[{"abstract":[{"lang":"eng","text":"Cerebral organoids differentiated from human-induced pluripotent stem cells (hiPSC) provide a unique opportunity to investigate brain development. However, organoids usually lack microglia, brain-resident immune cells, which are present in the early embryonic brain and participate in neuronal circuit development. Here, we find IBA1+ microglia-like cells alongside retinal cups between week 3 and 4 in 2.5D culture with an unguided retinal organoid differentiation protocol. Microglia do not infiltrate the neuroectoderm and instead enrich within non-pigmented, 3D-cystic compartments that develop in parallel to the 3D-retinal organoids. When we guide the retinal organoid differentiation with low-dosed BMP4, we prevent cup development and enhance microglia and 3D-cysts formation. Mass spectrometry identifies these 3D-cysts to express mesenchymal and epithelial markers. We confirmed this microglia-preferred environment also within the unguided protocol, providing insight into microglial behavior and migration and offer a model to study how they enter and distribute within the human brain."}],"issue":"7","doi":"10.1016/j.isci.2022.104580","title":"A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation","author":[{"full_name":"Bartalska, Katarina","last_name":"Bartalska","id":"4D883232-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina"},{"last_name":"Hübschmann","full_name":"Hübschmann, Verena","first_name":"Verena","id":"32B7C918-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4309-2251","id":"4B51CE74-F248-11E8-B48F-1D18A9856A87","first_name":"Medina","full_name":"Korkut, Medina","last_name":"Korkut"},{"orcid":"0000-0003-0002-1867","last_name":"Cubero","full_name":"Cubero, Ryan J","first_name":"Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425"},{"orcid":"0000-0003-2356-9403","full_name":"Venturino, Alessandro","last_name":"Venturino","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","first_name":"Alessandro"},{"last_name":"Rössler","full_name":"Rössler, Karl","first_name":"Karl"},{"first_name":"Thomas","last_name":"Czech","full_name":"Czech, Thomas"},{"orcid":"0000-0001-8635-0877","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","full_name":"Siegert, Sandra"}],"_id":"11478","status":"public","acknowledgement":"We thank the scientific service units at ISTA, specifically the lab support facility and imaging & optics facility for their support; Nicolas Armel for performing the Mass Spectrometry. We thank Alexandra Lang and Tanja Peilnsteiner for their help in human brain tissue collection, Rouven Schulz for his insights into the functional assays We thank all members of the Siegert group for constant feedback on the project and Margaret Maes, Rouven Schulz, and Marco Benevento for feedback on the manuscript. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant No. 715571 to S.S.) and from the Gesellschaft für Forschungsförderung Niederösterreich (grant No. Sc19-017 to V.H.).","publication_status":"published","ec_funded":1,"publication_identifier":{"eissn":["2589-0042"]},"project":[{"call_identifier":"H2020","name":"Microglia action towards neuronal circuit formation and function in health and disease","_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"name":"How human microglia shape developing neurons during health and inflammation","grant_number":"SC19-017","_id":"9B99D380-BA93-11EA-9121-9846C619BF3A"}],"oa_version":"Published Version","citation":{"apa":"Bartalska, K., Hübschmann, V., Korkut, M., Cubero, R. J., Venturino, A., Rössler, K., … Siegert, S. (2022). A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2022.104580\">https://doi.org/10.1016/j.isci.2022.104580</a>","ieee":"K. Bartalska <i>et al.</i>, “A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation,” <i>iScience</i>, vol. 25, no. 7. Elsevier, 2022.","ista":"Bartalska K, Hübschmann V, Korkut M, Cubero RJ, Venturino A, Rössler K, Czech T, Siegert S. 2022. A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation. iScience. 25(7), 104580.","ama":"Bartalska K, Hübschmann V, Korkut M, et al. A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation. <i>iScience</i>. 2022;25(7). doi:<a href=\"https://doi.org/10.1016/j.isci.2022.104580\">10.1016/j.isci.2022.104580</a>","short":"K. Bartalska, V. Hübschmann, M. Korkut, R.J. Cubero, A. Venturino, K. Rössler, T. Czech, S. Siegert, IScience 25 (2022).","mla":"Bartalska, Katarina, et al. “A Systematic Characterization of Microglia-like Cell Occurrence during Retinal Organoid Differentiation.” <i>IScience</i>, vol. 25, no. 7, 104580, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.isci.2022.104580\">10.1016/j.isci.2022.104580</a>.","chicago":"Bartalska, Katarina, Verena Hübschmann, Medina Korkut, Ryan J Cubero, Alessandro Venturino, Karl Rössler, Thomas Czech, and Sandra Siegert. “A Systematic Characterization of Microglia-like Cell Occurrence during Retinal Organoid Differentiation.” <i>IScience</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.isci.2022.104580\">https://doi.org/10.1016/j.isci.2022.104580</a>."},"day":"15","ddc":["610"],"month":"07","file_date_updated":"2022-07-04T08:19:25Z","has_accepted_license":"1","volume":25,"article_processing_charge":"Yes","file":[{"content_type":"application/pdf","checksum":"a470b74e1b3796c710189c81a4cd4329","access_level":"open_access","date_updated":"2022-07-04T08:19:25Z","success":1,"creator":"cchlebak","relation":"main_file","file_size":19400048,"file_name":"2022_iScience_Bartalska.pdf","date_created":"2022-07-04T08:19:25Z","file_id":"11480"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2022","oa":1,"related_material":{"record":[{"status":"public","relation":"other","id":"12117"}]},"article_number":"104580","article_type":"original","publication":"iScience","date_updated":"2023-11-02T12:21:33Z","external_id":{"isi":["000830428500005"]},"date_published":"2022-07-15T00:00:00Z","date_created":"2022-07-03T22:01:33Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"scopus_import":"1","department":[{"_id":"SaSi"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","publisher":"Elsevier","intvolume":"        25"},{"article_type":"original","page":"6352","publication":"International Journal of Molecular Sciences","date_updated":"2023-08-09T10:13:57Z","year":"2022","oa":1,"isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"        23","publisher":"MDPI","date_published":"2022-06-06T00:00:00Z","external_id":{"pmid":["35683031"],"isi":["000808733300001"]},"date_created":"2022-07-05T15:14:34Z","department":[{"_id":"JiFr"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","acknowledgement":"We thank Charo del Genio from Coventry University and Richard Napier from the University of Warwick for helpful discussion concerning protein modeling and inspiration concerning CD spectroscopy, respectively. We thank Jan Hejatko for sharing the published AHP2 construct. We also thank Josef Houser from the core facility BIC CEITEC for valuable assistance, discussions, and ideas relating to CD. We acknowledge the: Core Facility CELLIM of CEITEC supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR), part of the Euro-BioImaging (www.eurobioimaging.eu accessed on 1 January 2016) ALM and medical imaging Node (Brno, CZ), CF Biomolecular Interactions and Crystallization of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127) and European Regional Development Fund-Project “UP CIISB“ (No. CZ.02.1.01/0.0/0.0/18_046/0015974) for their support with obtaining scientific data presented in this paper; Plant Sciences Core Facility of CEITEC Masaryk University for technical support. Open Access Funding by the Austrian Science Fund (FWF).","publication_identifier":{"issn":["1422-0067"]},"project":[{"call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425","grant_number":"P29988"}],"issue":"11","abstract":[{"text":"Much of plant development depends on cell-to-cell redistribution of the plant hormone auxin, which is facilitated by the plasma membrane (PM) localized PIN FORMED (PIN) proteins. Auxin export activity, developmental roles, subcellular trafficking, and polarity of PINs have been well studied, but their structure remains elusive besides a rough outline that they contain two groups of 5 alpha-helices connected by a large hydrophilic loop (HL). Here, we focus on the PIN1 HL as we could produce it in sufficient quantities for biochemical investigations to provide insights into its secondary structure. Circular dichroism (CD) studies revealed its nature as an intrinsically disordered protein (IDP), manifested by the increase of structure content upon thermal melting. Consistent with IDPs serving as interaction platforms, PIN1 loops homodimerize. PIN1 HL cytoplasmic overexpression in Arabidopsis disrupts early endocytic trafficking of PIN1 and PIN2 and causes defects in the cotyledon vasculature formation. In summary, we demonstrate that PIN1 HL has an intrinsically disordered nature, which must be considered to gain further structural insights. Some secondary structures may form transiently during pairing with known and yet-to-be-discovered interactors.","lang":"eng"}],"doi":"10.3390/ijms23116352","author":[{"full_name":"Bilanovičová, V","last_name":"Bilanovičová","first_name":"V"},{"full_name":"Rýdza, N","last_name":"Rýdza","first_name":"N"},{"last_name":"Koczka","full_name":"Koczka, L","first_name":"L"},{"first_name":"M","last_name":"Hess","full_name":"Hess, M"},{"first_name":"E","last_name":"Feraru","full_name":"Feraru, E"},{"last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"full_name":"Nodzyński, T","last_name":"Nodzyński","first_name":"T"}],"title":"The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein","_id":"11489","has_accepted_license":"1","volume":23,"article_processing_charge":"Yes","file":[{"file_id":"11492","date_created":"2022-07-06T07:36:59Z","access_level":"open_access","checksum":"e997a57a928ec9d51fad8ce824a05935","content_type":"application/pdf","success":1,"date_updated":"2022-07-06T07:36:59Z","file_name":"2022_IntJMolSci_Bilanovicova.pdf","relation":"main_file","file_size":2324542,"creator":"cchlebak"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","day":"06","citation":{"ista":"Bilanovičová V, Rýdza N, Koczka L, Hess M, Feraru E, Friml J, Nodzyński T. 2022. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. International Journal of Molecular Sciences. 23(11), 6352.","short":"V. Bilanovičová, N. Rýdza, L. Koczka, M. Hess, E. Feraru, J. Friml, T. Nodzyński, International Journal of Molecular Sciences 23 (2022) 6352.","ama":"Bilanovičová V, Rýdza N, Koczka L, et al. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. <i>International Journal of Molecular Sciences</i>. 2022;23(11):6352. doi:<a href=\"https://doi.org/10.3390/ijms23116352\">10.3390/ijms23116352</a>","ieee":"V. Bilanovičová <i>et al.</i>, “The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein,” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 11. MDPI, p. 6352, 2022.","apa":"Bilanovičová, V., Rýdza, N., Koczka, L., Hess, M., Feraru, E., Friml, J., &#38; Nodzyński, T. (2022). The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms23116352\">https://doi.org/10.3390/ijms23116352</a>","mla":"Bilanovičová, V., et al. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 11, MDPI, 2022, p. 6352, doi:<a href=\"https://doi.org/10.3390/ijms23116352\">10.3390/ijms23116352</a>.","chicago":"Bilanovičová, V, N Rýdza, L Koczka, M Hess, E Feraru, Jiří Friml, and T Nodzyński. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” <i>International Journal of Molecular Sciences</i>. MDPI, 2022. <a href=\"https://doi.org/10.3390/ijms23116352\">https://doi.org/10.3390/ijms23116352</a>."},"ddc":["570"],"file_date_updated":"2022-07-06T07:36:59Z","month":"06","pmid":1},{"_id":"11542","author":[{"last_name":"Schulz","full_name":"Schulz, Rouven","first_name":"Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5297-733X"}],"title":"Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses)","oa":1,"doi":"10.15479/AT:ISTA:11542","year":"2022","date_updated":"2024-02-21T12:34:51Z","status":"public","related_material":{"record":[{"id":"11995","status":"public","relation":"used_in_publication"}],"link":[{"relation":"contains","url":"https://www.biorxiv.org/content/10.1101/2021.06.21.449162v1"}]},"file_date_updated":"2022-07-08T10:56:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"citation":{"short":"R. Schulz, (2022).","ama":"Schulz R. Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>","ista":"Schulz R. 2022. Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses), Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>.","ieee":"R. Schulz, “Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses).” Institute of Science and Technology Austria, 2022.","apa":"Schulz, R. (2022). Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">https://doi.org/10.15479/AT:ISTA:11542</a>","chicago":"Schulz, Rouven. “Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses).” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">https://doi.org/10.15479/AT:ISTA:11542</a>.","mla":"Schulz, Rouven. <i>Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses)</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>."},"date_created":"2022-07-08T11:03:02Z","oa_version":"None","date_published":"2022-01-01T00:00:00Z","file":[{"creator":"rschulz","relation":"main_file","file_size":135784571,"file_name":"Source Data.xlsx","date_updated":"2022-07-08T10:56:52Z","success":1,"checksum":"71e8186583f3adbb6c69a88ac9e6e49b","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","access_level":"open_access","date_created":"2022-07-08T10:56:52Z","file_id":"11543"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Institute of Science and Technology Austria","type":"research_data","article_processing_charge":"No","contributor":[{"last_name":"Siegert","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","contributor_type":"contact_person","orcid":"0000-0001-8635-0877"}],"has_accepted_license":"1"},{"publication_identifier":{"issn":["0021-8693"]},"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"status":"public","publication_status":"published","acknowledgement":"We thank Catharina Stroppel and Jens Niklas Eberhardt for interesting discussions. The first author acknowledges the support of the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. The second author is supported by the National Science Foundation Award No. 1803059 and the Australian Research Council grant DP170101579.","ec_funded":1,"author":[{"last_name":"Brown","full_name":"Brown, Adam","first_name":"Adam","id":"70B7FDF6-608D-11E9-9333-8535E6697425"},{"first_name":"Anna","last_name":"Romanov","full_name":"Romanov, Anna"}],"title":"Contravariant pairings between standard Whittaker modules and Verma modules","_id":"11545","issue":"11","abstract":[{"lang":"eng","text":"We classify contravariant pairings between standard Whittaker modules and Verma modules over a complex semisimple Lie algebra. These contravariant pairings are useful in extending several classical techniques for category O to the Miličić–Soergel category N . We introduce a class of costandard modules which generalize dual Verma modules, and describe canonical maps from standard to costandard modules in terms of contravariant pairings.\r\nWe show that costandard modules have unique irreducible submodules and share the same composition factors as the corresponding standard Whittaker modules. We show that costandard modules give an algebraic characterization of the global sections of costandard twisted Harish-Chandra sheaves on the associated flag variety, which are defined using holonomic duality of D-modules. We prove that with these costandard modules, blocks of category\r\nN have the structure of highest weight categories and we establish a BGG reciprocity theorem for N ."}],"doi":"10.1016/j.jalgebra.2022.06.017","file":[{"date_created":"2023-02-02T07:32:48Z","file_id":"12473","relation":"main_file","file_size":582962,"creator":"dernst","file_name":"2022_JournalAlgebra_Brown.pdf","content_type":"application/pdf","checksum":"82abaee3d7837f703e499a9ecbb25b7c","access_level":"open_access","date_updated":"2023-02-02T07:32:48Z","success":1}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","volume":609,"article_processing_charge":"Yes (via OA deal)","day":"01","citation":{"mla":"Brown, Adam, and Anna Romanov. “Contravariant Pairings between Standard Whittaker Modules and Verma Modules.” <i>Journal of Algebra</i>, vol. 609, no. 11, Elsevier, 2022, pp. 145–79, doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">10.1016/j.jalgebra.2022.06.017</a>.","chicago":"Brown, Adam, and Anna Romanov. “Contravariant Pairings between Standard Whittaker Modules and Verma Modules.” <i>Journal of Algebra</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">https://doi.org/10.1016/j.jalgebra.2022.06.017</a>.","ista":"Brown A, Romanov A. 2022. Contravariant pairings between standard Whittaker modules and Verma modules. Journal of Algebra. 609(11), 145–179.","ama":"Brown A, Romanov A. Contravariant pairings between standard Whittaker modules and Verma modules. <i>Journal of Algebra</i>. 2022;609(11):145-179. doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">10.1016/j.jalgebra.2022.06.017</a>","short":"A. Brown, A. Romanov, Journal of Algebra 609 (2022) 145–179.","apa":"Brown, A., &#38; Romanov, A. (2022). Contravariant pairings between standard Whittaker modules and Verma modules. <i>Journal of Algebra</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">https://doi.org/10.1016/j.jalgebra.2022.06.017</a>","ieee":"A. Brown and A. Romanov, “Contravariant pairings between standard Whittaker modules and Verma modules,” <i>Journal of Algebra</i>, vol. 609, no. 11. Elsevier, pp. 145–179, 2022."},"ddc":["510"],"file_date_updated":"2023-02-02T07:32:48Z","month":"11","oa_version":"Published Version","publication":"Journal of Algebra","date_updated":"2023-08-03T11:56:30Z","article_type":"original","page":"145-179","oa":1,"year":"2022","keyword":["Algebra and Number Theory"],"intvolume":"       609","publisher":"Elsevier","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","department":[{"_id":"HeEd"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000861841100004"]},"date_published":"2022-11-01T00:00:00Z","scopus_import":"1","date_created":"2022-07-08T11:40:07Z"},{"isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","intvolume":"       377","publisher":"Royal Society of London","date_published":"2022-08-01T00:00:00Z","external_id":{"isi":["000812317300005"]},"scopus_import":"1","date_created":"2022-07-08T11:41:56Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","article_number":"20210203","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","date_updated":"2023-08-03T11:55:42Z","year":"2022","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"oa":1,"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","volume":377,"file":[{"date_updated":"2023-02-02T08:20:29Z","success":1,"checksum":"49f69428f3dcf5ce3ff281f7d199e9df","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"dernst","file_size":920304,"file_name":"2022_PhilosophicalTransactionsB_Westram.pdf","date_created":"2023-02-02T08:20:29Z","file_id":"12479"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","day":"01","citation":{"mla":"Westram, Anja M., et al. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856, 20210203, Royal Society of London, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>.","chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas H Barton. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>.","ieee":"A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions and parallel evolution,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856. Royal Society of London, 2022.","apa":"Westram, A. M., Faria, R., Johannesson, K., Butlin, R., &#38; Barton, N. H. (2022). Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>","ista":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. 2022. Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1856), 20210203.","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","ama":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1856). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>"},"month":"08","ddc":["570"],"file_date_updated":"2023-02-02T08:20:29Z","publication_status":"published","status":"public","acknowledgement":"We thank the editor and two anonymous reviewers for their helpful and interesting comments on this manuscript.","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"project":[{"name":"The maintenance of alternative adaptive peaks in snapdragons","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166"}],"issue":"1856","abstract":[{"lang":"eng","text":"Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions."}],"doi":"10.1098/rstb.2021.0203","author":[{"last_name":"Westram","full_name":"Westram, Anja M","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"title":"Inversions and parallel evolution","_id":"11546"},{"publisher":"Springer Nature","intvolume":"         5","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","department":[{"_id":"LeSa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":[" 35739187"],"isi":["000815098500002"]},"date_published":"2022-06-23T00:00:00Z","date_created":"2022-07-10T22:01:52Z","scopus_import":"1","publication":"Communications Biology","date_updated":"2023-08-03T11:51:58Z","article_number":"620","oa":1,"year":"2022","file":[{"content_type":"application/pdf","checksum":"965f88bbcef3fd0c3e121340555c4467","access_level":"open_access","date_updated":"2022-07-13T07:44:58Z","success":1,"relation":"main_file","creator":"kschuh","file_size":2335369,"file_name":"2022_communicationsbiology_Molina-Granada.pdf","date_created":"2022-07-13T07:44:58Z","file_id":"11571"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","article_processing_charge":"No","volume":5,"citation":{"mla":"Molina-Granada, David, et al. “Most Mitochondrial DGTP Is Tightly Bound to Respiratory Complex I through the NDUFA10 Subunit.” <i>Communications Biology</i>, vol. 5, no. 1, 620, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s42003-022-03568-6\">10.1038/s42003-022-03568-6</a>.","chicago":"Molina-Granada, David, Emiliano González-Vioque, Marris G. Dibley, Raquel Cabrera-Pérez, Antoni Vallbona-Garcia, Javier Torres-Torronteras, Leonid A Sazanov, Michael T. Ryan, Yolanda Cámara, and Ramon Martí. “Most Mitochondrial DGTP Is Tightly Bound to Respiratory Complex I through the NDUFA10 Subunit.” <i>Communications Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s42003-022-03568-6\">https://doi.org/10.1038/s42003-022-03568-6</a>.","short":"D. Molina-Granada, E. González-Vioque, M.G. Dibley, R. Cabrera-Pérez, A. Vallbona-Garcia, J. Torres-Torronteras, L.A. Sazanov, M.T. Ryan, Y. Cámara, R. Martí, Communications Biology 5 (2022).","ista":"Molina-Granada D, González-Vioque E, Dibley MG, Cabrera-Pérez R, Vallbona-Garcia A, Torres-Torronteras J, Sazanov LA, Ryan MT, Cámara Y, Martí R. 2022. Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications Biology. 5(1), 620.","ama":"Molina-Granada D, González-Vioque E, Dibley MG, et al. Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. <i>Communications Biology</i>. 2022;5(1). doi:<a href=\"https://doi.org/10.1038/s42003-022-03568-6\">10.1038/s42003-022-03568-6</a>","ieee":"D. Molina-Granada <i>et al.</i>, “Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit,” <i>Communications Biology</i>, vol. 5, no. 1. Springer Nature, 2022.","apa":"Molina-Granada, D., González-Vioque, E., Dibley, M. G., Cabrera-Pérez, R., Vallbona-Garcia, A., Torres-Torronteras, J., … Martí, R. (2022). Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-022-03568-6\">https://doi.org/10.1038/s42003-022-03568-6</a>"},"day":"23","ddc":["570"],"file_date_updated":"2022-07-13T07:44:58Z","pmid":1,"month":"06","oa_version":"Published Version","publication_identifier":{"eissn":["23993642"]},"publication_status":"published","status":"public","acknowledgement":"We thank Dr, Luke Formosa (Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia) for his valuable advice and assistance on NDUFA10 molecular studies and Dr. Francesc Canals and his team (Proteomics Laboratory, Vall d’Hebron Institute of Oncology [VHIO], Universitat Autònoma de Barcelona, Barcelona, Spain) for their assistance with LC-MS/MS analyses. This work was supported by the Spanish Ministry of Industry, Economy and Competitiveness [grants BFU2014-52618-R, SAF2017-87506, and PID2020-112929RB-I00 to Y.C.], by the Spanish Instituto de Salud Carlos III [grants PI21/00554 and PMP15/00025 to R.M.], co-financed by the European Regional Development Fund (ERDF), and by an NHMRC Project grant to M.R. (GNT1164459).