[{"publication":"Annual Review of Fluid Mechanics","ec_funded":1,"page":"133-157","scopus_import":"1","type":"journal_article","status":"public","day":"01","publication_status":"published","doi":"10.1146/annurev-fluid-022421-011319","title":"Spontaneous aggregation of convective storms","corr_author":"1","publisher":"Annual Reviews","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        54","article_processing_charge":"No","date_updated":"2024-11-05T09:00:40Z","article_type":"original","citation":{"short":"C.J. Muller, D. Yang, G. Craig, T. Cronin, B. Fildier, J.O. Haerter, C. Hohenegger, B. Mapes, D. Randall, S. Shamekh, S.C. Sherwood, Annual Review of Fluid Mechanics 54 (2022) 133–157.","ista":"Muller CJ, Yang D, Craig G, Cronin T, Fildier B, Haerter JO, Hohenegger C, Mapes B, Randall D, Shamekh S, Sherwood SC. 2022. Spontaneous aggregation of convective storms. Annual Review of Fluid Mechanics. 54, 133–157.","apa":"Muller, C. J., Yang, D., Craig, G., Cronin, T., Fildier, B., Haerter, J. O., … Sherwood, S. C. (2022). Spontaneous aggregation of convective storms. <i>Annual Review of Fluid Mechanics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-fluid-022421-011319\">https://doi.org/10.1146/annurev-fluid-022421-011319</a>","mla":"Muller, Caroline J., et al. “Spontaneous Aggregation of Convective Storms.” <i>Annual Review of Fluid Mechanics</i>, vol. 54, Annual Reviews, 2022, pp. 133–57, doi:<a href=\"https://doi.org/10.1146/annurev-fluid-022421-011319\">10.1146/annurev-fluid-022421-011319</a>.","chicago":"Muller, Caroline J, Da Yang, George Craig, Timothy Cronin, Benjamin Fildier, Jan O. Haerter, Cathy Hohenegger, et al. “Spontaneous Aggregation of Convective Storms.” <i>Annual Review of Fluid Mechanics</i>. Annual Reviews, 2022. <a href=\"https://doi.org/10.1146/annurev-fluid-022421-011319\">https://doi.org/10.1146/annurev-fluid-022421-011319</a>.","ieee":"C. J. Muller <i>et al.</i>, “Spontaneous aggregation of convective storms,” <i>Annual Review of Fluid Mechanics</i>, vol. 54. Annual Reviews, pp. 133–157, 2022.","ama":"Muller CJ, Yang D, Craig G, et al. Spontaneous aggregation of convective storms. <i>Annual Review of Fluid Mechanics</i>. 2022;54:133-157. doi:<a href=\"https://doi.org/10.1146/annurev-fluid-022421-011319\">10.1146/annurev-fluid-022421-011319</a>"},"abstract":[{"lang":"eng","text":"Idealized simulations of the tropical atmosphere have predicted that clouds can spontaneously clump together in space, despite perfectly homogeneous settings. This phenomenon has been called self-aggregation, and it results in a state where a moist cloudy region with intense deep convective storms is surrounded by extremely dry subsiding air devoid of deep clouds. We review here the main findings from theoretical work and idealized models of this phenomenon, highlighting the physical processes believed to play a key role in convective self-aggregation. We also review the growing literature on the importance and implications of this phenomenon for the tropical atmosphere, notably, for the hydrological cycle and for precipitation extremes, in our current and in a warming climate."}],"oa_version":"Published Version","month":"01","acknowledgement":"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 805041). She also thanks Grand Équipement National de Calcul Intensif (GENCI), France, for providing access to their computing platforms at Très Grand Centre de Calcul (TGCC). J.O.H. gratefully acknowledges funding from the Villum Foundation (grant 13168), the ERC under the Horizon 2020 research and innovation program (grant 771859), and the Novo Nordisk Foundation's Interdisciplinary Synergy Program (grant NNF19OC0057374). G.C. gratefully acknowledges the support of the transregional collaborative research center (SFB/TRR 165) “Waves to Weather” (http://www.wavestoweather.de) funded by the German Research Foundation (DFG). D.Y. is supported by a Packard Fellowship in Science and Engineering, the France–Berkeley Fund, Laboratory Directed Research and Development (LDRD) funding from the Lawrence Berkeley National Laboratory, and the US Department of Energy, Office of Science, Office of Biological and Environmental Research, Climate and Environmental Sciences Division, Regional and Global Climate Modeling Program under award DE-AC02-05CH11231.","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1146/annurev-fluid-022421-011319"}],"isi":1,"quality_controlled":"1","project":[{"name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate","grant_number":"805041","_id":"629205d8-2b32-11ec-9570-e1356ff73576","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"date_created":"2022-01-23T23:01:29Z","oa":1,"year":"2022","_id":"10656","author":[{"full_name":"Muller, Caroline J","first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","last_name":"Muller"},{"last_name":"Yang","full_name":"Yang, Da","first_name":"Da"},{"last_name":"Craig","full_name":"Craig, George","first_name":"George"},{"full_name":"Cronin, Timothy","first_name":"Timothy","last_name":"Cronin"},{"last_name":"Fildier","first_name":"Benjamin","full_name":"Fildier, Benjamin"},{"last_name":"Haerter","first_name":"Jan O.","full_name":"Haerter, Jan O."},{"last_name":"Hohenegger","full_name":"Hohenegger, Cathy","first_name":"Cathy"},{"first_name":"Brian","full_name":"Mapes, Brian","last_name":"Mapes"},{"full_name":"Randall, David","first_name":"David","last_name":"Randall"},{"last_name":"Shamekh","first_name":"Sara","full_name":"Shamekh, Sara"},{"first_name":"Steven C.","full_name":"Sherwood, Steven C.","last_name":"Sherwood"}],"external_id":{"isi":["000794152800006"]},"volume":54,"department":[{"_id":"CaMu"}],"date_published":"2022-01-01T00:00:00Z","publication_identifier":{"issn":["0066-4189"],"eissn":["1545-4479"]}},{"ddc":["576"],"date_updated":"2025-04-15T07:48:50Z","article_type":"original","title":"Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity","publisher":"The Royal Society","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"intvolume":"       377","article_processing_charge":"No","day":"24","publication_status":"published","status":"public","doi":"10.1098/rstb.2021.0010","publication":"Philosophical Transactions of the Royal Society B","scopus_import":"1","has_accepted_license":"1","type":"journal_article","external_id":{"isi":["000745854300008"],"pmid":["35067097"]},"volume":377,"article_number":"20210010","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"date_published":"2022-01-24T00:00:00Z","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"related_material":{"link":[{"url":"https://doi.org/10.1101/2021.08.05.455207","relation":"earlier_version"}],"record":[{"status":"public","relation":"dissertation_contains","id":"14711"}]},"author":[{"last_name":"Sachdeva","first_name":"Himani","full_name":"Sachdeva, Himani"},{"orcid":"0000-0003-1971-8314","last_name":"Olusanya","first_name":"Oluwafunmilola O","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","full_name":"Olusanya, Oluwafunmilola O"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"_id":"10658","project":[{"_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","name":"Causes and consequences of population fragmentation","grant_number":"P32896"}],"quality_controlled":"1","file_date_updated":"2022-01-24T10:34:45Z","language":[{"iso":"eng"}],"date_created":"2022-01-24T10:34:53Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2022","oa":1,"issue":"1846","citation":{"ama":"Sachdeva H, Olusanya OO, Barton NH. Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. <i>Philosophical Transactions of the Royal Society B</i>. 2022;377(1846). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0010\">10.1098/rstb.2021.0010</a>","ieee":"H. Sachdeva, O. O. Olusanya, and N. H. Barton, “Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity,” <i>Philosophical Transactions of the Royal Society B</i>, vol. 377, no. 1846. The Royal Society, 2022.","chicago":"Sachdeva, Himani, Oluwafunmilola O Olusanya, and Nicholas H Barton. “Genetic Load and Extinction in Peripheral Populations: The Roles of Migration, Drift and Demographic Stochasticity.” <i>Philosophical Transactions of the Royal Society B</i>. The Royal Society, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0010\">https://doi.org/10.1098/rstb.2021.0010</a>.","ista":"Sachdeva H, Olusanya OO, Barton NH. 2022. Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. Philosophical Transactions of the Royal Society B. 377(1846), 20210010.","apa":"Sachdeva, H., Olusanya, O. O., &#38; Barton, N. H. (2022). Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. <i>Philosophical Transactions of the Royal Society B</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2021.0010\">https://doi.org/10.1098/rstb.2021.0010</a>","mla":"Sachdeva, Himani, et al. “Genetic Load and Extinction in Peripheral Populations: The Roles of Migration, Drift and Demographic Stochasticity.” <i>Philosophical Transactions of the Royal Society B</i>, vol. 377, no. 1846, 20210010, The Royal Society, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0010\">10.1098/rstb.2021.0010</a>.","short":"H. Sachdeva, O.O. Olusanya, N.H. Barton, Philosophical Transactions of the Royal Society B 377 (2022)."},"abstract":[{"text":"We analyse how migration from a large mainland influences genetic load and population numbers on an island, in a scenario where fitness-affecting variants are unconditionally deleterious, and where numbers decline with increasing load. Our analysis shows that migration can have qualitatively different effects, depending on the total mutation target and fitness effects of deleterious variants. In particular, we find that populations exhibit a genetic Allee effect across a wide range of parameter combinations, when variants are partially recessive, cycling between low-load (large-population) and high-load (sink) states. Increased migration reduces load in the sink state (by increasing heterozygosity) but further inflates load in the large-population state (by hindering purging). We identify various critical parameter thresholds at which one or other stable state collapses, and discuss how these thresholds are influenced by the genetic versus demographic effects of migration. Our analysis is based on a ‘semi-deterministic’ analysis, which accounts for genetic drift but neglects demographic stochasticity. We also compare against simulations which account for both demographic stochasticity and drift. Our results clarify the importance of gene flow as a key determinant of extinction risk in peripheral populations, even in the absence of ecological gradients. This article is part of the theme issue ‘Species’ ranges in the face of changing environments (part I)’.","lang":"eng"}],"file":[{"checksum":"04ca9e2f0e344d680b947f2457df8d0a","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"rstb.2021.0010.pdf","file_id":"10659","creator":"oolusany","date_created":"2022-01-24T10:34:45Z","file_size":1845792,"date_updated":"2022-01-24T10:34:45Z"}],"oa_version":"Published Version","month":"01","acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) (grant no. P-32896B).","isi":1},{"date_updated":"2025-06-11T13:54:53Z","article_type":"original","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Blood-based epigenome-wide analyses of cognitive abilities","corr_author":"1","publisher":"Springer Nature","article_processing_charge":"No","pmid":1,"intvolume":"        23","status":"public","publication_status":"published","day":"17","doi":"10.1186/s13059-021-02596-5","publication":"Genome Biology","has_accepted_license":"1","type":"journal_article","scopus_import":"1","article_number":"26","external_id":{"pmid":["35039062"],"isi":["000744358300002"]},"volume":23,"publication_identifier":{"eissn":["1474-760X"],"issn":["1474-7596"]},"department":[{"_id":"MaRo"}],"date_published":"2022-01-17T00:00:00Z","related_material":{"link":[{"url":"https://doi.org/10.1101/2021.05.24.21257698","relation":"earlier_version"}],"record":[{"relation":"research_data","status":"public","id":"13072"}]},"_id":"10702","author":[{"last_name":"McCartney","full_name":"McCartney, Daniel L.","first_name":"Daniel L."},{"last_name":"Hillary","full_name":"Hillary, Robert F.","first_name":"Robert F."},{"first_name":"Eleanor L.S.","full_name":"Conole, Eleanor L.S.","last_name":"Conole"},{"full_name":"Banos, Daniel Trejo","first_name":"Daniel Trejo","last_name":"Banos"},{"first_name":"Danni A.","full_name":"Gadd, Danni A.","last_name":"Gadd"},{"full_name":"Walker, Rosie M.","first_name":"Rosie M.","last_name":"Walker"},{"full_name":"Nangle, Cliff","first_name":"Cliff","last_name":"Nangle"},{"full_name":"Flaig, Robin","first_name":"Robin","last_name":"Flaig"},{"first_name":"Archie","full_name":"Campbell, Archie","last_name":"Campbell"},{"last_name":"Murray","first_name":"Alison D.","full_name":"Murray, Alison D."