[{"publication":"Science Advances","date_updated":"2023-11-21T08:05:35Z","related_material":{"record":[{"id":"14562","relation":"research_data","status":"public"}]},"article_type":"original","article_number":"add6495","oa":1,"year":"2023","keyword":["Multidisciplinary"],"intvolume":"         9","publisher":"American Association for the Advancement of Science","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000964550100015"]},"date_published":"2023-01-20T00:00:00Z","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"scopus_import":"1","date_created":"2023-01-23T07:26:42Z","publication_identifier":{"issn":["2375-2548"]},"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"acknowledgement":"We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nThis research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R.","publication_status":"published","status":"public","author":[{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Fäßler, Florian","last_name":"Fäßler","orcid":"0000-0001-7149-769X"},{"first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","last_name":"Javoor","full_name":"Javoor, Manjunath"},{"orcid":"0000-0002-3616-8580","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","full_name":"Datler, Julia","last_name":"Datler"},{"first_name":"Hermann","last_name":"Döring","full_name":"Döring, Hermann"},{"full_name":"Hofer, Florian","last_name":"Hofer","id":"b9d234ba-9e33-11ed-95b6-cd561df280e6","first_name":"Florian"},{"full_name":"Dimchev, Georgi A","last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","first_name":"Georgi A","orcid":"0000-0001-8370-6161"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau"},{"first_name":"Jan","last_name":"Faix","full_name":"Faix, Jan"},{"first_name":"Klemens","last_name":"Rottner","full_name":"Rottner, Klemens"},{"last_name":"Schur","full_name":"Schur, Florian KM","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"}],"title":"ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning","_id":"12334","issue":"3","abstract":[{"text":"Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.</jats:p>","lang":"eng"}],"doi":"10.1126/sciadv.add6495","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":[{"date_created":"2023-01-23T07:45:54Z","file_id":"12335","file_size":1756234,"relation":"main_file","creator":"dernst","file_name":"2023_ScienceAdvances_Faessler.pdf","date_updated":"2023-01-23T07:45:54Z","success":1,"content_type":"application/pdf","checksum":"ce81a6d0b84170e5e8c62f6acfa15d9e","access_level":"open_access"}],"has_accepted_license":"1","volume":9,"article_processing_charge":"No","day":"20","citation":{"mla":"Fäßler, Florian, et al. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” <i>Science Advances</i>, vol. 9, no. 3, add6495, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciadv.add6495\">10.1126/sciadv.add6495</a>.","chicago":"Fäßler, Florian, Manjunath Javoor, Julia Datler, Hermann Döring, Florian Hofer, Georgi A Dimchev, Victor-Valentin Hodirnau, Jan Faix, Klemens Rottner, and Florian KM Schur. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” <i>Science Advances</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciadv.add6495\">https://doi.org/10.1126/sciadv.add6495</a>.","ama":"Fäßler F, Javoor M, Datler J, et al. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. <i>Science Advances</i>. 2023;9(3). doi:<a href=\"https://doi.org/10.1126/sciadv.add6495\">10.1126/sciadv.add6495</a>","short":"F. Fäßler, M. Javoor, J. Datler, H. Döring, F. Hofer, G.A. Dimchev, V.-V. Hodirnau, J. Faix, K. Rottner, F.K. Schur, Science Advances 9 (2023).","ista":"Fäßler F, Javoor M, Datler J, Döring H, Hofer F, Dimchev GA, Hodirnau V-V, Faix J, Rottner K, Schur FK. 2023. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. 9(3), add6495.","ieee":"F. Fäßler <i>et al.</i>, “ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning,” <i>Science Advances</i>, vol. 9, no. 3. American Association for the Advancement of Science, 2023.","apa":"Fäßler, F., Javoor, M., Datler, J., Döring, H., Hofer, F., Dimchev, G. A., … Schur, F. K. (2023). ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.add6495\">https://doi.org/10.1126/sciadv.add6495</a>"},"ddc":["570"],"month":"01","file_date_updated":"2023-01-23T07:45:54Z","oa_version":"Published Version"},{"date_published":"2023-04-01T00:00:00Z","external_id":{"isi":["000955258300002"],"pmid":["36959418"]},"date_created":"2023-01-23T14:14:19Z","scopus_import":"1","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"Bio"}],"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Springer Nature","intvolume":"        26","year":"2023","oa":1,"related_material":{"record":[{"id":"12370","relation":"research_data","status":"public"}]},"page":"606-614","article_type":"original","publication":"Nature Neuroscience","date_updated":"2023-10-04T11:41:05Z","oa_version":"Published Version","citation":{"mla":"Gupta, Divyansh, et al. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” <i>Nature Neuroscience</i>, vol. 26, Springer Nature, 2023, pp. 606–14, doi:<a href=\"https://doi.org/10.1038/s41593-023-01280-0\">10.1038/s41593-023-01280-0</a>.","chicago":"Gupta, Divyansh, Wiktor F Mlynarski, Anton L Sumser, Olga Symonova, Jan Svaton, and Maximilian A Jösch. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” <i>Nature Neuroscience</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41593-023-01280-0\">https://doi.org/10.1038/s41593-023-01280-0</a>.","ieee":"D. Gupta, W. F. Mlynarski, A. L. Sumser, O. Symonova, J. Svaton, and M. A. Jösch, “Panoramic visual statistics shape retina-wide organization of receptive fields,” <i>Nature Neuroscience</i>, vol. 26. Springer Nature, pp. 606–614, 2023.","apa":"Gupta, D., Mlynarski, W. F., Sumser, A. L., Symonova, O., Svaton, J., &#38; Jösch, M. A. (2023). Panoramic visual statistics shape retina-wide organization of receptive fields. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41593-023-01280-0\">https://doi.org/10.1038/s41593-023-01280-0</a>","ama":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. Panoramic visual statistics shape retina-wide organization of receptive fields. <i>Nature Neuroscience</i>. 2023;26:606-614. doi:<a href=\"https://doi.org/10.1038/s41593-023-01280-0\">10.1038/s41593-023-01280-0</a>","ista":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. 2023. Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. 26, 606–614.","short":"D. Gupta, W.F. Mlynarski, A.L. Sumser, O. Symonova, J. Svaton, M.A. Jösch, Nature Neuroscience 26 (2023) 606–614."},"day":"01","file_date_updated":"2023-10-04T11:40:51Z","ddc":["570"],"pmid":1,"month":"04","has_accepted_license":"1","volume":26,"article_processing_charge":"Yes (in subscription journal)","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":"14395","date_created":"2023-10-04T11:40:51Z","file_name":"2023_NatureNeuroscience_Gupta.pdf","relation":"main_file","file_size":6144866,"creator":"dernst","access_level":"open_access","content_type":"application/pdf","checksum":"a33d91e398e548f34003170e10988368","success":1,"date_updated":"2023-10-04T11:40:51Z"}],"abstract":[{"text":"Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types.","lang":"eng"}],"doi":"10.1038/s41593-023-01280-0","title":"Panoramic visual statistics shape retina-wide organization of receptive fields","author":[{"orcid":"0000-0001-7400-6665","first_name":"Divyansh","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta","full_name":"Gupta, Divyansh"},{"last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F","first_name":"Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sumser","full_name":"Sumser, Anton L","first_name":"Anton L","id":"3320A096-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4792-1881"},{"full_name":"Symonova, Olga","last_name":"Symonova","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga","orcid":"0000-0003-2012-9947"},{"full_name":"Svaton, Jan","last_name":"Svaton","id":"f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2","first_name":"Jan","orcid":"0000-0002-6198-2939"},{"orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A"}],"_id":"12349","status":"public","publication_status":"published","acknowledgement":"We thank Hiroki Asari for sharing the dataset of naturalistic images, Anton Sumser for sharing visual stimulus code, Yoav Ben Simon for initial explorative work with the generation of AAVs, and Tomas Vega-Zuñiga for help with immunostainings. We also thank Gasper Tkacik and members of the Neuroethology group for their comments on the manuscript. This research was supported by the Scientific Service Units of IST Austria through resources provided by Scientific Computing, the Preclinical Facility, the Lab Support Facility, and the Imaging and Optics Facility. This work was supported by European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 (DG), Austrian Science Fund (FWF) stand-alone grant P 34015 (WM), Human Frontiers Science Program LT000256/2018-L (AS), EMBO ALTF 1098-2017 (AS) and the European Research Council Starting Grant 756502 (MJ).","ec_funded":1,"publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015"},{"grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","name":"Circuits of Visual Attention","call_identifier":"H2020"},{"name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","_id":"266D407A-B435-11E9-9278-68D0E5697425","grant_number":"LT000256"},{"name":"Connecting sensory with motor processing in the superior colliculus","_id":"264FEA02-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1098-2017"}]},{"date_updated":"2023-10-04T11:41:04Z","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"name":"Efficient coding with biophysical realism","grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"name":"Circuits of Visual Attention","call_identifier":"H2020","grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"},{"grant_number":"LT000256","_id":"266D407A-B435-11E9-9278-68D0E5697425","name":"Neuronal networks of salience and spatial detection in the murine superior colliculus"},{"name":"Connecting sensory with motor processing in the superior colliculus","grant_number":"ALTF 1098-2017","_id":"264FEA02-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"related_material":{"record":[{"id":"12349","status":"public","relation":"used_in_publication"}]},"status":"public","_id":"12370","oa":1,"title":"Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields","author":[{"last_name":"Gupta","full_name":"Gupta, Divyansh","first_name":"Divyansh","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7400-6665"},{"orcid":"0000-0002-4792-1881","first_name":"Anton L","id":"3320A096-F248-11E8-B48F-1D18A9856A87","last_name":"Sumser","full_name":"Sumser, Anton L"},{"orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","full_name":"Jösch, Maximilian A","last_name":"Jösch"}],"doi":"10.15479/AT:ISTA:12370","abstract":[{"lang":"eng","text":"Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types. 