\r\n","title":"Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit","author":[{"last_name":"Molina-Granada","full_name":"Molina-Granada, David","first_name":"David"},{"last_name":"González-Vioque","full_name":"González-Vioque, Emiliano","first_name":"Emiliano"},{"full_name":"Dibley, Marris G.","last_name":"Dibley","first_name":"Marris G."},{"last_name":"Cabrera-Pérez","full_name":"Cabrera-Pérez, Raquel","first_name":"Raquel"},{"first_name":"Antoni","last_name":"Vallbona-Garcia","full_name":"Vallbona-Garcia, Antoni"},{"full_name":"Torres-Torronteras, Javier","last_name":"Torres-Torronteras","first_name":"Javier"},{"full_name":"Sazanov, Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","orcid":"0000-0002-0977-7989"},{"full_name":"Ryan, Michael T.","last_name":"Ryan","first_name":"Michael T."},{"last_name":"Cámara","full_name":"Cámara, Yolanda","first_name":"Yolanda"},{"first_name":"Ramon","last_name":"Martí","full_name":"Martí, Ramon"}],"_id":"11551","abstract":[{"text":"Imbalanced mitochondrial dNTP pools are known players in the pathogenesis of multiple human diseases. Here we show that, even under physiological conditions, dGTP is largely overrepresented among other dNTPs in mitochondria of mouse tissues and human cultured cells. In addition, a vast majority of mitochondrial dGTP is tightly bound to NDUFA10, an accessory subunit of complex I of the mitochondrial respiratory chain. NDUFA10 shares a deoxyribonucleoside kinase (dNK) domain with deoxyribonucleoside kinases in the nucleotide salvage pathway, though no specific function beyond stabilizing the complex I holoenzyme has been described for this subunit. We mutated the dNK domain of NDUFA10 in human HEK-293T cells while preserving complex I assembly and activity. The NDUFA10E160A/R161A shows reduced dGTP binding capacity in vitro and leads to a 50% reduction in mitochondrial dGTP content, proving that most dGTP is directly bound to the dNK domain of NDUFA10. This interaction may represent a hitherto unknown mechanism regulating mitochondrial dNTP availability and linking oxidative metabolism to DNA maintenance.","lang":"eng"}],"issue":"1","doi":"10.1038/s42003-022-03568-6"},{"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"intvolume":"       128","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2201.09281","open_access":"1"}],"publisher":"American Physical Society","scopus_import":"1","date_created":"2022-07-10T22:01:52Z","external_id":{"isi":["000820659700002"],"arxiv":["2201.09281"]},"date_published":"2022-06-16T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MiLe"}],"article_number":"243201","date_updated":"2023-08-03T11:54:14Z","publication":"Physical Review Letters","year":"2022","oa":1,"article_processing_charge":"No","volume":128,"arxiv":1,"oa_version":"Submitted Version","month":"06","day":"16","citation":{"mla":"Qiang, Junjie, et al. “Femtosecond Rotational Dynamics of D2 Molecules in Superfluid Helium Nanodroplets.” <i>Physical Review Letters</i>, vol. 128, no. 24, 243201, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.128.243201\">10.1103/PhysRevLett.128.243201</a>.","chicago":"Qiang, Junjie, Lianrong Zhou, Peifen Lu, Kang Lin, Yongzhe Ma, Shengzhe Pan, Chenxu Lu, et al. “Femtosecond Rotational Dynamics of D2 Molecules in Superfluid Helium Nanodroplets.” <i>Physical Review Letters</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevLett.128.243201\">https://doi.org/10.1103/PhysRevLett.128.243201</a>.","ieee":"J. Qiang <i>et al.</i>, “Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets,” <i>Physical Review Letters</i>, vol. 128, no. 24. American Physical Society, 2022.","apa":"Qiang, J., Zhou, L., Lu, P., Lin, K., Ma, Y., Pan, S., … Wu, J. (2022). Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.128.243201\">https://doi.org/10.1103/PhysRevLett.128.243201</a>","ama":"Qiang J, Zhou L, Lu P, et al. Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets. <i>Physical Review Letters</i>. 2022;128(24). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.128.243201\">10.1103/PhysRevLett.128.243201</a>","short":"J. Qiang, L. Zhou, P. Lu, K. Lin, Y. Ma, S. Pan, C. Lu, W. Jiang, F. Sun, W. Zhang, H. Li, X. Gong, I.S. Averbukh, Y. Prior, C.A. Schouder, H. Stapelfeldt, I. Cherepanov, M. Lemeshko, W. Jäger, J. Wu, Physical Review Letters 128 (2022).","ista":"Qiang J, Zhou L, Lu P, Lin K, Ma Y, Pan S, Lu C, Jiang W, Sun F, Zhang W, Li H, Gong X, Averbukh IS, Prior Y, Schouder CA, Stapelfeldt H, Cherepanov I, Lemeshko M, Jäger W, Wu J. 2022. Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets. Physical Review Letters. 128(24), 243201."},"ec_funded":1,"publication_status":"published","status":"public","project":[{"call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"doi":"10.1103/PhysRevLett.128.243201","issue":"24","abstract":[{"lang":"eng","text":"Rotational dynamics of D2 molecules inside helium nanodroplets is induced by a moderately intense femtosecond pump pulse and measured as a function of time by recording the yield of HeD+ ions, created through strong-field dissociative ionization with a delayed femtosecond probe pulse. The yield oscillates with a period of 185 fs, reflecting field-free rotational wave packet dynamics, and the oscillation persists for more than 500 periods. Within the experimental uncertainty, the rotational constant BHe of the in-droplet D2 molecule, determined by Fourier analysis, is the same as Bgas for an isolated D2 molecule. Our observations show that the D2 molecules inside helium nanodroplets essentially rotate as free D2 molecules."}],"_id":"11552","author":[{"first_name":"Junjie","last_name":"Qiang","full_name":"Qiang, Junjie"},{"first_name":"Lianrong","full_name":"Zhou, Lianrong","last_name":"Zhou"},{"last_name":"Lu","full_name":"Lu, Peifen","first_name":"Peifen"},{"full_name":"Lin, Kang","last_name":"Lin","first_name":"Kang"},{"first_name":"Yongzhe","full_name":"Ma, Yongzhe","last_name":"Ma"},{"last_name":"Pan","full_name":"Pan, Shengzhe","first_name":"Shengzhe"},{"first_name":"Chenxu","full_name":"Lu, Chenxu","last_name":"Lu"},{"first_name":"Wenyu","last_name":"Jiang","full_name":"Jiang, Wenyu"},{"first_name":"Fenghao","full_name":"Sun, Fenghao","last_name":"Sun"},{"first_name":"Wenbin","full_name":"Zhang, Wenbin","last_name":"Zhang"},{"first_name":"Hui","full_name":"Li, Hui","last_name":"Li"},{"first_name":"Xiaochun","last_name":"Gong","full_name":"Gong, Xiaochun"},{"full_name":"Averbukh, Ilya Sh","last_name":"Averbukh","first_name":"Ilya Sh"},{"first_name":"Yehiam","last_name":"Prior","full_name":"Prior, Yehiam"},{"first_name":"Constant A.","last_name":"Schouder","full_name":"Schouder, Constant A."},{"first_name":"Henrik","last_name":"Stapelfeldt","full_name":"Stapelfeldt, Henrik"},{"full_name":"Cherepanov, Igor","last_name":"Cherepanov","id":"339C7E5A-F248-11E8-B48F-1D18A9856A87","first_name":"Igor"},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"},{"full_name":"Jäger, Wolfgang","last_name":"Jäger","first_name":"Wolfgang"},{"full_name":"Wu, Jian","last_name":"Wu","first_name":"Jian"}],"title":"Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets"},{"publication":"Arnold Mathematical Journal","date_updated":"2023-02-16T10:02:12Z","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s40598-022-00209-y"},{"relation":"erratum","url":"https://doi.org/10.1007/s40598-022-00218-x"}]},"page":"319-410","article_type":"original","oa":1,"year":"2022","publisher":"Springer Nature","intvolume":"         8","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"VaKa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-06-01T00:00:00Z","date_created":"2022-07-10T22:01:53Z","scopus_import":"1","publication_identifier":{"issn":["2199-6792"],"eissn":["2199-6806"]},"project":[{"grant_number":"885707","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","name":"Spectral rigidity and integrability for billiards and geodesic flows","call_identifier":"H2020"}],"status":"public","acknowledgement":"We would also like to thank Dzmitry Dudko and Dierk Schleicher for many stimulating discussions and encouragement during our work on this project, and Weixiao Shen, Mikhail Hlushchanka and the referee for helpful comments. We are grateful to Leon Staresinic who carefully read the revised version of the manuscript and provided many helpful suggestions.","publication_status":"published","ec_funded":1,"title":"The dynamics of complex box mappings","author":[{"first_name":"Trevor","last_name":"Clark","full_name":"Clark, Trevor"},{"first_name":"Kostiantyn","id":"fe8209e2-906f-11eb-847d-950f8fc09115","last_name":"Drach","full_name":"Drach, Kostiantyn","orcid":"0000-0002-9156-8616"},{"first_name":"Oleg","full_name":"Kozlovski, Oleg","last_name":"Kozlovski"},{"first_name":"Sebastian Van","full_name":"Strien, Sebastian Van","last_name":"Strien"}],"_id":"11553","abstract":[{"text":"In holomorphic dynamics, complex box mappings arise as first return maps to wellchosen domains. They are a generalization of polynomial-like mapping, where the domain of the return map can have infinitely many components. They turned out to be extremely useful in tackling diverse problems. The purpose of this paper is:\r\n• To illustrate some pathologies that can occur when a complex box mapping is not induced by a globally defined map and when its domain has infinitely many components, and to give conditions to avoid these issues.\r\n• To show that once one has a box mapping for a rational map, these conditions can be assumed to hold in a very natural setting. Thus, we call such complex box mappings dynamically natural. Having such box mappings is the first step in tackling many problems in one-dimensional dynamics.\r\n• Many results in holomorphic dynamics rely on an interplay between combinatorial and analytic techniques. In this setting, some of these tools are:\r\n  • the Enhanced Nest (a nest of puzzle pieces around critical points) from Kozlovski, Shen, van Strien (AnnMath 165:749–841, 2007), referred to below as KSS;\r\n  • the Covering Lemma (which controls the moduli of pullbacks of annuli) from Kahn and Lyubich (Ann Math 169(2):561–593, 2009);\r\n   • the QC-Criterion and the Spreading Principle from KSS.\r\nThe purpose of this paper is to make these tools more accessible so that they can be used as a ‘black box’, so one does not have to redo the proofs in new settings.\r\n• To give an intuitive, but also rather detailed, outline of the proof from KSS and Kozlovski and van Strien (Proc Lond Math Soc (3) 99:275–296, 2009) of the following results for non-renormalizable dynamically natural complex box mappings:\r\n   • puzzle pieces shrink to points,\r\n   • (under some assumptions) topologically conjugate non-renormalizable polynomials and box mappings are quasiconformally conjugate.\r\n• We prove the fundamental ergodic properties for dynamically natural box mappings. This leads to some necessary conditions for when such a box mapping supports a measurable invariant line field on its filled Julia set. These mappings\r\nare the analogues of Lattès maps in this setting.