},{"full_name":"Maniega, Susana Muñoz","first_name":"Susana Muñoz","last_name":"Maniega"},{"full_name":"Valdés-Hernández, María Del C.","first_name":"María Del C.","last_name":"Valdés-Hernández"},{"first_name":"Mathew A.","full_name":"Harris, Mathew A.","last_name":"Harris"},{"first_name":"Mark E.","full_name":"Bastin, Mark E.","last_name":"Bastin"},{"first_name":"Joanna M.","full_name":"Wardlaw, Joanna M.","last_name":"Wardlaw"},{"last_name":"Harris","first_name":"Sarah E.","full_name":"Harris, Sarah E."},{"first_name":"David J.","full_name":"Porteous, David J.","last_name":"Porteous"},{"last_name":"Tucker-Drob","first_name":"Elliot M.","full_name":"Tucker-Drob, Elliot M."},{"last_name":"McIntosh","full_name":"McIntosh, Andrew M.","first_name":"Andrew M."},{"full_name":"Evans, Kathryn L.","first_name":"Kathryn L.","last_name":"Evans"},{"first_name":"Ian J.","full_name":"Deary, Ian J.","last_name":"Deary"},{"first_name":"Simon R.","full_name":"Cox, Simon R.","last_name":"Cox"},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","last_name":"Robinson","orcid":"0000-0001-8982-8813"},{"first_name":"Riccardo E.","full_name":"Marioni, Riccardo E.","last_name":"Marioni"}],"language":[{"iso":"eng"}],"date_created":"2022-01-30T23:01:33Z","project":[{"_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","grant_number":"PCEGP3_181181","name":"Improving estimation and prediction of common complex disease risk"}],"quality_controlled":"1","file_date_updated":"2022-01-31T13:16:05Z","issue":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2022","oa":1,"oa_version":"Published Version","file":[{"creator":"cchlebak","date_created":"2022-01-31T13:16:05Z","file_size":1540606,"date_updated":"2022-01-31T13:16:05Z","checksum":"34f10bb2b0594189dcac24d13b691d52","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2022_GenomeBio_McCartney.pdf","file_id":"10708"}],"citation":{"ista":"McCartney DL, Hillary RF, Conole ELS, Banos DT, Gadd DA, Walker RM, Nangle C, Flaig R, Campbell A, Murray AD, Maniega SM, Valdés-Hernández MDC, Harris MA, Bastin ME, Wardlaw JM, Harris SE, Porteous DJ, Tucker-Drob EM, McIntosh AM, Evans KL, Deary IJ, Cox SR, Robinson MR, Marioni RE. 2022. Blood-based epigenome-wide analyses of cognitive abilities. Genome Biology. 23(1), 26.","apa":"McCartney, D. L., Hillary, R. F., Conole, E. L. S., Banos, D. T., Gadd, D. A., Walker, R. M., … Marioni, R. E. (2022). Blood-based epigenome-wide analyses of cognitive abilities. <i>Genome Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13059-021-02596-5\">https://doi.org/10.1186/s13059-021-02596-5</a>","mla":"McCartney, Daniel L., et al. “Blood-Based Epigenome-Wide Analyses of Cognitive Abilities.” <i>Genome Biology</i>, vol. 23, no. 1, 26, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13059-021-02596-5\">10.1186/s13059-021-02596-5</a>.","chicago":"McCartney, Daniel L., Robert F. Hillary, Eleanor L.S. Conole, Daniel Trejo Banos, Danni A. Gadd, Rosie M. Walker, Cliff Nangle, et al. “Blood-Based Epigenome-Wide Analyses of Cognitive Abilities.” <i>Genome Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1186/s13059-021-02596-5\">https://doi.org/10.1186/s13059-021-02596-5</a>.","short":"D.L. McCartney, R.F. Hillary, E.L.S. Conole, D.T. Banos, D.A. Gadd, R.M. Walker, C. Nangle, R. Flaig, A. Campbell, A.D. Murray, S.M. Maniega, M.D.C. Valdés-Hernández, M.A. Harris, M.E. Bastin, J.M. Wardlaw, S.E. Harris, D.J. Porteous, E.M. Tucker-Drob, A.M. McIntosh, K.L. Evans, I.J. Deary, S.R. Cox, M.R. Robinson, R.E. Marioni, Genome Biology 23 (2022).","ama":"McCartney DL, Hillary RF, Conole ELS, et al. Blood-based epigenome-wide analyses of cognitive abilities. <i>Genome Biology</i>. 2022;23(1). doi:<a href=\"https://doi.org/10.1186/s13059-021-02596-5\">10.1186/s13059-021-02596-5</a>","ieee":"D. L. McCartney <i>et al.</i>, “Blood-based epigenome-wide analyses of cognitive abilities,” <i>Genome Biology</i>, vol. 23, no. 1. Springer Nature, 2022."},"abstract":[{"text":"Background: Blood-based markers of cognitive functioning might provide an accessible way to track neurodegeneration years prior to clinical manifestation of cognitive impairment and dementia. Results: Using blood-based epigenome-wide analyses of general cognitive function, we show that individual differences in DNA methylation (DNAm) explain 35.0% of the variance in general cognitive function (g). A DNAm predictor explains ~4% of the variance, independently of a polygenic score, in two external cohorts. It also associates with circulating levels of neurology- and inflammation-related proteins, global brain imaging metrics, and regional cortical volumes. Conclusions: As sample sizes increase, the ability to assess cognitive function from DNAm data may be informative in settings where cognitive testing is unreliable or unavailable.","lang":"eng"}],"isi":1,"acknowledgement":"GS received core support from the Chief Scientist Office of the Scottish Government Health Directorates (CZD/16/6) and the Scottish Funding Council (HR03006). Genotyping and DNA methylation profiling of the GS samples was carried out by the Genetics Core Laboratory at the Edinburgh Clinical Research Facility, Edinburgh, Scotland, and was funded by the Medical Research Council UK and the Wellcome Trust (Wellcome Trust Strategic Award STratifying Resilience and Depression Longitudinally (STRADL; Reference 104036/Z/14/Z). The DNA methylation data assayed for Generation Scotland was partially funded by a 2018 NARSAD Young Investigator Grant from the Brain & Behavior Research Foundation (Ref: 27404; awardee: Dr David M Howard) and by a JMAS SIM fellowship from the Royal College of Physicians of Edinburgh (Awardee: Dr Heather C Whalley). LBC1936 MRI brain imaging was supported by Medical Research Council (MRC) grants [G0701120], [G1001245], [MR/M013111/1] and [MR/R024065/1]. Magnetic resonance image acquisition and analyses were conducted at the Brain Research Imaging Centre, Neuroimaging Sciences, University of Edinburgh (www.bric.ed.ac.uk) which is part of SINAPSE (Scottish Imaging Network: A Platform for Scientific Excellence) collaboration (www.sinapse.ac.uk) funded by the Scottish Funding Council and the Chief Scientist Office. This work was supported by the European Union Horizon 2020 (PHC.03.15, project No 666881), SVDs@Target, the Fondation Leducq Transatlantic Network of Excellence for the Study of Perivascular Spaces in Small Vessel Disease [ref no. 16 CVD 05]. We thank the LBC1936 participants and team members who contributed to these studies. The LBC1936 is supported by Age UK (Disconnected Mind project, which supports S.E.H.), the Medical Research Council (G0701120, G1001245, MR/M013111/1, MR/R024065/1) and the University of Edinburgh. Methylation typing of LBC1936 was supported by the Centre for Cognitive Ageing and Cognitive Epidemiology (Pilot Fund award), Age UK, The Wellcome Trust Institutional Strategic Support Fund, The University of Edinburgh, and The University of Queensland. Genotyping was funded by the Biotechnology and Biological Sciences Research Council (BB/F019394/1). Proteomic analyses in LBC1936 were supported by the Age UK grant and NIH Grants R01AG054628 and R01AG05462802S1. M.V.H. is funded by the Row Fogo Charitable Trust (Grant no. BROD.FID3668413). J.M.W is supported by the UK Dementia Research Institute which receives its funding from DRI Ltd, funded by the UK Medical Research Council, Alzheimers Society and Alzheimers Research UK. R.F.H., E.L.S.C and D.A.G. are supported by funding from the Wellcome Trust 4 year PhD in Translational Neuroscience: training the next generation of basic neuroscientists to embrace clinical research [108890/Z/15/Z]. E.M.T.D. was supported by the National Institutes of Health (NIH) grants R01AG054628, R01MH120219, R01HD083613, P2CHD042849 and P30AG066614. S.R.C. was also supported by a National Institutes of Health (NIH) research grant R01AG054628 and is supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (Grant Number 221890/Z/20/Z). D.L.Mc.C. and R.E.M. are supported by Alzheimers Research UK major project grant ARUK/PG2017B/10. R.E.M. is supported by Alzheimer’s Society major project grant AS-PG-19b-010. This research was funded in whole, or in part, by Wellcome [104036/Z/14/Z and 108890/Z/15/Z]. For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","month":"01"},{"article_type":"original","date_updated":"2025-04-15T06:53:08Z","ddc":["510"],"arxiv":1,"article_processing_charge":"Yes (via OA deal)","intvolume":"       228","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Very stable Higgs bundles, equivariant multiplicity and mirror symmetry","publisher":"Springer Nature","corr_author":"1","doi":"10.1007/s00222-021-01093-7","status":"public","day":"01","publication_status":"published","has_accepted_license":"1","type":"journal_article","scopus_import":"1","page":"893-989","publication":"Inventiones Mathematicae","publication_identifier":{"eissn":["1432-1297"],"issn":["0020-9910"]},"department":[{"_id":"TaHa"}],"date_published":"2022-05-01T00:00:00Z","volume":228,"external_id":{"isi":["000745495400001"],"arxiv":["2101.08583"]},"_id":"10704","author":[{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","first_name":"Tamás","full_name":"Hausel, Tamás","last_name":"Hausel","orcid":"0000-0002-9582-2634"},{"last_name":"Hitchin","full_name":"Hitchin, Nigel","first_name":"Nigel"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/the-tip-of-the-mathematical-iceberg/","description":"News on the ISTA Website","relation":"press_release"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2022","oa":1,"language":[{"iso":"eng"}],"date_created":"2022-01-30T23:01:34Z","quality_controlled":"1","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"file_date_updated":"2023-02-27T07:30:47Z","isi":1,"month":"05","acknowledgement":"We would like to thank Brian Collier, Davide Gaiotto, Peter Gothen, Jochen Heinloth, Daniel Huybrechts, Quoc Ho, Joel Kamnitzer, Gérard Laumon, Luca Migliorini, Alexander Minets, Brent Pym, Peng Shan, Carlos Simpson, András Szenes, Fernando R. Villegas, Richard Wentworth, Edward Witten and Kōta Yoshioka for interesting comments and discussions. Most of all we are grateful for a long list of very helpful comments by the referee. We would also like to thank the organizers of the Summer School on Higgs bundles in Hamburg in September 2018, where the authors and Richard Wentworth were giving lectures and where the work in this paper started by considering the mirror of the Lagrangian upward flows W+E investigated in [17]. The second author wishes to thank EPSRC and ICMAT for support. Open access funding provided by Institute of Science and Technology (IST Austria).","oa_version":"Published Version","file":[{"date_created":"2023-02-27T07:30:47Z","creator":"dernst","date_updated":"2023-02-27T07:30:47Z","file_size":1069538,"content_type":"application/pdf","access_level":"open_access","checksum":"a382ba75acebc9adfb8fe56247cb410e","relation":"main_file","file_id":"12687","file_name":"2022_InventionesMahtematicae_Hausel.pdf","success":1}],"citation":{"ama":"Hausel T, Hitchin N. Very stable Higgs bundles, equivariant multiplicity and mirror symmetry. <i>Inventiones Mathematicae</i>. 2022;228:893-989. doi:<a href=\"https://doi.org/10.1007/s00222-021-01093-7\">10.1007/s00222-021-01093-7</a>","ieee":"T. Hausel and N. Hitchin, “Very stable Higgs bundles, equivariant multiplicity and mirror symmetry,” <i>Inventiones Mathematicae</i>, vol. 228. Springer Nature, pp. 893–989, 2022.","chicago":"Hausel, Tamás, and Nigel Hitchin. “Very Stable Higgs Bundles, Equivariant Multiplicity and Mirror Symmetry.” <i>Inventiones Mathematicae</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00222-021-01093-7\">https://doi.org/10.1007/s00222-021-01093-7</a>.","ista":"Hausel T, Hitchin N. 2022. Very stable Higgs bundles, equivariant multiplicity and mirror symmetry. Inventiones Mathematicae. 228, 893–989.","mla":"Hausel, Tamás, and Nigel Hitchin. “Very Stable Higgs Bundles, Equivariant Multiplicity and Mirror Symmetry.” <i>Inventiones Mathematicae</i>, vol. 228, Springer Nature, 2022, pp. 893–989, doi:<a href=\"https://doi.org/10.1007/s00222-021-01093-7\">10.1007/s00222-021-01093-7</a>.","apa":"Hausel, T., &#38; Hitchin, N. (2022). Very stable Higgs bundles, equivariant multiplicity and mirror symmetry. <i>Inventiones Mathematicae</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00222-021-01093-7\">https://doi.org/10.1007/s00222-021-01093-7</a>","short":"T. Hausel, N. Hitchin, Inventiones Mathematicae 228 (2022) 893–989."