[{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15146","title":"Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix","ddc":["570"],"status":"public","intvolume":" 223","oa_version":"Published Version","file":[{"date_created":"2024-03-25T12:52:04Z","date_updated":"2024-03-25T12:52:04Z","checksum":"90d1984a93660735e506c2a304bc3f73","success":1,"relation":"main_file","file_id":"15188","content_type":"application/pdf","file_size":11907016,"creator":"dernst","file_name":"2024_JCB_Zens.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The extracellular matrix (ECM) serves as a scaffold for cells and plays an essential role in regulating numerous cellular processes, including cell migration and proliferation. Due to limitations in specimen preparation for conventional room-temperature electron microscopy, we lack structural knowledge on how ECM components are secreted, remodeled, and interact with surrounding cells. We have developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion beam milling, the lift-out extraction procedure, and cryo-electron tomography. Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting in a versatile tool closely mimicking ECM environments. This allows us to visualize ECM for the first time in its hydrated, native context. Our data reveal an intricate network of extracellular fibers, their positioning relative to matrix-secreting cells, and previously unresolved structural entities. Our workflow and results add to the structural atlas of the ECM, providing novel insights into its secretion and assembly."}],"issue":"6","publication":"Journal of Cell Biology","citation":{"chicago":"Zens, Bettina, Florian Fäßler, Jesse Hansen, Robert Hauschild, Julia Datler, Victor-Valentin Hodirnau, Vanessa Zheden, Jonna H Alanko, Michael K Sixt, and Florian KM Schur. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” Journal of Cell Biology. Rockefeller University Press, 2024. https://doi.org/10.1083/jcb.202309125.","mla":"Zens, Bettina, et al. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” Journal of Cell Biology, vol. 223, no. 6, e202309125, Rockefeller University Press, 2024, doi:10.1083/jcb.202309125.","short":"B. Zens, F. Fäßler, J. Hansen, R. Hauschild, J. Datler, V.-V. Hodirnau, V. Zheden, J.H. Alanko, M.K. Sixt, F.K. Schur, Journal of Cell Biology 223 (2024).","ista":"Zens B, Fäßler F, Hansen J, Hauschild R, Datler J, Hodirnau V-V, Zheden V, Alanko JH, Sixt MK, Schur FK. 2024. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 223(6), e202309125.","apa":"Zens, B., Fäßler, F., Hansen, J., Hauschild, R., Datler, J., Hodirnau, V.-V., … Schur, F. K. (2024). Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202309125","ieee":"B. Zens et al., “Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix,” Journal of Cell Biology, vol. 223, no. 6. Rockefeller University Press, 2024.","ama":"Zens B, Fäßler F, Hansen J, et al. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 2024;223(6). doi:10.1083/jcb.202309125"},"article_type":"original","date_published":"2024-03-20T00:00:00Z","scopus_import":"1","day":"20","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","acknowledgement":"Open Access funding provided by IST Austria. We thank Armel Nicolas and his team at the ISTA proteomics facility, Alois Schloegl, Stefano Elefante, and colleagues at the ISTA Scientific Computing facility, Tommaso Constanzo and Ludek Lovicar at the Electron Microsocpy Facility (EMF), and Thomas Menner at the Miba Machine shop for their support. We also thank Wanda Kukulski (University of Bern) as well as Darío Porley, Andreas Thader, and other members of the Schur group for helpful discussions. Matt Swulius and Jessica Heebner provided great support in using Dragonfly. We thank Dorotea Fracciolla (Art & Science) for support in figure illustration.\r\n\r\nThis research was supported by the Scientific Service Units of ISTA through resources provided by Scientific Computing, the Lab Support Facility, and the Electron Microscopy Facility. We acknowledge funding support from the following sources: Austrian Science Fund (FWF) grant P33367 (to F.K.M. Schur), the Federation of European Biochemical Societies (to F.K.M. Schur), Niederösterreich (NÖ) Fonds (to B. Zens), FWF grant E435 (to J.M. Hansen), European Research Council under the European Union’s Horizon 2020 research (grant agreement No. 724373) (to M. Sixt), and Jenny and Antti Wihuri Foundation (to J. Alanko). This publication has been made possible in part by CZI grant DAF2021-234754 and grant DOI https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (to F.K.M. Schur).","year":"2024","pmid":1,"publication_status":"published","department":[{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"publisher":"Rockefeller University Press","author":[{"id":"45FD126C-F248-11E8-B48F-1D18A9856A87","last_name":"Zens","first_name":"Bettina","full_name":"Zens, Bettina"},{"full_name":"Fäßler, Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","first_name":"Florian","last_name":"Fäßler"},{"last_name":"Hansen","first_name":"Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63","full_name":"Hansen, Jesse"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert"},{"orcid":"0000-0002-3616-8580","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler","first_name":"Julia","full_name":"Datler, Julia"},{"full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zheden, Vanessa","last_name":"Zheden","first_name":"Vanessa","orcid":"0000-0002-9438-4783","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jonna H","last_name":"Alanko","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7698-3061","full_name":"Alanko, Jonna H"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM"}],"date_created":"2024-03-21T06:45:51Z","date_updated":"2024-03-25T13:03:57Z","volume":223,"article_number":"e202309125","file_date_updated":"2024-03-25T12:52:04Z","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["38506714"]},"quality_controlled":"1","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"},{"_id":"7bd318a1-9f16-11ee-852c-cc9217763180","grant_number":"E435","name":"In Situ Actin Structures via Hybrid Cryo-electron Microscopy"},{"name":"Cellular navigation along spatial gradients","call_identifier":"H2020","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"},{"name":"Spatiotemporal regulation of chemokine-induced signalling in leukocyte chemotaxis","grant_number":"21317","_id":"2615199A-B435-11E9-9278-68D0E5697425"},{"name":"CryoMinflux-guided in-situ visual proteomics and structure determination","_id":"62909c6f-2b32-11ec-9570-e1476aab5308","grant_number":"CZI01"}],"doi":"10.1083/jcb.202309125","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]}},{"article_number":"110320","ec_funded":1,"acknowledgement":"A.B.L. would like to thank Johannes Agerskov and Jan Philip Solovej for valuable discussions. We thank Alessandro Giuliani for helpful discussions and for pointing out the reference [18]. Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is acknowledged. Financial support by the Austrian Science Fund (FWF) through project number I 6427-N (as part of the SFB/TRR 352) is gratefully acknowledged.","year":"2024","publication_status":"epub_ahead","publisher":"Elsevier","department":[{"_id":"RoSe"}],"author":[{"id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","orcid":"0000-0003-4476-2288","first_name":"Asbjørn Bækgaard","last_name":"Lauritsen","full_name":"Lauritsen, Asbjørn Bækgaard"},{"first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"date_updated":"2024-03-28T10:54:02Z","date_created":"2024-02-04T23:00:53Z","volume":286,"month":"01","publication_identifier":{"eissn":["1096--0783"],"issn":["0022-1236"]},"external_id":{"arxiv":["2301.04894"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jfa.2024.110320"}],"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"grant_number":"I06427","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","name":"Mathematical Challenges in BCS Theory of Superconductivity"}],"doi":"10.1016/j.jfa.2024.110320","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We prove an upper bound on the ground state energy of the dilute spin-polarized Fermi gas capturing the leading correction to the kinetic energy resulting from repulsive interactions. One of the main ingredients in the proof is a rigorous implementation of the fermionic cluster expansion of Gaudin et al. (1971) [15]."}],"issue":"7","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"14931","title":"Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion","status":"public","intvolume":" 286","oa_version":"Published Version","scopus_import":"1","day":"24","article_processing_charge":"Yes (via OA deal)","publication":"Journal of Functional Analysis","citation":{"chicago":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal of Functional Analysis. Elsevier, 2024. https://doi.org/10.1016/j.jfa.2024.110320.","mla":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal of Functional Analysis, vol. 286, no. 7, 110320, Elsevier, 2024, doi:10.1016/j.jfa.2024.110320.","short":"A.B. Lauritsen, R. Seiringer, Journal of Functional Analysis 286 (2024).","ista":"Lauritsen AB, Seiringer R. 2024. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. 286(7), 110320.","ieee":"A. B. Lauritsen and R. Seiringer, “Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion,” Journal of Functional Analysis, vol. 286, no. 7. Elsevier, 2024.","apa":"Lauritsen, A. B., & Seiringer, R. (2024). Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2024.110320","ama":"Lauritsen AB, Seiringer R. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. 