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Gupta, A. L. Sumser, and M. A. Jösch, “Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields.” Institute of Science and Technology Austria, 2023.","apa":"Gupta, D., Sumser, A. L., &#38; Jösch, M. A. (2023). Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12370\">https://doi.org/10.15479/AT:ISTA:12370</a>","short":"D. Gupta, A.L. Sumser, M.A. Jösch, (2023).","ista":"Gupta D, Sumser AL, Jösch MA. 2023. Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12370\">10.15479/AT:ISTA:12370</a>.","ama":"Gupta D, Sumser AL, Jösch MA. Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12370\">10.15479/AT:ISTA:12370</a>","mla":"Gupta, Divyansh, et al. <i>Research Data for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12370\">10.15479/AT:ISTA:12370</a>.","chicago":"Gupta, Divyansh, Anton L Sumser, and Maximilian A Jösch. “Research Data for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12370\">https://doi.org/10.15479/AT:ISTA:12370</a>."},"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"day":"26","oa_version":"Published Version","date_created":"2023-01-25T12:45:18Z","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"date_published":"2023-01-26T00:00:00Z"},{"volume":207,"article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","citation":{"ieee":"Y. Diao, “Density of the union of positive diagonal binary quadratic forms,” <i>Acta Arithmetica</i>, vol. 207. Instytut Matematyczny, pp. 1–17, 2023.","apa":"Diao, Y. (2023). Density of the union of positive diagonal binary quadratic forms. <i>Acta Arithmetica</i>. Instytut Matematyczny. <a href=\"https://doi.org/10.4064/aa210830-24-11\">https://doi.org/10.4064/aa210830-24-11</a>","short":"Y. Diao, Acta Arithmetica 207 (2023) 1–17.","ama":"Diao Y. Density of the union of positive diagonal binary quadratic forms. <i>Acta Arithmetica</i>. 2023;207:1-17. doi:<a href=\"https://doi.org/10.4064/aa210830-24-11\">10.4064/aa210830-24-11</a>","ista":"Diao Y. 2023. Density of the union of positive diagonal binary quadratic forms. Acta Arithmetica. 207, 1–17.","chicago":"Diao, Yijie. “Density of the Union of Positive Diagonal Binary Quadratic Forms.” <i>Acta Arithmetica</i>. Instytut Matematyczny, 2023. <a href=\"https://doi.org/10.4064/aa210830-24-11\">https://doi.org/10.4064/aa210830-24-11</a>.","mla":"Diao, Yijie. “Density of the Union of Positive Diagonal Binary Quadratic Forms.” <i>Acta Arithmetica</i>, vol. 207, Instytut Matematyczny, 2023, pp. 1–17, doi:<a href=\"https://doi.org/10.4064/aa210830-24-11\">10.4064/aa210830-24-11</a>."},"day":"09","month":"01","status":"public","acknowledgement":"This article is a version the author’s master thesis at the University of Bonn. The author would like to thank his advisor Valentin Blomer for introducing the problem, and giving generous feedback and encouragement along the way, especially during the global pandemic.\r\nThe author thanks Edgar Assing for his lectures on analytic number theory. Finally, the author is grateful to the anonymous referees for their valuable time and comments.\r\n","publication_status":"published","publication_identifier":{"eissn":["1730-6264"],"issn":["0065-1036"]},"abstract":[{"text":"Let X be a sufficiently large positive integer. We prove that one may choose a subset S of primes with cardinality O(logX) such that a positive proportion of integers less than X can be represented by x2+py2 for at least one p∈S.","lang":"eng"}],"doi":"10.4064/aa210830-24-11","title":"Density of the union of positive diagonal binary quadratic forms","author":[{"orcid":"0000-0002-4989-5330","id":"7b7eb4ca-eb2c-11ec-b98b-accec0b20c3b","first_name":"Yijie","full_name":"Diao, Yijie","last_name":"Diao"}],"_id":"12406","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Instytut Matematyczny","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2103.08268","open_access":"1"}],"intvolume":"       207","date_published":"2023-01-09T00:00:00Z","external_id":{"arxiv":["2103.08268"],"isi":["000912903000001"]},"date_created":"2023-01-26T21:17:04Z","department":[{"_id":"GradSch"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1-17","article_type":"original","publication":"Acta Arithmetica","date_updated":"2023-10-17T09:15:17Z","year":"2023","keyword":["Algebra","Number Theory"],"oa":1},{"department":[{"_id":"ToHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-01-27T00:00:00Z","date_created":"2023-01-27T03:18:08Z","publisher":"Institute of Science and Technology Austria","type":"technical_report","language":[{"iso":"eng"}],"oa":1,"year":"2023","alternative_title":["IST Austria Technical Report"],"keyword":["runtime monitoring","best effort","third party"],"date_updated":"2023-04-25T07:19:06Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"12856"}]},"page":"38","day":"27","citation":{"chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. <i>VAMOS: Middleware for Best-Effort Third-Party Monitoring</i>. Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12407\">https://doi.org/10.15479/AT:ISTA:12407</a>.","mla":"Chalupa, Marek, et al. <i>VAMOS: Middleware for Best-Effort Third-Party Monitoring</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12407\">10.15479/AT:ISTA:12407</a>.","ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. <i>VAMOS: Middleware for Best-Effort Third-Party Monitoring</i>. Institute of Science and Technology Austria; 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12407\">10.15479/AT:ISTA:12407</a>","ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. VAMOS: Middleware for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria, 38p.","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, VAMOS: Middleware for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria, 2023.","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., &#38; Henzinger, T. A. (2023). <i>VAMOS: Middleware for Best-Effort Third-Party Monitoring</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12407\">https://doi.org/10.15479/AT:ISTA:12407</a>","ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, <i>VAMOS: Middleware for Best-Effort Third-Party Monitoring</i>. Institute of Science and Technology Austria, 2023."},"ddc":["005"],"month":"01","file_date_updated":"2023-01-27T03:18:34Z","oa_version":"Published Version","file":[{"success":1,"date_updated":"2023-01-27T03:18:34Z","access_level":"open_access","content_type":"application/pdf","checksum":"55426e463fdeafe9777fc3ff635154c7","file_name":"main.pdf","relation":"main_file","file_size":662409,"creator":"fmuehlbo","file_id":"12408","date_created":"2023-01-27T03:18:34Z"}],"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","author":[{"last_name":"Chalupa","full_name":"Chalupa, Marek","first_name":"Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463"},{"id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","first_name":"Fabian","full_name":"Mühlböck, Fabian","last_name":"Mühlböck","orcid":"0000-0003-1548-0177"},{"last_name":"Muroya Lei","full_name":"Muroya Lei, Stefanie","first_name":"Stefanie","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff"},{"orcid":"0000-0002-2985-7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"title":"VAMOS: Middleware for Best-Effort Third-Party Monitoring","_id":"12407","abstract":[{"lang":"eng","text":"As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both.\r\n\r\nWe present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\n\r\nWe implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch."}],"doi":"10.15479/AT:ISTA:12407","publication_identifier":{"eissn":["2664-1690"]},"project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"status":"public","publication_status":"published","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. \r\nThe authors would like to thank the anonymous FASE reviewers for their valuable feedback and suggestions.","ec_funded":1},{"doi":"10.1042/bst20220221","abstract":[{"lang":"eng","text":"The actin cytoskeleton plays a key role in cell migration and cellular morphodynamics in most eukaryotes. The ability of the actin cytoskeleton to assemble and disassemble in a spatiotemporally controlled manner allows it to form higher-order structures, which can generate forces required for a cell to explore and navigate through its environment. It is regulated not only via a complex synergistic and competitive interplay between actin-binding proteins (ABP), but also by filament biochemistry and filament geometry. The lack of structural insights into how geometry and ABPs regulate the actin cytoskeleton limits our understanding of the molecular mechanisms that define actin cytoskeleton remodeling and, in turn, impact emerging cell migration characteristics. With the advent of cryo-electron microscopy (cryo-EM) and advanced computational methods, it is now possible to define these molecular mechanisms involving actin and its interactors at both atomic and ultra-structural levels in vitro and in cellulo. In this review, we will provide an overview of the available cryo-EM methods, applicable to further our understanding of the actin cytoskeleton, specifically in the context of cell migration. We will discuss how these methods have been employed to elucidate ABP- and geometry-defined regulatory mechanisms in initiating, maintaining, and disassembling cellular actin networks in migratory protrusions."}],"issue":"1","_id":"12421","title":"Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM","author":[{"first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X"},{"id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","first_name":"Manjunath","full_name":"Javoor, Manjunath","last_name":"Javoor"},{"orcid":"0000-0003-4790-8078","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","full_name":"Schur, Florian KM"}],"publication_status":"published","acknowledgement":"We apologize for not being able to mention and cite additional excellent work that would have fit the scope of this review, due to space restraints. We thank Jesse Hansen for comments on the manuscript. We acknowledge support from the Austrian Science Fund (FWF): P33367 and the Institute of Science and Technology Austria.","status":"public","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"publication_identifier":{"issn":["0300-5127"],"eissn":["1470-8752"]},"oa_version":"Published Version","ddc":["570"],"file_date_updated":"2023-03-16T07:58:16Z","month":"02","citation":{"apa":"Fäßler, F., Javoor, M., &#38; Schur, F. K. (2023). Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. <i>Biochemical Society Transactions</i>. Portland Press. <a href=\"https://doi.org/10.1042/bst20220221\">https://doi.org/10.1042/bst20220221</a>","ieee":"F. Fäßler, M. Javoor, and F. K. Schur, “Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM,” <i>Biochemical Society Transactions</i>, vol. 51, no. 1. Portland Press, pp. 87–99, 2023.","ista":"Fäßler F, Javoor M, Schur FK. 2023. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. 