},"abstract":[{"lang":"eng","text":"We define and study the existence of very stable Higgs bundles on Riemann surfaces, how it implies a precise formula for the multiplicity of the very stable components of the global nilpotent cone and its relationship to mirror symmetry. The main ingredients are the Bialynicki-Birula theory of C∗-actions on semiprojective varieties, C∗ characters of indices of C∗-equivariant coherent sheaves, Hecke transformation for Higgs bundles, relative Fourier–Mukai transform along the Hitchin fibration, hyperholomorphic structures on universal bundles and cominuscule Higgs bundles."}]},{"_id":"10705","author":[{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"external_id":{"pmid":["35058104"],"isi":["000795773900009"]},"volume":32,"date_published":"2022-05-01T00:00:00Z","department":[{"_id":"EdHa"},{"_id":"CaHe"}],"publication_identifier":{"issn":["0962-8924"],"eissn":["1879-3088"]},"abstract":[{"lang":"eng","text":"Although rigidity and jamming transitions have been widely studied in physics and material science, their importance in a number of biological processes, including embryo development, tissue homeostasis, wound healing, and disease progression, has only begun to be recognized in the past few years. The hypothesis that biological systems can undergo rigidity/jamming transitions is attractive, as it would allow these systems to change their material properties rapidly and strongly. However, whether such transitions indeed occur in biological systems, how they are being regulated, and what their physiological relevance might be, is still being debated. Here, we review theoretical and experimental advances from the past few years, focusing on the regulation and role of potential tissue rigidity transitions in different biological processes."}],"citation":{"chicago":"Hannezo, Edouard B, and Carl-Philipp J Heisenberg. “Rigidity Transitions in Development and Disease.” <i>Trends in Cell Biology</i>. Cell Press, 2022. <a href=\"https://doi.org/10.1016/j.tcb.2021.12.006\">https://doi.org/10.1016/j.tcb.2021.12.006</a>.","ista":"Hannezo EB, Heisenberg C-PJ. 2022. Rigidity transitions in development and disease. Trends in Cell Biology. 32(5), P433-444.","apa":"Hannezo, E. B., &#38; Heisenberg, C.-P. J. (2022). Rigidity transitions in development and disease. <i>Trends in Cell Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tcb.2021.12.006\">https://doi.org/10.1016/j.tcb.2021.12.006</a>","mla":"Hannezo, Edouard B., and Carl-Philipp J. Heisenberg. “Rigidity Transitions in Development and Disease.” <i>Trends in Cell Biology</i>, vol. 32, no. 5, Cell Press, 2022, pp. P433-444, doi:<a href=\"https://doi.org/10.1016/j.tcb.2021.12.006\">10.1016/j.tcb.2021.12.006</a>.","short":"E.B. Hannezo, C.-P.J. Heisenberg, Trends in Cell Biology 32 (2022) P433-444.","ama":"Hannezo EB, Heisenberg C-PJ. Rigidity transitions in development and disease. <i>Trends in Cell Biology</i>. 2022;32(5):P433-444. doi:<a href=\"https://doi.org/10.1016/j.tcb.2021.12.006\">10.1016/j.tcb.2021.12.006</a>","ieee":"E. B. Hannezo and C.-P. J. Heisenberg, “Rigidity transitions in development and disease,” <i>Trends in Cell Biology</i>, vol. 32, no. 5. Cell Press, pp. P433-444, 2022."},"oa_version":"None","month":"05","acknowledgement":"We thank present and former members of the Heisenberg and Hannezo groups, in particular Bernat Corominas-Murtra and Nicoletta Petridou, for helpful discussions, and Claudia Flandoli for the artwork. We apologize for not being able to cite a number of highly relevant studies, to stay within the maximum allowed number of citations.","isi":1,"quality_controlled":"1","date_created":"2022-01-30T23:01:34Z","language":[{"iso":"eng"}],"year":"2022","issue":"5","corr_author":"1","publisher":"Cell Press","title":"Rigidity transitions in development and disease","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"intvolume":"        32","article_processing_charge":"No","article_type":"original","date_updated":"2024-10-09T21:01:30Z","publication":"Trends in Cell Biology","page":"P433-444","scopus_import":"1","type":"journal_article","publication_status":"published","status":"public","day":"01","doi":"10.1016/j.tcb.2021.12.006"},{"doi":"10.1007/s40598-022-00198-y","day":"01","publication_status":"published","status":"public","conference":{"name":"CIRM: Centre International de Rencontres Mathématiques","end_date":"2021-10-08","location":"Hybrid","start_date":"2021-10-04"},"scopus_import":"1","type":"journal_article","publication":"Arnold Mathematical Journal","page":"411-422","article_type":"original","date_updated":"2023-02-27T07:34:08Z","arxiv":1,"intvolume":"         8","article_processing_charge":"No","publisher":"Springer Nature","title":"Open problems on billiards and geometric optics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"year":"2022","quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2022-01-30T23:01:34Z","month":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2110.10750"}],"citation":{"ieee":"M. Bialy, C. Fiorebe, A. Glutsyuk, M. Levi, A. Plakhov, and S. Tabachnikov, “Open problems on billiards and geometric optics,” <i>Arnold Mathematical Journal</i>, vol. 8. Springer Nature, pp. 411–422, 2022.","ama":"Bialy M, Fiorebe C, Glutsyuk A, Levi M, Plakhov A, Tabachnikov S. Open problems on billiards and geometric optics. <i>Arnold Mathematical Journal</i>. 2022;8:411-422. doi:<a href=\"https://doi.org/10.1007/s40598-022-00198-y\">10.1007/s40598-022-00198-y</a>","short":"M. Bialy, C. Fiorebe, A. Glutsyuk, M. Levi, A. Plakhov, S. Tabachnikov, Arnold Mathematical Journal 8 (2022) 411–422.","mla":"Bialy, Misha, et al. “Open Problems on Billiards and Geometric Optics.” <i>Arnold Mathematical Journal</i>, vol. 8, Springer Nature, 2022, pp. 411–22, doi:<a href=\"https://doi.org/10.1007/s40598-022-00198-y\">10.1007/s40598-022-00198-y</a>.","apa":"Bialy, M., Fiorebe, C., Glutsyuk, A., Levi, M., Plakhov, A., &#38; Tabachnikov, S. (2022). Open problems on billiards and geometric optics. <i>Arnold Mathematical Journal</i>. Hybrid: Springer Nature. <a href=\"https://doi.org/10.1007/s40598-022-00198-y\">https://doi.org/10.1007/s40598-022-00198-y</a>","ista":"Bialy M, Fiorebe C, Glutsyuk A, Levi M, Plakhov A, Tabachnikov S. 2022. Open problems on billiards and geometric optics. Arnold Mathematical Journal. 8, 411–422.","chicago":"Bialy, Misha, Corentin Fiorebe, Alexey Glutsyuk, Mark Levi, Alexander Plakhov, and Serge Tabachnikov. “Open Problems on Billiards and Geometric Optics.” <i>Arnold Mathematical Journal</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s40598-022-00198-y\">https://doi.org/10.1007/s40598-022-00198-y</a>."},"abstract":[{"text":"This is a collection of problems composed by some participants of the workshop “Differential Geometry, Billiards, and Geometric Optics” that took place at CIRM on October 4–8, 2021.","lang":"eng"}],"oa_version":"Preprint","date_published":"2022-10-01T00:00:00Z","department":[{"_id":"VaKa"}],"publication_identifier":{"eissn":["2199-6806"],"issn":["2199-6792"]},"external_id":{"arxiv":["2110.10750"]},"volume":8,"author":[{"last_name":"Bialy","first_name":"Misha","full_name":"Bialy, Misha"},{"last_name":"Fiorebe","first_name":"Corentin","id":"06619f18-9070-11eb-847d-d1ee780bd88b","full_name":"Fiorebe, Corentin"},{"full_name":"Glutsyuk, Alexey","first_name":"Alexey","last_name":"Glutsyuk"},{"first_name":"Mark","full_name":"Levi, Mark","last_name":"Levi"},{"full_name":"Plakhov, Alexander","first_name":"Alexander","last_name":"Plakhov"},{"last_name":"Tabachnikov","first_name":"Serge","full_name":"Tabachnikov, Serge"}],"_id":"10706","related_material":{"link":[{"url":"https://conferences.cirm-math.fr/2383.html","relation":"earlier_version"}]}},{"related_material":{"link":[{"url":"https://ist.ac.at/en/news/suppressing-the-spread-of-tumors/","description":"News on IST Homepage","relation":"confirmation"}]},"_id":"10712","author":[{"last_name":"Roblek","orcid":"0000-0001-9588-1389","full_name":"Roblek, Marko","id":"3047D808-F248-11E8-B48F-1D18A9856A87","first_name":"Marko"},{"full_name":"Bicher, Julia","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Bicher"},{"last_name":"van Gogh","full_name":"van Gogh, Merel","first_name":"Merel"},{"id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","first_name":"Attila","full_name":"György, Attila","orcid":"0000-0002-1819-198X","last_name":"György"},{"full_name":"Seeböck, Rita","first_name":"Rita","last_name":"Seeböck"},{"last_name":"Szulc","first_name":"Bozena","full_name":"Szulc, Bozena"},{"last_name":"Damme","first_name":"Markus","full_name":"Damme, Markus"},{"last_name":"Olczak","full_name":"Olczak, Mariusz","first_name":"Mariusz"},{"full_name":"Borsig, Lubor","first_name":"Lubor","last_name":"Borsig"},{"full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","last_name":"Siekhaus","orcid":"0000-0001-8323-8353"}],"external_id":{"isi":["000760618800001"],"pmid":["35211397"]},"volume":12,"acknowledged_ssus":[{"_id":"Bio"}],"article_number":"777634","date_published":"2022-02-08T00:00:00Z","department":[{"_id":"DaSi"}],"publication_identifier":{"issn":["2234-943X"]},"abstract":[{"text":"Solute carriers are increasingly recognized as participating in a plethora of pathologies, including cancer. We describe here the involvement of the orphan solute carrier MFSD1 in the regulation of tumor cell migration. Loss of MFSD1 enabled higher levels of metastasis in a mouse model. We identified an increased migratory potential in MFSD1-/- tumor cells which was mediated by increased focal adhesion turn-over, reduced stability of mature inactive β1 integrin, and the resulting increased integrin activation index. We show that MFSD1 promoted recycling to the cell surface of endocytosed inactive β1 integrin and thereby protected β1 integrin from proteolytic degradation; this led to dampening of the integrin activation index. Furthermore, down-regulation of MFSD1 expression was observed during early steps of tumorigenesis and higher MFSD1 expression levels correlate with a better cancer patient prognosis. In sum, we describe a requirement for endolysosomal MFSD1 in efficient β1 integrin recycling to suppress tumor spread.","lang":"eng"}],"citation":{"short":"M. Roblek, J. Bicher, M. van Gogh, A. György, R. Seeböck, B. Szulc, M. Damme, M. Olczak, L. Borsig, D.E. Siekhaus, Frontiers in Oncology 12 (2022).","chicago":"Roblek, Marko, Julia Bicher, Merel van Gogh, Attila György, Rita Seeböck, Bozena Szulc, Markus Damme, Mariusz Olczak, Lubor Borsig, and Daria E Siekhaus. “The Solute Carrier MFSD1 Decreases Β1 Integrin’s Activation Status and Thus Tumor Metastasis.” <i>Frontiers in Oncology</i>. Frontiers, 2022. <a href=\"https://doi.org/10.3389/fonc.2022.777634\">https://doi.org/10.3389/fonc.2022.777634</a>.","apa":"Roblek, M., Bicher, J., van Gogh, M., György, A., Seeböck, R., Szulc, B., … Siekhaus, D. E. (2022). The solute carrier MFSD1 decreases β1 integrin’s activation status and thus tumor metastasis. <i>Frontiers in Oncology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fonc.2022.777634\">https://doi.org/10.3389/fonc.2022.777634</a>","ista":"Roblek M, Bicher J, van Gogh M, György A, Seeböck R, Szulc B, Damme M, Olczak M, Borsig L, Siekhaus DE. 2022. The solute carrier MFSD1 decreases β1 integrin’s activation status and thus tumor metastasis. Frontiers in Oncology. 12, 777634.","mla":"Roblek, Marko, et al. “The Solute Carrier MFSD1 Decreases Β1 Integrin’s Activation Status and Thus Tumor Metastasis.” <i>Frontiers in Oncology</i>, vol. 12, 777634, Frontiers, 2022, doi:<a href=\"https://doi.org/10.3389/fonc.2022.777634\">10.3389/fonc.2022.777634</a>.","ieee":"M. Roblek <i>et al.</i>, “The solute carrier MFSD1 decreases β1 integrin’s activation status and thus tumor metastasis,” <i>Frontiers in Oncology</i>, vol. 12. Frontiers, 2022.","ama":"Roblek M, Bicher J, van Gogh M, et al. The solute carrier MFSD1 decreases β1 integrin’s activation status and thus tumor metastasis. <i>Frontiers in Oncology</i>. 