\r\n• We prove a version of Mañé’s Theorem for complex box mappings concerning expansion along orbits of points that avoid a neighborhood of the set of critical points.","lang":"eng"}],"issue":"2","doi":"10.1007/s40598-022-00200-7","file":[{"file_id":"11559","date_created":"2022-07-12T10:04:55Z","success":1,"date_updated":"2022-07-12T10:04:55Z","access_level":"open_access","content_type":"application/pdf","checksum":"16e7c659dee9073c6c8aeb87316ef201","file_name":"2022_ArnoldMathematicalJournal_Clark.pdf","relation":"main_file","creator":"kschuh","file_size":2509915}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","volume":8,"article_processing_charge":"No","citation":{"chicago":"Clark, Trevor, Kostiantyn Drach, Oleg Kozlovski, and Sebastian Van Strien. “The Dynamics of Complex Box Mappings.” <i>Arnold Mathematical Journal</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s40598-022-00200-7\">https://doi.org/10.1007/s40598-022-00200-7</a>.","mla":"Clark, Trevor, et al. “The Dynamics of Complex Box Mappings.” <i>Arnold Mathematical Journal</i>, vol. 8, no. 2, Springer Nature, 2022, pp. 319–410, doi:<a href=\"https://doi.org/10.1007/s40598-022-00200-7\">10.1007/s40598-022-00200-7</a>.","ieee":"T. Clark, K. Drach, O. Kozlovski, and S. V. Strien, “The dynamics of complex box mappings,” <i>Arnold Mathematical Journal</i>, vol. 8, no. 2. Springer Nature, pp. 319–410, 2022.","apa":"Clark, T., Drach, K., Kozlovski, O., &#38; Strien, S. V. (2022). The dynamics of complex box mappings. <i>Arnold Mathematical Journal</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40598-022-00200-7\">https://doi.org/10.1007/s40598-022-00200-7</a>","ama":"Clark T, Drach K, Kozlovski O, Strien SV. The dynamics of complex box mappings. <i>Arnold Mathematical Journal</i>. 2022;8(2):319-410. doi:<a href=\"https://doi.org/10.1007/s40598-022-00200-7\">10.1007/s40598-022-00200-7</a>","short":"T. Clark, K. Drach, O. Kozlovski, S.V. Strien, Arnold Mathematical Journal 8 (2022) 319–410.","ista":"Clark T, Drach K, Kozlovski O, Strien SV. 2022. The dynamics of complex box mappings. Arnold Mathematical Journal. 8(2), 319–410."},"day":"01","ddc":["500"],"month":"06","file_date_updated":"2022-07-12T10:04:55Z","oa_version":"None"},{"acknowledgement":"Zhores supercomputer of Skolkovo Institute of Science and Technology [68] has been used in the present research. S.A.M. was supported by Moscow Center for Fundamental and Applied Mathematics (the agreement with the Ministry of Education and Science of the Russian Federation No. 075-15-2019-1624). A.I.O. acknowledges RFBR project No. 20-31-90022. N.V.B. acknowledges the support of the Analytical Center (subsidy agreement 000000D730321P5Q0002, Grant No. 70-2021-00145 02.11.2021).","status":"public","publication_status":"published","publication_identifier":{"issn":["0021-9991"]},"abstract":[{"lang":"eng","text":"We revisit two basic Direct Simulation Monte Carlo Methods to model aggregation kinetics and extend them for aggregation processes with collisional fragmentation (shattering). We test the performance and accuracy of the extended methods and compare their performance with efficient deterministic finite-difference method applied to the same model. We validate the stochastic methods on the test problems and apply them to verify the existence of oscillating regimes in the aggregation-fragmentation kinetics recently detected in deterministic simulations. We confirm the emergence of steady oscillations of densities in such systems and prove the stability of the\r\noscillations with respect to fluctuations and noise."}],"doi":"10.1016/j.jcp.2022.111439","author":[{"full_name":"Kalinov, Aleksei","last_name":"Kalinov","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","first_name":"Aleksei","orcid":"0000-0003-2189-3904"},{"full_name":"Osinskiy, A.I.","last_name":"Osinskiy","first_name":"A.I."},{"full_name":"Matveev, S.A.","last_name":"Matveev","first_name":"S.A."},{"first_name":"W.","full_name":"Otieno, W.","last_name":"Otieno"},{"first_name":"N.V.","full_name":"Brilliantov, N.V.","last_name":"Brilliantov"}],"title":"Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics","_id":"11556","article_processing_charge":"No","volume":467,"arxiv":1,"oa_version":"Preprint","day":"15","citation":{"chicago":"Kalinov, Aleksei, A.I. Osinskiy, S.A. Matveev, W. Otieno, and N.V. Brilliantov. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” <i>Journal of Computational Physics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>.","mla":"Kalinov, Aleksei, et al. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” <i>Journal of Computational Physics</i>, vol. 467, 111439, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>.","short":"A. Kalinov, A.I. Osinskiy, S.A. Matveev, W. Otieno, N.V. Brilliantov, Journal of Computational Physics 467 (2022).","ama":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. 2022;467. doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>","ista":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. 2022. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. Journal of Computational Physics. 467, 111439.","apa":"Kalinov, A., Osinskiy, A. I., Matveev, S. A., Otieno, W., &#38; Brilliantov, N. V. (2022). Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>","ieee":"A. Kalinov, A. I. Osinskiy, S. A. Matveev, W. Otieno, and N. V. Brilliantov, “Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics,” <i>Journal of Computational Physics</i>, vol. 467. Elsevier, 2022."},"month":"10","ddc":["518"],"article_type":"original","article_number":"111439","publication":"Journal of Computational Physics","date_updated":"2023-08-03T11:55:06Z","year":"2022","keyword":["Computer Science Applications","Physics and Astronomy (miscellaneous)","Applied Mathematics","Computational Mathematics","Modeling and Simulation","Numerical Analysis"],"oa":1,"isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2103.09481"}],"intvolume":"       467","publisher":"Elsevier","external_id":{"isi":["000917225500013"],"arxiv":["2103.09481"]},"date_published":"2022-10-15T00:00:00Z","date_created":"2022-07-11T12:19:59Z","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"publisher":"BioMed Central","intvolume":"        23","external_id":{"isi":["000821915500002"]},"date_published":"2022-07-07T00:00:00Z","date_created":"2022-07-17T22:01:53Z","scopus_import":"1","department":[{"_id":"FyKo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"149","article_type":"original","publication":"Genome Biology","date_updated":"2023-08-03T12:04:18Z","year":"2022","oa":1,"has_accepted_license":"1","volume":23,"article_processing_charge":"No","file":[{"content_type":"application/pdf","checksum":"2c30ef84151d257a6b835b4e069b70ac","access_level":"open_access","date_updated":"2022-07-18T08:15:24Z","success":1,"relation":"main_file","creator":"dernst","file_size":3146207,"file_name":"2022_GenomeBiology_Zhang.pdf","date_created":"2022-07-18T08:15:24Z","file_id":"11597"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","citation":{"mla":"Zhang, Runxuan, et al. “A High-Resolution Single-Molecule Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.” <i>Genome Biology</i>, vol. 23, 149, BioMed Central, 2022, doi:<a href=\"https://doi.org/10.1186/s13059-022-02711-0\">10.1186/s13059-022-02711-0</a>.","chicago":"Zhang, Runxuan, Richard Kuo, Max Coulter, Cristiane P.G. Calixto, Juan Carlos Entizne, Wenbin Guo, Yamile Marquez, et al. “A High-Resolution Single-Molecule Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.” <i>Genome Biology</i>. BioMed Central, 2022. <a href=\"https://doi.org/10.1186/s13059-022-02711-0\">https://doi.org/10.1186/s13059-022-02711-0</a>.","apa":"Zhang, R., Kuo, R., Coulter, M., Calixto, C. P. G., Entizne, J. C., Guo, W., … Brown, J. W. S. (2022). A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-022-02711-0\">https://doi.org/10.1186/s13059-022-02711-0</a>","ieee":"R. Zhang <i>et al.</i>, “A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis,” <i>Genome Biology</i>, vol. 23. BioMed Central, 2022.","short":"R. Zhang, R. Kuo, M. Coulter, C.P.G. Calixto, J.C. Entizne, W. Guo, Y. Marquez, L. Milne, S. Riegler, A. Matsui, M. Tanaka, S. Harvey, Y. Gao, T. Wießner-Kroh, A. Paniagua, M. Crespi, K. Denby, A.B. Hur, E. Huq, M. Jantsch, A. Jarmolowski, T. Koester, S. Laubinger, Q.Q. Li, L. Gu, M. Seki, D. Staiger, R. Sunkar, Z. Szweykowska-Kulinska, S.L. Tu, A. Wachter, R. Waugh, L. Xiong, X.N. Zhang, A. Conesa, A.S.N. Reddy, A. Barta, M. Kalyna, J.W.S. Brown, Genome Biology 23 (2022).","ama":"Zhang R, Kuo R, Coulter M, et al. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. <i>Genome Biology</i>. 2022;23. doi:<a href=\"https://doi.org/10.1186/s13059-022-02711-0\">10.1186/s13059-022-02711-0</a>","ista":"Zhang R, Kuo R, Coulter M, Calixto CPG, Entizne JC, Guo W, Marquez Y, Milne L, Riegler S, Matsui A, Tanaka M, Harvey S, Gao Y, Wießner-Kroh T, Paniagua A, Crespi M, Denby K, Hur AB, Huq E, Jantsch M, Jarmolowski A, Koester T, Laubinger S, Li QQ, Gu L, Seki M, Staiger D, Sunkar R, Szweykowska-Kulinska Z, Tu SL, Wachter A, Waugh R, Xiong L, Zhang XN, Conesa A, Reddy ASN, Barta A, Kalyna M, Brown JWS. 2022. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biology. 23, 149."},"day":"07","file_date_updated":"2022-07-18T08:15:24Z","ddc":["570"],"month":"07","publication_status":"published","acknowledgement":"This work was jointly supported by funding from the Biotechnology and Biological Sciences Research Council (BBSRC) BB/P009751/1 to JB; BB/R014582/1 to RW and RZ; BB/S020160/1 to RZ; BB/S004610/1 (16 ERA-CAPS BARN) to RW; the Scottish Government Rural and Environment Science and Analytical Services division (RESAS) [to RZ, RW, and JB]; the\r\nNational Science Foundation (MCB-2014408) and the National Institute of Health (NIH) (GM-114297) to E.H.; S. H. was supported by funding to K.D. from the University of York; the Austrian Science Fund (FWF) SFB F43 to AB and MJ and [P26333] to MK; The French Agence Nationale de la Recherche grant ANR-16-CE12-0032 to MC; the Japan Science and\r\nTechnology Agency (JST), the Core Research for Evolutionary Science and Technology (CREST; Grant Number JPMJCR13B4) to M.S.; the National Science Foundation (Grant No. DBI1949036 to A.b.H and A.S.N.R, and Grant No. MCB 2014542 to E.H. and A.S.N.R.); and the DOE Office of Science, Office of Biological and Environmental Research (Grant\r\nNo. DE-SC0010733) to A.S.N.R and A.b.H.; the Deutsche Forschungsgemeinschaft (DFG) STA653/14-1 and STA653/15-1 to DS; the National Science Foundation grant (IOS-154173) to Q.Q.L.; the German Research Foundation (DFG) WA2167/8-1 to AW and SFB1101/C03 to AW and TWK; the Research Grants Council (RGC) of Hong Kong (GRF 12103020) to LX. NSF grant IOS-1849708 and NSF EPSCoR grant 1826836 to RS; the Academia Sinica to S.-L. T.","status":"public","publication_identifier":{"eissn":["1474-760X"]},"abstract":[{"text":"Background: Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis.\r\nResults: We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts—twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage.\r\nConclusions: AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species.","lang":"eng"}],"doi":"10.1186/s13059-022-02711-0","title":"A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis","author":[{"first_name":"Runxuan","full_name":"Zhang, Runxuan","last_name":"Zhang"},{"first_name":"Richard","last_name":"Kuo","full_name":"Kuo, Richard"},{"first_name":"Max","full_name":"Coulter, Max","last_name":"Coulter"},{"last_name":"Calixto","full_name":"Calixto, Cristiane P.G.","first_name":"Cristiane P.G."