2024;286(7). doi:10.1016/j.jfa.2024.110320"},"article_type":"original","date_published":"2024-01-24T00:00:00Z"},{"month":"01","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"language":[{"iso":"eng"}],"doi":"10.1093/mnras/stae012","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://academic.oup.com/mnras/article/528/1/676/7511123","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2401.04178"]},"extern":"1","date_created":"2024-03-26T09:43:55Z","date_updated":"2024-03-29T09:52:36Z","volume":528,"author":[{"full_name":"Galiullin, Ilkham","first_name":"Ilkham","last_name":"Galiullin"},{"full_name":"Rodriguez, Antonio C","first_name":"Antonio C","last_name":"Rodriguez"},{"full_name":"Kulkarni, Shrinivas R","first_name":"Shrinivas R","last_name":"Kulkarni"},{"full_name":"Sunyaev, Rashid","last_name":"Sunyaev","first_name":"Rashid"},{"full_name":"Gilfanov, Marat","last_name":"Gilfanov","first_name":"Marat"},{"full_name":"Bikmaev, Ilfan","first_name":"Ilfan","last_name":"Bikmaev"},{"last_name":"Yungelson","first_name":"Lev","full_name":"Yungelson, Lev"},{"full_name":"van Roestel, Jan","first_name":"Jan","last_name":"van Roestel"},{"last_name":"Gänsicke","first_name":"Boris T","full_name":"Gänsicke, Boris T"},{"last_name":"Khamitov","first_name":"Irek","full_name":"Khamitov, Irek"},{"first_name":"Paula","last_name":"Szkody","full_name":"Szkody, Paula"},{"full_name":"El-Badry, Kareem","last_name":"El-Badry","first_name":"Kareem"},{"first_name":"Mikhail","last_name":"Suslikov","full_name":"Suslikov, Mikhail"},{"full_name":"Prince, Thomas A","first_name":"Thomas A","last_name":"Prince"},{"full_name":"Buntov, Mikhail","last_name":"Buntov","first_name":"Mikhail"},{"first_name":"Ilaria","last_name":"Caiazzo","id":"8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d","orcid":"0000-0002-4770-5388","full_name":"Caiazzo, Ilaria"},{"full_name":"Gorbachev, Mark","first_name":"Mark","last_name":"Gorbachev"},{"first_name":"Matthew J","last_name":"Graham","full_name":"Graham, Matthew J"},{"full_name":"Gumerov, Rustam","last_name":"Gumerov","first_name":"Rustam"},{"first_name":"Eldar","last_name":"Irtuganov","full_name":"Irtuganov, Eldar"},{"full_name":"Laher, Russ R","last_name":"Laher","first_name":"Russ R"},{"full_name":"Medvedev, Pavel","first_name":"Pavel","last_name":"Medvedev"},{"first_name":"Reed","last_name":"Riddle","full_name":"Riddle, Reed"},{"last_name":"Rusholme","first_name":"Ben","full_name":"Rusholme, Ben"},{"full_name":"Sakhibullin, Nail","first_name":"Nail","last_name":"Sakhibullin"},{"full_name":"Sklyanov, Alexander","last_name":"Sklyanov","first_name":"Alexander"},{"full_name":"Vanderbosch, Zachary P","first_name":"Zachary P","last_name":"Vanderbosch"}],"publication_status":"published","publisher":"Oxford University Press","year":"2024","day":"04","article_processing_charge":"No","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"scopus_import":"1","date_published":"2024-01-04T00:00:00Z","article_type":"original","page":"676-692","publication":"Monthly Notices of the Royal Astronomical Society","citation":{"chicago":"Galiullin, Ilkham, Antonio C Rodriguez, Shrinivas R Kulkarni, Rashid Sunyaev, Marat Gilfanov, Ilfan Bikmaev, Lev Yungelson, et al. “A Joint SRG/EROSITA + ZTF Search: Discovery of a 97-Min Period Eclipsing Cataclysmic Variable with Evidence of a Brown Dwarf Secondary.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2024. https://doi.org/10.1093/mnras/stae012.","short":"I. Galiullin, A.C. Rodriguez, S.R. Kulkarni, R. Sunyaev, M. Gilfanov, I. Bikmaev, L. Yungelson, J. van Roestel, B.T. Gänsicke, I. Khamitov, P. Szkody, K. El-Badry, M. Suslikov, T.A. Prince, M. Buntov, I. Caiazzo, M. Gorbachev, M.J. Graham, R. Gumerov, E. Irtuganov, R.R. Laher, P. Medvedev, R. Riddle, B. Rusholme, N. Sakhibullin, A. Sklyanov, Z.P. Vanderbosch, Monthly Notices of the Royal Astronomical Society 528 (2024) 676–692.","mla":"Galiullin, Ilkham, et al. “A Joint SRG/EROSITA + ZTF Search: Discovery of a 97-Min Period Eclipsing Cataclysmic Variable with Evidence of a Brown Dwarf Secondary.” Monthly Notices of the Royal Astronomical Society, vol. 528, no. 1, Oxford University Press, 2024, pp. 676–92, doi:10.1093/mnras/stae012.","apa":"Galiullin, I., Rodriguez, A. C., Kulkarni, S. R., Sunyaev, R., Gilfanov, M., Bikmaev, I., … Vanderbosch, Z. P. (2024). A joint SRG/eROSITA + ZTF search: Discovery of a 97-min period eclipsing cataclysmic variable with evidence of a brown dwarf secondary. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stae012","ieee":"I. Galiullin et al., “A joint SRG/eROSITA + ZTF search: Discovery of a 97-min period eclipsing cataclysmic variable with evidence of a brown dwarf secondary,” Monthly Notices of the Royal Astronomical Society, vol. 528, no. 1. Oxford University Press, pp. 676–692, 2024.","ista":"Galiullin I, Rodriguez AC, Kulkarni SR, Sunyaev R, Gilfanov M, Bikmaev I, Yungelson L, van Roestel J, Gänsicke BT, Khamitov I, Szkody P, El-Badry K, Suslikov M, Prince TA, Buntov M, Caiazzo I, Gorbachev M, Graham MJ, Gumerov R, Irtuganov E, Laher RR, Medvedev P, Riddle R, Rusholme B, Sakhibullin N, Sklyanov A, Vanderbosch ZP. 2024. A joint SRG/eROSITA + ZTF search: Discovery of a 97-min period eclipsing cataclysmic variable with evidence of a brown dwarf secondary. Monthly Notices of the Royal Astronomical Society. 528(1), 676–692.","ama":"Galiullin I, Rodriguez AC, Kulkarni SR, et al. A joint SRG/eROSITA + ZTF search: Discovery of a 97-min period eclipsing cataclysmic variable with evidence of a brown dwarf secondary. Monthly Notices of the Royal Astronomical Society. 2024;528(1):676-692. doi:10.1093/mnras/stae012"},"abstract":[{"lang":"eng","text":"Cataclysmic variables (CVs) that have evolved past the period minimum during their lifetimes are predicted to be systems with a brown dwarf donor. While population synthesis models predict that around 40–70 per cent of the Galactic CVs are post-period minimum systems referred to as ‘period bouncers’, only a few dozen confirmed systems are known. We report the study and characterization of a new eclipsing CV, SRGeJ041130.3+685350 (SRGeJ0411), discovered from a joint SRG/eROSITA and ZTF programme. The optical spectrum of SRGeJ0411 shows prominent hydrogen and helium emission lines, typical for CVs. We obtained optical high-speed photometry to confirm the eclipse of SRGeJ0411 and determine the orbital period to be Porb ≈ 97.530 min. The spectral energy distribution suggests that the donor has an effective temperature of ≲ 1800 K. We constrain the donor mass with the period–density relationship for Roche lobe-filling stars and find that Mdonor ≲ 0.04 M⊙. The binary parameters are consistent with evolutionary models for post-period minimum CVs, suggesting that SRGeJ0411 is a new period bouncer. The optical emission lines of SRGeJ0411 are single-peaked despite the system being eclipsing, which is typically only seen due to stream-fed accretion in polars. X-ray spectroscopy hints that the white dwarf in SRGeJ0411 could be magnetic, but verifying the magnetic nature of SRGeJ0411 requires further investigation. The lack of optical outbursts has made SRGeJ0411 elusive in previous surveys, and joint X-ray and optical surveys highlight the potential for discovering similar systems in the near future."}],"issue":"1","type":"journal_article","oa_version":"Published Version","status":"public","title":"A joint SRG/eROSITA + ZTF search: Discovery of a 97-min period eclipsing cataclysmic variable with evidence of a brown dwarf secondary","intvolume":" 528","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"15189"},{"extern":"1","article_number":"139","author":[{"first_name":"Roman","last_name":"Gerasimov","full_name":"Gerasimov, Roman"},{"last_name":"Burgasser","first_name":"Adam J.","full_name":"Burgasser, Adam J."},{"first_name":"Ilaria","last_name":"Caiazzo","id":"8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d","orcid":"0000-0002-4770-5388","full_name":"Caiazzo, Ilaria"},{"full_name":"Homeier, Derek","last_name":"Homeier","first_name":"Derek"},{"full_name":"Richer, Harvey B.","last_name":"Richer","first_name":"Harvey B."},{"last_name":"Correnti","first_name":"Matteo","full_name":"Correnti, Matteo"},{"first_name":"Jeremy","last_name":"Heyl","full_name":"Heyl, Jeremy"}],"volume":961,"date_updated":"2024-03-29T10:06:31Z","date_created":"2024-03-26T09:44:50Z","year":"2024","publisher":"American Astronomical Society","publication_status":"published","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"month":"01","doi":"10.3847/1538-4357/ad08bf","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://iopscience.iop.org/article/10.3847/1538-4357/ad08bf","open_access":"1"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2310.11800"]},"quality_controlled":"1","issue":"1","abstract":[{"lang":"eng","text":"Despite their shared origin, members of globular clusters display star-to-star variations in composition. The observed pattern of element abundances is unique to these stellar environments and cannot be fully explained by any proposed mechanism. It remains unclear whether stars form with chemical heterogeneity or inherit it from interactions with other members. These scenarios may be differentiated by the dependence of chemical spread on stellar mass; however, obtaining a sufficiently large mass baseline requires abundance measurements on the lower main sequence, which is too faint for spectroscopy even in the nearest globular clusters. We developed a stellar modeling method to obtain precise chemical abundances for stars near the end of the main sequence from multiband photometry, and we applied it to the globular cluster 47 Tucanae. The computational efficiency is attained by matching chemical elements to the model components that are most sensitive to their abundance. We determined [O/Fe] for ∼5000 members below the main-sequence knee at the level of accuracy, comparable to the spectroscopic measurements of evolved members in the literature. The inferred distribution disfavors stellar interactions as the origin of chemical spread; however, an accurate theory of accretion is required to draw a more definitive conclusion. We anticipate that future observations of 47 Tucanae with the James Webb Space Telescope will extend the mass baseline of our analysis into the substellar regime. Therefore, we present predicted color–magnitude diagrams and mass–magnitude relations for the brown dwarf members of 47 Tucanae."}],"type":"journal_article","oa_version":"Published Version","_id":"15191","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 961","status":"public","title":"Exploring the chemistry and mass function of the globular cluster 47 Tucanae with new theoretical color–magnitude diagrams","article_processing_charge":"No","day":"22","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"date_published":"2024-01-22T00:00:00Z","citation":{"short":"R. Gerasimov, A.J. Burgasser, I. Caiazzo, D. Homeier, H.B. Richer, M. Correnti, J. Heyl, The Astrophysical Journal 961 (2024).","mla":"Gerasimov, Roman, et al. “Exploring the Chemistry and Mass Function of the Globular Cluster 47 Tucanae with New Theoretical Color–Magnitude Diagrams.” The Astrophysical Journal, vol. 961, no. 1, 139, American Astronomical Society, 2024, doi:10.3847/1538-4357/ad08bf.","chicago":"Gerasimov, Roman, Adam J. Burgasser, Ilaria Caiazzo, Derek Homeier, Harvey B. Richer, Matteo Correnti, and Jeremy Heyl. “Exploring the Chemistry and Mass Function of the Globular Cluster 47 Tucanae with New Theoretical Color–Magnitude Diagrams.” The Astrophysical Journal. American Astronomical Society, 2024. https://doi.org/10.3847/1538-4357/ad08bf.","ama":"Gerasimov R, Burgasser AJ, Caiazzo I, et al. Exploring the chemistry and mass function of the globular cluster 47 Tucanae with new theoretical color–magnitude diagrams. The Astrophysical Journal. 