2022;12. doi:<a href=\"https://doi.org/10.3389/fonc.2022.777634\">10.3389/fonc.2022.777634</a>"},"file":[{"relation":"main_file","access_level":"open_access","checksum":"63dfecf30c5bbf9408b3512bd603f78c","content_type":"application/pdf","success":1,"file_name":"2022_FrontiersOncol_Roblek.pdf","file_id":"10751","creator":"cchlebak","date_created":"2022-02-08T13:26:40Z","file_size":6303227,"date_updated":"2022-02-08T13:26:40Z"}],"oa_version":"Published Version","month":"02","acknowledgement":"We thank M. Sixt, A. Leithner, and J. Alanko for helpful advice and the BioImaging Facility at IST Austria for technical support and assistance. We thank the Siekhaus Lab for the careful review of the manuscript and their input. MR and DS were funded by the NO Forschungs- und Bildungsges.m.b.H. (LS16-021) and IST core funding. MD was funded by Deutsche Forschungsgemeinschaft (DA 1785-1).","isi":1,"file_date_updated":"2022-02-08T13:26:40Z","quality_controlled":"1","project":[{"name":"Investigating the role of the novel major superfamily facilitator transporter family member MFSD1 in metastasis","grant_number":"LSC16-021","_id":"2637E9C0-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"date_created":"2022-02-01T10:33:50Z","year":"2022","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"corr_author":"1","publisher":"Frontiers","title":"The solute carrier MFSD1 decreases β1 integrin’s activation status and thus tumor metastasis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"intvolume":"        12","article_processing_charge":"Yes (via OA deal)","ddc":["570"],"article_type":"original","date_updated":"2025-06-11T13:56:08Z","publication":"Frontiers in Oncology","scopus_import":"1","type":"journal_article","has_accepted_license":"1","status":"public","day":"08","publication_status":"published","doi":"10.3389/fonc.2022.777634"},{"doi":"10.1126/science.abj0425","day":"22","status":"public","publication_status":"published","type":"journal_article","scopus_import":"1","page":"394-396","publication":"Science","date_updated":"2025-04-15T07:25:41Z","article_type":"original","article_processing_charge":"No","pmid":1,"intvolume":"       376","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Cell division in tissues enables macrophage infiltration","publisher":"American Association for the Advancement of Science","corr_author":"1","issue":"6591","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"oa":1,"year":"2022","date_created":"2022-02-01T11:23:18Z","language":[{"iso":"eng"}],"project":[{"call_identifier":"FWF","_id":"264CBBAC-B435-11E9-9278-68D0E5697425","grant_number":"M02379","name":"Modeling epithelial tissue mechanics during cell invasion"}],"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://doi.org/10.1101/2021.04.19.438995","open_access":"1"}],"month":"04","acknowledgement":"We thank J. Friml, C. Guet, T. Hurd, M. Fendrych and members of the laboratory for comments on the manuscript; the Bioimaging Facility of IST Austria for excellent support and T. Lecuit, E. Hafen, R. Levayer and A. Martin for fly strains. This work was supported by a grant from the Austrian Science Fund FWF: Lise Meitner Fellowship M2379-B28 to M.A and D.S., and internal funding from IST Austria to D.S. and EMBL to S.D.R.","oa_version":"Preprint","abstract":[{"text":"Cells migrate through crowded microenvironments within tissues during normal development, immune response, and cancer metastasis. Although migration through pores and tracks in the extracellular matrix (ECM) has been well studied, little is known about cellular traversal into confining cell-dense tissues. We find that embryonic tissue invasion by Drosophila macrophages requires division of an epithelial ectodermal cell at the site of entry. Dividing ectodermal cells disassemble ECM attachment formed by integrin-mediated focal adhesions next to mesodermal cells, allowing macrophages to move their nuclei ahead and invade between two immediately adjacent tissues. Invasion efficiency depends on division frequency, but reduction of adhesion strength allows macrophage entry independently of division. This work demonstrates that tissue dynamics can regulate cellular infiltration.","lang":"eng"}],"citation":{"ama":"Akhmanova M, Emtenani S, Krueger D, et al. Cell division in tissues enables macrophage infiltration. <i>Science</i>. 2022;376(6591):394-396. doi:<a href=\"https://doi.org/10.1126/science.abj0425\">10.1126/science.abj0425</a>","ieee":"M. Akhmanova <i>et al.</i>, “Cell division in tissues enables macrophage infiltration,” <i>Science</i>, vol. 376, no. 6591. American Association for the Advancement of Science, pp. 394–396, 2022.","chicago":"Akhmanova, Maria, Shamsi Emtenani, Daniel Krueger, Attila György, Mariana Pereira Guarda, Mikhail Vlasov, Fedor Vlasov, et al. “Cell Division in Tissues Enables Macrophage Infiltration.” <i>Science</i>. American Association for the Advancement of Science, 2022. <a href=\"https://doi.org/10.1126/science.abj0425\">https://doi.org/10.1126/science.abj0425</a>.","apa":"Akhmanova, M., Emtenani, S., Krueger, D., György, A., Pereira Guarda, M., Vlasov, M., … Siekhaus, D. E. (2022). Cell division in tissues enables macrophage infiltration. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.abj0425\">https://doi.org/10.1126/science.abj0425</a>","ista":"Akhmanova M, Emtenani S, Krueger D, György A, Pereira Guarda M, Vlasov M, Vlasov F, Akopian A, Ratheesh A, De Renzis S, Siekhaus DE. 2022. Cell division in tissues enables macrophage infiltration. Science. 376(6591), 394–396.","mla":"Akhmanova, Maria, et al. “Cell Division in Tissues Enables Macrophage Infiltration.” <i>Science</i>, vol. 376, no. 6591, American Association for the Advancement of Science, 2022, pp. 394–96, doi:<a href=\"https://doi.org/10.1126/science.abj0425\">10.1126/science.abj0425</a>.","short":"M. Akhmanova, S. Emtenani, D. Krueger, A. György, M. Pereira Guarda, M. Vlasov, F. Vlasov, A. Akopian, A. Ratheesh, S. De Renzis, D.E. Siekhaus, Science 376 (2022) 394–396."},"publication_identifier":{"issn":["0036-8075"]},"department":[{"_id":"DaSi"}],"date_published":"2022-04-22T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"}],"volume":376,"external_id":{"pmid":["35446632"],"isi":["000788553700039"]},"_id":"10713","author":[{"full_name":"Akhmanova, Maria","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Akhmanova","orcid":"0000-0003-1522-3162"},{"id":"49D32318-F248-11E8-B48F-1D18A9856A87","first_name":"Shamsi","full_name":"Emtenani, Shamsi","orcid":"0000-0001-6981-6938","last_name":"Emtenani"},{"last_name":"Krueger","full_name":"Krueger, Daniel","first_name":"Daniel"},{"full_name":"György, Attila","first_name":"Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1819-198X","last_name":"György"},{"orcid":"0000-0001-8238-480X","last_name":"Pereira Guarda","id":"6de81d9d-e2f2-11eb-945a-af8bc2a60b26","first_name":"Mariana","full_name":"Pereira Guarda, Mariana"},{"first_name":"Mikhail","full_name":"Vlasov, Mikhail","last_name":"Vlasov"},{"full_name":"Vlasov, Fedor","first_name":"Fedor","last_name":"Vlasov"},{"last_name":"Akopian","first_name":"Andrei","full_name":"Akopian, Andrei"},{"orcid":"0000-0001-7190-0776","last_name":"Ratheesh","first_name":"Aparna","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","full_name":"Ratheesh, Aparna"},{"first_name":"Stefano","full_name":"De Renzis, Stefano","last_name":"De Renzis"},{"last_name":"Siekhaus","orcid":"0000-0001-8323-8353","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E"}]},{"author":[{"last_name":"Martin","full_name":"Martin, Elliot T.","first_name":"Elliot T."},{"full_name":"Blatt, Patrick","first_name":"Patrick","last_name":"Blatt"},{"last_name":"Ngyuen","first_name":"Elaine","full_name":"Ngyuen, Elaine"},{"first_name":"Roni","full_name":"Lahr, Roni","last_name":"Lahr"},{"last_name":"Selvam","first_name":"Sangeetha","full_name":"Selvam, Sangeetha"},{"first_name":"Hyun Ah M.","full_name":"Yoon, Hyun Ah M.","last_name":"Yoon"},{"full_name":"Pocchiari, Tyler","first_name":"Tyler","last_name":"Pocchiari"},{"id":"49D32318-F248-11E8-B48F-1D18A9856A87","first_name":"Shamsi","full_name":"Emtenani, Shamsi","last_name":"Emtenani","orcid":"0000-0001-6981-6938"},{"orcid":"0000-0001-8323-8353","last_name":"Siekhaus","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E"},{"last_name":"Berman","full_name":"Berman, Andrea","first_name":"Andrea"},{"full_name":"Fuchs, Gabriele","first_name":"Gabriele","last_name":"Fuchs"},{"last_name":"Rangan","first_name":"Prashanth","full_name":"Rangan, Prashanth"}],"_id":"10714","department":[{"_id":"DaSi"}],"date_published":"2022-04-11T00:00:00Z","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"volume":57,"external_id":{"pmid":["35413237"],"isi":["000789021800005"]},"acknowledgement":"We are grateful to all members of the Rangan and Fuchs labs for their discussion and comments on the manuscript. We also thanks Dr. Sammons, Dr. Marlow, Life Science Editors, for their thoughts and comments the manuscript Additionally, we thank the Bloomington Stock Center, the Vienna Drosophila Resource Center, the BDGP Gene Disruption Project, and Flybase for fly stocks, reagents, and other resources. P.R. is funded by the NIH/NIGMS (R01GM111779-06 and RO1GM135628-01), G.F. is funded by NSF MCB-2047629 and NIH RO3 AI144839, D.E.S. was funded by Marie Curie CIG 334077/IRTIM and the Austrian Science Fund (FWF) grant ASI_FWF01_P29638S, and A.B is funded by NIH R01GM116889 and American Cancer Society RSG-17-197-01-RMC.","month":"04","isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2021.04.04.438367"}],"abstract":[{"text":"Ribosomal defects perturb stem cell differentiation, causing diseases called ribosomopathies. How ribosome levels control stem cell differentiation is not fully known. Here, we discovered three RNA helicases are required for ribosome biogenesis and for Drosophila oogenesis. Loss of these helicases, which we named Aramis, Athos and Porthos, lead to aberrant stabilization of p53, cell cycle arrest and stalled GSC differentiation. Unexpectedly, Aramis is required for efficient translation of a cohort of mRNAs containing a 5’-Terminal-Oligo-Pyrimidine (TOP)-motif, including mRNAs that encode ribosomal proteins and a conserved p53 inhibitor, Novel Nucleolar protein 1 (Non1). The TOP-motif co-regulates the translation of growth-related mRNAs in mammals. As in mammals, the La-related protein co-regulates the translation of TOP-motif containing RNAs during Drosophila oogenesis. Thus, a previously unappreciated TOP-motif in Drosophila responds to reduced ribosome biogenesis to co-regulate the translation of ribosomal proteins and a p53 repressor, thus coupling ribosome biogenesis to GSC differentiation.","lang":"eng"}],"citation":{"short":"E.T. Martin, P. Blatt, E. Ngyuen, R. Lahr, S. Selvam, H.A.M. Yoon, T. Pocchiari, S. Emtenani, D.E. Siekhaus, A. Berman, G. Fuchs, P. Rangan, Developmental Cell 57 (2022) 883–900.e10.","ista":"Martin ET, Blatt P, Ngyuen E, Lahr R, Selvam S, Yoon HAM, Pocchiari T, Emtenani S, Siekhaus DE, Berman A, Fuchs G, Rangan P. 2022. A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis. Developmental Cell. 57(7), 883–900.e10.","apa":"Martin, E. T., Blatt, P., Ngyuen, E., Lahr, R., Selvam, S., Yoon, H. A. M., … Rangan, P. (2022). A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2022.03.005\">https://doi.org/10.1016/j.devcel.2022.03.005</a>","mla":"Martin, Elliot T., et al. “A Translation Control Module Coordinates Germline Stem Cell Differentiation with Ribosome Biogenesis during Drosophila Oogenesis.” <i>Developmental Cell</i>, vol. 57, no. 7, Elsevier, 2022, p. 883–900.e10, doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.03.005\">10.1016/j.devcel.2022.03.005</a>.","chicago":"Martin, Elliot T., Patrick Blatt, Elaine Ngyuen, Roni Lahr, Sangeetha Selvam, Hyun Ah M. Yoon, Tyler Pocchiari, et al. “A Translation Control Module Coordinates Germline Stem Cell Differentiation with Ribosome Biogenesis during Drosophila Oogenesis.” <i>Developmental Cell</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.devcel.2022.03.005\">https://doi.org/10.1016/j.devcel.2022.03.005</a>.","ieee":"E. T. Martin <i>et al.</i>, “A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis,” <i>Developmental Cell</i>, vol. 57, no. 7. Elsevier, p. 883–900.e10, 2022.","ama":"Martin ET, Blatt P, Ngyuen E, et al. A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis. <i>Developmental Cell</i>. 