},{"first_name":"Juan Carlos","full_name":"Entizne, Juan Carlos","last_name":"Entizne"},{"full_name":"Guo, Wenbin","last_name":"Guo","first_name":"Wenbin"},{"first_name":"Yamile","full_name":"Marquez, Yamile","last_name":"Marquez"},{"first_name":"Linda","last_name":"Milne","full_name":"Milne, Linda"},{"orcid":"0000-0003-3413-1343","last_name":"Riegler","full_name":"Riegler, Stefan","first_name":"Stefan","id":"FF6018E0-D806-11E9-8E43-0B14E6697425"},{"first_name":"Akihiro","last_name":"Matsui","full_name":"Matsui, Akihiro"},{"first_name":"Maho","last_name":"Tanaka","full_name":"Tanaka, Maho"},{"full_name":"Harvey, Sarah","last_name":"Harvey","first_name":"Sarah"},{"full_name":"Gao, Yubang","last_name":"Gao","first_name":"Yubang"},{"first_name":"Theresa","full_name":"Wießner-Kroh, Theresa","last_name":"Wießner-Kroh"},{"first_name":"Alejandro","last_name":"Paniagua","full_name":"Paniagua, Alejandro"},{"first_name":"Martin","last_name":"Crespi","full_name":"Crespi, Martin"},{"first_name":"Katherine","full_name":"Denby, Katherine","last_name":"Denby"},{"full_name":"Hur, Asa Ben","last_name":"Hur","first_name":"Asa Ben"},{"first_name":"Enamul","full_name":"Huq, Enamul","last_name":"Huq"},{"first_name":"Michael","last_name":"Jantsch","full_name":"Jantsch, Michael"},{"full_name":"Jarmolowski, Artur","last_name":"Jarmolowski","first_name":"Artur"},{"first_name":"Tino","last_name":"Koester","full_name":"Koester, Tino"},{"first_name":"Sascha","last_name":"Laubinger","full_name":"Laubinger, Sascha"},{"first_name":"Qingshun Quinn","last_name":"Li","full_name":"Li, Qingshun Quinn"},{"last_name":"Gu","full_name":"Gu, Lianfeng","first_name":"Lianfeng"},{"first_name":"Motoaki","last_name":"Seki","full_name":"Seki, Motoaki"},{"first_name":"Dorothee","full_name":"Staiger, Dorothee","last_name":"Staiger"},{"full_name":"Sunkar, Ramanjulu","last_name":"Sunkar","first_name":"Ramanjulu"},{"last_name":"Szweykowska-Kulinska","full_name":"Szweykowska-Kulinska, Zofia","first_name":"Zofia"},{"last_name":"Tu","full_name":"Tu, Shih Long","first_name":"Shih Long"},{"full_name":"Wachter, Andreas","last_name":"Wachter","first_name":"Andreas"},{"first_name":"Robbie","last_name":"Waugh","full_name":"Waugh, Robbie"},{"first_name":"Liming","last_name":"Xiong","full_name":"Xiong, Liming"},{"full_name":"Zhang, Xiao Ning","last_name":"Zhang","first_name":"Xiao Ning"},{"first_name":"Ana","last_name":"Conesa","full_name":"Conesa, Ana"},{"full_name":"Reddy, Anireddy S.N.","last_name":"Reddy","first_name":"Anireddy S.N."},{"first_name":"Andrea","last_name":"Barta","full_name":"Barta, Andrea"},{"first_name":"Maria","full_name":"Kalyna, Maria","last_name":"Kalyna"},{"last_name":"Brown","full_name":"Brown, John W.S.","first_name":"John W.S."}],"_id":"11587"},{"title":"Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo","author":[{"first_name":"Leo","last_name":"Nicolai","full_name":"Nicolai, Leo"},{"first_name":"Rainer","full_name":"Kaiser, Rainer","last_name":"Kaiser"},{"first_name":"Raphael","full_name":"Escaig, Raphael","last_name":"Escaig"},{"full_name":"Hoffknecht, Marie Louise","last_name":"Hoffknecht","first_name":"Marie Louise"},{"last_name":"Anjum","full_name":"Anjum, Afra","first_name":"Afra"},{"full_name":"Leunig, Alexander","last_name":"Leunig","first_name":"Alexander"},{"last_name":"Pircher","full_name":"Pircher, Joachim","first_name":"Joachim"},{"first_name":"Andreas","last_name":"Ehrlich","full_name":"Ehrlich, Andreas"},{"first_name":"Michael","full_name":"Lorenz, Michael","last_name":"Lorenz"},{"first_name":"Hellen","last_name":"Ishikawa-Ankerhold","full_name":"Ishikawa-Ankerhold, Hellen"},{"full_name":"Aird, William C.","last_name":"Aird","first_name":"William C."},{"full_name":"Massberg, Steffen","last_name":"Massberg","first_name":"Steffen"},{"orcid":"0000-0001-6120-3723","last_name":"Gärtner","full_name":"Gärtner, Florian R","first_name":"Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87"}],"_id":"11588","abstract":[{"lang":"eng","text":"Visualizing cell behavior and effector function on a single cell level has been crucial for understanding key aspects of mammalian biology. Due to their small size, large number and rapid recruitment into thrombi, there is a lack of data on fate and behavior of individual platelets in thrombosis and hemostasis. Here we report the use of platelet lineage restricted multi-color reporter mouse strains to delineate platelet function on a single cell level. We show that genetic labeling allows for single platelet and megakaryocyte (MK) tracking and morphological analysis in vivo and in vitro, while not affecting lineage functions. Using Cre-driven Confetti expression, we provide insights into temporal gene expression patterns as well as spatial clustering of MK in the bone marrow. In the vasculature, shape analysis of activated platelets recruited to thrombi identifies ubiquitous filopodia formation with no evidence of lamellipodia formation. Single cell tracking in complex thrombi reveals prominent myosin-dependent motility of platelets and highlights thrombus formation as a highly dynamic process amenable to modification and intervention of the acto-myosin cytoskeleton. Platelet function assays combining flow cytrometry, as well as in vivo, ex vivo and in vitro imaging show unaltered platelet functions of multicolor reporter mice compared to wild-type controls. In conclusion, platelet lineage multicolor reporter mice prove useful in furthering our understanding of platelet and MK biology on a single cell level."}],"issue":"7","doi":"10.3324/haematol.2021.278896","publication_identifier":{"eissn":["1592-8721"],"issn":["0390-6078"]},"project":[{"_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020"}],"status":"public","publication_status":"published","acknowledgement":"This study was supported by the Deutsche Forschungsgemeinschaft (DFG) SFB 914 ( to SM [B02 and Z01]), the DFG SFB 1123 (to SM [B06]), the DFG FOR 2033 (to SM), the German\r\nCenter for Cardiovascular Research (DZHK) (Clinician Scientist Programme), MHA 1.4VD (to SM), Postdoc Start-up Grant, 81X3600213 (to FG), 81X3600222 (to LN), the FP7 program\r\n(project 260309, PRESTIGE [to SM]). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 83344, ERC-2018-ADG “IMMUNOTHROMBOSIS” [to SM] and the Marie Skłodowska Curie Individual Fellowship (EU project 747687, LamelliActin [to FG]). ","ec_funded":1,"citation":{"short":"L. Nicolai, R. Kaiser, R. Escaig, M.L. Hoffknecht, A. Anjum, A. Leunig, J. Pircher, A. Ehrlich, M. Lorenz, H. Ishikawa-Ankerhold, W.C. Aird, S. Massberg, F.R. Gärtner, Haematologica 107 (2022) 1669–1680.","ama":"Nicolai L, Kaiser R, Escaig R, et al. Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo. <i>Haematologica</i>. 2022;107(7):1669-1680. doi:<a href=\"https://doi.org/10.3324/haematol.2021.278896\">10.3324/haematol.2021.278896</a>","ista":"Nicolai L, Kaiser R, Escaig R, Hoffknecht ML, Anjum A, Leunig A, Pircher J, Ehrlich A, Lorenz M, Ishikawa-Ankerhold H, Aird WC, Massberg S, Gärtner FR. 2022. Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo. Haematologica. 107(7), 1669–1680.","apa":"Nicolai, L., Kaiser, R., Escaig, R., Hoffknecht, M. L., Anjum, A., Leunig, A., … Gärtner, F. R. (2022). Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo. <i>Haematologica</i>. Ferrata Storti Foundation. <a href=\"https://doi.org/10.3324/haematol.2021.278896\">https://doi.org/10.3324/haematol.2021.278896</a>","ieee":"L. Nicolai <i>et al.</i>, “Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo,” <i>Haematologica</i>, vol. 107, no. 7. Ferrata Storti Foundation, pp. 1669–1680, 2022.","mla":"Nicolai, Leo, et al. “Single Platelet and Megakaryocyte Morpho-Dynamics Uncovered by Multicolor Reporter Mouse Strains in Vitro and in Vivo.” <i>Haematologica</i>, vol. 107, no. 7, Ferrata Storti Foundation, 2022, pp. 1669–80, doi:<a href=\"https://doi.org/10.3324/haematol.2021.278896\">10.3324/haematol.2021.278896</a>.","chicago":"Nicolai, Leo, Rainer Kaiser, Raphael Escaig, Marie Louise Hoffknecht, Afra Anjum, Alexander Leunig, Joachim Pircher, et al. “Single Platelet and Megakaryocyte Morpho-Dynamics Uncovered by Multicolor Reporter Mouse Strains in Vitro and in Vivo.” <i>Haematologica</i>. Ferrata Storti Foundation, 2022. <a href=\"https://doi.org/10.3324/haematol.2021.278896\">https://doi.org/10.3324/haematol.2021.278896</a>."},"day":"01","file_date_updated":"2022-07-18T07:51:55Z","month":"07","ddc":["570"],"license":"https://creativecommons.org/licenses/by-nc/4.0/","oa_version":"Published Version","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"file":[{"file_name":"2022_Haematologica_Nicolai.pdf","creator":"dernst","relation":"main_file","file_size":1722094,"success":1,"date_updated":"2022-07-18T07:51:55Z","access_level":"open_access","checksum":"9b47830945f3c30428fe9cfee2dc4a8a","content_type":"application/pdf","file_id":"11595","date_created":"2022-07-18T07:51:55Z"}],"has_accepted_license":"1","article_processing_charge":"No","volume":107,"oa":1,"year":"2022","publication":"Haematologica","date_updated":"2023-08-03T12:01:01Z","page":"1669-1680","article_type":"original","department":[{"_id":"MiSi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000823746100018"]},"date_published":"2022-07-01T00:00:00Z","date_created":"2022-07-17T22:01:54Z","scopus_import":"1","publisher":"Ferrata Storti Foundation","intvolume":"       107","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1"},{"doi":"10.3389/fpls.2022.862398","abstract":[{"lang":"eng","text":"Calcium-dependent protein kinases (CPK) are key components of a wide array of signaling pathways, translating stress and nutrient signaling into the modulation of cellular processes such as ion transport and transcription. However, not much is known about CPKs in endomembrane trafficking. Here, we screened for CPKs that impact on root growth and gravitropism, by overexpressing constitutively active forms of CPKs under the control of an inducible promoter in Arabidopsis thaliana. We found that inducible overexpression of an constitutive active CPK30 (CA-CPK30) resulted in a loss of root gravitropism and ectopic auxin accumulation in the root tip. Immunolocalization revealed that CA-CPK30 roots have reduced PIN protein levels, PIN1 polarity defects and impaired Brefeldin A (BFA)-sensitive trafficking. Moreover, FM4-64 uptake was reduced, indicative of a defect in endocytosis. The effects on BFA-sensitive trafficking were not specific to PINs, as BFA could not induce aggregation of ARF1- and CHC-labeled endosomes in CA-CPK30. Interestingly, the interference with BFA-body formation, could be reverted by increasing the extracellular pH, indicating a pH-dependence of this CA-CPK30 effect. Altogether, our data reveal an important role for CPK30 in root growth regulation and endomembrane trafficking in Arabidopsis thaliana."}],"_id":"11589","author":[{"full_name":"Wang, Ren","last_name":"Wang","first_name":"Ren"},{"first_name":"Ellie","last_name":"Himschoot","full_name":"Himschoot, Ellie"},{"last_name":"Chen","full_name":"Chen, Jian","first_name":"Jian"},{"full_name":"Boudsocq, Marie","last_name":"Boudsocq","first_name":"Marie"},{"first_name":"Danny","full_name":"Geelen, Danny","last_name":"Geelen"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"}],"title":"Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana","publication_status":"published","status":"public","acknowledgement":"RW and JC predoctoral fellows that were supported by the Chinese Science Counsil. The IPS2 benefits from the support of the LabEx Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS).\r\nWe thank Jen Sheen for establishing and generously sharing the CKP family clone sets, and for providing useful feedback on the manuscript.","publication_identifier":{"eissn":["1664-462X"]},"oa_version":"Published Version","pmid":1,"month":"06","ddc":["580"],"file_date_updated":"2022-07-18T08:05:15Z","day":"16","citation":{"chicago":"Wang, Ren, Ellie Himschoot, Jian Chen, Marie Boudsocq, Danny Geelen, Jiří Friml, Tom Beeckman, and Steffen Vanneste. “Constitutive Active CPK30 Interferes with Root Growth and Endomembrane Trafficking in Arabidopsis Thaliana.” <i>Frontiers in Plant Science</i>. Frontiers, 2022. <a href=\"https://doi.org/10.3389/fpls.2022.862398\">https://doi.org/10.3389/fpls.2022.862398</a>.","mla":"Wang, Ren, et al. “Constitutive Active CPK30 Interferes with Root Growth and Endomembrane Trafficking in Arabidopsis Thaliana.” <i>Frontiers in Plant Science</i>, vol. 13, 862398, Frontiers, 2022, doi:<a href=\"https://doi.org/10.3389/fpls.2022.862398\">10.3389/fpls.2022.862398</a>.","ieee":"R. Wang <i>et al.</i>, “Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana,” <i>Frontiers in Plant Science</i>, vol. 13. Frontiers, 2022.","apa":"Wang, R., Himschoot, E., Chen, J., Boudsocq, M., Geelen, D., Friml, J., … Vanneste, S. (2022). Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. <i>Frontiers in Plant Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fpls.2022.862398\">https://doi.org/10.3389/fpls.2022.862398</a>","ista":"Wang R, Himschoot E, Chen J, Boudsocq M, Geelen D, Friml J, Beeckman T, Vanneste S. 2022. Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. Frontiers in Plant Science. 