51(1), 87–99.","short":"F. Fäßler, M. Javoor, F.K. Schur, Biochemical Society Transactions 51 (2023) 87–99.","ama":"Fäßler F, Javoor M, Schur FK. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. <i>Biochemical Society Transactions</i>. 2023;51(1):87-99. doi:<a href=\"https://doi.org/10.1042/bst20220221\">10.1042/bst20220221</a>","chicago":"Fäßler, Florian, Manjunath Javoor, and Florian KM Schur. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” <i>Biochemical Society Transactions</i>. Portland Press, 2023. <a href=\"https://doi.org/10.1042/bst20220221\">https://doi.org/10.1042/bst20220221</a>.","mla":"Fäßler, Florian, et al. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” <i>Biochemical Society Transactions</i>, vol. 51, no. 1, Portland Press, 2023, pp. 87–99, doi:<a href=\"https://doi.org/10.1042/bst20220221\">10.1042/bst20220221</a>."},"day":"01","article_processing_charge":"No","volume":51,"has_accepted_license":"1","file":[{"creator":"dernst","relation":"main_file","file_size":10045006,"file_name":"2023_BioChemicalSocietyTransactions_Faessler.pdf","checksum":"4e7069845e3dad22bb44fb71ec624c60","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-03-16T07:58:16Z","success":1,"date_created":"2023-03-16T07:58:16Z","file_id":"12728"}],"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"},"keyword":["Biochemistry"],"year":"2023","oa":1,"page":"87-99","article_type":"original","date_updated":"2023-08-01T12:55:32Z","publication":"Biochemical Society Transactions","date_created":"2023-01-27T10:08:19Z","scopus_import":"1","date_published":"2023-02-01T00:00:00Z","external_id":{"isi":["000926043100001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"FlSc"}],"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"publisher":"Portland Press","intvolume":"        51"},{"oa":1,"year":"2023","publication":"Proceedings of the American Mathematical Society","date_updated":"2023-08-01T13:03:32Z","article_type":"original","page":"907-914","department":[{"_id":"TiBr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2023-01-01T00:00:00Z","external_id":{"isi":["000898440000001"]},"scopus_import":"1","date_created":"2023-01-29T23:00:58Z","main_file_link":[{"open_access":"1","url":"https://hal.science/hal-03013498/"}],"intvolume":"       151","publisher":"American Mathematical Society","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","author":[{"id":"3ACCD756-F248-11E8-B48F-1D18A9856A87","first_name":"Francesca","full_name":"Balestrieri, Francesca","last_name":"Balestrieri"}],"title":"Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups","_id":"12427","issue":"3","abstract":[{"lang":"eng","text":"Let k be a number field and X a smooth, geometrically integral quasi-projective variety over k. For any linear algebraic group G over k and any G-torsor g : Z → X, we observe that if the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for all twists of Z by elements in H^1(k, G), then the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for X. As an application, we show that any homogeneous space of the form G/H with G a connected linear algebraic group over k satisfies strong approximation off the infinite places with étale-Brauer obstruction, under some compactness assumptions when k is totally real. We also prove more refined strong approximation results for homogeneous spaces of the form G/H with G semisimple simply connected and H finite, using the theory of torsors and descent."}],"doi":"10.1090/proc/15239","publication_identifier":{"eissn":["1088-6826"],"issn":["0002-9939"]},"publication_status":"published","status":"public","day":"01","citation":{"chicago":"Balestrieri, Francesca. “Some Remarks on Strong Approximation and Applications to Homogeneous Spaces of Linear Algebraic Groups.” <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society, 2023. <a href=\"https://doi.org/10.1090/proc/15239\">https://doi.org/10.1090/proc/15239</a>.","mla":"Balestrieri, Francesca. “Some Remarks on Strong Approximation and Applications to Homogeneous Spaces of Linear Algebraic Groups.” <i>Proceedings of the American Mathematical Society</i>, vol. 151, no. 3, American Mathematical Society, 2023, pp. 907–14, doi:<a href=\"https://doi.org/10.1090/proc/15239\">10.1090/proc/15239</a>.","ista":"Balestrieri F. 2023. Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. 151(3), 907–914.","ama":"Balestrieri F. Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. <i>Proceedings of the American Mathematical Society</i>. 2023;151(3):907-914. doi:<a href=\"https://doi.org/10.1090/proc/15239\">10.1090/proc/15239</a>","short":"F. Balestrieri, Proceedings of the American Mathematical Society 151 (2023) 907–914.","ieee":"F. Balestrieri, “Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups,” <i>Proceedings of the American Mathematical Society</i>, vol. 151, no. 3. American Mathematical Society, pp. 907–914, 2023.","apa":"Balestrieri, F. (2023). Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/proc/15239\">https://doi.org/10.1090/proc/15239</a>"},"month":"01","oa_version":"Preprint","article_processing_charge":"No","volume":151},{"oa_version":"Published Version","citation":{"mla":"Hannezo, Edouard B., and Colinda L. G. J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” <i>Cell Migration in Three Dimensions</i>, edited by Coert Margadant, vol. 2608, Springer Nature, 2023, pp. 183–205, doi:<a href=\"https://doi.org/10.1007/978-1-0716-2887-4_12\">10.1007/978-1-0716-2887-4_12</a>.","chicago":"Hannezo, Edouard B, and Colinda L.G.J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” In <i>Cell Migration in Three Dimensions</i>, edited by Coert Margadant, 2608:183–205. MIMB. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-1-0716-2887-4_12\">https://doi.org/10.1007/978-1-0716-2887-4_12</a>.","ieee":"E. B. Hannezo and C. L. G. J. Scheele, “A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland,” in <i>Cell Migration in Three Dimensions</i>, vol. 2608, C. Margadant, Ed. Springer Nature, 2023, pp. 183–205.","apa":"Hannezo, E. B., &#38; Scheele, C. L. G. J. (2023). A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In C. Margadant (Ed.), <i>Cell Migration in Three Dimensions</i> (Vol. 2608, pp. 183–205). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-2887-4_12\">https://doi.org/10.1007/978-1-0716-2887-4_12</a>","ista":"Hannezo EB, Scheele CLGJ. 2023.A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Cell Migration in Three Dimensions. Methods in Molecular Biology, vol. 2608, 183–205.","ama":"Hannezo EB, Scheele CLGJ. A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Margadant C, ed. <i>Cell Migration in Three Dimensions</i>. Vol 2608. MIMB. Springer Nature; 2023:183-205. doi:<a href=\"https://doi.org/10.1007/978-1-0716-2887-4_12\">10.1007/978-1-0716-2887-4_12</a>","short":"E.B. Hannezo, C.L.G.J. Scheele, in:, C. Margadant (Ed.), Cell Migration in Three Dimensions, Springer Nature, 2023, pp. 183–205."},"day":"19","file_date_updated":"2023-02-03T10:56:39Z","ddc":["570"],"pmid":1,"month":"01","has_accepted_license":"1","article_processing_charge":"No","volume":2608,"file":[{"creator":"dernst","relation":"main_file","file_size":826598,"file_name":"2023_MIMB_Hannezo.pdf","date_updated":"2023-02-03T10:56:39Z","success":1,"content_type":"application/pdf","checksum":"aec1b8d3ba938ddf9d8fcb777f3c38ee","access_level":"open_access","date_created":"2023-02-03T10:56:39Z","file_id":"12500"}],"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"},"abstract":[{"text":"The mammary gland consists of a bilayered epithelial structure with an extensively branched morphology. The majority of this epithelial tree is laid down during puberty, during which actively proliferating terminal end buds repeatedly elongate and bifurcate to form the basic structure of the ductal tree. Mammary ducts consist of a basal and luminal cell layer with a multitude of identified sub-lineages within both layers. The understanding of how these different cell lineages are cooperatively driving branching morphogenesis is a problem of crossing multiple scales, as this requires information on the macroscopic branched structure of the gland, as well as data on single-cell dynamics driving the morphogenic program. Here we describe a method to combine genetic lineage tracing with whole-gland branching analysis. Quantitative data on the global organ structure can be used to derive a model for mammary gland branching morphogenesis and provide a backbone on which the dynamics of individual cell lineages can be simulated and compared to lineage-tracing approaches. Eventually, these quantitative models and experiments allow to understand the couplings between the macroscopic shape of the mammary gland and the underlying single-cell dynamics driving branching morphogenesis.","lang":"eng"}],"doi":"10.1007/978-1-0716-2887-4_12","title":"A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland","author":[{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561"},{"last_name":"Scheele","full_name":"Scheele, Colinda L.G.J.","first_name":"Colinda L.G.J."}],"_id":"12428","editor":[{"first_name":"Coert","full_name":"Margadant, Coert","last_name":"Margadant"}],"status":"public","publication_status":"published","publication_identifier":{"eisbn":["9781071628874"],"isbn":["9781071628867"],"eissn":["1940-6029"]},"external_id":{"pmid":["36653709"]},"date_published":"2023-01-19T00:00:00Z","date_created":"2023-01-29T23:00:58Z","scopus_import":"1","department":[{"_id":"EdHa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","type":"book_chapter","language":[{"iso":"eng"}],"series_title":"MIMB","publisher":"Springer Nature","intvolume":"      2608","year":"2023","alternative_title":["Methods in Molecular Biology"],"oa":1,"page":"183-205","publication":"Cell Migration in Three Dimensions","date_updated":"2023-02-03T10:58:56Z"},{"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)"},"arxiv":1,"file":[{"file_id":"14067","date_created":"2023-08-16T11:40:02Z","success":1,"date_updated":"2023-08-16T11:40:02Z","access_level":"open_access","checksum":"6f099f1d064173784d1a27716a2cc795","content_type":"application/pdf","file_name":"2023_MathNachrichten_Agresti.pdf","file_size":449280,"creator":"dernst","relation":"main_file"}],"has_accepted_license":"1","volume":296,"article_processing_charge":"No","day":"01","citation":{"ieee":"A. Agresti, N. Lindemulder, and M. Veraar, “On the trace embedding and its applications to evolution equations,” <i>Mathematische Nachrichten</i>, vol. 296, no. 4. Wiley, pp. 1319–1350, 2023.","apa":"Agresti, A., Lindemulder, N., &#38; Veraar, M. (2023). On the trace embedding and its applications to evolution equations. <i>Mathematische Nachrichten</i>. Wiley. <a href=\"https://doi.org/10.1002/mana.202100192\">https://doi.org/10.1002/mana.202100192</a>","short":"A. Agresti, N. Lindemulder, M. Veraar, Mathematische Nachrichten 296 (2023) 1319–1350.","ama":"Agresti A, Lindemulder N, Veraar M. On the trace embedding and its applications to evolution equations. <i>Mathematische Nachrichten</i>. 