2022;57(7):883-900.e10. doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.03.005\">10.1016/j.devcel.2022.03.005</a>"},"oa_version":"Preprint","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"year":"2022","oa":1,"issue":"7","project":[{"grant_number":"334077","name":"Investigating the role of transporters in invasive migration through junctions","_id":"2536F660-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"253B6E48-B435-11E9-9278-68D0E5697425","name":"The role of Drosophila TNF alpha in immune cell invasion","grant_number":"P29638","call_identifier":"FWF"}],"quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2022-02-01T13:15:05Z","pmid":1,"intvolume":"        57","article_processing_charge":"No","title":"A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","date_updated":"2025-06-12T06:19:50Z","scopus_import":"1","type":"journal_article","ec_funded":1,"publication":"Developmental Cell","page":"883-900.e10","doi":"10.1016/j.devcel.2022.03.005","status":"public","day":"11","publication_status":"published"},{"_id":"10717","author":[{"last_name":"Wang","first_name":"R","full_name":"Wang, R"},{"last_name":"Himschoot","full_name":"Himschoot, E","first_name":"E"},{"full_name":"Grenzi, M","first_name":"M","last_name":"Grenzi"},{"first_name":"J","full_name":"Chen, J","last_name":"Chen"},{"full_name":"Safi, A","first_name":"A","last_name":"Safi"},{"last_name":"Krebs","full_name":"Krebs, M","first_name":"M"},{"full_name":"Schumacher, K","first_name":"K","last_name":"Schumacher"},{"last_name":"Nowack","full_name":"Nowack, MK","first_name":"MK"},{"full_name":"Moeder, W","first_name":"W","last_name":"Moeder"},{"last_name":"Yoshioka","full_name":"Yoshioka, K","first_name":"K"},{"full_name":"Van Damme, D","first_name":"D","last_name":"Van Damme"},{"last_name":"De Smet","first_name":"I","full_name":"De Smet, I"},{"first_name":"D","full_name":"Geelen, D","last_name":"Geelen"},{"first_name":"T","full_name":"Beeckman, T","last_name":"Beeckman"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"last_name":"Costa","first_name":"A","full_name":"Costa, A"},{"last_name":"Vanneste","full_name":"Vanneste, S","first_name":"S"}],"department":[{"_id":"JiFr"}],"date_published":"2022-04-18T00:00:00Z","publication_identifier":{"eissn":["1460-2431"],"issn":["0022-0957"]},"external_id":{"pmid":["35085386"],"isi":["000764220900001"]},"volume":73,"article_number":"erac019","acknowledgement":"We thank Joerg Kudla (WWU Munster, Germany), Petra Dietrich (F.A. University of Erlangen-Nurnberg, Germany) for sharing published materials, and NASC for providing seeds. We thank Veronique Storme for help with the statistical analyses. Part of the imaging analysis was carried out at NOLIMITS, an advanced imaging facility established by the University of Milan.\r\nThis work was supported by grants of the China Scholarship Council (CSC) to RW and JC; Fonds Wetenschappelijk Onderzoek (FWO) to TB and (G002220N) SV; the special research fund of Ghent University to EH; the Deutsche Forschungsgemeinschaft (DFG) through Grants within FOR964 (MK and KS); Piano di Sviluppo di Ateneo 2019 (University of Milan) to AC; the European Research Council (ERC) T-Rex project 682436 to DVD; the ERC ETAP project 742985 to JF, and by a PhD fellowship from the University of Milan to MG.","month":"04","main_file_link":[{"open_access":"1","url":"https://biblio.ugent.be/publication/8738721"}],"isi":1,"citation":{"ama":"Wang R, Himschoot E, Grenzi M, et al. Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots. <i>Journal of Experimental Botany</i>. 2022;73(8). doi:<a href=\"https://doi.org/10.1093/jxb/erac019\">10.1093/jxb/erac019</a>","ieee":"R. Wang <i>et al.</i>, “Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots,” <i>Journal of Experimental Botany</i>, vol. 73, no. 8. Oxford University Press, 2022.","apa":"Wang, R., Himschoot, E., Grenzi, M., Chen, J., Safi, A., Krebs, M., … Vanneste, S. (2022). Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/erac019\">https://doi.org/10.1093/jxb/erac019</a>","mla":"Wang, R., et al. “Auxin Analog-Induced Ca2+ Signaling Is Independent of Inhibition of Endosomal Aggregation in Arabidopsis Roots.” <i>Journal of Experimental Botany</i>, vol. 73, no. 8, erac019, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/jxb/erac019\">10.1093/jxb/erac019</a>.","ista":"Wang R, Himschoot E, Grenzi M, Chen J, Safi A, Krebs M, Schumacher K, Nowack M, Moeder W, Yoshioka K, Van Damme D, De Smet I, Geelen D, Beeckman T, Friml J, Costa A, Vanneste S. 2022. Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots. Journal of Experimental Botany. 73(8), erac019.","chicago":"Wang, R, E Himschoot, M Grenzi, J Chen, A Safi, M Krebs, K Schumacher, et al. “Auxin Analog-Induced Ca2+ Signaling Is Independent of Inhibition of Endosomal Aggregation in Arabidopsis Roots.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/jxb/erac019\">https://doi.org/10.1093/jxb/erac019</a>.","short":"R. Wang, E. Himschoot, M. Grenzi, J. Chen, A. Safi, M. Krebs, K. Schumacher, M. Nowack, W. Moeder, K. Yoshioka, D. Van Damme, I. De Smet, D. Geelen, T. Beeckman, J. Friml, A. Costa, S. Vanneste, Journal of Experimental Botany 73 (2022)."},"abstract":[{"lang":"eng","text":"Much of what we know about the role of auxin in plant development derives from exogenous manipulations of auxin distribution and signaling, using inhibitors, auxins and auxin analogs. In this context, synthetic auxin analogs, such as 1-Naphtalene Acetic Acid (1-NAA), are often favored over the endogenous auxin indole-3-acetic acid (IAA), in part due to their higher stability. While such auxin analogs have proven to be instrumental to reveal the various faces of auxin, they display in some cases distinct bioactivities compared to IAA. Here, we focused on the effect of auxin analogs on the accumulation of PIN proteins in Brefeldin A-sensitive endosomal aggregations (BFA bodies), and the correlation with the ability to elicit Ca 2+ responses. For a set of commonly used auxin analogs, we evaluated if auxin-analog induced Ca 2+ signaling inhibits PIN accumulation. Not all auxin analogs elicited a Ca 2+ response, and their differential ability to elicit Ca 2+ responses correlated partially with their ability to inhibit BFA-body formation. However, in tir1/afb and cngc14, 1-NAA-induced Ca 2+ signaling was strongly impaired, yet 1-NAA still could inhibit PIN accumulation in BFA bodies. This demonstrates that TIR1/AFB-CNGC14-dependent Ca 2+ signaling does not inhibit BFA body formation in Arabidopsis roots."}],"oa_version":"Submitted Version","oa":1,"year":"2022","issue":"8","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020"}],"quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2022-02-03T09:19:01Z","pmid":1,"intvolume":"        73","article_processing_charge":"No","title":"Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots","publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-05-14T11:06:37Z","article_type":"original","scopus_import":"1","type":"journal_article","ec_funded":1,"publication":"Journal of Experimental Botany","doi":"10.1093/jxb/erac019","day":"18","status":"public","publication_status":"published"},{"external_id":{"pmid":["35018726"],"isi":["000761281200011"]},"volume":64,"publication_identifier":{"issn":["1672-9072"],"eissn":["1744-7909"]},"department":[{"_id":"JiFr"}],"date_published":"2022-02-01T00:00:00Z","_id":"10719","author":[{"first_name":"Z","full_name":"Yu, Z","last_name":"Yu"},{"last_name":"Zhang","full_name":"Zhang, F","first_name":"F"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří"},{"full_name":"Ding, Z","first_name":"Z","last_name":"Ding"}],"language":[{"iso":"eng"}],"date_created":"2022-02-03T09:52:59Z","quality_controlled":"1","issue":"2","oa":1,"year":"2022","oa_version":"Published Version","citation":{"ama":"Yu Z, Zhang F, Friml J, Ding Z. Auxin signaling: Research advances over the past 30 years. <i>Journal of Integrative Plant Biology</i>. 2022;64(2):371-392. doi:<a href=\"https://doi.org/10.1111/jipb.13225\">10.1111/jipb.13225</a>","ieee":"Z. Yu, F. Zhang, J. Friml, and Z. Ding, “Auxin signaling: Research advances over the past 30 years,” <i>Journal of Integrative Plant Biology</i>, vol. 64, no. 2. Wiley, pp. 371–392, 2022.","apa":"Yu, Z., Zhang, F., Friml, J., &#38; Ding, Z. (2022). Auxin signaling: Research advances over the past 30 years. <i>Journal of Integrative Plant Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jipb.13225\">https://doi.org/10.1111/jipb.13225</a>","ista":"Yu Z, Zhang F, Friml J, Ding Z. 2022. Auxin signaling: Research advances over the past 30 years. Journal of Integrative Plant Biology. 64(2), 371–392.","mla":"Yu, Z., et al. “Auxin Signaling: Research Advances over the Past 30 Years.” <i>Journal of Integrative Plant Biology</i>, vol. 64, no. 2, Wiley, 2022, pp. 371–92, doi:<a href=\"https://doi.org/10.1111/jipb.13225\">10.1111/jipb.13225</a>.","chicago":"Yu, Z, F Zhang, Jiří Friml, and Z Ding. “Auxin Signaling: Research Advances over the Past 30 Years.” <i>Journal of Integrative Plant Biology</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/jipb.13225\">https://doi.org/10.1111/jipb.13225</a>.","short":"Z. Yu, F. Zhang, J. Friml, Z. Ding, Journal of Integrative Plant Biology 64 (2022) 371–392."},"abstract":[{"lang":"eng","text":"Auxin, one of the first identified and most widely studied phytohormones, has been and will remain a hot topic in plant biology. After more than a century of passionate exploration, the mysteries of its synthesis, transport, signaling, and metabolism have largely been unlocked. Due to the rapid development of new technologies, new methods, and new genetic materials, the study of auxin has entered the fast lane over the past 30 years. Here, we highlight advances in understanding auxin signaling, including auxin perception, rapid auxin responses, TRANSPORT INHIBITOR RESPONSE 1 and AUXIN SIGNALING F-boxes (TIR1/AFBs)-mediated transcriptional and non-transcriptional branches, and the epigenetic regulation of auxin signaling. We also focus on feedback inhibition mechanisms that prevent the over-amplification of auxin signals. In addition, we cover the TRANSMEMBRANE KINASEs (TMKs)-mediated non-canonical signaling, which converges with TIR1/AFBs-mediated transcriptional regulation to coordinate plant growth and development. The identification of additional auxin signaling components and their regulation will continue to open new avenues of research in this field, leading to an increasingly deeper, more comprehensive understanding of how auxin signals are interpreted at the cellular level to regulate plant growth and development."}],"isi":1,"main_file_link":[{"url":"https://doi.org/10.1111/jipb.13225","open_access":"1"}],"acknowledgement":"This research was financially supported by the National Natural Science Foundation of China and the Israel Science Foundation (NSFC-ISF; 32061143005), National Natural Science Foundation of China (32000225), Natural Science Foundation of Shandong Province (ZR2020QC036), and China Postdoctoral Science Foundation (2020M682165).\r\n","month":"02","article_type":"review","date_updated":"2024-10-09T21:01:32Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Auxin signaling: Research advances over the past 30 years","publisher":"Wiley","corr_author":"1","article_processing_charge":"No","intvolume":"        64","pmid":1,"day":"01","publication_status":"published","status":"public","doi":"10.1111/jipb.13225","page":"371-392","publication":"Journal of Integrative Plant Biology","type":"journal_article","scopus_import":"1"},{"publication":"Scientific Reports","ec_funded":1,"type":"journal_article","has_accepted_license":"1","scopus_import":"1","publication_status":"published","day":"27","status":"public","doi":"10.1038/s41598-022-05333-5","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","title":"Infection dynamics of COVID-19 virus under lockdown and reopening","article_processing_charge":"No","intvolume":"        12","arxiv":1,"date_updated":"2025-04-14T07:52:45Z","article_type":"original","ddc":["570"],"file":[{"file_id":"10744","file_name":"2022_ScientificReports_Svoboda.pdf","success":1,"access_level":"open_access","relation":"main_file","checksum":"247afd30c173390940f099ead35a28ed","content_type":"application/pdf","date_updated":"2022-02-07T14:57:59Z","file_size":2971922,"date_created":"2022-02-07T14:57:59Z","creator":"alisjak"}],"oa_version":"Published Version","citation":{"ista":"Svoboda J, Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2022. Infection dynamics of COVID-19 virus under lockdown and reopening. Scientific Reports. 12(1), 1526.","mla":"Svoboda, Jakub, et al. “Infection Dynamics of COVID-19 Virus under Lockdown and Reopening.” <i>Scientific Reports</i>, vol. 12, no. 1, 1526, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41598-022-05333-5\">10.1038/s41598-022-05333-5</a>.","apa":"Svoboda, J., Tkadlec, J., Pavlogiannis, A., Chatterjee, K., &#38; Nowak, M. A. (2022). Infection dynamics of COVID-19 virus under lockdown and reopening. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-022-05333-5\">https://doi.org/10.1038/s41598-022-05333-5</a>","chicago":"Svoboda, Jakub, Josef Tkadlec, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Infection Dynamics of COVID-19 Virus under Lockdown and Reopening.” <i>Scientific Reports</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41598-022-05333-5\">https://doi.org/10.1038/s41598-022-05333-5</a>.","short":"J. Svoboda, J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Scientific Reports 12 (2022).","ama":"Svoboda J, Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Infection dynamics of COVID-19 virus under lockdown and reopening. <i>Scientific Reports</i>. 2022;12(1). doi:<a href=\"https://doi.org/10.1038/s41598-022-05333-5\">10.1038/s41598-022-05333-5</a>","ieee":"J. Svoboda, J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Infection dynamics of COVID-19 virus under lockdown and reopening,” <i>Scientific Reports</i>, vol. 12, no. 1. Springer Nature, 2022."