2024;961(1). doi:10.3847/1538-4357/ad08bf","apa":"Gerasimov, R., Burgasser, A. J., Caiazzo, I., Homeier, D., Richer, H. B., Correnti, M., & Heyl, J. (2024). Exploring the chemistry and mass function of the globular cluster 47 Tucanae with new theoretical color–magnitude diagrams. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/ad08bf","ieee":"R. Gerasimov et al., “Exploring the chemistry and mass function of the globular cluster 47 Tucanae with new theoretical color–magnitude diagrams,” The Astrophysical Journal, vol. 961, no. 1. American Astronomical Society, 2024.","ista":"Gerasimov R, Burgasser AJ, Caiazzo I, Homeier D, Richer HB, Correnti M, Heyl J. 2024. Exploring the chemistry and mass function of the globular cluster 47 Tucanae with new theoretical color–magnitude diagrams. The Astrophysical Journal. 961(1), 139."},"publication":"The Astrophysical Journal","article_type":"original"},{"scopus_import":"1","series_title":"MIMB","has_accepted_license":"1","article_processing_charge":"No","day":"19","citation":{"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.","ieee":"E. B. Hannezo and C. L. G. J. Scheele, “A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland,” in Cell Migration in Three Dimensions, vol. 2608, C. Margadant, Ed. Springer Nature, 2023, pp. 183–205.","apa":"Hannezo, E. B., & Scheele, C. L. G. J. (2023). A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In C. Margadant (Ed.), Cell Migration in Three Dimensions (Vol. 2608, pp. 183–205). Springer Nature. https://doi.org/10.1007/978-1-0716-2887-4_12","ama":"Hannezo EB, Scheele CLGJ. A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Margadant C, ed. Cell Migration in Three Dimensions. Vol 2608. MIMB. Springer Nature; 2023:183-205. doi:10.1007/978-1-0716-2887-4_12","chicago":"Hannezo, Edouard B, and Colinda L.G.J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” In Cell Migration in Three Dimensions, edited by Coert Margadant, 2608:183–205. MIMB. Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-2887-4_12.","mla":"Hannezo, Edouard B., and Colinda L. G. J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” Cell Migration in Three Dimensions, edited by Coert Margadant, vol. 2608, Springer Nature, 2023, pp. 183–205, doi:10.1007/978-1-0716-2887-4_12.","short":"E.B. Hannezo, C.L.G.J. Scheele, in:, C. Margadant (Ed.), Cell Migration in Three Dimensions, Springer Nature, 2023, pp. 183–205."},"publication":"Cell Migration in Three Dimensions","page":"183-205","date_published":"2023-01-19T00:00:00Z","type":"book_chapter","alternative_title":["Methods in Molecular Biology"],"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"}],"_id":"12428","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 2608","ddc":["570"],"title":"A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland","status":"public","file":[{"content_type":"application/pdf","file_size":826598,"creator":"dernst","access_level":"open_access","file_name":"2023_MIMB_Hannezo.pdf","checksum":"aec1b8d3ba938ddf9d8fcb777f3c38ee","success":1,"date_created":"2023-02-03T10:56:39Z","date_updated":"2023-02-03T10:56:39Z","relation":"main_file","file_id":"12500"}],"oa_version":"Published Version","publication_identifier":{"eisbn":["9781071628874"],"eissn":["1940-6029"],"isbn":["9781071628867"]},"month":"01","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["36653709"]},"oa":1,"quality_controlled":"1","doi":"10.1007/978-1-0716-2887-4_12","language":[{"iso":"eng"}],"file_date_updated":"2023-02-03T10:56:39Z","pmid":1,"year":"2023","publisher":"Springer Nature","editor":[{"full_name":"Margadant, Coert","last_name":"Margadant","first_name":"Coert"}],"department":[{"_id":"EdHa"}],"publication_status":"published","author":[{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"},{"full_name":"Scheele, Colinda L.G.J.","first_name":"Colinda L.G.J.","last_name":"Scheele"}],"volume":2608,"date_updated":"2023-02-03T10:58:56Z","date_created":"2023-01-29T23:00:58Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12534","ddc":["530"],"title":"Dissipative dynamics of an impurity with spin-orbit coupling","status":"public","intvolume":" 5","file":[{"date_created":"2023-02-13T10:38:10Z","date_updated":"2023-02-13T10:38:10Z","checksum":"6068b62874c0099628a108bb9c5c6bd2","success":1,"relation":"main_file","file_id":"12546","file_size":865150,"content_type":"application/pdf","creator":"dernst","file_name":"2023_PhysicalReviewResearch_Ghazaryan.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Brownian motion of a mobile impurity in a bath is affected by spin-orbit coupling (SOC). Here, we discuss a Caldeira-Leggett-type model that can be used to propose and interpret quantum simulators of this problem in cold Bose gases. First, we derive a master equation that describes the model and explore it in a one-dimensional (1D) setting. To validate the standard assumptions needed for our derivation, we analyze available experimental data without SOC; as a byproduct, this analysis suggests that the quench dynamics of the impurity is beyond the 1D Bose-polaron approach at temperatures currently accessible in a cold-atom laboratory—motion of the impurity is mainly driven by dissipation. For systems with SOC, we demonstrate that 1D spin-orbit coupling can be gauged out even in the presence of dissipation—the information about SOC is incorporated in the initial conditions. Observables sensitive to this information (such as spin densities) can be used to study formation of steady spin polarization domains during quench dynamics."}],"issue":"1","publication":"Physical Review Research","citation":{"ista":"Ghazaryan A, Cappellaro A, Lemeshko M, Volosniev A. 2023. Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. 5(1), 013029.","apa":"Ghazaryan, A., Cappellaro, A., Lemeshko, M., & Volosniev, A. (2023). Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.5.013029","ieee":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Dissipative dynamics of an impurity with spin-orbit coupling,” Physical Review Research, vol. 5, no. 1. American Physical Society, 2023.","ama":"Ghazaryan A, Cappellaro A, Lemeshko M, Volosniev A. Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. 2023;5(1). doi:10.1103/physrevresearch.5.013029","chicago":"Ghazaryan, Areg, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev. “Dissipative Dynamics of an Impurity with Spin-Orbit Coupling.” Physical Review Research. American Physical Society, 2023. https://doi.org/10.1103/physrevresearch.5.013029.","mla":"Ghazaryan, Areg, et al. “Dissipative Dynamics of an Impurity with Spin-Orbit Coupling.” Physical Review Research, vol. 5, no. 1, 013029, American Physical Society, 2023, doi:10.1103/physrevresearch.5.013029.","short":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, A. Volosniev, Physical Review Research 5 (2023)."},"article_type":"original","date_published":"2023-01-20T00:00:00Z","scopus_import":"1","day":"20","article_processing_charge":"No","has_accepted_license":"1","acknowledgement":"We thank Rafael Barfknecht for help at the initial stages of this project; Fabian Brauneis for useful discussions; Miguel A. Garcia-March, Georgios Koutentakis, and Simeon Mistakidis\r\nfor comments on the paper. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","year":"2023","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","author":[{"full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","first_name":"Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cappellaro, Alberto","first_name":"Alberto","last_name":"Cappellaro","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","orcid":"0000-0001-6110-2359"},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail"},{"full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem"}],"date_updated":"2023-02-20T07:02:00Z","date_created":"2023-02-10T09:02:26Z","volume":5,"article_number":"013029","file_date_updated":"2023-02-13T10:38:10Z","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770"}],"doi":"10.1103/physrevresearch.5.013029","language":[{"iso":"eng"}],"month":"01","publication_identifier":{"issn":["2643-1564"]}},{"date_published":"2023-02-01T00:00:00Z","article_type":"review","page":"333-345","publication":"Nature Genetics","citation":{"chicago":"Zeller, Peter, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, and Alexander van Oudenaarden. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” Nature Genetics. Springer Nature, 2023. https://doi.org/10.1038/s41588-022-01260-3.","short":"P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu, R. van der Linden, A. van Oudenaarden, Nature Genetics 55 (2023) 333–345.","mla":"Zeller, Peter, et al. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” Nature Genetics, vol. 55, Springer Nature, 2023, pp. 333–45, doi:10.1038/s41588-022-01260-3.","apa":"Zeller, P., Yeung, J., Viñas Gaza, H., de Barbanson, B. A., Bhardwaj, V., Florescu, M., … van Oudenaarden, A. (2023). Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-022-01260-3","ieee":"P. Zeller et al., “Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis,” Nature Genetics, vol. 55. Springer Nature, pp. 333–345, 2023.","ista":"Zeller P, Yeung J, Viñas Gaza H, de Barbanson BA, Bhardwaj V, Florescu M, van der Linden R, van Oudenaarden A. 2023. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 55, 333–345.","ama":"Zeller P, Yeung J, Viñas Gaza H, et al. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 2023;55:333-345. doi:10.1038/s41588-022-01260-3"},"day":"01","article_processing_charge":"No","has_accepted_license":"1","keyword":["Genetics"],"scopus_import":"1","file":[{"file_name":"2023_NatureGenetics_Zeller.pdf","access_level":"open_access","file_size":21484855,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"12688","date_updated":"2023-02-27T07:46:45Z","date_created":"2023-02-27T07:46:45Z","checksum":"6fdb8e34fbeea63edd0f2c6c2cc5823e","success":1}],"oa_version":"Published Version","title":"Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis","status":"public","ddc":["570","000"],"intvolume":" 55","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12158","abstract":[{"text":"Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41588-022-01260-3","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"02","publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"date_created":"2023-01-12T12:09:09Z","date_updated":"2023-02-27T07:48:24Z","volume":55,"author":[{"last_name":"Zeller","first_name":"Peter","full_name":"Zeller, Peter"},{"first_name":"Jake","last_name":"Yeung","id":"123012b2-db30-11eb-b4d8-a35840c0551b","orcid":"0000-0003-1732-1559","full_name":"Yeung, Jake"},{"full_name":"Viñas Gaza, Helena","first_name":"Helena","last_name":"Viñas Gaza"},{"first_name":"Buys Anton","last_name":"de Barbanson","full_name":"de Barbanson, Buys Anton"},{"last_name":"Bhardwaj","first_name":"Vivek","full_name":"Bhardwaj, Vivek"},{"full_name":"Florescu, Maria","last_name":"Florescu","first_name":"Maria"},{"last_name":"van der Linden","first_name":"Reinier","full_name":"van der Linden, Reinier"},{"full_name":"van Oudenaarden, Alexander","first_name":"Alexander","last_name":"van Oudenaarden"}],"publication_status":"published","department":[{"_id":"ScienComp"}],"publisher":"Springer Nature","acknowledgement":"We thank A. Giladi for sharing mRNA abundance tables of cell types together with J. van den Berg for critical reading of the manuscript. We thank M. Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973). Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström under CC-BY-SA 3.0 license. This work was supported by European Research Council Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991), HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z. The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF (ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","year":"2023","file_date_updated":"2023-02-27T07:46:45Z"},{"date_published":"2023-02-01T00:00:00Z","publication":"Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms","citation":{"short":"K. Chatterjee, T. Meggendorfer, R.J. Saona Urmeneta, J. Svoboda, in:, Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 4590–4605.","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 4590–605, doi:10.1137/1.9781611977554.ch173.","chicago":"Chatterjee, Krishnendu, Tobias Meggendorfer, Raimundo J Saona Urmeneta, and Jakub Svoboda. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, 4590–4605. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/1.9781611977554.ch173.","ama":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. Faster algorithm for turn-based stochastic games with bounded treewidth. In: Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2023:4590-4605. doi:10.1137/1.9781611977554.ch173","apa":"Chatterjee, K., Meggendorfer, T., Saona Urmeneta, R. J., & Svoboda, J. (2023). Faster algorithm for turn-based stochastic games with bounded treewidth. In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 4590–4605). Florence, Italy: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977554.ch173","ieee":"K. Chatterjee, T. Meggendorfer, R. J. Saona Urmeneta, and J. Svoboda, “Faster algorithm for turn-based stochastic games with bounded treewidth,” in Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Florence, Italy, 2023, pp. 4590–4605.","ista":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. 2023. Faster algorithm for turn-based stochastic games with bounded treewidth. Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 4590–4605."},"page":"4590-4605","day":"01","article_processing_charge":"No","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12676","status":"public","title":"Faster algorithm for turn-based stochastic games with bounded treewidth","abstract":[{"lang":"eng","text":"Turn-based stochastic games (aka simple stochastic games) are two-player zero-sum games played on directed graphs with probabilistic transitions. The goal of player-max is to maximize the probability to reach a target state against the adversarial player-min. These games lie in NP ∩ coNP and are among the rare combinatorial problems that belong to this complexity class for which the existence of polynomial-time algorithm is a major open question. While randomized sub-exponential time algorithm exists, all known deterministic algorithms require exponential time in the worst-case. An important open question has been whether faster algorithms can be obtained parametrized by the treewidth of the game graph. Even deterministic sub-exponential time algorithm for constant treewidth turn-based stochastic games has remain elusive. In this work our main result is a deterministic algorithm to solve turn-based stochastic games that, given a game with n states, treewidth at most t, and the bit-complexity of the probabilistic transition function log D, has running time O ((tn2 log D)t log n). In particular, our algorithm is quasi-polynomial time for games with constant or poly-logarithmic treewidth."}],"type":"conference","conference":{"end_date":"2023-01-25","location":"Florence, Italy","start_date":"2023-01-22","name":"SODA: Symposium on Discrete Algorithms"},"doi":"10.1137/1.9781611977554.ch173","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1137/1.9781611977554.ch173","open_access":"1"}],"oa":1,"quality_controlled":"1","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"month":"02","publication_identifier":{"isbn":["9781611977554"]},"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Tobias","last_name":"Meggendorfer","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","full_name":"Meggendorfer, Tobias"},{"first_name":"Raimundo J","last_name":"Saona Urmeneta","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","orcid":"0000-0001-5103-038X","full_name":"Saona Urmeneta, Raimundo J"},{"last_name":"Svoboda","first_name":"Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","full_name":"Svoboda, Jakub"}],"date_updated":"2023-02-27T09:01:16Z","date_created":"2023-02-24T12:20:47Z","year":"2023","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant.","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publisher":"Society for Industrial and Applied Mathematics","ec_funded":1},{"publication_identifier":{"isbn":["978-1-0716-3003-7"],"eissn":["1940-6029"],"issn":["1064-3745"],"eisbn":["978-1-0716-3004-4"]},"month":"03","doi":"10.1007/978-1-0716-3004-4_3","language":[{"iso":"eng"}],"external_id":{"pmid":["36853454"]},"quality_controlled":"1","place":"New York, NY, United States","author":[{"first_name":"Sandra","last_name":"Arroyo-Urea","full_name":"Arroyo-Urea, Sandra"},{"last_name":"Watson","first_name":"Jake","orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E","full_name":"Watson, Jake"},{"first_name":"Javier","last_name":"García-Nafría","full_name":"García-Nafría, Javier"}],"volume":2633,"date_updated":"2023-03-16T08:34:24Z","date_created":"2023-03-12T23:01:02Z","pmid":1,"year":"2023","editor":[{"full_name":"Scarlett, Garry","last_name":"Scarlett","first_name":"Garry"}],"department":[{"_id":"PeJo"}],"publisher":"Springer Nature","publication_status":"published","article_processing_charge":"No","day":"01","scopus_import":"1","series_title":"MIMB","date_published":"2023-03-01T00:00:00Z","citation":{"chicago":"Arroyo-Urea, Sandra, Jake Watson, and Javier García-Nafría. “Molecular Cloning Using In Vivo DNA Assembly.” In DNA Manipulation and Analysis, edited by Garry Scarlett, 2633:33–44. MIMB. New York, NY, United States: Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-3004-4_3.","mla":"Arroyo-Urea, Sandra, et al. “Molecular Cloning Using In Vivo DNA Assembly.” DNA Manipulation and Analysis, edited by Garry Scarlett, vol. 2633, Springer Nature, 2023, pp. 33–44, doi:10.1007/978-1-0716-3004-4_3.","short":"S. Arroyo-Urea, J. Watson, J. García-Nafría, in:, G. Scarlett (Ed.), DNA Manipulation and Analysis, Springer Nature, New York, NY, United States, 2023, pp. 33–44.","ista":"Arroyo-Urea S, Watson J, García-Nafría J. 2023.Molecular Cloning Using In Vivo DNA Assembly. In: DNA Manipulation and Analysis. Methods in Molecular Biology, vol. 2633, 33–44.","apa":"Arroyo-Urea, S., Watson, J., & García-Nafría, J. (2023). Molecular Cloning Using In Vivo DNA Assembly. In G. Scarlett (Ed.), DNA Manipulation and Analysis (Vol. 2633, pp. 33–44). New York, NY, United States: Springer Nature. https://doi.org/10.1007/978-1-0716-3004-4_3","ieee":"S. Arroyo-Urea, J. Watson, and J. García-Nafría, “Molecular Cloning Using In Vivo DNA Assembly,” in DNA Manipulation and Analysis, vol. 2633, G. Scarlett, Ed. New York, NY, United States: Springer Nature, 2023, pp. 33–44.","ama":"Arroyo-Urea S, Watson J, García-Nafría J. Molecular Cloning Using In Vivo DNA Assembly. In: Scarlett G, ed. DNA Manipulation and Analysis. Vol 2633. MIMB. New York, NY, United States: Springer Nature; 2023:33-44. doi:10.1007/978-1-0716-3004-4_3"},"publication":"DNA Manipulation and Analysis","page":"33-44","abstract":[{"text":"Here we describe the in vivo DNA assembly approach, where molecular cloning procedures are performed using an E. coli recA-independent recombination pathway, which assembles linear fragments of DNA with short homologous termini. This pathway is present in all standard laboratory E. coli strains and, by bypassing the need for in vitro DNA assembly, allows simplified molecular cloning to be performed without the plasmid instability issues associated with specialized recombination-cloning bacterial strains. The methodology requires specific primer design and can perform all standard plasmid modifications (insertions, deletions, mutagenesis, and sub-cloning) in a rapid, simple, and cost-efficient manner, as it does not require commercial kits or specialized bacterial strains. Additionally, this approach can be used to perform complex procedures such as multiple modifications to a plasmid, as up to 6 linear fragments can be assembled in vivo by this recombination pathway. Procedures generally require less than 3 h, involving PCR amplification, DpnI digestion of template DNA, and transformation, upon which circular plasmids are assembled. In this chapter we describe the requirements, procedure, and potential pitfalls when using this technique, as well as protocol variations to overcome the most common issues.","lang":"eng"}],"type":"book_chapter","alternative_title":["Methods in Molecular Biology"],"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12720","intvolume":" 2633","status":"public","title":"Molecular Cloning Using In Vivo DNA Assembly"},{"external_id":{"arxiv":["2211.04986"]},"citation":{"ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, “Fast and scalable channels in Kotlin Coroutines,” in Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Montreal, QC, Canada, 2023, pp. 107–118.","apa":"Koval, N., Alistarh, D.-A., & Elizarov, R. (2023). Fast and scalable channels in Kotlin Coroutines. In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 107–118). Montreal, QC, Canada: Association for Computing Machinery. https://doi.org/10.1145/3572848.3577481","ista":"Koval N, Alistarh D-A, Elizarov R. 2023. Fast and scalable channels in Kotlin Coroutines. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 107–118.","ama":"Koval N, Alistarh D-A, Elizarov R. Fast and scalable channels in Kotlin Coroutines. In: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2023:107-118. doi:10.1145/3572848.3577481","chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Fast and Scalable Channels in Kotlin Coroutines.” In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 107–18. Association for Computing Machinery, 2023. https://doi.org/10.1145/3572848.3577481.","short":"N. Koval, D.-A. Alistarh, R. Elizarov, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 107–118.","mla":"Koval, Nikita, et al. “Fast and Scalable Channels in Kotlin Coroutines.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 107–18, doi:10.1145/3572848.3577481."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.04986"}],"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","page":"107-118","quality_controlled":"1","doi":"10.1145/3572848.3577481","date_published":"2023-02-25T00:00:00Z","conference":{"name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming","end_date":"2023-03-01","location":"Montreal, QC, Canada","start_date":"2023-02-25"},"language":[{"iso":"eng"}],"scopus_import":"1","publication_identifier":{"isbn":["9798400700156"]},"article_processing_charge":"No","month":"02","day":"25","_id":"12735","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"}],"publication_status":"published","title":"Fast and scalable channels in Kotlin Coroutines","status":"public","author":[{"id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","first_name":"Nikita","last_name":"Koval","full_name":"Koval, Nikita"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"full_name":"Elizarov, Roman","first_name":"Roman","last_name":"Elizarov"}],"oa_version":"Preprint","date_created":"2023-03-19T23:00:58Z","date_updated":"2023-03-20T07:29:28Z","type":"conference","abstract":[{"text":"Asynchronous programming has gained significant popularity over the last decade: support for this programming pattern is available in many popular languages via libraries and native language implementations, typically in the form of coroutines or the async/await construct. Instead of programming via shared memory, this concept assumes implicit synchronization through message passing. The key data structure enabling such communication is the rendezvous channel. Roughly, a rendezvous channel is a blocking queue of size zero, so both send(e) and receive() operations wait for each other, performing a rendezvous when they meet. To optimize the message passing pattern, channels are usually equipped with a fixed-size buffer, so sends do not suspend and put elements into the buffer until its capacity is exceeded. This primitive is known as a buffered channel.\r\n\r\nThis paper presents a fast and scalable algorithm for both rendezvous and buffered channels. Similarly to modern queues, our solution is based on an infinite array with two positional counters for send(e) and receive() operations, leveraging the unconditional Fetch-And-Add instruction to update them. Yet, the algorithm requires non-trivial modifications of this classic pattern, in order to support the full channel semantics, such as buffering and cancellation of waiting requests. We compare the performance of our solution to that of the Kotlin implementation, as well as against other academic proposals, showing up to 9.8× speedup. To showcase its expressiveness and performance, we also integrated the proposed algorithm into the standard Kotlin Coroutines library, replacing the previous channel implementations.","lang":"eng"}]},{"abstract":[{"text":"Although a wide variety of handcrafted concurrent data structures have been proposed, there is considerable interest in universal approaches (Universal Constructions or UCs) for building concurrent data structures. UCs (semi-)automatically convert a sequential data structure into a concurrent one. The simplest approach uses locks [3, 6] that protect a sequential data structure and allow only one process to access it at a time. However, the resulting data structure is blocking. Most work on UCs instead focuses on obtaining non-blocking progress guarantees such as obstruction-freedom, lock-freedom or wait-freedom. Many non-blocking UCs have appeared. Key examples include the seminal wait-free UC [2] by Herlihy, a NUMA-aware UC [10] by Yi et al., and an efficient UC for large objects [1] by Fatourou et al.","lang":"eng"}],"type":"conference_poster","author":[{"last_name":"Aksenov","first_name":"Vitaly","full_name":"Aksenov, Vitaly"},{"first_name":"Trevor A","last_name":"Brown","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Trevor A"},{"full_name":"Fedorov, Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","first_name":"Alexander","last_name":"Fedorov"},{"first_name":"Ilya","last_name":"Kokorin","full_name":"Kokorin, Ilya"}],"date_created":"2023-03-19T23:00:58Z","date_updated":"2023-03-20T07:57:27Z","oa_version":"Published Version","acknowledgement":"This work was supported by: the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Program grant: RGPIN-2019-04227, and the Canada Foundation for Innovation John R. Evans Leaders Fund (CFI-JELF) with equal support from the Ontario Research Fund CFI Leaders Opportunity Fund: 38512.","_id":"12736","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","publication_status":"published","title":"Unexpected scaling in path copying trees","status":"public","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"publisher":"Association for Computing Machinery","day":"25","month":"02","publication_identifier":{"isbn":["9798400700156"]},"article_processing_charge":"No","conference":{"name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming","location":"Montreal, QB, Canada","start_date":"2023-02-25","end_date":"2023-03-01"},"date_published":"2023-02-25T00:00:00Z","doi":"10.1145/3572848.3577512","language":[{"iso":"eng"}],"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","citation":{"chicago":"Aksenov, Vitaly, Trevor A Brown, Alexander Fedorov, and Ilya Kokorin. Unexpected Scaling in Path Copying Trees. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery, 2023. https://doi.org/10.1145/3572848.3577512.","mla":"Aksenov, Vitaly, et al. “Unexpected Scaling in Path Copying Trees.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 438–40, doi:10.1145/3572848.3577512.","short":"V. Aksenov, T.A. Brown, A. Fedorov, I. Kokorin, Unexpected Scaling in Path Copying Trees, Association for Computing Machinery, 2023.","ista":"Aksenov V, Brown TA, Fedorov A, Kokorin I. 2023. Unexpected scaling in path copying trees, Association for Computing Machinery,p.","ieee":"V. Aksenov, T. A. Brown, A. Fedorov, and I. Kokorin, Unexpected scaling in path copying trees. Association for Computing Machinery, 2023, pp. 438–440.","apa":"Aksenov, V., Brown, T. A., Fedorov, A., & Kokorin, I. (2023). Unexpected scaling in path copying trees. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 438–440). Montreal, QB, Canada: Association for Computing Machinery. https://doi.org/10.1145/3572848.3577512","ama":"Aksenov V, Brown TA, Fedorov A, Kokorin I. Unexpected Scaling in Path Copying Trees. Association for Computing Machinery; 2023:438-440. doi:10.1145/3572848.3577512"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3572848.3577512"}],"quality_controlled":"1","page":"438-440"},{"date_published":"2023-03-01T00:00:00Z","publication":"40th International Symposium on Theoretical Aspects of Computer Science","citation":{"ista":"Henzinger MH, Neumann S, Räcke H, Schmid S. 2023. Dynamic maintenance of monotone dynamic programs and applications. 40th International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 254, 36.","apa":"Henzinger, M. H., Neumann, S., Räcke, H., & Schmid, S. (2023). Dynamic maintenance of monotone dynamic programs and applications. In 40th International Symposium on Theoretical Aspects of Computer Science (Vol. 254). Hamburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2023.36","ieee":"M. H. Henzinger, S. Neumann, H. Räcke, and S. Schmid, “Dynamic maintenance of monotone dynamic programs and applications,” in 40th International Symposium on Theoretical Aspects of Computer Science, Hamburg, Germany, 2023, vol. 254.","ama":"Henzinger MH, Neumann S, Räcke H, Schmid S. Dynamic maintenance of monotone dynamic programs and applications. In: 40th International Symposium on Theoretical Aspects of Computer Science. Vol 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.STACS.2023.36","chicago":"Henzinger, Monika H, Stefan Neumann, Harald Räcke, and Stefan Schmid. “Dynamic Maintenance of Monotone Dynamic Programs and Applications.” In 40th International Symposium on Theoretical Aspects of Computer Science, Vol. 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.STACS.2023.36.","mla":"Henzinger, Monika H., et al. “Dynamic Maintenance of Monotone Dynamic Programs and Applications.” 40th International Symposium on Theoretical Aspects of Computer Science, vol. 254, 36, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.STACS.2023.36.","short":"M.H. Henzinger, S. Neumann, H. Räcke, S. Schmid, in:, 40th International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023."},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","file":[{"file_size":872706,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_LIPICS_HenzingerM.pdf","checksum":"22141ab8bc55188e2dfff665e5daecbd","success":1,"date_updated":"2023-03-27T06:37:22Z","date_created":"2023-03-27T06:37:22Z","relation":"main_file","file_id":"12769"}],"_id":"12760","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"status":"public","title":"Dynamic maintenance of monotone dynamic programs and applications","intvolume":" 254","abstract":[{"text":"Dynamic programming (DP) is one of the fundamental paradigms in algorithm design. However,\r\nmany DP algorithms have to fill in large DP tables, represented by two-dimensional arrays, which causes at least quadratic running times and space usages. This has led to the development of improved algorithms for special cases when the DPs satisfy additional properties like, e.g., the Monge property or total monotonicity.