2023;296(4):1319-1350. doi:<a href=\"https://doi.org/10.1002/mana.202100192\">10.1002/mana.202100192</a>","ista":"Agresti A, Lindemulder N, Veraar M. 2023. On the trace embedding and its applications to evolution equations. Mathematische Nachrichten. 296(4), 1319–1350.","mla":"Agresti, Antonio, et al. “On the Trace Embedding and Its Applications to Evolution Equations.” <i>Mathematische Nachrichten</i>, vol. 296, no. 4, Wiley, 2023, pp. 1319–50, doi:<a href=\"https://doi.org/10.1002/mana.202100192\">10.1002/mana.202100192</a>.","chicago":"Agresti, Antonio, Nick Lindemulder, and Mark Veraar. “On the Trace Embedding and Its Applications to Evolution Equations.” <i>Mathematische Nachrichten</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/mana.202100192\">https://doi.org/10.1002/mana.202100192</a>."},"file_date_updated":"2023-08-16T11:40:02Z","month":"04","ddc":["510"],"oa_version":"Published Version","publication_identifier":{"eissn":["1522-2616"],"issn":["0025-584X"]},"acknowledgement":"The first author has been partially supported by the Nachwuchsring—Network for the promotion of young scientists—at TU Kaiserslautern. The second and third authors were supported by the Vidi subsidy 639.032.427 of the Netherlands Organisation for Scientific Research (NWO).","status":"public","publication_status":"published","author":[{"orcid":"0000-0002-9573-2962","full_name":"Agresti, Antonio","last_name":"Agresti","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","first_name":"Antonio"},{"last_name":"Lindemulder","full_name":"Lindemulder, Nick","first_name":"Nick"},{"first_name":"Mark","last_name":"Veraar","full_name":"Veraar, Mark"}],"title":"On the trace embedding and its applications to evolution equations","_id":"12429","issue":"4","abstract":[{"lang":"eng","text":"In this paper, we consider traces at initial times for functions with mixed time-space smoothness. Such results are often needed in the theory of evolution equations. Our result extends and unifies many previous results. Our main improvement is that we can allow general interpolation couples. The abstract results are applied to regularity problems for fractional evolution equations and stochastic evolution equations, where uniform trace estimates on the half-line are shown."}],"doi":"10.1002/mana.202100192","intvolume":"       296","publisher":"Wiley","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"JuFi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2104.05063"],"isi":["000914134900001"]},"date_published":"2023-04-01T00:00:00Z","scopus_import":"1","date_created":"2023-01-29T23:00:59Z","publication":"Mathematische Nachrichten","date_updated":"2023-08-16T11:41:42Z","article_type":"original","page":"1319-1350","oa":1,"year":"2023"},{"article_processing_charge":"No","volume":35,"arxiv":1,"oa_version":"Preprint","citation":{"mla":"Falconi, Marco, et al. “Bogoliubov Dynamics and Higher-Order Corrections for the Regularized Nelson Model.” <i>Reviews in Mathematical Physics</i>, vol. 35, no. 4, 2350006, World Scientific Publishing, 2023, doi:<a href=\"https://doi.org/10.1142/S0129055X2350006X\">10.1142/S0129055X2350006X</a>.","chicago":"Falconi, Marco, Nikolai K Leopold, David Johannes Mitrouskas, and Sören P Petrat. “Bogoliubov Dynamics and Higher-Order Corrections for the Regularized Nelson Model.” <i>Reviews in Mathematical Physics</i>. World Scientific Publishing, 2023. <a href=\"https://doi.org/10.1142/S0129055X2350006X\">https://doi.org/10.1142/S0129055X2350006X</a>.","ieee":"M. Falconi, N. K. Leopold, D. J. Mitrouskas, and S. P. Petrat, “Bogoliubov dynamics and higher-order corrections for the regularized Nelson model,” <i>Reviews in Mathematical Physics</i>, vol. 35, no. 4. World Scientific Publishing, 2023.","apa":"Falconi, M., Leopold, N. K., Mitrouskas, D. J., &#38; Petrat, S. P. (2023). Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. <i>Reviews in Mathematical Physics</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0129055X2350006X\">https://doi.org/10.1142/S0129055X2350006X</a>","short":"M. Falconi, N.K. Leopold, D.J. Mitrouskas, S.P. Petrat, Reviews in Mathematical Physics 35 (2023).","ama":"Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. <i>Reviews in Mathematical Physics</i>. 2023;35(4). doi:<a href=\"https://doi.org/10.1142/S0129055X2350006X\">10.1142/S0129055X2350006X</a>","ista":"Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. 2023. Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. Reviews in Mathematical Physics. 35(4), 2350006."},"day":"09","month":"01","publication_status":"published","status":"public","publication_identifier":{"issn":["0129-055X"]},"abstract":[{"text":"We study the time evolution of the Nelson model in a mean-field limit in which N nonrelativistic bosons weakly couple (with respect to the particle number) to a positive or zero mass quantized scalar field. Our main result is the derivation of the Bogoliubov dynamics and higher-order corrections. More precisely, we prove the convergence of the approximate wave function to the many-body wave function in norm, with a convergence rate proportional to the number of corrections taken into account in the approximation. We prove an analogous result for the unitary propagator. As an application, we derive a simple system of partial differential equations describing the time evolution of the first- and second-order approximations to the one-particle reduced density matrices of the particles and the quantum field, respectively.","lang":"eng"}],"issue":"4","doi":"10.1142/S0129055X2350006X","title":"Bogoliubov dynamics and higher-order corrections for the regularized Nelson model","author":[{"full_name":"Falconi, Marco","last_name":"Falconi","first_name":"Marco"},{"full_name":"Leopold, Nikolai K","last_name":"Leopold","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","first_name":"Nikolai K","orcid":"0000-0002-0495-6822"},{"id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","first_name":"David Johannes","full_name":"Mitrouskas, David Johannes","last_name":"Mitrouskas"},{"first_name":"Sören P","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrat","full_name":"Petrat, Sören P","orcid":"0000-0002-9166-5889"}],"_id":"12430","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","publisher":"World Scientific Publishing","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2110.00458","open_access":"1"}],"intvolume":"        35","external_id":{"arxiv":["2110.00458"],"isi":["000909760300001"]},"date_published":"2023-01-09T00:00:00Z","date_created":"2023-01-29T23:00:59Z","scopus_import":"1","department":[{"_id":"RoSe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"2350006","article_type":"original","publication":"Reviews in Mathematical Physics","date_updated":"2023-08-16T11:47:27Z","year":"2023","oa":1},{"page":"349-370","date_updated":"2023-07-14T11:20:27Z","publication":"26th International Conference Foundations of Software Science and Computation Structures","alternative_title":["LNCS"],"year":"2023","oa":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","publisher":"Springer Nature","intvolume":"     13992","date_created":"2023-01-31T07:23:56Z","scopus_import":"1","external_id":{"arxiv":["2301.11175"]},"date_published":"2023-04-21T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"ec_funded":1,"publication_status":"published","acknowledgement":"We thank the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093.","status":"public","project":[{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"publication_identifier":{"isbn":["9783031308284"],"issn":["0302-9743"],"eissn":["1611-3349"]},"doi":"10.1007/978-3-031-30829-1_17","abstract":[{"lang":"eng","text":"Safety and liveness are elementary concepts of computation, and the foundation of many verification paradigms. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In quantitative specification and verification, properties assign not truth values, but quantitative values to infinite traces (e.g., a cost, or the distance to a boolean property). We introduce quantitative safety and liveness, and we prove that our definitions induce conservative quantitative generalizations of both (1)~the safety-progress hierarchy of boolean properties and (2)~the safety-liveness decomposition of boolean properties. In particular, we show that every quantitative property can be written as the pointwise minimum of a quantitative safety property and a quantitative liveness property. Consequently, like boolean properties, also quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. Moreover, quantitative properties can be approximated naturally. We prove that every quantitative property that has both safe and co-safe approximations can be monitored arbitrarily precisely by a monitor that uses only a finite number of states."}],"_id":"12467","title":"Quantitative safety and liveness","author":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000-0002-2985-7724"},{"last_name":"Mazzocchi","full_name":"Mazzocchi, Nicolas Adrien","first_name":"Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85"},{"first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","last_name":"Sarac","full_name":"Sarac, Naci E"}],"article_processing_charge":"No","volume":13992,"has_accepted_license":"1","file":[{"creator":"esarac","file_size":449027,"relation":"main_file","file_name":"qsl.pdf","date_updated":"2023-01-31T07:22:21Z","success":1,"content_type":"application/pdf","checksum":"981025aed580b6b27c426cb8856cf63e","access_level":"open_access","date_created":"2023-01-31T07:22:21Z","file_id":"12468"},{"creator":"dernst","relation":"main_file","file_size":1048171,"file_name":"2023_LNCS_HenzingerT.pdf","content_type":"application/pdf","checksum":"f16e2af1e0eb243158ab0f0fe74e7d5a","access_level":"open_access","date_updated":"2023-06-19T10:28:09Z","success":1,"date_created":"2023-06-19T10:28:09Z","file_id":"13153"}],"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"},"arxiv":1,"oa_version":"Published Version","conference":{"end_date":"2023-04-27","start_date":"2023-04-22","location":"Paris, France","name":"FOSSACS: Foundations of Software Science and Computation Structures"},"file_date_updated":"2023-06-19T10:28:09Z","ddc":["000"],"month":"04","citation":{"chicago":"Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Quantitative Safety and Liveness.” In <i>26th International Conference Foundations of Software Science and Computation Structures</i>, 13992:349–70. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-30829-1_17\">https://doi.org/10.1007/978-3-031-30829-1_17</a>.","mla":"Henzinger, Thomas A., et al. “Quantitative Safety and Liveness.” <i>26th International Conference Foundations of Software Science and Computation Structures</i>, vol. 13992, Springer Nature, 2023, pp. 349–70, doi:<a href=\"https://doi.org/10.1007/978-3-031-30829-1_17\">10.1007/978-3-031-30829-1_17</a>.","ieee":"T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Quantitative safety and liveness,” in <i>26th International Conference Foundations of Software Science and Computation Structures</i>, Paris, France, 2023, vol. 13992, pp. 349–370.","apa":"Henzinger, T. A., Mazzocchi, N. A., &#38; Sarac, N. E. (2023). Quantitative safety and liveness. In <i>26th International Conference Foundations of Software Science and Computation Structures</i> (Vol. 13992, pp. 349–370). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-30829-1_17\">https://doi.org/10.1007/978-3-031-30829-1_17</a>","ista":"Henzinger TA, Mazzocchi NA, Sarac NE. 2023. Quantitative safety and liveness. 26th International Conference Foundations of Software Science and Computation Structures. FOSSACS: Foundations of Software Science and Computation Structures, LNCS, vol. 13992, 349–370.","short":"T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 26th International Conference Foundations of Software Science and Computation Structures, Springer Nature, 2023, pp. 349–370.","ama":"Henzinger TA, Mazzocchi NA, Sarac NE. Quantitative safety and liveness. In: <i>26th International Conference Foundations of Software Science and Computation Structures</i>. Vol 13992. Springer Nature; 2023:349-370. doi:<a href=\"https://doi.org/10.1007/978-3-031-30829-1_17\">10.1007/978-3-031-30829-1_17</a>"},"day":"21"},{"date_published":"2023-03-16T00:00:00Z","external_id":{"isi":["000961542100001"],"pmid":["PPR559293 "]},"scopus_import":"1","date_created":"2023-01-31T08:13:40Z","department":[{"_id":"SyCr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","intvolume":"        14","publisher":"Frontiers","year":"2023","oa":1,"article_type":"original","article_number":"1119002","publication":"Frontiers in Microbiology","date_updated":"2023-08-01T12:39:58Z","oa_version":"Published Version","day":"16","citation":{"chicago":"Viljakainen, Lumi, Matthias Fürst, Anna V Grasse, Jaana Jurvansuu, Jinook Oh, Lassi Tolonen, Thomas Eder, Thomas Rattei, and Sylvia Cremer. “Antiviral Immune Response Reveals Host-Specific Virus Infections in Natural Ant Populations.” <i>Frontiers in Microbiology</i>. Frontiers, 2023. <a href=\"https://doi.org/10.3389/fmicb.2023.1119002\">https://doi.org/10.3389/fmicb.2023.1119002</a>.","mla":"Viljakainen, Lumi, et al. “Antiviral Immune Response Reveals Host-Specific Virus Infections in Natural Ant Populations.” <i>Frontiers in Microbiology</i>, vol. 14, 1119002, Frontiers, 2023, doi:<a href=\"https://doi.org/10.3389/fmicb.2023.1119002\">10.3389/fmicb.2023.1119002</a>.","ama":"Viljakainen L, Fürst M, Grasse AV, et al. Antiviral immune response reveals host-specific virus infections in natural ant populations. <i>Frontiers in Microbiology</i>. 2023;14. doi:<a href=\"https://doi.org/10.3389/fmicb.2023.1119002\">10.3389/fmicb.2023.1119002</a>","ista":"Viljakainen L, Fürst M, Grasse AV, Jurvansuu J, Oh J, Tolonen L, Eder T, Rattei T, Cremer S. 2023. Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. 14, 1119002.","short":"L. Viljakainen, M. Fürst, A.V. Grasse, J. Jurvansuu, J. Oh, L. Tolonen, T. Eder, T. Rattei, S. Cremer, Frontiers in Microbiology 14 (2023).","apa":"Viljakainen, L., Fürst, M., Grasse, A. V., Jurvansuu, J., Oh, J., Tolonen, L., … Cremer, S. (2023). Antiviral immune response reveals host-specific virus infections in natural ant populations. <i>Frontiers in Microbiology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fmicb.2023.1119002\">https://doi.org/10.3389/fmicb.2023.1119002</a>","ieee":"L. Viljakainen <i>et al.</i>, “Antiviral immune response reveals host-specific virus infections in natural ant populations,” <i>Frontiers in Microbiology</i>, vol. 14. Frontiers, 2023."},"ddc":["570"],"file_date_updated":"2023-04-17T07:49:09Z","pmid":1,"month":"03","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","volume":14,"file":[{"file_id":"12843","date_created":"2023-04-17T07:49:09Z","success":1,"date_updated":"2023-04-17T07:49:09Z","access_level":"open_access","checksum":"cd52292963acce1111634d9fac08c699","content_type":"application/pdf","file_name":"2023_FrontMicrobiology_Viljakainen.pdf","file_size":4866332,"relation":"main_file","creator":"dernst"}],"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"},"abstract":[{"lang":"eng","text":"Hosts can carry many viruses in their bodies, but not all of them cause disease. We studied ants as a social host to determine both their overall viral repertoire and the subset of actively infecting viruses across natural populations of three subfamilies: the Argentine ant (Linepithema humile, Dolichoderinae), the invasive garden ant (Lasius neglectus, Formicinae) and the red ant (Myrmica rubra, Myrmicinae). We used a dual sequencing strategy to reconstruct complete virus genomes by RNA-seq and to simultaneously determine the small interfering RNAs (siRNAs) by small RNA sequencing (sRNA-seq), which constitute the host antiviral RNAi immune response. This approach led to the discovery of 41 novel viruses in ants and revealed a host ant-specific RNAi response (21 vs. 22 nt siRNAs) in the different ant species. The efficiency of the RNAi response (sRNA/RNA read count ratio) depended on the virus and the respective ant species, but not its population. Overall, we found the highest virus abundance and diversity per population in Li. humile, followed by La. neglectus and M. rubra. Argentine ants also shared a high proportion of viruses between populations, whilst overlap was nearly absent in M. rubra. Only one of the 59 viruses was found to infect two of the ant species as hosts, revealing high host-specificity in active infections. In contrast, six viruses actively infected one ant species, but were found as contaminants only in the others. Disentangling spillover of disease-causing infection from non-infecting contamination across species is providing relevant information for disease ecology and ecosystem management."}],"doi":"10.3389/fmicb.2023.1119002","author":[{"full_name":"Viljakainen, Lumi","last_name":"Viljakainen","first_name":"Lumi"},{"id":"393B1196-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","full_name":"Fürst, Matthias","last_name":"Fürst","orcid":"0000-0002-3712-925X"},{"first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","full_name":"Grasse, Anna V"},{"full_name":"Jurvansuu, Jaana","last_name":"Jurvansuu","first_name":"Jaana"},{"id":"403169A4-080F-11EA-9993-BF3F3DDC885E","first_name":"Jinook","full_name":"Oh, Jinook","last_name":"Oh","orcid":"0000-0001-7425-2372"},{"last_name":"Tolonen","full_name":"Tolonen, Lassi","first_name":"Lassi"},{"full_name":"Eder, Thomas","last_name":"Eder","first_name":"Thomas"},{"full_name":"Rattei, Thomas","last_name":"Rattei","first_name":"Thomas"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"}],"title":"Antiviral immune response reveals host-specific virus infections in natural ant populations","_id":"12469","publication_status":"published","acknowledgement":"We thank D.J. Obbard for sharing the details of the dual RNA-seq/sRNA-seq approach, S.\r\nMetzler and R. Ferrigato for the photographs (Figure 1), M. Konrad, B. Casillas-Perez, C.D.\r\nPull and X. Espadaler for help with ant collection, and the Social Immunity Team at IST\r\nAustria, in particular J. Robb, A. Franschitz, E. Naderlinger, E. Dawson and B. Casillas-Perez\r\nfor support and comments on the manuscript. The study was funded by the Austrian Science\r\nFund (FWF; M02076-B25 to MAF) and the Academy of Finland (343022 to LV). ","status":"public","publication_identifier":{"eissn":["1664-302X"]},"project":[{"call_identifier":"FWF","name":"Viral pathogens and social immunity in ants","grant_number":"M02076","_id":"25DF61D8-B435-11E9-9278-68D0E5697425"}]},{"publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"date_created":"2023-01-31T15:10:53Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"date_published":"2023-01-09T00:00:00Z","date_updated":"2023-08-31T12:26:58Z","page":"201","related_material":{"record":[{"id":"11943","relation":"part_of_dissertation","status":"public"},{"id":"11950","status":"public","relation":"part_of_dissertation"}]},"oa":1,"alternative_title":["ISTA Thesis"],"year":"2023","file":[{"relation":"main_file","file_size":41771714,"creator":"cchlebak","file_name":"20230109_PhD_thesis_JM_final.pdf","embargo":"2023-07-09","content_type":"application/pdf","checksum":"1a2306e5f59f52df598e7ecfadf921ac","access_level":"open_access","date_updated":"2023-07-27T22:30:54Z","date_created":"2023-01-31T15:11:42Z","file_id":"12471"},{"file_name":"20230109_PhD_thesis_JM_final.docx","creator":"cchlebak","file_size":66983464,"relation":"source_file","date_updated":"2023-07-10T22:30:04Z","access_level":"closed","checksum":"0bebbdee0773443959e1f6ab8caf281f","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12472","date_created":"2023-01-31T15:11:51Z","embargo_to":"open_access"}],"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"},"degree_awarded":"PhD","article_processing_charge":"No","has_accepted_license":"1","ddc":["610"],"file_date_updated":"2023-07-27T22:30:54Z","month":"01","citation":{"mla":"Michalska, Julia M. <i>A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12470\">10.15479/at:ista:12470</a>.","chicago":"Michalska, Julia M. “A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12470\">https://doi.org/10.15479/at:ista:12470</a>.","ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria.","ama":"Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12470\">10.15479/at:ista:12470</a>","short":"J.M. Michalska, A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy, Institute of Science and Technology Austria, 2023.","ieee":"J. M. Michalska, “A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy,” Institute of Science and Technology Austria, 2023.","apa":"Michalska, J. M. (2023). <i>A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12470\">https://doi.org/10.15479/at:ista:12470</a>"},"day":"09","oa_version":"Published Version","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","call_identifier":"FWF"}],"publication_identifier":{"issn":["2663-337X"],"isbn":[" 978-3-99078-026-8"]},"ec_funded":1,"publication_status":"published","status":"public","_id":"12470","title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","supervisor":[{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"}],"author":[{"orcid":"0000-0003-3862-1235","full_name":"Michalska, Julia M","last_name":"Michalska","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","first_name":"Julia M"}],"doi":"10.15479/at:ista:12470","abstract":[{"text":"The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of \r\nconnections that orchestrate our cognition and behavior. To decode its complex connectivity, it is \r\npivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (super\u0002resolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular\r\nspace, that is compatible with chemical fixation, with information on molecular markers, super\u0002resolved data acquisition and machine-learning based data analysis for segmentation and synapse \r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with light microscopy.","lang":"eng"}]},{"file":[{"file_id":"13322","date_created":"2023-07-31T07:16:34Z","access_level":"open_access","content_type":"application/pdf","checksum":"7dd322347512afaa5daf72a0154f2f07","success":1,"date_updated":"2023-07-31T07:16:34Z","file_name":"2023_FrontiersMicrobiology_Guet.pdf","creator":"dernst","file_size":6452841,"relation":"main_file"}],"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":14,"article_processing_charge":"Yes","citation":{"chicago":"Guet, Calin C, L Bruneaux, P Oikonomou, M Aldana, and P Cluzel. “Monitoring Lineages of Growing and Dividing Bacteria Reveals an Inducible Memory of <i>Mar</i> Operon Expression.” <i>Frontiers in Microbiology</i>. Frontiers, 2023. <a href=\"https://doi.org/10.3389/fmicb.2023.1049255\">https://doi.org/10.3389/fmicb.2023.1049255</a>.","mla":"Guet, Calin C., et al. “Monitoring Lineages of Growing and Dividing Bacteria Reveals an Inducible Memory of <i>Mar</i> Operon Expression.” <i>Frontiers in Microbiology</i>, vol. 14, 1049255, Frontiers, 2023, doi:<a href=\"https://doi.org/10.3389/fmicb.2023.1049255\">10.3389/fmicb.2023.1049255</a>.","ista":"Guet CC, Bruneaux L, Oikonomou P, Aldana M, Cluzel P. 2023. Monitoring lineages of growing and dividing bacteria reveals an inducible memory of <i>mar</i> operon expression. Frontiers in Microbiology. 