},"abstract":[{"lang":"eng","text":"Motivated by COVID-19, we develop and analyze a simple stochastic model for the spread of disease in human population. We track how the number of infected and critically ill people develops over time in order to estimate the demand that is imposed on the hospital system. To keep this demand under control, we consider a class of simple policies for slowing down and reopening society and we compare their efficiency in mitigating the spread of the virus from several different points of view. We find that in order to avoid overwhelming of the hospital system, a policy must impose a harsh lockdown or it must react swiftly (or both). While reacting swiftly is universally beneficial, being harsh pays off only when the country is patient about reopening and when the neighboring countries coordinate their mitigation efforts. Our work highlights the importance of acting decisively when closing down and the importance of patience and coordination between neighboring countries when reopening."}],"isi":1,"acknowledgement":"K.C. acknowledges support from ERC Consolidator Grant No. (863818: ForM-SMart). A.P. acknowledges support from FWF Grant No. J-4220. M.A.N. acknowledges support from Office of Naval Research grant N00014-16-1-2914 and from the John Templeton Foundation.","month":"01","date_created":"2022-02-06T23:01:30Z","language":[{"iso":"eng"}],"file_date_updated":"2022-02-07T14:57:59Z","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020"}],"quality_controlled":"1","issue":"1","oa":1,"year":"2022","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"_id":"10731","author":[{"orcid":"0000-0002-1419-3267","last_name":"Svoboda","full_name":"Svoboda, Jakub","first_name":"Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425"},{"last_name":"Tkadlec","first_name":"Josef","full_name":"Tkadlec, Josef"},{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"first_name":"Martin A.","full_name":"Nowak, Martin A.","last_name":"Nowak"}],"article_number":"1526","external_id":{"isi":["000749198000039"],"arxiv":["2012.15155"]},"volume":12,"publication_identifier":{"eissn":["2045-2322"]},"date_published":"2022-01-27T00:00:00Z","department":[{"_id":"KrCh"}]},{"has_accepted_license":"1","type":"journal_article","scopus_import":"1","publication":"Journal of Functional Analysis","doi":"10.1016/j.jfa.2022.109394","publication_status":"published","day":"15","status":"public","article_processing_charge":"Yes (via OA deal)","intvolume":"       282","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Thermalisation for Wigner matrices","corr_author":"1","publisher":"Elsevier","article_type":"original","date_updated":"2024-10-09T21:01:33Z","ddc":["500"],"arxiv":1,"isi":1,"month":"04","acknowledgement":"We compute the deterministic approximation of products of Sobolev functions of large Wigner matrices W and provide an optimal error bound on their fluctuation with very high probability. This generalizes Voiculescu's seminal theorem from polynomials to general Sobolev functions, as well as from tracial quantities to individual matrix elements. Applying the result to  for large t, we obtain a precise decay rate for the overlaps of several deterministic matrices with temporally well separated Heisenberg time evolutions; thus we demonstrate the thermalisation effect of the unitary group generated by Wigner matrices.","oa_version":"Published Version","file":[{"creator":"dernst","date_created":"2022-07-29T07:22:08Z","file_size":652573,"date_updated":"2022-07-29T07:22:08Z","access_level":"open_access","relation":"main_file","checksum":"b75fdad606ab507dc61109e0907d86c0","content_type":"application/pdf","success":1,"file_id":"11690","file_name":"2022_JourFunctionalAnalysis_Cipolloni.pdf"}],"abstract":[{"lang":"eng","text":"We compute the deterministic approximation of products of Sobolev functions of large Wigner matrices W and provide an optimal error bound on their fluctuation with very high probability. This generalizes Voiculescu's seminal theorem from polynomials to general Sobolev functions, as well as from tracial quantities to individual matrix elements. Applying the result to eitW for large t, we obtain a precise decay rate for the overlaps of several deterministic matrices with temporally well separated Heisenberg time evolutions; thus we demonstrate the thermalisation effect of the unitary group generated by Wigner matrices."}],"citation":{"short":"G. Cipolloni, L. Erdös, D.J. Schröder, Journal of Functional Analysis 282 (2022).","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Thermalisation for Wigner Matrices.” <i>Journal of Functional Analysis</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jfa.2022.109394\">https://doi.org/10.1016/j.jfa.2022.109394</a>.","mla":"Cipolloni, Giorgio, et al. “Thermalisation for Wigner Matrices.” <i>Journal of Functional Analysis</i>, vol. 282, no. 8, 109394, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jfa.2022.109394\">10.1016/j.jfa.2022.109394</a>.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2022). Thermalisation for Wigner matrices. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2022.109394\">https://doi.org/10.1016/j.jfa.2022.109394</a>","ista":"Cipolloni G, Erdös L, Schröder DJ. 2022. Thermalisation for Wigner matrices. Journal of Functional Analysis. 282(8), 109394.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Thermalisation for Wigner matrices,” <i>Journal of Functional Analysis</i>, vol. 282, no. 8. Elsevier, 2022.","ama":"Cipolloni G, Erdös L, Schröder DJ. Thermalisation for Wigner matrices. <i>Journal of Functional Analysis</i>. 2022;282(8). doi:<a href=\"https://doi.org/10.1016/j.jfa.2022.109394\">10.1016/j.jfa.2022.109394</a>"},"issue":"8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2022","oa":1,"language":[{"iso":"eng"}],"date_created":"2022-02-06T23:01:30Z","quality_controlled":"1","file_date_updated":"2022-07-29T07:22:08Z","_id":"10732","author":[{"full_name":"Cipolloni, Giorgio","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","last_name":"Cipolloni"},{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös"},{"first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","last_name":"Schröder"}],"publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"department":[{"_id":"LaEr"}],"date_published":"2022-04-15T00:00:00Z","article_number":"109394","volume":282,"external_id":{"arxiv":["2102.09975"],"isi":["000781239100004"]}},{"arxiv":1,"date_updated":"2023-08-02T14:10:13Z","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Intruders cooperatively interact with a wall into granular matter","publisher":"Springer Nature","article_processing_charge":"No","intvolume":"        24","day":"24","status":"public","publication_status":"published","doi":"10.1007/s10035-021-01200-8","publication":"Granular Matter","type":"journal_article","scopus_import":"1","article_number":"39","keyword":["granular matter","boundary effects","intruder penetration","sedimentation"],"external_id":{"arxiv":["2110.15311"],"isi":["000746623000001"]},"volume":24,"publication_identifier":{"eissn":["1434-7636"],"issn":["1434-5021"]},"department":[{"_id":"ScWa"}],"date_published":"2022-01-24T00:00:00Z","author":[{"last_name":"Espinosa","first_name":"M.","full_name":"Espinosa, M."},{"last_name":"Diaz Melian","id":"b6798902-eea0-11ea-9cbc-a8e14286c631","first_name":"Vicente L","full_name":"Diaz Melian, Vicente L"},{"last_name":"Serrano-Muñoz","first_name":"A.","full_name":"Serrano-Muñoz, A."},{"last_name":"Altshuler","full_name":"Altshuler, E.","first_name":"E."}],"_id":"10733","language":[{"iso":"eng"}],"date_created":"2022-02-06T23:01:30Z","quality_controlled":"1","issue":"1","oa":1,"year":"2022","oa_version":"Preprint","citation":{"ista":"Espinosa M, Diaz Melian VL, Serrano-Muñoz A, Altshuler E. 2022. Intruders cooperatively interact with a wall into granular matter. Granular Matter. 24(1), 39.","apa":"Espinosa, M., Diaz Melian, V. L., Serrano-Muñoz, A., &#38; Altshuler, E. (2022). Intruders cooperatively interact with a wall into granular matter. <i>Granular Matter</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10035-021-01200-8\">https://doi.org/10.1007/s10035-021-01200-8</a>","mla":"Espinosa, M., et al. “Intruders Cooperatively Interact with a Wall into Granular Matter.” <i>Granular Matter</i>, vol. 24, no. 1, 39, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s10035-021-01200-8\">10.1007/s10035-021-01200-8</a>.","chicago":"Espinosa, M., Vicente L Diaz Melian, A. Serrano-Muñoz, and E. Altshuler. “Intruders Cooperatively Interact with a Wall into Granular Matter.” <i>Granular Matter</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s10035-021-01200-8\">https://doi.org/10.1007/s10035-021-01200-8</a>.","short":"M. Espinosa, V.L. Diaz Melian, A. Serrano-Muñoz, E. Altshuler, Granular Matter 24 (2022).","ama":"Espinosa M, Diaz Melian VL, Serrano-Muñoz A, Altshuler E. Intruders cooperatively interact with a wall into granular matter. <i>Granular Matter</i>. 2022;24(1). doi:<a href=\"https://doi.org/10.1007/s10035-021-01200-8\">10.1007/s10035-021-01200-8</a>","ieee":"M. Espinosa, V. L. Diaz Melian, A. Serrano-Muñoz, and E. Altshuler, “Intruders cooperatively interact with a wall into granular matter,” <i>Granular Matter</i>, vol. 24, no. 1. Springer Nature, 2022."},"abstract":[{"lang":"eng","text":"When a cylindrical object penetrates granular matter near a vertical boundary, it experiences two effects: its center of mass moves horizontally away from the wall, and it rotates around its symmetry axis. Here we show experimentally that, if two identical intruders instead of one are released side-by-side near the wall, both effects are also detected. However, unexpected phenomena appear due to a cooperative dynamics between the intruders. The net horizontal distance traveled by the common center of mass of the twin intruders is much larger than that traveled by one intruder released at the same initial distance from the wall, and the rotation is also larger. The experimental results are well described by the Discrete Element Method (DEM), which reveals that, as the number of intruders horizontally released side-by-side increases, the total energy dissipation per intruder decreases. Finally, DEM simulations demonstrate that the horizontal repulsion is substantially enhanced if groups of intruders are released forming a column near the wall."}],"isi":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2110.15311"}],"month":"01","acknowledgement":"We acknowledge the University of Havana’s institutional project “Granular media: creating tools for the prevention of catastrophes”. The Institute “Pedro Kourí” is thanked for allowing us using their computing cluster. E. Altshuler found inspiration in the late M. Álvarez-Ponte."},{"article_number":"135802","external_id":{"pmid":["34986467"],"isi":["000775191800001"]},"volume":34,"publication_identifier":{"eissn":["1361-648X"]},"department":[{"_id":"KiMo"}],"date_published":"2022-01-20T00:00:00Z","author":[{"full_name":"Nauman, Muhammad","first_name":"Muhammad","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","orcid":"0000-0002-2111-4846","last_name":"Nauman"},{"first_name":"Tayyaba","full_name":"Hussain, Tayyaba","last_name":"Hussain"},{"last_name":"Choi","first_name":"Joonyoung","full_name":"Choi, Joonyoung"},{"first_name":"Nara","full_name":"Lee, Nara","last_name":"Lee"},{"last_name":"Choi","first_name":"Young Jai","full_name":"Choi, Young Jai"},{"first_name":"Woun","full_name":"Kang, Woun","last_name":"Kang"},{"last_name":"Jo","first_name":"Younjung","full_name":"Jo, Younjung"}],"_id":"10735","language":[{"iso":"eng"}],"date_created":"2022-02-06T23:01:31Z","quality_controlled":"1","file_date_updated":"2022-02-07T10:35:28Z","issue":"13","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2022","oa":1,"oa_version":"Published Version","file":[{"date_created":"2022-02-07T10:35:28Z","creator":"cchlebak","date_updated":"2022-02-07T10:35:28Z","file_size":1742414,"checksum":"b6c705c7f03dcb1dbcb06b1b4d4938d6","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2022_JPhysCondensMatter_Nauman.pdf","file_id":"10741","success":1}],"citation":{"ieee":"M. Nauman <i>et al.</i>, “Low-field magnetic anisotropy of Sr2IrO4,” <i>Journal of physics: Condensed matter</i>, vol. 34, no. 13. IOP Publishing, 2022.","ama":"Nauman M, Hussain T, Choi J, et al. Low-field magnetic anisotropy of Sr2IrO4. <i>Journal of physics: Condensed matter</i>. 