\r\nIn this paper, we consider a new condition which assumes (among some other technical assumptions) that the rows of the DP table are monotone. Under this assumption, we introduce\r\na novel data structure for computing (1 + ϵ)-approximate DP solutions in near-linear time and\r\nspace in the static setting, and with polylogarithmic update times when the DP entries change\r\ndynamically. To the best of our knowledge, our new condition is incomparable to previous conditions and is the first which allows to derive dynamic algorithms based on existing DPs. Instead of using two-dimensional arrays to store the DP tables, we store the rows of the DP tables using monotone piecewise constant functions. This allows us to store length-n DP table rows with entries in [0, W] using only polylog(n, W) bits, and to perform operations, such as (min, +)-convolution or rounding, on these functions in polylogarithmic time.\r\nWe further present several applications of our data structure. For bicriteria versions of k-balanced graph partitioning and simultaneous source location, we obtain the first dynamic algorithms with subpolynomial update times, as well as the first static algorithms using only near-linear time and space. Additionally, we obtain the currently fastest algorithm for fully dynamic knapsack.","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"conference":{"name":"STACS: Symposium on Theoretical Aspects of Computer Science","location":"Hamburg, Germany","start_date":"2023-03-07","end_date":"2023-03-09"},"doi":"10.4230/LIPIcs.STACS.2023.36","language":[{"iso":"eng"}],"external_id":{"arxiv":["2301.01744"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","month":"03","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772662"]},"author":[{"first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"full_name":"Neumann, Stefan","first_name":"Stefan","last_name":"Neumann"},{"last_name":"Räcke","first_name":"Harald","full_name":"Räcke, Harald"},{"first_name":"Stefan","last_name":"Schmid","full_name":"Schmid, Stefan"}],"date_created":"2023-03-26T22:01:07Z","date_updated":"2023-03-27T06:46:27Z","volume":254,"acknowledgement":"Monika Henzinger: This project has received funding from the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nStefan Neumann: This research is supported by the the ERC Advanced Grant REBOUND (834862) and the EC H2020 RIA project SoBigData++ (871042).\r\nStefan Schmid: Research supported by Austrian Science Fund (FWF) project I 5025-N (DELTA), 2020-2024.","year":"2023","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"MoHe"}],"file_date_updated":"2023-03-27T06:37:22Z","article_number":"36"},{"abstract":[{"lang":"eng","text":"The process of detecting and evaluating sensory information to guide behaviour is termed perceptual decision-making (PDM), and is critical for the ability of an organism to interact with its external world. Individuals with autism, a neurodevelopmental condition primarily characterised by social and communication difficulties, frequently exhibit altered sensory processing and PDM difficulties are widely reported. Recent technological advancements have pushed forward our understanding of the genetic changes accompanying this condition, however our understanding of how these mutations affect the function of specific neuronal circuits and bring about the corresponding behavioural changes remains limited. Here, we use an innate PDM task, the looming avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality across three molecularly distinct genetic mouse models of autism (Cul3, Setd5 and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli, their responses are consistently delayed, requiring longer to initiate an appropriate response than their wild-type siblings. Mutant animals show abnormal adaptation in both their stimulus- evoked escape responses and exploratory dynamics following repeated stimulus presentations. Similarly delayed behavioural responses are observed in wild-type animals when faced with more ambiguous threats, suggesting the mutant phenotype could arise from a dysfunction in the flexible control of this PDM process.\r\nOur knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed dissection of the neuronal mechanisms underlying the behavioural impairment. In vivo extracellular recording revealed that visual responses were unaffected within a key brain region for the rapid processing of visual threats, the superior colliculus (SC), indicating that the behavioural delay was unlikely to originate from sensory impairments. Delayed behavioural responses were recapitulated in the Setd5 model following optogenetic stimulation of the excitatory output neurons of the SC, which are known to mediate escape initiation through the activation of cells in the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by the misregulation of voltage-gated potassium channels. Overall, our results show that the ability to use visual information to drive efficient escape responses is impaired in three diverse genetic mouse models of autism and that, in one of the models studied, this behavioural delay likely originates from differences in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore, this work showcases the use of an innate behavioural paradigm to mechanistically dissect PDM processes in autism."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"file_name":"Burnett_Thesis_2023.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":23029260,"creator":"lburnett","relation":"source_file","file_id":"12717","date_created":"2023-03-08T15:08:46Z","date_updated":"2023-03-08T15:08:46Z","checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332"},{"content_type":"application/pdf","file_size":11959869,"creator":"lburnett","access_level":"open_access","file_name":"Burnett_Thesis_2023_pdfA.pdf","checksum":"cebc77705288bf4382db9b3541483cd0","success":1,"date_updated":"2023-03-08T15:08:46Z","date_created":"2023-03-08T15:08:46Z","relation":"main_file","file_id":"12718"}],"title":"To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism","status":"public","ddc":["599","573"],"_id":"12716","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","has_accepted_license":"1","day":"10","date_published":"2023-03-10T00:00:00Z","page":"178","citation":{"chicago":"Burnett, Laura. “To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12716.","mla":"Burnett, Laura. To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12716.","short":"L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism, Institute of Science and Technology Austria, 2023.","ista":"Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria.","apa":"Burnett, L. (2023). To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12716","ieee":"L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism,” Institute of Science and Technology Austria, 2023.","ama":"Burnett L. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. 2023. doi:10.15479/at:ista:12716"},"ec_funded":1,"file_date_updated":"2023-03-08T15:08:46Z","date_updated":"2023-04-05T10:59:04Z","date_created":"2023-03-08T15:19:45Z","author":[{"first_name":"Laura","last_name":"Burnett","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8937-410X","full_name":"Burnett, Laura"}],"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2023","publication_identifier":{"issn":["2663-337X"]},"month":"03","language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"supervisor":[{"full_name":"Jösch, Maximilian A","first_name":"Maximilian A","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330"}],"doi":"10.15479/at:ista:12716","project":[{"call_identifier":"H2020","name":"Circuits of Visual Attention","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","grant_number":"756502"}],"oa":1},{"date_published":"2023-04-20T00:00:00Z","citation":{"ama":"Chalupa M, Henzinger TA. Bubaak: Runtime monitoring of program verifiers. In: Tools and Algorithms for the Construction and Analysis of Systems. Vol 13994. Springer Nature; 2023:535-540. doi:10.1007/978-3-031-30820-8_32","ieee":"M. Chalupa and T. A. Henzinger, “Bubaak: Runtime monitoring of program verifiers,” in Tools and Algorithms for the Construction and Analysis of Systems, Paris, France, 2023, vol. 13994, pp. 535–540.","apa":"Chalupa, M., & Henzinger, T. A. (2023). Bubaak: Runtime monitoring of program verifiers. In Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13994, pp. 535–540). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30820-8_32","ista":"Chalupa M, Henzinger TA. 2023. Bubaak: Runtime monitoring of program verifiers. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994, 535–540.","short":"M. Chalupa, T.A. Henzinger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 535–540.","mla":"Chalupa, Marek, and Thomas A. Henzinger. “Bubaak: Runtime Monitoring of Program Verifiers.” Tools and Algorithms for the Construction and Analysis of Systems, vol. 13994, Springer Nature, 2023, pp. 535–40, doi:10.1007/978-3-031-30820-8_32.","chicago":"Chalupa, Marek, and Thomas A Henzinger. “Bubaak: Runtime Monitoring of Program Verifiers.” In Tools and Algorithms for the Construction and Analysis of Systems, 13994:535–40. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30820-8_32."},"publication":"Tools and Algorithms for the Construction and Analysis of Systems","page":"535-540","has_accepted_license":"1","article_processing_charge":"No","day":"20","file":[{"file_id":"12864","relation":"main_file","date_updated":"2023-04-25T06:58:36Z","date_created":"2023-04-25T06:58:36Z","success":1,"checksum":"120d2c2a38384058ad0630fdf8288312","file_name":"2023_LNCS_Chalupa.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":16096413}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12854","intvolume":" 13994","status":"public","title":"Bubaak: Runtime monitoring of program verifiers","ddc":["000"],"abstract":[{"lang":"eng","text":"The main idea behind BUBAAK is to run multiple program analyses in parallel and use runtime monitoring and enforcement to observe and control their progress in real time. The analyses send information about (un)explored states of the program and discovered invariants to a monitor. The monitor processes the received data and can force an analysis to stop the search of certain program parts (which have already been analyzed by other analyses), or to make it utilize a program invariant found by another analysis.\r\nAt SV-COMP 2023, the implementation of data exchange between the monitor and the analyses was not yet completed, which is why BUBAAK only ran several analyses in parallel, without any coordination. Still, BUBAAK won the meta-category FalsificationOverall and placed very well in several other (sub)-categories of the competition."