14, 1049255.","short":"C.C. Guet, L. Bruneaux, P. Oikonomou, M. Aldana, P. Cluzel, Frontiers in Microbiology 14 (2023).","ama":"Guet CC, Bruneaux L, Oikonomou P, Aldana M, Cluzel P. Monitoring lineages of growing and dividing bacteria reveals an inducible memory of <i>mar</i> operon expression. <i>Frontiers in Microbiology</i>. 2023;14. doi:<a href=\"https://doi.org/10.3389/fmicb.2023.1049255\">10.3389/fmicb.2023.1049255</a>","apa":"Guet, C. C., Bruneaux, L., Oikonomou, P., Aldana, M., &#38; Cluzel, P. (2023). Monitoring lineages of growing and dividing bacteria reveals an inducible memory of <i>mar</i> operon expression. <i>Frontiers in Microbiology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fmicb.2023.1049255\">https://doi.org/10.3389/fmicb.2023.1049255</a>","ieee":"C. C. Guet, L. Bruneaux, P. Oikonomou, M. Aldana, and P. Cluzel, “Monitoring lineages of growing and dividing bacteria reveals an inducible memory of <i>mar</i> operon expression,” <i>Frontiers in Microbiology</i>, vol. 14. Frontiers, 2023."},"day":"20","month":"06","pmid":1,"file_date_updated":"2023-07-31T07:16:34Z","ddc":["570"],"oa_version":"Published Version","publication_identifier":{"eissn":["1664-302X"]},"acknowledgement":"This work was supported by NIH P50 award P50GM081892-02 to the University of Chicago, a catalyst grant from the Chicago Biomedical Consortium with support from The Searle Funds at The Chicago Community Trust to PC, and a Yen Fellowship to CCG. MA was partially supported by PAPIIT-UNAM grant IN-11322.","status":"public","publication_status":"published","title":"Monitoring lineages of growing and dividing bacteria reveals an inducible memory of <i>mar</i> operon expression","author":[{"last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"full_name":"Bruneaux, L","last_name":"Bruneaux","first_name":"L"},{"last_name":"Oikonomou","full_name":"Oikonomou, P","first_name":"P"},{"full_name":"Aldana, M","last_name":"Aldana","first_name":"M"},{"first_name":"P","full_name":"Cluzel, P","last_name":"Cluzel"}],"_id":"12478","abstract":[{"text":"In Gram negative bacteria, the multiple antibiotic resistance or mar operon, is known to control the expression of multi-drug efflux genes that protect bacteria from a wide range of drugs. As many different chemical compounds can induce this operon, identifying the parameters that govern the dynamics of its induction is crucial to better characterize the processes of tolerance and resistance. Most experiments have assumed that the properties of the mar transcriptional network can be inferred from population measurements. However, measurements from an asynchronous population of cells can mask underlying phenotypic variations of single cells. We monitored the activity of the mar promoter in single Escherichia coli cells in linear micro-colonies and established that the response to a steady level of inducer was most heterogeneous within individual colonies for an intermediate value of inducer. Specifically, sub-lineages defined by contiguous daughter-cells exhibited similar promoter activity, whereas activity was greatly variable between different sub-lineages. Specific sub-trees of uniform promoter activity persisted over several generations. Statistical analyses of the lineages suggest that the presence of these sub-trees is the signature of an inducible memory of the promoter state that is transmitted from mother to daughter cells. This single-cell study reveals that the degree of epigenetic inheritance changes as a function of inducer concentration, suggesting that phenotypic inheritance may be an inducible phenotype.","lang":"eng"}],"doi":"10.3389/fmicb.2023.1049255","publisher":"Frontiers","intvolume":"        14","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"CaGu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["37485524"],"isi":["001030002600001"]},"date_published":"2023-06-20T00:00:00Z","date_created":"2023-02-02T08:13:28Z","scopus_import":"1","publication":"Frontiers in Microbiology","date_updated":"2023-08-02T06:25:04Z","article_number":"1049255","article_type":"original","oa":1,"year":"2023"},{"oa_version":"Submitted Version","citation":{"chicago":"Agresti, Antonio. “Delayed Blow-up and Enhanced Diffusion by Transport Noise for Systems of Reaction-Diffusion Equations.” <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s40072-023-00319-4\">https://doi.org/10.1007/s40072-023-00319-4</a>.","mla":"Agresti, Antonio. “Delayed Blow-up and Enhanced Diffusion by Transport Noise for Systems of Reaction-Diffusion Equations.” <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s40072-023-00319-4\">10.1007/s40072-023-00319-4</a>.","ama":"Agresti A. Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations. <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>. 2023. doi:<a href=\"https://doi.org/10.1007/s40072-023-00319-4\">10.1007/s40072-023-00319-4</a>","ista":"Agresti A. 2023. Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations. Stochastics and Partial Differential Equations: Analysis and Computations.","short":"A. Agresti, Stochastics and Partial Differential Equations: Analysis and Computations (2023).","ieee":"A. Agresti, “Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations,” <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>. Springer Nature, 2023.","apa":"Agresti, A. (2023). Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations. <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40072-023-00319-4\">https://doi.org/10.1007/s40072-023-00319-4</a>"},"day":"28","month":"11","ddc":["510"],"has_accepted_license":"1","article_processing_charge":"No","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"},"abstract":[{"lang":"eng","text":"This paper is concerned with the problem of regularization by noise of systems of reaction–diffusion equations with mass control. It is known that strong solutions to such systems of PDEs may blow-up in finite time. Moreover, for many systems of practical interest, establishing whether the blow-up occurs or not is an open question. Here we prove that a suitable multiplicative noise of transport type has a regularizing effect. More precisely, for both a sufficiently noise intensity and a high spectrum, the blow-up of strong solutions is delayed up to an arbitrary large time. Global existence is shown for the case of exponentially decreasing mass. The proofs combine and extend recent developments in regularization by noise and in the Lp(Lq)-approach to stochastic PDEs, highlighting new connections between the two areas."}],"doi":"10.1007/s40072-023-00319-4","title":"Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations","author":[{"full_name":"Agresti, Antonio","last_name":"Agresti","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","first_name":"Antonio","orcid":"0000-0002-9573-2962"}],"_id":"12486","status":"public","publication_status":"epub_ahead","acknowledgement":"The author has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 948819).\r\nThe author thanks Lorenzo Dello Schiavo, Lucio Galeati and Mark Veraar for helpful comments. The author acknowledges Caterina Balzotti for her support in creating the picture. The author\r\nthanks the anonymous referee for helpful comments. ","ec_funded":1,"publication_identifier":{"eissn":["2194-041X"],"issn":["2194-0401"]},"project":[{"_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819","call_identifier":"H2020","name":"Bridging Scales in Random Materials"}],"date_published":"2023-11-28T00:00:00Z","external_id":{"arxiv":["2207.08293"]},"date_created":"2023-02-02T10:45:47Z","scopus_import":"1","department":[{"_id":"JuFi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s40072-023-00319-4"}],"year":"2023","oa":1,"article_type":"original","publication":"Stochastics and Partial Differential Equations: Analysis and Computations","date_updated":"2023-12-18T07:53:45Z"},{"citation":{"mla":"Scarpetta, Silvia, et al. “Criticality of Neuronal Avalanches in Human Sleep and Their Relationship with Sleep Macro- and Micro-Architecture.” <i>IScience</i>, vol. 26, no. 10, Elsevier, 2023, p. 107840, doi:<a href=\"https://doi.org/10.1016/j.isci.2023.107840\">10.1016/j.isci.2023.107840</a>.","chicago":"Scarpetta, Silvia, Niccolò Morrisi, Carlotta Mutti, Nicoletta Azzi, Irene Trippi, Rosario Ciliento, Ilenia Apicella, et al. “Criticality of Neuronal Avalanches in Human Sleep and Their Relationship with Sleep Macro- and Micro-Architecture.” <i>IScience</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.isci.2023.107840\">https://doi.org/10.1016/j.isci.2023.107840</a>.","apa":"Scarpetta, S., Morrisi, N., Mutti, C., Azzi, N., Trippi, I., Ciliento, R., … Vaudano, A. E. (2023). Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2023.107840\">https://doi.org/10.1016/j.isci.2023.107840</a>","ieee":"S. Scarpetta <i>et al.</i>, “Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture,” <i>iScience</i>, vol. 26, no. 10. Elsevier, p. 107840, 2023.","ama":"Scarpetta S, Morrisi N, Mutti C, et al. Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. <i>iScience</i>. 2023;26(10):107840. doi:<a href=\"https://doi.org/10.1016/j.isci.2023.107840\">10.1016/j.isci.2023.107840</a>","short":"S. Scarpetta, N. Morrisi, C. Mutti, N. Azzi, I. Trippi, R. Ciliento, I. Apicella, G. Messuti, M. Angiolelli, F. Lombardi, L. Parrino, A.E. Vaudano, IScience 26 (2023) 107840.","ista":"Scarpetta S, Morrisi N, Mutti C, Azzi N, Trippi I, Ciliento R, Apicella I, Messuti G, Angiolelli M, Lombardi F, Parrino L, Vaudano AE. 2023. Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. iScience. 26(10), 107840."},"day":"20","ddc":["570"],"pmid":1,"month":"10","file_date_updated":"2023-10-09T07:23:46Z","oa_version":"Published Version","file":[{"file_name":"2023_iScience_Scarpetta.pdf","creator":"dernst","relation":"main_file","file_size":4872708,"access_level":"open_access","content_type":"application/pdf","checksum":"f499836af172ecc9865de4bb41fa99d1","success":1,"date_updated":"2023-10-09T07:23:46Z","file_id":"14412","date_created":"2023-10-09T07:23:46Z"}],"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":26,"article_processing_charge":"Yes","title":"Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture","author":[{"last_name":"Scarpetta","full_name":"Scarpetta, Silvia","first_name":"Silvia"},{"first_name":"Niccolò","last_name":"Morrisi","full_name":"Morrisi, Niccolò"},{"first_name":"Carlotta","last_name":"Mutti","full_name":"Mutti, Carlotta"},{"first_name":"Nicoletta","last_name":"Azzi","full_name":"Azzi, Nicoletta"},{"last_name":"Trippi","full_name":"Trippi, Irene","first_name":"Irene"},{"first_name":"Rosario","full_name":"Ciliento, Rosario","last_name":"Ciliento"},{"last_name":"Apicella","full_name":"Apicella, Ilenia","first_name":"Ilenia"},{"full_name":"Messuti, Giovanni","last_name":"Messuti","first_name":"Giovanni"},{"last_name":"Angiolelli","full_name":"Angiolelli, Marianna","first_name":"Marianna"},{"orcid":"0000-0003-2623-5249","last_name":"Lombardi","full_name":"Lombardi, Fabrizio","first_name":"Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"first_name":"Liborio","last_name":"Parrino","full_name":"Parrino, Liborio"},{"last_name":"Vaudano","full_name":"Vaudano, Anna Elisabetta","first_name":"Anna Elisabetta"}],"_id":"12487","abstract":[{"lang":"eng","text":"Sleep plays a key role in preserving brain function, keeping the brain network in a state that ensures optimal computational capabilities. Empirical evidence indicates that such a state is consistent with criticality, where scale-free neuronal avalanches emerge. However, the relationship between sleep, emergent avalanches, and criticality remains poorly understood. Here we fully characterize the critical behavior of avalanches during sleep, and study their relationship with the sleep macro- and micro-architecture, in particular the cyclic alternating pattern (CAP). We show that avalanche size and duration distributions exhibit robust power laws with exponents approximately equal to −3/2 e −2, respectively. Importantly, we find that sizes scale as a power law of the durations, and that all critical exponents for neuronal avalanches obey robust scaling relations, which are consistent with the mean-field directed percolation universality class. Our analysis demonstrates that avalanche dynamics depends on the position within the NREM-REM cycles, with the avalanche density increasing in the descending phases and decreasing in the ascending phases of sleep cycles. Moreover, we show that, within NREM sleep, avalanche occurrence correlates with CAP activation phases, particularly A1, which are the expression of slow wave sleep propensity and have been proposed to be beneficial for cognitive processes. The results suggest that neuronal avalanches, and thus tuning to criticality, actively contribute to sleep development and play a role in preserving network function. Such findings, alongside characterization of the universality class for avalanches, open new avenues to the investigation of functional role of criticality during sleep with potential clinical application.</jats:p><jats:sec><jats:title>Significance statement</jats:title><jats:p>We fully characterize the critical behavior of neuronal avalanches during sleep, and show that avalanches follow precise scaling laws that are consistent with the mean-field directed percolation universality class. The analysis provides first evidence of a functional relationship between avalanche occurrence, slow-wave sleep dynamics, sleep stage transitions and occurrence of CAP phase A during NREM sleep. Because CAP is considered one of the major guardians of NREM sleep that allows the brain to dynamically react to external perturbation and contributes to the cognitive consolidation processes occurring in sleep, our observations suggest that neuronal avalanches at criticality are associated with flexible response to external inputs and to cognitive processes, a key assumption of the critical brain hypothesis."}],"issue":"10","doi":"10.1016/j.isci.2023.107840","publication_identifier":{"eissn":["2589-0042"]},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"M03318","_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67","name":"Functional Advantages of Critical Brain Dynamics"}],"publication_status":"published","status":"public","acknowledgement":"FL acknowledges support from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411, and from the Austrian Science Fund (FWF) under the Lise Meitner fellowship No. PT1013M03318. IA acknowledges financial support from the MIUR PRIN 2017WZFTZP.","ec_funded":1,"department":[{"_id":"GaTk"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["37766992"],"isi":["001082331200001"]},"date_published":"2023-10-20T00:00:00Z","date_created":"2023-02-02T10:50:17Z","scopus_import":"1","publisher":"Elsevier","intvolume":"        26","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"oa":1,"year":"2023","publication":"iScience","date_updated":"2023-12-13T11:11:24Z","page":"107840","article_type":"original"},{"abstract":[{"lang":"eng","text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions."}],"doi":"10.15479/at:ista:12491","supervisor":[{"full_name":"Schur, Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","orcid":"0000-0003-4790-8078"}],"title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","author":[{"full_name":"Zens, Bettina","last_name":"Zens","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina"}],"_id":"12491","status":"public","publication_status":"published","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-027-5"]},"project":[{"_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3","name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"}],"oa_version":"Published Version","citation":{"mla":"Zens, Bettina. <i>Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12491\">10.15479/at:ista:12491</a>.","chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12491\">https://doi.org/10.15479/at:ista:12491</a>.","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12491\">10.15479/at:ista:12491</a>","ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","apa":"Zens, B. (2023). <i>Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12491\">https://doi.org/10.15479/at:ista:12491</a>"},"day":"02","month":"02","ddc":["570"],"file_date_updated":"2024-02-08T23:30:04Z","has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","file":[{"file_id":"12527","date_created":"2023-02-07T13:07:38Z","access_level":"open_access","content_type":"application/pdf","checksum":"069d87f025e0799bf9e3c375664264f2","date_updated":"2024-02-08T23:30:04Z","file_name":"PhDThesis_BettinaZens_2023_final.pdf","file_size":23082464,"relation":"main_file","creator":"bzens","embargo":"2024-02-07"},{"file_id":"12528","date_created":"2023-02-07T13:09:05Z","embargo_to":"open_access","date_updated":"2024-02-08T23:30:04Z","access_level":"closed","checksum":"8c66ed203495d6e078ed1002a866520c","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"PhDThesis_BettinaZens_2023_final.docx","creator":"bzens","file_size":106169509,"relation":"source_file"}],"year":"2023","alternative_title":["ISTA Thesis"],"keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"],"oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8586"}]},"page":"187","date_updated":"2024-02-08T23:30:05Z","date_published":"2023-02-02T00:00:00Z","date_created":"2023-02-02T14:50:20Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"department":[{"_id":"GradSch"},{"_id":"FlSc"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria"},{"status":"public","related_material":{"record":[{"id":"12675","status":"public","relation":"used_in_publication"}]},"date_updated":"2024-02-21T12:14:06Z","keyword":["aromatic side chains","isotopic labeling","protein dynamics","ring flips","spin relaxation"],"doi":"10.15479/AT:ISTA:12497","year":"2023","abstract":[{"lang":"eng","text":"Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein–protein interactions. We studied aromatic residues in the two structurally homologous cross-β amyloid fibrils HET-s, and  HELLF by employing a specific isotope-labeling approach and magic-angle-spinning NMR. The dynamic behavior of the aromatic residues Phe and Tyr indicates that the hydrophobic amyloid core is rigid, without any sign of \"breathing motions\" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips on a variety of time scales from nanoseconds to microseconds. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from an NMR structural ensemble of such amyloid cross-β architecture."}],"_id":"12497","author":[{"full_name":"Becker, Lea Marie","last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","first_name":"Lea Marie","orcid":"0000-0002-6401-5151"},{"orcid":"0000-0002-9350-7606","last_name":"Schanda","full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"title":"Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues","oa":1,"type":"research_data","article_processing_charge":"No","contributor":[{"first_name":"Mélanie","last_name":"Berbon","contributor_type":"researcher"},{"contributor_type":"researcher","last_name":"Vallet","first_name":"Alicia"},{"contributor_type":"researcher","first_name":"Axelle","last_name":"Grelard"},{"first_name":"Estelle","last_name":"Morvan","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Benjamin","last_name":"Bardiaux"},{"last_name":"Lichtenecker","first_name":"Roman","contributor_type":"researcher"},{"last_name":"Ernst","first_name":"Matthias","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Antoine","last_name":"Loquet"},{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","orcid":"0000-0002-9350-7606","contributor_type":"contact_person"},{"contributor_type":"researcher","orcid":"0000-0002-6401-5151","last_name":"Becker","first_name":"Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79"}],"has_accepted_license":"1","file":[{"file_name":"Research_Data.zip","file_size":87018103,"relation":"main_file","creator":"lbecker","date_updated":"2023-03-24T09:34:20Z","access_level":"open_access","content_type":"application/zip","checksum":"fd9a28620a81a82991fb70f4fd6591d9","file_id":"12743","date_created":"2023-03-23T10:03:16Z"},{"date_created":"2023-03-24T07:13:55Z","file_id":"12755","creator":"dernst","relation":"main_file","file_size":747,"file_name":"README.txt","checksum":"30ebdfb600af118fcf8518b6efe0b7e9","content_type":"text/plain","access_level":"open_access","date_updated":"2023-03-24T09:42:03Z"}],"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)"},"publisher":"Institute of Science and Technology Austria","date_created":"2023-02-03T08:08:02Z","oa_version":"Published Version","date_published":"2023-03-23T00:00:00Z","month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-03-24T09:42:03Z","ddc":["572"],"day":"23","department":[{"_id":"GradSch"},{"_id":"PaSc"}],"citation":{"ista":"Becker LM, Schanda P. 2023. Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12497\">10.15479/AT:ISTA:12497</a>.","ama":"Becker LM, Schanda P. Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12497\">10.15479/AT:ISTA:12497</a>","short":"L.M. Becker, P. Schanda, (2023).","ieee":"L. M. Becker and P. Schanda, “Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues.” Institute of Science and Technology Austria, 2023.","apa":"Becker, L. M., &#38; Schanda, P. (2023). Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12497\">https://doi.org/10.15479/AT:ISTA:12497</a>","mla":"Becker, Lea Marie, and Paul Schanda. <i>Research Data to: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12497\">10.15479/AT:ISTA:12497</a>.","chicago":"Becker, Lea Marie, and Paul Schanda. “Research Data to: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12497\">https://doi.org/10.15479/AT:ISTA:12497</a>."}},{"page":"318-328","article_type":"original","date_updated":"2023-08-01T12:58:30Z","publication":"Evolution: International journal of organic evolution","year":"2023","oa":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"publisher":"Oxford University Press","main_file_link":[{"url":"https://doi.org/10.1093/evolut/qpac004","open_access":"1"}],"intvolume":"        77","date_created":"2023-02-05T23:00:59Z","scopus_import":"1","date_published":"2023-01-01T00:00:00Z","external_id":{"pmid":["36622661"],"isi":["001021686300024"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"NiBa"}],"status":"public","publication_status":"published","acknowledgement":"The authors of this article were supported by LMU Munich (J.B.W.W.), a James S. McDonnell Foundation postdoctoral fellowship (A.K.H.). P.N. received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant agreement No. 770826 EE-Dynamics).\r\nWe thank participants in the 2019 Gordon Conference on Speciation for the extensive conversation on this topic. Thanks to Dan Funk for providing permission to use data from Funk et al. 2006, and for comments on the manuscript.","publication_identifier":{"eissn":["1558-5646"]},"doi":"10.1093/evolut/qpac004","abstract":[{"text":"The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model.","lang":"eng"}],"issue":"1","_id":"12514","title":"A multivariate view of the speciation continuum","author":[{"last_name":"Bolnick","full_name":"Bolnick, Daniel I.","first_name":"Daniel I."},{"last_name":"Hund","full_name":"Hund, Amanda K.","first_name":"Amanda K."},{"full_name":"Nosil, Patrik","last_name":"Nosil","first_name":"Patrik"},{"full_name":"Peng, Foen","last_name":"Peng","first_name":"Foen"},{"last_name":"Ravinet","full_name":"Ravinet, Mark","first_name":"Mark"},{"full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"},{"last_name":"Subramanian","full_name":"Subramanian, Swapna","first_name":"Swapna"},{"last_name":"Wolf","full_name":"Wolf, Jochen B.W.","first_name":"Jochen B.W."},{"first_name":"Roman","last_name":"Yukilevich","full_name":"Yukilevich, Roman"}],"volume":77,"article_processing_charge":"No","oa_version":"Published Version","pmid":1,"month":"01","citation":{"mla":"Bolnick, Daniel I., et al. “A Multivariate View of the Speciation Continuum.” <i>Evolution: International Journal of Organic Evolution</i>, vol. 77, no. 1, Oxford University Press, 2023, pp. 318–28, doi:<a href=\"https://doi.org/10.1093/evolut/qpac004\">10.1093/evolut/qpac004</a>.","chicago":"Bolnick, Daniel I., Amanda K. Hund, Patrik Nosil, Foen Peng, Mark Ravinet, Sean Stankowski, Swapna Subramanian, Jochen B.W. Wolf, and Roman Yukilevich. “A Multivariate View of the Speciation Continuum.” <i>Evolution: International Journal of Organic Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evolut/qpac004\">https://doi.org/10.1093/evolut/qpac004</a>.","ista":"Bolnick DI, Hund AK, Nosil P, Peng F, Ravinet M, Stankowski S, Subramanian S, Wolf JBW, Yukilevich R. 2023. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 77(1), 318–328.","short":"D.I. Bolnick, A.K. Hund, P. Nosil, F. Peng, M. Ravinet, S. Stankowski, S. Subramanian, J.B.W. Wolf, R. Yukilevich, Evolution: International Journal of Organic Evolution 77 (2023) 318–328.","ama":"Bolnick DI, Hund AK, Nosil P, et al. A multivariate view of the speciation continuum. <i>Evolution: International journal of organic evolution</i>. 2023;77(1):318-328. doi:<a href=\"https://doi.org/10.1093/evolut/qpac004\">10.1093/evolut/qpac004</a>","ieee":"D. I. Bolnick <i>et al.</i>, “A multivariate view of the speciation continuum,” <i>Evolution: International journal of organic evolution</i>, vol. 77, no. 1. Oxford University Press, pp. 318–328, 2023.","apa":"Bolnick, D. I., Hund, A. K., Nosil, P., Peng, F., Ravinet, M., Stankowski, S., … Yukilevich, R. (2023). A multivariate view of the speciation continuum. <i>Evolution: International Journal of Organic Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolut/qpac004\">https://doi.org/10.1093/evolut/qpac004</a>"},"day":"01"},{"publisher":"Frontiers","intvolume":"        16","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"PeJo"}],"date_created":"2023-02-05T23:01:00Z","scopus_import":"1","external_id":{"pmid":["36704406"],"isi":["000919786900001"]},"date_published":"2023-01-10T00:00:00Z","date_updated":"2023-08-16T11:37:52Z","publication":"Frontiers in Neuroanatomy","article_number":"1097467","article_type":"original","oa":1,"year":"2023","file":[{"file_id":"12518","date_created":"2023-02-06T07:56:14Z","access_level":"open_access","checksum":"49cd40f3bda6f267079427042e7d15e3","content_type":"application/pdf","success":1,"date_updated":"2023-02-06T07:56:14Z","file_name":"2022_FrontiersNeuroanatomy_OrtizLeal.pdf","creator":"dernst","relation":"main_file","file_size":21943473}],"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"},"article_processing_charge":"No","volume":16,"has_accepted_license":"1","pmid":1,"month":"01","file_date_updated":"2023-02-06T07:56:14Z","ddc":["570"],"citation":{"ista":"Ortiz-Leal I, Torres MV, Vargas Barroso VM, Fidalgo LE, López-Beceiro AM, Larriva-Sahd JA, Sánchez-Quinteiro P. 2023. The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. 16, 1097467.","short":"I. Ortiz-Leal, M.V. Torres, V.M. Vargas Barroso, L.E. Fidalgo, A.M. López-Beceiro, J.A. Larriva-Sahd, P. Sánchez-Quinteiro, Frontiers in Neuroanatomy 16 (2023).","ama":"Ortiz-Leal I, Torres MV, Vargas Barroso VM, et al. The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. <i>Frontiers in Neuroanatomy</i>. 2023;16. doi:<a href=\"https://doi.org/10.3389/fnana.2022.1097467\">10.3389/fnana.2022.1097467</a>","ieee":"I. Ortiz-Leal <i>et al.</i>, “The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway,” <i>Frontiers in Neuroanatomy</i>, vol. 16. Frontiers, 2023.","apa":"Ortiz-Leal, I., Torres, M. V., Vargas Barroso, V. M., Fidalgo, L. E., López-Beceiro, A. M., Larriva-Sahd, J. A., &#38; Sánchez-Quinteiro, P. (2023). The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. <i>Frontiers in Neuroanatomy</i>. Frontiers. <a href=\"https://doi.org/10.3389/fnana.2022.1097467\">https://doi.org/10.3389/fnana.2022.1097467</a>","chicago":"Ortiz-Leal, Irene, Mateo V. Torres, Victor M Vargas Barroso, Luis Eusebio Fidalgo, Ana María López-Beceiro, Jorge A. Larriva-Sahd, and Pablo Sánchez-Quinteiro. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” <i>Frontiers in Neuroanatomy</i>. Frontiers, 2023. <a href=\"https://doi.org/10.3389/fnana.2022.1097467\">https://doi.org/10.3389/fnana.2022.1097467</a>.","mla":"Ortiz-Leal, Irene, et al. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” <i>Frontiers in Neuroanatomy</i>, vol. 16, 1097467, Frontiers, 2023, doi:<a href=\"https://doi.org/10.3389/fnana.2022.1097467\">10.3389/fnana.2022.1097467</a>."},"day":"10","oa_version":"Published Version","publication_identifier":{"eissn":["1662-5129"]},"status":"public","acknowledgement":"This work was partially supported by a grant from “Consello Social Universidade de Santiago de Compostela” 2022-PU004.We would like to show special gratitude to Prof. Ludwig Wagner (Medical University, Vienna) for kindly providing us with the secretagogin antibody. We thank the Wildlife Recovery Centres of Galicia, Dirección Xeral de Patrimonio Natural (Xunta de Galicia, Spain), and Federación Galega de Caza for providing the red foxes used in this study.","publication_status":"published","_id":"12515","title":"The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway","author":[{"first_name":"Irene","full_name":"Ortiz-Leal, Irene","last_name":"Ortiz-Leal"},{"first_name":"Mateo V.","full_name":"Torres, Mateo V.","last_name":"Torres"},{"first_name":"Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","last_name":"Vargas Barroso","full_name":"Vargas Barroso, Victor M"},{"first_name":"Luis Eusebio","last_name":"Fidalgo","full_name":"Fidalgo, Luis Eusebio"},{"last_name":"López-Beceiro","full_name":"López-Beceiro, Ana María","first_name":"Ana María"},{"first_name":"Jorge A.","last_name":"Larriva-Sahd","full_name":"Larriva-Sahd, Jorge A."},{"full_name":"Sánchez-Quinteiro, Pablo","last_name":"Sánchez-Quinteiro","first_name":"Pablo"}],"doi":"10.3389/fnana.2022.1097467","abstract":[{"text":"Introduction: The olfactory system in most mammals is divided into several subsystems based on the anatomical locations of the neuroreceptor cells involved and the receptor families that are expressed. In addition to the main olfactory system and the vomeronasal system, a range of olfactory subsystems converge onto the transition zone located between the main olfactory bulb (MOB) and the accessory olfactory bulb (AOB), which has been termed the olfactory limbus (OL). The OL contains specialized glomeruli that receive noncanonical sensory afferences and which interact with the MOB and AOB. Little is known regarding the olfactory subsystems of mammals other than laboratory rodents.\r\nMethods: We have focused on characterizing the OL in the red fox by performing general and specific histological stainings on serial sections, using both single and double immunohistochemical and lectin-histochemical labeling techniques.\r\nResults: As a result, we have been able to determine that the OL of the red fox (Vulpes vulpes) displays an uncommonly high degree of development and complexity.\r\nDiscussion: This makes this species a novel mammalian model, the study of which could improve our understanding of the noncanonical pathways involved in the processing of chemosensory cues.","lang":"eng"}]}]