2022;34(13). doi:<a href=\"https://doi.org/10.1088/1361-648X/ac484d\">10.1088/1361-648X/ac484d</a>","short":"M. Nauman, T. Hussain, J. Choi, N. Lee, Y.J. Choi, W. Kang, Y. Jo, Journal of Physics: Condensed Matter 34 (2022).","chicago":"Nauman, Muhammad, Tayyaba Hussain, Joonyoung Choi, Nara Lee, Young Jai Choi, Woun Kang, and Younjung Jo. “Low-Field Magnetic Anisotropy of Sr2IrO4.” <i>Journal of Physics: Condensed Matter</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.1088/1361-648X/ac484d\">https://doi.org/10.1088/1361-648X/ac484d</a>.","apa":"Nauman, M., Hussain, T., Choi, J., Lee, N., Choi, Y. J., Kang, W., &#38; Jo, Y. (2022). Low-field magnetic anisotropy of Sr2IrO4. <i>Journal of Physics: Condensed Matter</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-648X/ac484d\">https://doi.org/10.1088/1361-648X/ac484d</a>","mla":"Nauman, Muhammad, et al. “Low-Field Magnetic Anisotropy of Sr2IrO4.” <i>Journal of Physics: Condensed Matter</i>, vol. 34, no. 13, 135802, IOP Publishing, 2022, doi:<a href=\"https://doi.org/10.1088/1361-648X/ac484d\">10.1088/1361-648X/ac484d</a>.","ista":"Nauman M, Hussain T, Choi J, Lee N, Choi YJ, Kang W, Jo Y. 2022. Low-field magnetic anisotropy of Sr2IrO4. Journal of physics: Condensed matter. 34(13), 135802."},"abstract":[{"text":"Magnetic anisotropy in strontium iridate (Sr2IrO4) is essential because of its strong spin–orbit coupling and crystal field effect. In this paper, we present a detailed mapping of the out-of-plane (OOP) magnetic anisotropy in Sr2IrO4 for different sample orientations using torque magnetometry measurements in the low-magnetic-field region before the isospins are completely ordered. Dominant in-plane anisotropy was identified at low fields, confirming the b axis as an easy magnetization axis. Based on the fitting analysis of the strong uniaxial magnetic anisotropy, we observed that the main anisotropic effect arises from a spin–orbit-coupled magnetic exchange interaction affecting the OOP interaction. The effect of interlayer exchange interaction results in additional anisotropic terms owing to the tilting of the isospins. The results are relevant for understanding OOP magnetic anisotropy and provide a new way to analyze the effects of spin–orbit-coupling and interlayer magnetic exchange interactions. This study provides insight into the understanding of bulk magnetic, magnetotransport, and spintronic behavior on Sr2IrO4 for future studies.","lang":"eng"}],"isi":1,"acknowledgement":"YJ was supported by the National Research Foundation of Korea (NRF) (Grant Nos. NRF-2018K2A9A1A06069211 and NRF-2019R1A2C1089017). The work at Yonsei was supported by the NRF (Grant Nos. NRF-2017R1A5A-1014862 (SRC program: vdWMRC center), NRF-2019R1A2C2002601, and NRF-2021R1A2C1006375). WK acknowledges the support by the NRF (Grant Nos. 2018R1D1A1B07050087, 2018R1A6A1A03025340).","month":"01","date_updated":"2023-08-02T14:12:01Z","article_type":"original","ddc":["530"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Low-field magnetic anisotropy of Sr2IrO4","publisher":"IOP Publishing","article_processing_charge":"No","intvolume":"        34","pmid":1,"publication_status":"published","day":"20","status":"public","doi":"10.1088/1361-648X/ac484d","publication":"Journal of physics: Condensed matter","has_accepted_license":"1","type":"journal_article","scopus_import":"1"},{"ddc":["576"],"article_type":"original","date_updated":"2025-03-31T16:00:23Z","title":"Predicting bacterial promoter function and evolution from random sequences","corr_author":"1","publisher":"eLife Sciences Publications","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        11","pmid":1,"article_processing_charge":"No","day":"26","status":"public","publication_status":"published","doi":"10.7554/eLife.64543","publication":"eLife","ec_funded":1,"scopus_import":"1","has_accepted_license":"1","type":"journal_article","external_id":{"isi":["000751104400001"],"pmid":["35080492"]},"volume":11,"article_number":"e64543","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"NiBa"}],"date_published":"2022-01-26T00:00:00Z","publication_identifier":{"eissn":["2050-084X"]},"_id":"10736","author":[{"first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato","last_name":"Lagator"},{"full_name":"Sarikas, Srdjan","first_name":"Srdjan","id":"35F0286E-F248-11E8-B48F-1D18A9856A87","last_name":"Sarikas"},{"id":"2C023F40-F248-11E8-B48F-1D18A9856A87","first_name":"Magdalena","full_name":"Steinrück, Magdalena","last_name":"Steinrück","orcid":"0000-0003-1229-9719"},{"first_name":"David","full_name":"Toledo-Aparicio, David","last_name":"Toledo-Aparicio"},{"orcid":"0000-0002-4624-4612","last_name":"Bollback","full_name":"Bollback, Jonathan P","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"},{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"quality_controlled":"1","project":[{"call_identifier":"H2020","grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2022-02-07T07:14:09Z","language":[{"iso":"eng"}],"date_created":"2022-02-06T23:01:32Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2022","oa":1,"abstract":[{"lang":"eng","text":"Predicting function from sequence is a central problem of biology. Currently, this is possible only locally in a narrow mutational neighborhood around a wildtype sequence rather than globally from any sequence. Using random mutant libraries, we developed a biophysical model that accounts for multiple features of σ70 binding bacterial promoters to predict constitutive gene expression levels from any sequence. We experimentally and theoretically estimated that 10–20% of random sequences lead to expression and ~80% of non-expressing sequences are one mutation away from a functional promoter. The potential for generating expression from random sequences is so pervasive that selection acts against σ70-RNA polymerase binding sites even within inter-genic, promoter-containing regions. This pervasiveness of σ70-binding sites implies that emergence of promoters is not the limiting step in gene regulatory evolution. Ultimately, the inclusion of novel features of promoter function into a mechanistic model enabled not only more accurate predictions of gene expression levels, but also identified that promoters evolve more rapidly than previously thought."}],"citation":{"ieee":"M. Lagator <i>et al.</i>, “Predicting bacterial promoter function and evolution from random sequences,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","ama":"Lagator M, Sarikas S, Steinrück M, et al. Predicting bacterial promoter function and evolution from random sequences. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.64543\">10.7554/eLife.64543</a>","short":"M. Lagator, S. Sarikas, M. Steinrück, D. Toledo-Aparicio, J.P. Bollback, C.C. Guet, G. Tkačik, ELife 11 (2022).","mla":"Lagator, Mato, et al. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” <i>ELife</i>, vol. 11, e64543, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.64543\">10.7554/eLife.64543</a>.","apa":"Lagator, M., Sarikas, S., Steinrück, M., Toledo-Aparicio, D., Bollback, J. P., Guet, C. C., &#38; Tkačik, G. (2022). Predicting bacterial promoter function and evolution from random sequences. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.64543\">https://doi.org/10.7554/eLife.64543</a>","ista":"Lagator M, Sarikas S, Steinrück M, Toledo-Aparicio D, Bollback JP, Guet CC, Tkačik G. 2022. Predicting bacterial promoter function and evolution from random sequences. eLife. 11, e64543.","chicago":"Lagator, Mato, Srdjan Sarikas, Magdalena Steinrück, David Toledo-Aparicio, Jonathan P Bollback, Calin C Guet, and Gašper Tkačik. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.64543\">https://doi.org/10.7554/eLife.64543</a>."},"file":[{"file_id":"10739","file_name":"2022_ELife_Lagator.pdf","success":1,"content_type":"application/pdf","checksum":"decdcdf600ff51e9a9703b49ca114170","relation":"main_file","access_level":"open_access","date_updated":"2022-02-07T07:14:09Z","file_size":5604343,"date_created":"2022-02-07T07:14:09Z","creator":"cchlebak"}],"oa_version":"Published Version","acknowledgement":"We thank Hande Acar, Nicholas H Barton, Rok Grah, Tiago Paixao, Maros Pleska, Anna Staron, and Murat Tugrul for insightful comments and input on the manuscript. This work was supported by: Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (grant number 216779/Z/19/Z) to ML; IPC Grant from IST Austria to ML and SS; European Research Council Funding Programme 7 (2007–2013, grant agreement number 648440) to JPB.","month":"01","isi":1},{"year":"2022","oa":1,"issue":"1","quality_controlled":"1","date_created":"2022-02-06T23:01:32Z","language":[{"iso":"eng"}],"month":"01","main_file_link":[{"url":"https://arxiv.org/abs/1404.5475","open_access":"1"}],"isi":1,"abstract":[{"text":"We consider two models for the sequence labeling (tagging) problem. The first one is a Pattern-Based Conditional Random Field (PB), in which the energy of a string (chain labeling) x=x1⁢…⁢xn∈Dn is a sum of terms over intervals [i,j] where each term is non-zero only if the substring xi⁢…⁢xj equals a prespecified word w∈Λ. The second model is a Weighted Context-Free Grammar (WCFG) frequently used for natural language processing. PB and WCFG encode local and non-local interactions respectively, and thus can be viewed as complementary. We propose a Grammatical Pattern-Based CRF model (GPB) that combines the two in a natural way. We argue that it has certain advantages over existing approaches such as the Hybrid model of Benedí and Sanchez that combines N-grams and WCFGs. The focus of this paper is to analyze the complexity of inference tasks in a GPB such as computing MAP. We present a polynomial-time algorithm for general GPBs and a faster version for a special case that we call Interaction Grammars.","lang":"eng"}],"citation":{"ama":"Takhanov R, Kolmogorov V. Combining pattern-based CRFs and weighted context-free grammars. <i>Intelligent Data Analysis</i>. 2022;26(1):257-272. doi:<a href=\"https://doi.org/10.3233/IDA-205623\">10.3233/IDA-205623</a>","ieee":"R. Takhanov and V. Kolmogorov, “Combining pattern-based CRFs and weighted context-free grammars,” <i>Intelligent Data Analysis</i>, vol. 26, no. 1. IOS Press, pp. 257–272, 2022.","chicago":"Takhanov, Rustem, and Vladimir Kolmogorov. “Combining Pattern-Based CRFs and Weighted Context-Free Grammars.” <i>Intelligent Data Analysis</i>. IOS Press, 2022. <a href=\"https://doi.org/10.3233/IDA-205623\">https://doi.org/10.3233/IDA-205623</a>.","ista":"Takhanov R, Kolmogorov V. 2022. Combining pattern-based CRFs and weighted context-free grammars. Intelligent Data Analysis. 26(1), 257–272.","mla":"Takhanov, Rustem, and Vladimir Kolmogorov. “Combining Pattern-Based CRFs and Weighted Context-Free Grammars.” <i>Intelligent Data Analysis</i>, vol. 26, no. 1, IOS Press, 2022, pp. 257–72, doi:<a href=\"https://doi.org/10.3233/IDA-205623\">10.3233/IDA-205623</a>.","apa":"Takhanov, R., &#38; Kolmogorov, V. (2022). Combining pattern-based CRFs and weighted context-free grammars. <i>Intelligent Data Analysis</i>. IOS Press. <a href=\"https://doi.org/10.3233/IDA-205623\">https://doi.org/10.3233/IDA-205623</a>","short":"R. Takhanov, V. Kolmogorov, Intelligent Data Analysis 26 (2022) 257–272."},"oa_version":"Preprint","date_published":"2022-01-14T00:00:00Z","department":[{"_id":"VlKo"}],"publication_identifier":{"eissn":["1571-4128"],"issn":["1088-467X"]},"volume":26,"external_id":{"arxiv":["1404.5475"],"isi":["000749997700015"]},"author":[{"last_name":"Takhanov","id":"2CCAC26C-F248-11E8-B48F-1D18A9856A87","first_name":"Rustem","full_name":"Takhanov, Rustem"},{"last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"_id":"10737","doi":"10.3233/IDA-205623","status":"public","day":"14","publication_status":"published","scopus_import":"1","type":"journal_article","publication":"Intelligent Data Analysis","page":"257-272","date_updated":"2024-10-09T21:01:33Z","article_type":"original","arxiv":1,"intvolume":"        26","article_processing_charge":"No","corr_author":"1","publisher":"IOS Press","title":"Combining pattern-based CRFs and weighted context-free grammars","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"isi":1,"month":"01","acknowledgement":"This research was funded in parts by the FORTE program of the Austrian Research Promotion Agency (FFG) and the Federal Ministry of Agriculture, Regions and Tourism (BMLRT) as part of the AMMONIS project (grant no. 879705). The research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","oa_version":"None","citation":{"ieee":"J. Lampert and C. Lampert, “Overcoming rare-language discrimination in multi-lingual sentiment analysis,” in <i>2021 IEEE International Conference on Big Data</i>, Orlando, FL, United States, 2022, pp. 5185–5192.","ama":"Lampert J, Lampert C. Overcoming rare-language discrimination in multi-lingual sentiment analysis. In: <i>2021 IEEE International Conference on Big Data</i>. IEEE; 2022:5185-5192. doi:<a href=\"https://doi.org/10.1109/bigdata52589.2021.9672003\">10.1109/bigdata52589.2021.9672003</a>","short":"J. Lampert, C. Lampert, in:, 2021 IEEE International Conference on Big Data, IEEE, 2022, pp. 5185–5192.","mla":"Lampert, Jasmin, and Christoph Lampert. “Overcoming Rare-Language Discrimination in Multi-Lingual Sentiment Analysis.” <i>2021 IEEE International Conference on Big Data</i>, IEEE, 2022, pp. 5185–92, doi:<a href=\"https://doi.org/10.1109/bigdata52589.2021.9672003\">10.1109/bigdata52589.2021.9672003</a>.","apa":"Lampert, J., &#38; Lampert, C. (2022). Overcoming rare-language discrimination in multi-lingual sentiment analysis. In <i>2021 IEEE International Conference on Big Data</i> (pp. 5185–5192). Orlando, FL, United States: IEEE. <a href=\"https://doi.org/10.1109/bigdata52589.2021.9672003\">https://doi.org/10.1109/bigdata52589.2021.9672003</a>","ista":"Lampert J, Lampert C. 2022. Overcoming rare-language discrimination in multi-lingual sentiment analysis. 