13, 862398.","short":"R. Wang, E. Himschoot, J. Chen, M. Boudsocq, D. Geelen, J. Friml, T. Beeckman, S. Vanneste, Frontiers in Plant Science 13 (2022).","ama":"Wang R, Himschoot E, Chen J, et al. Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. <i>Frontiers in Plant Science</i>. 2022;13. doi:<a href=\"https://doi.org/10.3389/fpls.2022.862398\">10.3389/fpls.2022.862398</a>"},"volume":13,"article_processing_charge":"No","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"2022_FrontiersPlantScience_Wang.pdf","creator":"dernst","relation":"main_file","file_size":5040638,"success":1,"date_updated":"2022-07-18T08:05:15Z","access_level":"open_access","checksum":"95313515637c0f84de591d204375d764","content_type":"application/pdf","file_id":"11596","date_created":"2022-07-18T08:05:15Z"}],"year":"2022","oa":1,"article_type":"original","article_number":"862398","related_material":{"link":[{"url":"https://doi.org/10.3389/fpls.2022.1100792","relation":"erratum"}]},"date_updated":"2023-08-03T12:01:47Z","publication":"Frontiers in Plant Science","scopus_import":"1","date_created":"2022-07-17T22:01:54Z","date_published":"2022-06-16T00:00:00Z","external_id":{"pmid":["35783951"],"isi":["000819250500001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"intvolume":"        13","publisher":"Frontiers"},{"date_published":"2022-06-01T00:00:00Z","external_id":{"isi":["000818530000001"]},"date_created":"2022-07-17T22:01:55Z","scopus_import":"1","department":[{"_id":"MiLe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"IOP Publishing","intvolume":"        24","year":"2022","oa":1,"article_number":"063036","article_type":"original","publication":"New Journal of Physics","date_updated":"2023-08-03T11:57:41Z","oa_version":"Published Version","citation":{"apa":"Brauneis, F., Backert, T. G., Mistakidis, S. I., Lemeshko, M., Hammer, H. W., &#38; Volosniev, A. (2022). Artificial atoms from cold bosons in one dimension. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ac78d8\">https://doi.org/10.1088/1367-2630/ac78d8</a>","ieee":"F. Brauneis, T. G. Backert, S. I. Mistakidis, M. Lemeshko, H. W. Hammer, and A. Volosniev, “Artificial atoms from cold bosons in one dimension,” <i>New Journal of Physics</i>, vol. 24, no. 6. IOP Publishing, 2022.","short":"F. Brauneis, T.G. Backert, S.I. Mistakidis, M. Lemeshko, H.W. Hammer, A. Volosniev, New Journal of Physics 24 (2022).","ama":"Brauneis F, Backert TG, Mistakidis SI, Lemeshko M, Hammer HW, Volosniev A. Artificial atoms from cold bosons in one dimension. <i>New Journal of Physics</i>. 2022;24(6). doi:<a href=\"https://doi.org/10.1088/1367-2630/ac78d8\">10.1088/1367-2630/ac78d8</a>","ista":"Brauneis F, Backert TG, Mistakidis SI, Lemeshko M, Hammer HW, Volosniev A. 2022. Artificial atoms from cold bosons in one dimension. New Journal of Physics. 24(6), 063036.","mla":"Brauneis, Fabian, et al. “Artificial Atoms from Cold Bosons in One Dimension.” <i>New Journal of Physics</i>, vol. 24, no. 6, 063036, IOP Publishing, 2022, doi:<a href=\"https://doi.org/10.1088/1367-2630/ac78d8\">10.1088/1367-2630/ac78d8</a>.","chicago":"Brauneis, Fabian, Timothy G. Backert, Simeon I. Mistakidis, Mikhail Lemeshko, Hans Werner Hammer, and Artem Volosniev. “Artificial Atoms from Cold Bosons in One Dimension.” <i>New Journal of Physics</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.1088/1367-2630/ac78d8\">https://doi.org/10.1088/1367-2630/ac78d8</a>."},"day":"01","ddc":["530"],"file_date_updated":"2022-07-18T06:33:13Z","month":"06","has_accepted_license":"1","volume":24,"article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"11594","date_created":"2022-07-18T06:33:13Z","file_name":"2022_NewJournalPhysics_Brauneis.pdf","file_size":3415721,"relation":"main_file","creator":"dernst","success":1,"date_updated":"2022-07-18T06:33:13Z","access_level":"open_access","checksum":"dc67b60f2e50e9ef2bd820ca0d7333d2","content_type":"application/pdf"}],"abstract":[{"lang":"eng","text":"We investigate the ground-state properties of weakly repulsive one-dimensional bosons in the presence of an attractive zero-range impurity potential. First, we derive mean-field solutions to the problem on a finite ring for the two asymptotic cases: (i) all bosons are bound to the impurity and (ii) all bosons are in a scattering state. Moreover, we derive the critical line that separates these regimes in the parameter space. In the thermodynamic limit, this critical line determines the maximum number of bosons that can be bound by the impurity potential, forming an artificial atom. Second, we validate the mean-field results using the flow equation approach and the multi-layer multi-configuration time-dependent Hartree method for atomic mixtures. While beyond-mean-field effects destroy long-range order in the Bose gas, the critical boson number is unaffected. Our findings are important for understanding such artificial atoms in low-density Bose gases with static and mobile impurities."}],"issue":"6","doi":"10.1088/1367-2630/ac78d8","title":"Artificial atoms from cold bosons in one dimension","author":[{"first_name":"Fabian","full_name":"Brauneis, Fabian","last_name":"Brauneis"},{"last_name":"Backert","full_name":"Backert, Timothy G.","first_name":"Timothy G."},{"last_name":"Mistakidis","full_name":"Mistakidis, Simeon I.","first_name":"Simeon I."},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","orcid":"0000-0002-6990-7802"},{"last_name":"Hammer","full_name":"Hammer, Hans Werner","first_name":"Hans Werner"},{"orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","full_name":"Volosniev, Artem","last_name":"Volosniev"}],"_id":"11590","publication_status":"published","status":"public","acknowledgement":"This work has received funding from the DFG Project No. 413495248 [VO 2437/1-1] (FB, H-WH, AGV) and European Union's Horizon 2020 research and innovation programme under the Marie Skĺodowska-Curie Grant Agreement No. 754411 (AGV). ML acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). SIM acknowledges support from the NSF through a grant for ITAMP at Harvard University.","ec_funded":1,"publication_identifier":{"issn":["1367-2630"]},"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}]},{"article_number":"062454","article_type":"original","date_updated":"2023-08-03T11:58:16Z","publication":"Physical Review A","year":"2022","oa":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"publisher":"American Physical Society","intvolume":"       105","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2204.02993"}],"date_created":"2022-07-17T22:01:55Z","scopus_import":"1","date_published":"2022-06-29T00:00:00Z","external_id":{"isi":["000824330200003"],"arxiv":["2204.02993"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JoFi"}],"ec_funded":1,"acknowledgement":"We thank T. Mavrogordatos and D. Zhu for initial contribution on the presented topic and K. Fedorov for stimulating discussions on entangled microwave beams. This work was supported by the Austrian Science Fund (FWF) through Grant No. P32299 (PHONED) and the European Union’s Horizon 2020 research and innovation programme under Grant Agreement No. 899354 (SuperQuLAN). Most of the computational results presented were obtained using the CLIP cluster [65].","publication_status":"published","status":"public","project":[{"call_identifier":"H2020","name":"Quantum Local Area Networks with Superconducting Qubits","grant_number":"899354","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A"}],"publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"doi":"10.1103/PhysRevA.105.062454","abstract":[{"lang":"eng","text":"We investigate the deterministic generation and distribution of entanglement in large quantum networks by driving distant qubits with the output fields of a nondegenerate parametric amplifier. In this setting, the amplifier produces a continuous Gaussian two-mode squeezed state, which acts as a quantum-correlated reservoir for the qubits and relaxes them into a highly entangled steady state. Here we are interested in the maximal amount of entanglement and the optimal entanglement generation rates that can be achieved with this scheme under realistic conditions taking, in particular, the finite amplifier bandwidth, waveguide losses, and propagation delays into account. By combining exact numerical simulations of the full network with approximate analytic results, we predict the optimal working point for the amplifier and the corresponding qubit-qubit entanglement under various conditions. Our findings show that this passive conversion of Gaussian into discrete-variable entanglement offers a robust and experimentally very attractive approach for operating large optical, microwave, or hybrid quantum networks, for which efficient parametric amplifiers are currently developed."}],"issue":"6","_id":"11591","title":"Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams","author":[{"first_name":"J.","last_name":"Agustí","full_name":"Agustí, J."},{"first_name":"Y.","last_name":"Minoguchi","full_name":"Minoguchi, Y."},{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"},{"full_name":"Rabl, P.","last_name":"Rabl","first_name":"P."}],"volume":105,"article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","month":"06","citation":{"chicago":"Agustí, J., Y. Minoguchi, Johannes M Fink, and P. Rabl. “Long-Distance Distribution of Qubit-Qubit Entanglement Using Gaussian-Correlated Photonic Beams.” <i>Physical Review A</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevA.105.062454\">https://doi.org/10.1103/PhysRevA.105.062454</a>.","mla":"Agustí, J., et al. “Long-Distance Distribution of Qubit-Qubit Entanglement Using Gaussian-Correlated Photonic Beams.” <i>Physical Review A</i>, vol. 105, no. 6, 062454, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevA.105.062454\">10.1103/PhysRevA.105.062454</a>.","apa":"Agustí, J., Minoguchi, Y., Fink, J. M., &#38; Rabl, P. (2022). Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.105.062454\">https://doi.org/10.1103/PhysRevA.105.062454</a>","ieee":"J. Agustí, Y. Minoguchi, J. M. Fink, and P. Rabl, “Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams,” <i>Physical Review A</i>, vol. 105, no. 6. American Physical Society, 2022.","short":"J. Agustí, Y. Minoguchi, J.M. Fink, P. Rabl, Physical Review A 105 (2022).","ista":"Agustí J, Minoguchi Y, Fink JM, Rabl P. 2022. Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams. Physical Review A. 105(6), 062454.","ama":"Agustí J, Minoguchi Y, Fink JM, Rabl P. Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams. <i>Physical Review A</i>. 2022;105(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.105.062454\">10.1103/PhysRevA.105.062454</a>"},"day":"29"},{"date_published":"2022-06-30T00:00:00Z","external_id":{"isi":["000829758500010"],"arxiv":["2206.03924"]},"date_created":"2022-07-17T22:01:55Z","scopus_import":"1","department":[{"_id":"MiLe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","publisher":"American Physical Society","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2206.03924"}],"intvolume":"       105","year":"2022","oa":1,"article_number":"063329","article_type":"original","publication":"Physical Review A","date_updated":"2023-08-03T12:00:11Z","oa_version":"Preprint","citation":{"ieee":"G. Bighin, A. Cappellaro, and L. Salasnich, “Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations,” <i>Physical Review A</i>, vol. 105, no. 6. American Physical Society, 2022.","apa":"Bighin, G., Cappellaro, A., &#38; Salasnich, L. (2022). Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.105.063329\">https://doi.org/10.1103/PhysRevA.105.063329</a>","short":"G. Bighin, A. Cappellaro, L. Salasnich, Physical Review A 105 (2022).","ista":"Bighin G, Cappellaro A, Salasnich L. 2022. Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations. Physical Review A. 105(6), 063329.","ama":"Bighin G, Cappellaro A, Salasnich L. Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations. <i>Physical Review A</i>. 