}],"type":"conference","alternative_title":["LNCS"],"doi":"10.1007/978-3-031-30820-8_32","conference":{"location":"Paris, France","start_date":"2023-04-22","end_date":"2023-04-27","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"quality_controlled":"1","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031308192"],"issn":["0302-9743"],"eisbn":["9783031308208"]},"month":"04","author":[{"last_name":"Chalupa","first_name":"Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","full_name":"Chalupa, Marek"},{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"volume":13994,"date_updated":"2023-04-25T07:02:43Z","date_created":"2023-04-20T08:22:53Z","acknowledgement":"This work was supported by the ERC-2020-AdG 10102009 grant.","year":"2023","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2023-04-25T06:58:36Z"},{"month":"03","day":"25","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2023-03-25T00:00:00Z","doi":"10.48550/arXiv.2303.14555","project":[{"grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"publication":"arXiv","citation":{"short":"A. Chern, S. Ishida, ArXiv (n.d.).","mla":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, 2303.14555, doi:10.48550/arXiv.2303.14555.","chicago":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2303.14555.","ama":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv. doi:10.48550/arXiv.2303.14555","ieee":"A. Chern and S. Ishida, “Area formula for spherical polygons via prequantization,” arXiv. .","apa":"Chern, A., & Ishida, S. (n.d.). Area formula for spherical polygons via prequantization. arXiv. https://doi.org/10.48550/arXiv.2303.14555","ista":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv, 2303.14555."},"main_file_link":[{"url":"https://arxiv.org/abs/2303.14555","open_access":"1"}],"external_id":{"arxiv":["2303.14555"]},"oa":1,"abstract":[{"text":"We present a formula for the signed area of a spherical polygon via prequantization. In contrast to the traditional formula based on the Gauss-Bonnet theorem that requires measuring angles, the new formula mimics Green's theorem and is applicable to a wider range of degenerate spherical curves and polygons.","lang":"eng"}],"article_number":"2303.14555","type":"preprint","date_created":"2023-04-18T19:16:06Z","date_updated":"2023-04-25T06:51:21Z","oa_version":"Preprint","author":[{"full_name":"Chern, Albert","first_name":"Albert","last_name":"Chern"},{"first_name":"Sadashige","last_name":"Ishida","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","full_name":"Ishida, Sadashige"}],"publication_status":"submitted","status":"public","title":"Area formula for spherical polygons via prequantization","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"acknowledgement":"The authors acknowledge Chris Wojtan for his continuous support to the present work through discussions and advice. The second author thanks Anna Sisak for a fruitful discussion on prequantum bundles. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).","_id":"12846","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023"},{"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\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."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":580828,"file_name":"2023_LNCS_ChalupaM.pdf","access_level":"open_access","date_updated":"2023-04-25T07:16:36Z","date_created":"2023-04-25T07:16:36Z","success":1,"checksum":"17a7c8e08be609cf2408d37ea55e322c","file_id":"12865","relation":"main_file"}],"intvolume":" 13991","title":"Vamos: Middleware for best-effort third-party monitoring","ddc":["000"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12856","has_accepted_license":"1","article_processing_charge":"No","day":"20","date_published":"2023-04-20T00:00:00Z","page":"260-281","citation":{"mla":"Chalupa, Marek, et al. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” Fundamental Approaches to Software Engineering, vol. 13991, Springer Nature, 2023, pp. 260–81, doi:10.1007/978-3-031-30826-0_15.","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, in:, Fundamental Approaches to Software Engineering, Springer Nature, 2023, pp. 260–281.","chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” In Fundamental Approaches to Software Engineering, 13991:260–81. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30826-0_15.","ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. Vamos: Middleware for best-effort third-party monitoring. In: Fundamental Approaches to Software Engineering. Vol 13991. Springer Nature; 2023:260-281. doi:10.1007/978-3-031-30826-0_15","ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. Vamos: Middleware for best-effort third-party monitoring. Fundamental Approaches to Software Engineering. FASE: Fundamental Approaches to Software Engineering, LNCS, vol. 13991, 260–281.","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023). Vamos: Middleware for best-effort third-party monitoring. In Fundamental Approaches to Software Engineering (Vol. 13991, pp. 260–281). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30826-0_15","ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, “Vamos: Middleware for best-effort third-party monitoring,” in Fundamental Approaches to Software Engineering, Paris, France, 2023, vol. 13991, pp. 260–281."},"publication":"Fundamental Approaches to Software Engineering","ec_funded":1,"file_date_updated":"2023-04-25T07:16:36Z","volume":13991,"date_updated":"2023-04-25T07:19:07Z","date_created":"2023-04-20T08:29:42Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"12407"}]},"author":[{"first_name":"Marek","last_name":"Chalupa","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","full_name":"Chalupa, Marek"},{"last_name":"Mühlböck","first_name":"Fabian","orcid":"0000-0003-1548-0177","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","full_name":"Mühlböck, Fabian"},{"last_name":"Muroya Lei","first_name":"Stefanie","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","full_name":"Muroya Lei, Stefanie"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"}],"department":[{"_id":"ToHe"}],"publisher":"Springer Nature","publication_status":"published","year":"2023","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. The authors would like to thank the anonymous FASE reviewers for their valuable feedback and suggestions.","publication_identifier":{"eisbn":["9783031308260"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031308253"]},"month":"04","language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-30826-0_15","conference":{"name":"FASE: Fundamental Approaches to Software Engineering","location":"Paris, France","start_date":"2023-04-22","end_date":"2023-04-27"},"project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"month":"01","publication_identifier":{"eissn":["2664-1690"]},"project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:12407","file_date_updated":"2023-01-27T03:18:34Z","ec_funded":1,"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Institute of Science and Technology Austria","year":"2023","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.","date_created":"2023-01-27T03:18:08Z","date_updated":"2023-04-25T07:19:06Z","author":[{"id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","first_name":"Marek","last_name":"Chalupa","full_name":"Chalupa, Marek"},{"full_name":"Mühlböck, Fabian","orcid":"0000-0003-1548-0177","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","last_name":"Mühlböck","first_name":"Fabian"},{"first_name":"Stefanie","last_name":"Muroya Lei","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","full_name":"Muroya Lei, Stefanie"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"12856","relation":"later_version","status":"public"}]},"keyword":["runtime monitoring","best effort","third party"],"day":"27","article_processing_charge":"No","has_accepted_license":"1","page":"38","citation":{"chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12407.","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.","mla":"Chalupa, Marek, et al. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12407.","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023). VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12407","ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023.","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.","ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria; 2023. doi:10.15479/AT:ISTA:12407"},"date_published":"2023-01-27T00:00:00Z","alternative_title":["IST Austria Technical Report"],"type":"technical_report","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."}],"status":"public","title":"VAMOS: Middleware for Best-Effort Third-Party Monitoring","ddc":["005"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12407","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12408","date_updated":"2023-01-27T03:18:34Z","date_created":"2023-01-27T03:18:34Z","checksum":"55426e463fdeafe9777fc3ff635154c7","success":1,"file_name":"main.pdf","access_level":"open_access","file_size":662409,"content_type":"application/pdf","creator":"fmuehlbo"}]},{"day":"01","month":"02","publication_identifier":{"isbn":["9780128188736"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2023-02-01T00:00:00Z","doi":"10.1016/b978-0-12-818872-9.00129-1","quality_controlled":"1","page":"86-98","publication":"Encyclopedia of Child and Adolescent Health","citation":{"short":"C. Currin, C. Beyer, in:, B. Halpern-Felsher (Ed.), Encyclopedia of Child and Adolescent Health, 1st ed., Elsevier, 2023, pp. 86–98.","mla":"Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development in Autism and Epilepsy.” Encyclopedia of Child and Adolescent Health, edited by Bonnie Halpern-Felsher, 1st ed., Elsevier, 2023, pp. 86–98, doi:10.1016/b978-0-12-818872-9.00129-1.","chicago":"Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development in Autism and Epilepsy.” In Encyclopedia of Child and Adolescent Health, edited by Bonnie Halpern-Felsher, 1st ed., 86–98. Elsevier, 2023. https://doi.org/10.1016/b978-0-12-818872-9.00129-1.","ama":"Currin C, Beyer C. Altered childhood brain development in autism and epilepsy. In: Halpern-Felsher B, ed. Encyclopedia of Child and Adolescent Health. 1st ed. Elsevier; 2023:86-98. doi:10.1016/b978-0-12-818872-9.00129-1","ieee":"C. Currin and C. Beyer, “Altered childhood brain development in autism and epilepsy,” in Encyclopedia of Child and Adolescent Health, 1st ed., B. Halpern-Felsher, Ed. Elsevier, 2023, pp. 86–98.","apa":"Currin, C., & Beyer, C. (2023). Altered childhood brain development in autism and epilepsy. In B. Halpern-Felsher (Ed.), Encyclopedia of Child and Adolescent Health (1st ed., pp. 86–98). Elsevier. https://doi.org/10.1016/b978-0-12-818872-9.00129-1","ista":"Currin C, Beyer C. 2023.Altered childhood brain development in autism and epilepsy. In: Encyclopedia of Child and Adolescent Health. Vol. 1: Biological Development and Physical Health, , 86–98."