2021 IEEE International Conference on Big Data. Big Data: International Conference on Big Data, 5185–5192.","chicago":"Lampert, Jasmin, and Christoph Lampert. “Overcoming Rare-Language Discrimination in Multi-Lingual Sentiment Analysis.” In <i>2021 IEEE International Conference on Big Data</i>, 5185–92. IEEE, 2022. <a href=\"https://doi.org/10.1109/bigdata52589.2021.9672003\">https://doi.org/10.1109/bigdata52589.2021.9672003</a>."},"abstract":[{"lang":"eng","text":"The digitalization of almost all aspects of our everyday lives has led to unprecedented amounts of data being freely available on the Internet. In particular social media platforms provide rich sources of user-generated data, though typically in unstructured form, and with high diversity, such as written in many different languages. Automatically identifying meaningful information in such big data resources and extracting it efficiently is one of the ongoing challenges of our time. A common step for this is sentiment analysis, which forms the foundation for tasks such as opinion mining or trend prediction. Unfortunately, publicly available tools for this task are almost exclusively available for English-language texts. Consequently, a large fraction of the Internet users, who do not communicate in English, are ignored in automatized studies, a phenomenon called rare-language discrimination.In this work we propose a technique to overcome this problem by a truly multi-lingual model, which can be trained automatically without linguistic knowledge or even the ability to read the many target languages. The main step is to combine self-annotation, specifically the use of emoticons as a proxy for labels, with multi-lingual sentence representations.To evaluate our method we curated several large datasets from data obtained via the free Twitter streaming API. The results show that our proposed multi-lingual training is able to achieve sentiment predictions at the same quality level for rare languages as for frequent ones, and in particular clearly better than what mono-lingual training achieves on the same data. "}],"year":"2022","date_created":"2022-02-10T14:08:23Z","language":[{"iso":"eng"}],"quality_controlled":"1","author":[{"full_name":"Lampert, Jasmin","first_name":"Jasmin","last_name":"Lampert"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0002-4561-241X","last_name":"Lampert"}],"_id":"10752","publication_identifier":{"isbn":["9781665439022"]},"date_published":"2022-01-13T00:00:00Z","department":[{"_id":"ChLa"}],"external_id":{"isi":["000800559505036"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"type":"conference","scopus_import":"1","page":"5185-5192","publication":"2021 IEEE International Conference on Big Data","doi":"10.1109/bigdata52589.2021.9672003","publication_status":"published","day":"13","conference":{"location":"Orlando, FL, United States","start_date":"2021-12-15","end_date":"2021-12-18","name":"Big Data: International Conference on Big Data"},"status":"public","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"IEEE","corr_author":"1","title":"Overcoming rare-language discrimination in multi-lingual sentiment analysis","date_updated":"2024-10-21T06:01:53Z"},{"page":"361-362","publication":"Neuron","type":"journal_article","scopus_import":"1","publication_status":"published","status":"public","day":"02","doi":"10.1016/j.neuron.2022.01.014","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","corr_author":"1","title":"A familiar thought: Machines that replace us?","article_processing_charge":"No","intvolume":"       110","pmid":1,"article_type":"letter_note","date_updated":"2024-10-09T21:01:34Z","oa_version":"Published Version","abstract":[{"text":"This is a comment on \"Meta-learning synaptic plasticity and memory addressing for continual familiarity detection.\" Neuron. 2022 Feb 2;110(3):544-557.e8.","lang":"eng"}],"citation":{"ama":"Confavreux BJ, Vogels TP. A familiar thought: Machines that replace us? <i>Neuron</i>. 2022;110(3):361-362. doi:<a href=\"https://doi.org/10.1016/j.neuron.2022.01.014\">10.1016/j.neuron.2022.01.014</a>","ieee":"B. J. Confavreux and T. P. Vogels, “A familiar thought: Machines that replace us?,” <i>Neuron</i>, vol. 110, no. 3. Elsevier, pp. 361–362, 2022.","chicago":"Confavreux, Basile J, and Tim P Vogels. “A Familiar Thought: Machines That Replace Us?” <i>Neuron</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.neuron.2022.01.014\">https://doi.org/10.1016/j.neuron.2022.01.014</a>.","ista":"Confavreux BJ, Vogels TP. 2022. A familiar thought: Machines that replace us? Neuron. 110(3), 361–362.","mla":"Confavreux, Basile J., and Tim P. Vogels. “A Familiar Thought: Machines That Replace Us?” <i>Neuron</i>, vol. 110, no. 3, Elsevier, 2022, pp. 361–62, doi:<a href=\"https://doi.org/10.1016/j.neuron.2022.01.014\">10.1016/j.neuron.2022.01.014</a>.","apa":"Confavreux, B. J., &#38; Vogels, T. P. (2022). A familiar thought: Machines that replace us? <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2022.01.014\">https://doi.org/10.1016/j.neuron.2022.01.014</a>","short":"B.J. Confavreux, T.P. Vogels, Neuron 110 (2022) 361–362."},"main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2022.01.014","open_access":"1"}],"isi":1,"month":"02","date_created":"2022-02-13T23:01:34Z","language":[{"iso":"eng"}],"quality_controlled":"1","issue":"3","year":"2022","oa":1,"author":[{"full_name":"Confavreux, Basile J","id":"C7610134-B532-11EA-BD9F-F5753DDC885E","first_name":"Basile J","last_name":"Confavreux"},{"orcid":"0000-0003-3295-6181","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","full_name":"Vogels, Tim P"}],"_id":"10753","external_id":{"isi":["000751819100005"],"pmid":["35114107"]},"volume":110,"publication_identifier":{"eissn":["1097-4199"]},"date_published":"2022-02-02T00:00:00Z","department":[{"_id":"TiVo"}]},{"_id":"10754","author":[{"full_name":"Chang, Yan","first_name":"Yan","last_name":"Chang"},{"full_name":"Funk, Marah","first_name":"Marah","last_name":"Funk"},{"last_name":"Roy","first_name":"Souvik","full_name":"Roy, Souvik"},{"last_name":"Stephenson","orcid":"0000-0002-6862-208X","full_name":"Stephenson, Elizabeth R","first_name":"Elizabeth R","id":"2D04F932-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sangyong","full_name":"Choi, Sangyong","last_name":"Choi"},{"last_name":"Kojouharov","first_name":"Hristo V.","full_name":"Kojouharov, Hristo V."},{"first_name":"Benito","full_name":"Chen, Benito","last_name":"Chen"},{"full_name":"Pan, Zui","first_name":"Zui","last_name":"Pan"}],"publication_identifier":{"eissn":["1422-0067"],"issn":["1661-6596"]},"date_published":"2022-02-01T00:00:00Z","department":[{"_id":"HeEd"}],"article_number":"1763","volume":23,"external_id":{"pmid":["35163685"],"isi":["000754773500001"]},"isi":1,"month":"02","acknowledgement":"This work was partially supported by grants from National Institutes of Health (NIH) (R01 CA185055, S10OD0252300) and The University of Texas System STARs Award (to Z.P.),\r\nThe University of Texas at Arlington Interdisciplinary Research Program (to B.C., H.V.K. and Z.P.). ","file":[{"success":1,"file_id":"10756","file_name":"2022_IJMS_Chang.pdf","content_type":"application/pdf","checksum":"8890ad20c54e90dc58ad5ea97c902998","access_level":"open_access","relation":"main_file","file_size":24416183,"date_updated":"2022-02-14T07:46:30Z","creator":"dernst","date_created":"2022-02-14T07:46:30Z"}],"oa_version":"Published Version","abstract":[{"text":"Targeting dysregulated Ca2+ signaling in cancer cells is an emerging chemotherapy approach. We previously reported that store-operated Ca2+ entry (SOCE) blockers, such as RP4010, are promising antitumor drugs for esophageal cancer. As a tyrosine kinase inhibitor (TKI), afatinib received FDA approval to be used in targeted therapy for patients with EGFR mutation-positive cancers. While preclinical studies and clinical trials have shown that afatinib has benefits for esophageal cancer patients, it is not known whether a combination of afatinib and RP4010 could achieve better anticancer effects. Since TKI can alter intracellular Ca2+ dynamics through EGFR/phospholipase C-γ pathway, in this study, we evaluated the inhibitory effect of afatinib and RP4010 on intracellular Ca2+ oscillations in KYSE-150, a human esophageal squamous cell carcinoma cell line, using both experimental and mathematical simulations. Our mathematical simulation of Ca2+ oscillations could fit well with experimental data responding to afatinib or RP4010, both separately or in combination. Guided by simulation, we were able to identify a proper ratio of afatinib and RP4010 for combined treatment, and such a combination presented synergistic anticancer-effect evidence by experimental measurement of intracellular Ca2+ and cell proliferation. This intracellular Ca2+ dynamic-based mathematical simulation approach could be useful for a rapid and cost-effective evaluation of combined targeting therapy drugs.","lang":"eng"}],"citation":{"mla":"Chang, Yan, et al. “Developing a Mathematical Model of Intracellular Calcium Dynamics for Evaluating Combined Anticancer Effects of Afatinib and RP4010 in Esophageal Cancer.” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 3, 1763, MDPI, 2022, doi:<a href=\"https://doi.org/10.3390/ijms23031763\">10.3390/ijms23031763</a>.","ista":"Chang Y, Funk M, Roy S, Stephenson ER, Choi S, Kojouharov HV, Chen B, Pan Z. 2022. Developing a mathematical model of intracellular Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer. International Journal of Molecular Sciences. 23(3), 1763.","apa":"Chang, Y., Funk, M., Roy, S., Stephenson, E. R., Choi, S., Kojouharov, H. V., … Pan, Z. (2022). Developing a mathematical model of intracellular Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms23031763\">https://doi.org/10.3390/ijms23031763</a>","chicago":"Chang, Yan, Marah Funk, Souvik Roy, Elizabeth R Stephenson, Sangyong Choi, Hristo V. Kojouharov, Benito Chen, and Zui Pan. “Developing a Mathematical Model of Intracellular Calcium Dynamics for Evaluating Combined Anticancer Effects of Afatinib and RP4010 in Esophageal Cancer.” <i>International Journal of Molecular Sciences</i>. MDPI, 2022. <a href=\"https://doi.org/10.3390/ijms23031763\">https://doi.org/10.3390/ijms23031763</a>.","short":"Y. Chang, M. Funk, S. Roy, E.R. Stephenson, S. Choi, H.V. Kojouharov, B. Chen, Z. Pan, International Journal of Molecular Sciences 23 (2022).","ama":"Chang Y, Funk M, Roy S, et al. Developing a mathematical model of intracellular Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer. <i>International Journal of Molecular Sciences</i>. 2022;23(3). doi:<a href=\"https://doi.org/10.3390/ijms23031763\">10.3390/ijms23031763</a>","ieee":"Y. Chang <i>et al.</i>, “Developing a mathematical model of intracellular Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer,” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 3. MDPI, 2022."},"issue":"3","oa":1,"year":"2022","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_created":"2022-02-13T23:01:35Z","language":[{"iso":"eng"}],"file_date_updated":"2022-02-14T07:46:30Z","quality_controlled":"1","article_processing_charge":"Yes","pmid":1,"intvolume":"        23","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"MDPI","title":"Developing a mathematical model of intracellular Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer","date_updated":"2025-06-11T13:46:46Z","article_type":"original","ddc":["510","576"],"type":"journal_article","has_accepted_license":"1","scopus_import":"1","publication":"International Journal of Molecular Sciences","doi":"10.3390/ijms23031763","status":"public","day":"01","publication_status":"published"}]