2022;105(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.105.063329\">10.1103/PhysRevA.105.063329</a>","mla":"Bighin, Giacomo, et al. “Unitary Fermi Superfluid near the Critical Temperature: Thermodynamics and Sound Modes from Elementary Excitations.” <i>Physical Review A</i>, vol. 105, no. 6, 063329, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevA.105.063329\">10.1103/PhysRevA.105.063329</a>.","chicago":"Bighin, Giacomo, Alberto Cappellaro, and L. Salasnich. “Unitary Fermi Superfluid near the Critical Temperature: Thermodynamics and Sound Modes from Elementary Excitations.” <i>Physical Review A</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevA.105.063329\">https://doi.org/10.1103/PhysRevA.105.063329</a>."},"day":"30","month":"06","article_processing_charge":"No","volume":105,"arxiv":1,"abstract":[{"text":"We compare recent experimental results [Science 375, 528 (2022)] of the superfluid unitary Fermi gas near the critical temperature with a thermodynamic model based on the elementary excitations of the system. We find good agreement between experimental data and our theory for several quantities such as first sound, second sound, and superfluid fraction. We also show that mode mixing between first and second sound occurs. Finally, we characterize the response amplitude to a density perturbation: Close to the critical temperature both first and second sound can be excited through a density perturbation, whereas at lower temperatures only the first sound mode exhibits a significant response.","lang":"eng"}],"issue":"6","doi":"10.1103/PhysRevA.105.063329","title":"Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations","author":[{"first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","last_name":"Bighin","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777"},{"first_name":"Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","last_name":"Cappellaro","full_name":"Cappellaro, Alberto","orcid":"0000-0001-6110-2359"},{"first_name":"L.","full_name":"Salasnich, L.","last_name":"Salasnich"}],"_id":"11592","status":"public","acknowledgement":"The authors gratefully acknowledge stimulating discussions with T. Enss, and thank an anonymous referee for suggestions and remarks that allowed us to improve the original manuscript. This work is supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy EXC2181/1-390900948 (the Heidelberg STRUCTURES Excellence Cluster).","publication_status":"published","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]}},{"month":"09","day":"01","citation":{"chicago":"Fulek, Radoslav, and Jan Kynčl. “The Z2-Genus of Kuratowski Minors.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00454-022-00412-w\">https://doi.org/10.1007/s00454-022-00412-w</a>.","mla":"Fulek, Radoslav, and Jan Kynčl. “The Z2-Genus of Kuratowski Minors.” <i>Discrete and Computational Geometry</i>, vol. 68, Springer Nature, 2022, pp. 425–47, doi:<a href=\"https://doi.org/10.1007/s00454-022-00412-w\">10.1007/s00454-022-00412-w</a>.","short":"R. Fulek, J. Kynčl, Discrete and Computational Geometry 68 (2022) 425–447.","ama":"Fulek R, Kynčl J. The Z2-Genus of Kuratowski minors. <i>Discrete and Computational Geometry</i>. 2022;68:425-447. doi:<a href=\"https://doi.org/10.1007/s00454-022-00412-w\">10.1007/s00454-022-00412-w</a>","ista":"Fulek R, Kynčl J. 2022. The Z2-Genus of Kuratowski minors. Discrete and Computational Geometry. 68, 425–447.","apa":"Fulek, R., &#38; Kynčl, J. (2022). The Z2-Genus of Kuratowski minors. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-022-00412-w\">https://doi.org/10.1007/s00454-022-00412-w</a>","ieee":"R. Fulek and J. Kynčl, “The Z2-Genus of Kuratowski minors,” <i>Discrete and Computational Geometry</i>, vol. 68. Springer Nature, pp. 425–447, 2022."},"oa_version":"Preprint","arxiv":1,"article_processing_charge":"No","volume":68,"_id":"11593","author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","full_name":"Fulek, Radoslav","last_name":"Fulek","orcid":"0000-0001-8485-1774"},{"first_name":"Jan","last_name":"Kynčl","full_name":"Kynčl, Jan"}],"title":"The Z2-Genus of Kuratowski minors","doi":"10.1007/s00454-022-00412-w","abstract":[{"text":"A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The Z2 -genus of a graph G is the minimum g such that G has an independently even drawing on the orientable surface of genus g. An unpublished result by Robertson and Seymour implies that for every t, every graph of sufficiently large genus contains as a minor a projective t×t grid or one of the following so-called t -Kuratowski graphs: K3,t, or t copies of K5 or K3,3 sharing at most two common vertices. We show that the Z2-genus of graphs in these families is unbounded in t; in fact, equal to their genus. Together, this implies that the genus of a graph is bounded from above by a function of its Z2-genus, solving a problem posed by Schaefer and Štefankovič, and giving an approximate version of the Hanani–Tutte theorem on orientable surfaces. We also obtain an analogous result for Euler genus and Euler Z2-genus of graphs.","lang":"eng"}],"project":[{"name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281"}],"publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"status":"public","acknowledgement":"We thank Zdeněk Dvořák, Xavier Goaoc, and Pavel Paták for helpful discussions. We also thank Bojan Mohar, Paul Seymour, Gelasio Salazar, Jim Geelen, and John Maharry for information about their unpublished results related to Conjecture 3.1. Finally we thank the reviewers for corrections and suggestions for improving the presentation.\r\nSupported by Austrian Science Fund (FWF): M2281-N35. Supported by project 19-04113Y of the Czech Science Foundation (GAČR), by the Czech-French collaboration project EMBEDS II (CZ: 7AMB17FR029, FR: 38087RM), and by Charles University project UNCE/SCI/004.","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"UlWa"}],"scopus_import":"1","date_created":"2022-07-17T22:01:56Z","date_published":"2022-09-01T00:00:00Z","external_id":{"isi":["000825014500001"],"arxiv":["1803.05085"]},"intvolume":"        68","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.05085"}],"publisher":"Springer Nature","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"oa":1,"year":"2022","date_updated":"2023-08-14T12:43:52Z","publication":"Discrete and Computational Geometry","article_type":"original","page":"425-447","related_material":{"record":[{"id":"186","status":"public","relation":"earlier_version"}]}},{"alternative_title":["ISTA Thesis"],"year":"2022","oa":1,"page":"248","related_material":{"record":[{"id":"9287","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7142"},{"status":"public","relation":"part_of_dissertation","id":"7465"},{"status":"public","relation":"part_of_dissertation","id":"8138"},{"id":"6260","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8931"},{"relation":"part_of_dissertation","status":"public","id":"10411"}]},"date_updated":"2024-10-29T10:22:45Z","date_created":"2022-07-20T11:21:53Z","date_published":"2022-07-20T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"language":[{"iso":"eng"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:11626","abstract":[{"text":"Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth.","lang":"eng"}],"_id":"11626","author":[{"full_name":"Gallei, Michelle C","last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","orcid":"0000-0003-1286-7368"}],"supervisor":[{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"last_name":"Shani","full_name":"Shani, Eilon","first_name":"Eilon"}],"title":"Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana","ec_funded":1,"status":"public","publication_status":"published","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"publication_identifier":{"isbn":["978-3-99078-019-0"],"issn":["2663-337X"]},"oa_version":"Published Version","ddc":["575"],"file_date_updated":"2022-07-25T11:48:45Z","month":"07","day":"20","citation":{"chicago":"Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11626\">https://doi.org/10.15479/at:ista:11626</a>.","mla":"Gallei, Michelle C. <i>Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11626\">10.15479/at:ista:11626</a>.","ieee":"M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2022.","apa":"Gallei, M. C. (2022). <i>Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11626\">https://doi.org/10.15479/at:ista:11626</a>","ista":"Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria.","ama":"Gallei MC. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11626\">10.15479/at:ista:11626</a>","short":"M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022."},"article_processing_charge":"No","has_accepted_license":"1","file":[{"file_id":"11645","date_created":"2022-07-25T09:08:47Z","access_level":"open_access","checksum":"bd7ac35403cf5b4b2607287d2a104b3a","content_type":"application/pdf","date_updated":"2022-07-25T09:08:47Z","file_name":"Thesis_Gallei.pdf","file_size":9730864,"creator":"mgallei","relation":"main_file"},{"file_id":"11646","date_created":"2022-07-25T09:09:09Z","file_name":"Thesis_Gallei_source.docx","file_size":19560720,"relation":"source_file","creator":"mgallei","date_updated":"2022-07-25T09:39:58Z","access_level":"closed","checksum":"a9e54fe5471ba25dc13c2150c1b8ccbb","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"date_updated":"2022-07-25T09:39:58Z","description":"This is the print version of the thesis including the full appendix","access_level":"closed","content_type":"application/pdf","checksum":"3994f7f20058941b5bb8a16886b21e71","file_name":"Thesis_Gallei_to_print.pdf","creator":"mgallei","relation":"source_file","file_size":24542837,"file_id":"11647","date_created":"2022-07-25T09:09:32Z"},{"date_created":"2022-07-25T11:48:45Z","file_id":"11650","relation":"main_file","creator":"mgallei","file_size":15435966,"file_name":"Thesis_Gallei_Appendix.pdf","date_updated":"2022-07-25T11:48:45Z","checksum":"f24acd3c0d864f4c6676e8b0d7bfa76b","content_type":"application/pdf","access_level":"open_access"}],"degree_awarded":"PhD"},{"article_type":"original","article_number":"102085","publication":"Finite Fields and their Applications","date_updated":"2023-08-03T12:12:57Z","year":"2022","oa":1,"isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","intvolume":"        83","publisher":"Elsevier","external_id":{"isi":["000835490600001"],"arxiv":["2111.06697"]},"date_published":"2022-10-01T00:00:00Z","scopus_import":"1","date_created":"2022-07-24T22:01:41Z","department":[{"_id":"TiBr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication_status":"published","publication_identifier":{"eissn":["10902465"],"issn":["10715797"]},"issue":"10","abstract":[{"lang":"eng","text":"In [3], Poonen and Slavov recently developed a novel approach to Bertini irreducibility theorems over an arbitrary field, based on random hyperplane slicing. In this paper, we extend their work by proving an analogous bound for the dimension of the exceptional locus in the setting of linear subspaces of higher codimensions."}],"doi":"10.1016/j.ffa.2022.102085","author":[{"id":"c90670c9-0bf0-11ed-86f5-ed522ece2fac","first_name":"Philip","full_name":"Kmentt, Philip","last_name":"Kmentt"},{"full_name":"Shute, Alec L","last_name":"Shute","id":"440EB050-F248-11E8-B48F-1D18A9856A87","first_name":"Alec L","orcid":"0000-0002-1812-2810"}],"title":"The Bertini irreducibility theorem for higher codimensional slices","_id":"11636","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","volume":83,"arxiv":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"12475","date_created":"2023-02-02T07:56:34Z","file_name":"2022_FiniteFields_Kmentt.pdf","relation":"main_file","file_size":247615,"creator":"dernst","success":1,"date_updated":"2023-02-02T07:56:34Z","access_level":"open_access","checksum":"3ca88decb1011180dc6de7e0862153e1","content_type":"application/pdf"}],"oa_version":"Published Version","day":"01","citation":{"ama":"Kmentt P, Shute AL. The Bertini irreducibility theorem for higher codimensional slices. <i>Finite Fields and their Applications</i>. 2022;83(10). doi:<a href=\"https://doi.org/10.1016/j.ffa.2022.102085\">10.1016/j.ffa.2022.102085</a>","short":"P. Kmentt, A.L. Shute, Finite Fields and Their Applications 83 (2022).","ista":"Kmentt P, Shute AL. 2022. The Bertini irreducibility theorem for higher codimensional slices. Finite Fields and their Applications. 