0178-2770"]},"author":[{"id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","last_name":"Baig","first_name":"Mirza Ahad","full_name":"Baig, Mirza Ahad"},{"last_name":"Hendler","full_name":"Hendler, Danny","first_name":"Danny"},{"last_name":"Milani","full_name":"Milani, Alessia","first_name":"Alessia"},{"last_name":"Travers","first_name":"Corentin","full_name":"Travers, Corentin"}],"doi":"10.1007/s00446-022-00439-5","_id":"12164","article_type":"original","citation":{"mla":"Baig, Mirza Ahad, et al. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” <i>Distributed Computing</i>, vol. 36, Springer Nature, 2023, pp. 29–43, doi:<a href=\"https://doi.org/10.1007/s00446-022-00439-5\">10.1007/s00446-022-00439-5</a>.","ista":"Baig MA, Hendler D, Milani A, Travers C. 2023. Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. 36, 29–43.","chicago":"Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” <i>Distributed Computing</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00446-022-00439-5\">https://doi.org/10.1007/s00446-022-00439-5</a>.","ieee":"M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived counters with polylogarithmic amortized step complexity,” <i>Distributed Computing</i>, vol. 36. Springer Nature, pp. 29–43, 2023.","ama":"Baig MA, Hendler D, Milani A, Travers C. Long-lived counters with polylogarithmic amortized step complexity. <i>Distributed Computing</i>. 2023;36:29-43. doi:<a href=\"https://doi.org/10.1007/s00446-022-00439-5\">10.1007/s00446-022-00439-5</a>","short":"M.A. Baig, D. Hendler, A. Milani, C. Travers, Distributed Computing 36 (2023) 29–43.","apa":"Baig, M. A., Hendler, D., Milani, A., &#38; Travers, C. (2023). Long-lived counters with polylogarithmic amortized step complexity. <i>Distributed Computing</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00446-022-00439-5\">https://doi.org/10.1007/s00446-022-00439-5</a>"},"date_created":"2023-01-12T12:10:08Z","keyword":["Computational Theory and Mathematics","Computer Networks and Communications","Hardware and Architecture","Theoretical Computer Science"],"acknowledgement":"A preliminary version of this work appeared in DISC’19. Mirza Ahad Baig, Alessia Milani and Corentin Travers are supported by ANR projects Descartes and FREDDA. Mirza Ahad Baig is supported by UMI Relax. Danny Hendler is supported by the Israel Science Foundation (Grants 380/18 and 1425/22).","year":"2023","page":"29-43","department":[{"_id":"KrPi"}],"volume":36,"quality_controlled":"1","publisher":"Springer Nature","date_published":"2023-03-01T00:00:00Z","external_id":{"isi":["000890138700001"]},"abstract":[{"lang":"eng","text":"A shared-memory counter is a widely-used and well-studied concurrent object. It supports two operations: An Inc operation that increases its value by 1 and a Read operation that returns its current value. In Jayanti et al (SIAM J Comput, 30(2), 2000), Jayanti, Tan and Toueg proved a linear lower bound on the worst-case step complexity of obstruction-free implementations, from read-write registers, of a large class of shared objects that includes counters. The lower bound leaves open the question of finding counter implementations with sub-linear amortized step complexity. In this work, we address this gap. We show that n-process, wait-free and linearizable counters can be implemented from read-write registers with O(log2n) amortized step complexity. This is the first counter algorithm from read-write registers that provides sub-linear amortized step complexity in executions of arbitrary length. Since a logarithmic lower bound on the amortized step complexity of obstruction-free counter implementations exists, our upper bound is within a logarithmic factor of the optimal. The worst-case step complexity of the construction remains linear, which is optimal. This is obtained thanks to a new max register construction with O(logn) amortized step complexity in executions of arbitrary length in which the value stored in the register does not grow too quickly. We then leverage an existing counter algorithm by Aspnes, Attiya and Censor-Hillel [1] in which we “plug” our max register implementation to show that it remains linearizable while achieving O(log2n) amortized step complexity."}],"publication_status":"published"}]