83(10), 102085.","apa":"Kmentt, P., &#38; Shute, A. L. (2022). The Bertini irreducibility theorem for higher codimensional slices. <i>Finite Fields and Their Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ffa.2022.102085\">https://doi.org/10.1016/j.ffa.2022.102085</a>","ieee":"P. Kmentt and A. L. Shute, “The Bertini irreducibility theorem for higher codimensional slices,” <i>Finite Fields and their Applications</i>, vol. 83, no. 10. Elsevier, 2022.","chicago":"Kmentt, Philip, and Alec L Shute. “The Bertini Irreducibility Theorem for Higher Codimensional Slices.” <i>Finite Fields and Their Applications</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.ffa.2022.102085\">https://doi.org/10.1016/j.ffa.2022.102085</a>.","mla":"Kmentt, Philip, and Alec L. Shute. “The Bertini Irreducibility Theorem for Higher Codimensional Slices.” <i>Finite Fields and Their Applications</i>, vol. 83, no. 10, 102085, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.ffa.2022.102085\">10.1016/j.ffa.2022.102085</a>."},"file_date_updated":"2023-02-02T07:56:34Z","month":"10","ddc":["510"]},{"external_id":{"isi":["000828679600001"],"pmid":["35727855"]},"date_published":"2022-06-21T00:00:00Z","scopus_import":"1","date_created":"2022-07-24T22:01:42Z","department":[{"_id":"MaDe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        20","publisher":"Public Library of Science","year":"2022","oa":1,"article_type":"original","article_number":"e3001684","publication":"PLoS Biology","date_updated":"2023-08-03T12:11:44Z","oa_version":"Published Version","day":"21","citation":{"apa":"Zhao, L., Fenk, L. A., Nilsson, L., Amin-Wetzel, N. P., Ramirez, N., de Bono, M., &#38; Chen, C. (2022). ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3001684\">https://doi.org/10.1371/journal.pbio.3001684</a>","ieee":"L. Zhao <i>et al.</i>, “ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans,” <i>PLoS Biology</i>, vol. 20, no. 6. Public Library of Science, 2022.","ista":"Zhao L, Fenk LA, Nilsson L, Amin-Wetzel NP, Ramirez N, de Bono M, Chen C. 2022. ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans. PLoS Biology. 20(6), e3001684.","ama":"Zhao L, Fenk LA, Nilsson L, et al. ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans. <i>PLoS Biology</i>. 2022;20(6). doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001684\">10.1371/journal.pbio.3001684</a>","short":"L. Zhao, L.A. Fenk, L. Nilsson, N.P. Amin-Wetzel, N. Ramirez, M. de Bono, C. Chen, PLoS Biology 20 (2022).","mla":"Zhao, Lina, et al. “ROS and CGMP Signaling Modulate Persistent Escape from Hypoxia in Caenorhabditis Elegans.” <i>PLoS Biology</i>, vol. 20, no. 6, e3001684, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001684\">10.1371/journal.pbio.3001684</a>.","chicago":"Zhao, Lina, Lorenz A. Fenk, Lars Nilsson, Niko Paresh Amin-Wetzel, Nelson Ramirez, Mario de Bono, and Changchun Chen. “ROS and CGMP Signaling Modulate Persistent Escape from Hypoxia in Caenorhabditis Elegans.” <i>PLoS Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pbio.3001684\">https://doi.org/10.1371/journal.pbio.3001684</a>."},"file_date_updated":"2022-07-25T07:38:49Z","month":"06","ddc":["570"],"pmid":1,"has_accepted_license":"1","article_processing_charge":"No","volume":20,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"checksum":"df4902f854ad76769d3203bfdc69f16c","content_type":"application/pdf","access_level":"open_access","date_updated":"2022-07-25T07:38:49Z","success":1,"file_size":3721585,"creator":"dernst","relation":"main_file","file_name":"2022_PLoSBiology_Zhao.pdf","date_created":"2022-07-25T07:38:49Z","file_id":"11643"}],"issue":"6","abstract":[{"text":"The ability to detect and respond to acute oxygen (O2) shortages is indispensable to aerobic life. The molecular mechanisms and circuits underlying this capacity are poorly understood. Here, we characterize the behavioral responses of feeding Caenorhabditis elegans to approximately 1% O2. Acute hypoxia triggers a bout of turning maneuvers followed by a persistent switch to rapid forward movement as animals seek to avoid and escape hypoxia. While the behavioral responses to 1% O2 closely resemble those evoked by 21% O2, they have distinct molecular and circuit underpinnings. Disrupting phosphodiesterases (PDEs), specific G proteins, or BBSome function inhibits escape from 1% O2 due to increased cGMP signaling. A primary source of cGMP is GCY-28, the ortholog of the atrial natriuretic peptide (ANP) receptor. cGMP activates the protein kinase G EGL-4 and enhances neuroendocrine secretion to inhibit acute responses to 1% O2. Triggering a rise in cGMP optogenetically in multiple neurons, including AIA interneurons, rapidly and reversibly inhibits escape from 1% O2. Ca2+ imaging reveals that a 7% to 1% O2 stimulus evokes a Ca2+ decrease in several neurons. Defects in mitochondrial complex I (MCI) and mitochondrial complex I (MCIII), which lead to persistently high reactive oxygen species (ROS), abrogate acute hypoxia responses. In particular, repressing the expression of isp-1, which encodes the iron sulfur protein of MCIII, inhibits escape from 1% O2 without affecting responses to 21% O2. Both genetic and pharmacological up-regulation of mitochondrial ROS increase cGMP levels, which contribute to the reduced hypoxia responses. Our results implicate ROS and precise regulation of intracellular cGMP in the modulation of acute responses to hypoxia by C. elegans.","lang":"eng"}],"doi":"10.1371/journal.pbio.3001684","author":[{"first_name":"Lina","last_name":"Zhao","full_name":"Zhao, Lina"},{"first_name":"Lorenz A.","full_name":"Fenk, Lorenz A.","last_name":"Fenk"},{"first_name":"Lars","last_name":"Nilsson","full_name":"Nilsson, Lars"},{"last_name":"Amin-Wetzel","full_name":"Amin-Wetzel, Niko Paresh","first_name":"Niko Paresh","id":"E95D3014-9D8C-11E9-9C80-D2F8E5697425"},{"first_name":"Nelson","id":"39831956-E4FE-11E9-85DE-0DC7E5697425","last_name":"Ramirez","full_name":"Ramirez, Nelson"},{"orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","full_name":"De Bono, Mario","last_name":"De Bono"},{"last_name":"Chen","full_name":"Chen, Changchun","first_name":"Changchun"}],"title":"ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans","_id":"11637","publication_status":"published","acknowledgement":" This work was funded by H2020 European Research Council (ERC Advanced grant, 269058 ACMO, https://erc.europa.eu/funding/advanced-grants) and Wellcome Trust UK (Wellcome Investigator Award, 209504/Z/17/Z, https://wellcome.org/grant-funding/people-and-projects/grants-awarded/molecular-mechanisms-neural-circuit-function-0) to M.d.B, and by H2020 European Research Council (ERC starting grant, 802653 OXYGEN SENSING, https://erc.europa.eu/funding/starting-grants) and Vetenskapsrådet (VR starting grant, 2018-02216, https://www.vr.se/english.html) to C.C. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","status":"public","publication_identifier":{"eissn":["1545-7885"]},"project":[{"_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","grant_number":"209504/A/17/Z","name":"Molecular mechanisms of neural circuit function"}]},{"oa_version":"Published Version","day":"24","citation":{"short":"V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D.J. Schwab, S.E. Palmer, Physical Review Research 4 (2022).","ista":"Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. 2022. Inferring couplings in networks across order-disorder phase transitions. Physical Review Research. 4(2), 023240.","ama":"Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. Inferring couplings in networks across order-disorder phase transitions. <i>Physical Review Research</i>. 2022;4(2). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">10.1103/PhysRevResearch.4.023240</a>","ieee":"V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D. J. Schwab, and S. E. Palmer, “Inferring couplings in networks across order-disorder phase transitions,” <i>Physical Review Research</i>, vol. 4, no. 2. American Physical Society, 2022.","apa":"Ngampruetikorn, V., Sachdeva, V., Torrence, J., Humplik, J., Schwab, D. J., &#38; Palmer, S. E. (2022). Inferring couplings in networks across order-disorder phase transitions. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">https://doi.org/10.1103/PhysRevResearch.4.023240</a>","chicago":"Ngampruetikorn, Vudtiwat, Vedant Sachdeva, Johanna Torrence, Jan Humplik, David J. Schwab, and Stephanie E. Palmer. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.” <i>Physical Review Research</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">https://doi.org/10.1103/PhysRevResearch.4.023240</a>.","mla":"Ngampruetikorn, Vudtiwat, et al. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.” <i>Physical Review Research</i>, vol. 4, no. 2, 023240, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">10.1103/PhysRevResearch.4.023240</a>."},"ddc":["530"],"month":"06","file_date_updated":"2022-07-25T07:47:23Z","has_accepted_license":"1","volume":4,"article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"11644","date_created":"2022-07-25T07:47:23Z","access_level":"open_access","checksum":"ed6fdc2a3a096df785fa5f7b17b716c6","content_type":"application/pdf","success":1,"date_updated":"2022-07-25T07:47:23Z","file_name":"2022_PhysicalReviewResearch_Ngampruetikorn.pdf","relation":"main_file","file_size":1379683,"creator":"dernst"}],"arxiv":1,"issue":"2","abstract":[{"text":"Statistical inference is central to many scientific endeavors, yet how it works remains unresolved. Answering this requires a quantitative understanding of the intrinsic interplay between statistical models, inference methods, and the structure in the data. To this end, we characterize the efficacy of direct coupling analysis (DCA)—a highly successful method for analyzing amino acid sequence data—in inferring pairwise interactions from samples of ferromagnetic Ising models on random graphs. Our approach allows for physically motivated exploration of qualitatively distinct data regimes separated by phase transitions. We show that inference quality depends strongly on the nature of data-generating distributions: optimal accuracy occurs at an intermediate temperature where the detrimental effects from macroscopic order and thermal noise are minimal. Importantly our results indicate that DCA does not always outperform its local-statistics-based predecessors; while DCA excels at low temperatures, it becomes inferior to simple correlation thresholding at virtually all temperatures when data are limited. Our findings offer insights into the regime in which DCA operates so successfully, and more broadly, how inference interacts with the structure in the data.","lang":"eng"}],"doi":"10.1103/PhysRevResearch.4.023240","author":[{"full_name":"Ngampruetikorn, Vudtiwat","last_name":"Ngampruetikorn","first_name":"Vudtiwat"},{"first_name":"Vedant","last_name":"Sachdeva","full_name":"Sachdeva, Vedant"},{"last_name":"Torrence","full_name":"Torrence, Johanna","first_name":"Johanna"},{"first_name":"Jan","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","last_name":"Humplik","full_name":"Humplik, Jan"},{"last_name":"Schwab","full_name":"Schwab, David J.","first_name":"David J."},{"full_name":"Palmer, Stephanie E.","last_name":"Palmer","first_name":"Stephanie E."}],"title":"Inferring couplings in networks across order-disorder phase transitions","_id":"11638","status":"public","publication_status":"published","acknowledgement":"This work was supported in part by the Alfred P. Sloan Foundation, the Simons Foundation, the National Institutes of Health under Award No. R01EB026943, and the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030).","publication_identifier":{"issn":["2643-1564"]},"external_id":{"arxiv":["2106.02349"]},"date_published":"2022-06-24T00:00:00Z","scopus_import":"1","date_created":"2022-07-24T22:01:42Z","department":[{"_id":"GaTk"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"         4","publisher":"American Physical Society","year":"2022","oa":1,"article_type":"original","article_number":"023240","funded_apc":"1","publication":"Physical Review Research","date_updated":"2022-07-25T07:52:35Z"}]