},"abstract":[{"text":"Autism spectrum disorder (ASD) and epilepsy are frequently comorbid neurodevelopmental disorders. Extensive research has demonstrated shared pathological pathways, etiologies, and phenotypes. Many risk factors for these disorders, like genetic mutations and environmental pressures, are linked to changes in childhood brain development, which is a critical period for their manifestation.\r\nDecades of research have yielded many signatures for ASD and epilepsy, some shared and others unique or opposing. The anatomical, physiological, and behavioral correlates of these disorders are discussed in this chapter in the context of understanding shared pathological pathways. We end with important takeaways on the presentation, prevention, intervention, and policy changes for ASD and epilepsy. This chapter aims to explore the complexity of these disorders, both in etiology and phenotypes, with the further goal of appreciating the expanse of unknowns still to explore about the brain.","lang":"eng"}],"alternative_title":["Vol. 1: Biological Development and Physical Health"],"type":"book_chapter","date_updated":"2023-04-25T09:25:40Z","date_created":"2023-04-25T07:52:43Z","oa_version":"None","author":[{"id":"e8321fc5-3091-11eb-8a53-83f309a11ac9","orcid":"0000-0002-4809-5059","first_name":"Christopher","last_name":"Currin","full_name":"Currin, Christopher"},{"last_name":"Beyer","first_name":"Chad","full_name":"Beyer, Chad"}],"edition":"1","title":"Altered childhood brain development in autism and epilepsy","status":"public","publication_status":"published","editor":[{"full_name":"Halpern-Felsher, Bonnie","first_name":"Bonnie","last_name":"Halpern-Felsher"}],"publisher":"Elsevier","department":[{"_id":"TiVo"}],"_id":"12866","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"project":[{"_id":"267DFB90-B435-11E9-9278-68D0E5697425","name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?"}],"doi":"10.15479/at:ista:12809","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"supervisor":[{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"issn":["2663 - 337X"]},"year":"2023","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"RySh"}],"author":[{"full_name":"Alcarva, Catarina","first_name":"Catarina","last_name":"Alcarva","id":"3A96634C-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-04-26T12:16:56Z","date_created":"2023-04-06T07:54:09Z","file_date_updated":"2023-04-07T06:18:05Z","citation":{"short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023.","mla":"Alcarva, Catarina. Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12809.","chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12809.","ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:10.15479/at:ista:12809","apa":"Alcarva, C. (2023). Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12809","ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023.","ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria."},"page":"115","date_published":"2023-04-06T00:00:00Z","day":"06","has_accepted_license":"1","article_processing_charge":"No","_id":"12809","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","ddc":["570"],"title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","file":[{"date_created":"2023-04-07T06:16:06Z","date_updated":"2023-04-07T06:16:06Z","checksum":"35b5997d2b0acb461f9d33d073da0df5","relation":"main_file","file_id":"12814","embargo":"2024-04-07","content_type":"application/pdf","file_size":9881969,"creator":"cchlebak","embargo_to":"open_access","file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf","access_level":"closed"},{"creator":"cchlebak","content_type":"application/pdf","file_size":44201583,"access_level":"closed","file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf","checksum":"81198f63c294890f6d58e8b29782efdc","date_created":"2023-04-07T06:17:11Z","date_updated":"2023-04-07T06:17:11Z","file_id":"12815","relation":"source_file"},{"relation":"source_file","file_id":"12816","date_created":"2023-04-07T06:18:05Z","date_updated":"2023-04-07T06:18:05Z","checksum":"0317bf7f457bb585f99d453ffa69eb53","file_name":"Thesis_CatarinaAlcarva_final.docx","access_level":"closed","file_size":84731244,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"cchlebak"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. "}]},{"extern":"1","article_number":"7","author":[{"last_name":"Zhao","first_name":"Long","full_name":"Zhao, Long"},{"first_name":"Yiman","last_name":"Yang","full_name":"Yang, Yiman"},{"first_name":"Jinchao","last_name":"Chen","full_name":"Chen, Jinchao"},{"last_name":"Lin","first_name":"Xuelei","full_name":"Lin, Xuelei"},{"first_name":"Hao","last_name":"Zhang","full_name":"Zhang, Hao"},{"full_name":"Wang, Hao","first_name":"Hao","last_name":"Wang"},{"full_name":"Wang, Hongzhe","last_name":"Wang","first_name":"Hongzhe"},{"full_name":"Bie, Xiaomin","last_name":"Bie","first_name":"Xiaomin"},{"full_name":"Jiang, Jiafu","last_name":"Jiang","first_name":"Jiafu"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","last_name":"Feng","full_name":"Feng, Xiaoqi"},{"first_name":"Xiangdong","last_name":"Fu","full_name":"Fu, Xiangdong"},{"full_name":"Zhang, Xiansheng","last_name":"Zhang","first_name":"Xiansheng"},{"first_name":"Zhuo","last_name":"Du","full_name":"Du, Zhuo"},{"first_name":"Jun","last_name":"Xiao","full_name":"Xiao, Jun"}],"volume":24,"date_created":"2023-02-23T09:13:49Z","date_updated":"2023-05-08T10:52:49Z","pmid":1,"year":"2023","department":[{"_id":"XiFe"}],"publisher":"Springer Nature","publication_status":"published","publication_identifier":{"issn":["1474-760X"]},"month":"01","doi":"10.1186/s13059-022-02844-2","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["36639687"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s13059-022-02844-2"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"Background: Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive.\r\n\r\nResults: Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal–distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome.\r\n\r\nConclusions: Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis."}],"type":"journal_article","oa_version":"Published Version","_id":"12668","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 24","status":"public","title":"Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat","article_processing_charge":"No","day":"13","scopus_import":"1","date_published":"2023-01-13T00:00:00Z","citation":{"short":"L. Zhao, Y. Yang, J. Chen, X. Lin, H. Zhang, H. Wang, H. Wang, X. Bie, J. Jiang, X. Feng, X. Fu, X. Zhang, Z. Du, J. Xiao, Genome Biology 24 (2023).","mla":"Zhao, Long, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” Genome Biology, vol. 24, 7, Springer Nature, 2023, doi:10.1186/s13059-022-02844-2.","chicago":"Zhao, Long, Yiman Yang, Jinchao Chen, Xuelei Lin, Hao Zhang, Hao Wang, Hongzhe Wang, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” Genome Biology. Springer Nature, 2023. https://doi.org/10.1186/s13059-022-02844-2.","ama":"Zhao L, Yang Y, Chen J, et al. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. 2023;24. doi:10.1186/s13059-022-02844-2","ieee":"L. Zhao et al., “Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat,” Genome Biology, vol. 24. Springer Nature, 2023.","apa":"Zhao, L., Yang, Y., Chen, J., Lin, X., Zhang, H., Wang, H., … Xiao, J. (2023). Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-022-02844-2","ista":"Zhao L, Yang Y, Chen J, Lin X, Zhang H, Wang H, Wang H, Bie X, Jiang J, Feng X, Fu X, Zhang X, Du Z, Xiao J. 2023. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. 24, 7."},"publication":"Genome Biology","article_type":"original"},{"date_published":"2023-01-18T00:00:00Z","article_type":"original","publication":"Chemistry – A European Journal","citation":{"ista":"Traxler M, Reischauer S, Vogl S, Roeser J, Rabeah J, Penschke C, Saalfrank P, Pieber B, Thomas A. 2023. Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts. Chemistry – A European Journal. 29(4), e202202967.","ieee":"M. Traxler et al., “Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts,” Chemistry – A European Journal, vol. 29, no. 4. Wiley, 2023.","apa":"Traxler, M., Reischauer, S., Vogl, S., Roeser, J., Rabeah, J., Penschke, C., … Thomas, A. (2023). Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts. Chemistry – A European Journal. Wiley. https://doi.org/10.1002/chem.202202967","ama":"Traxler M, Reischauer S, Vogl S, et al. Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts. Chemistry – A European Journal. 2023;29(4). doi:10.1002/chem.202202967","chicago":"Traxler, Michael, Susanne Reischauer, Sarah Vogl, Jérôme Roeser, Jabor Rabeah, Christopher Penschke, Peter Saalfrank, Bartholomäus Pieber, and Arne Thomas. “Programmable Photocatalytic Activity of Multicomponent Covalent Organic Frameworks Used as Metallaphotocatalysts.” Chemistry – A European Journal. Wiley, 2023. https://doi.org/10.1002/chem.202202967.","mla":"Traxler, Michael, et al. “Programmable Photocatalytic Activity of Multicomponent Covalent Organic Frameworks Used as Metallaphotocatalysts.” Chemistry – A European Journal, vol. 29, no. 4, e202202967, Wiley, 2023, doi:10.1002/chem.202202967.","short":"M. Traxler, S. Reischauer, S. Vogl, J. Roeser, J. Rabeah, C. Penschke, P. Saalfrank, B. Pieber, A. Thomas, Chemistry – A European Journal 29 (2023)."},"day":"18","article_processing_charge":"No","keyword":["General Chemistry","Catalysis","Organic Chemistry"],"scopus_import":"1","oa_version":"Published Version","status":"public","title":"Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts","intvolume":" 29","_id":"12920","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The multicomponent approach allows to incorporate several functionalities into a single covalent organic framework (COF) and consequently allows the construction of bifunctional materials for cooperative catalysis. The well-defined structure of such multicomponent COFs is furthermore ideally suited for structure-activity relationship studies. We report a series of multicomponent COFs that contain acridine- and 2,2’-bipyridine linkers connected through 1,3,5-benzenetrialdehyde derivatives. The acridine motif is responsible for broad light absorption, while the bipyridine unit enables complexation of nickel catalysts. These features enable the usage of the framework materials as catalysts for light-mediated carbon−heteroatom cross-couplings. Variation of the node units shows that the catalytic activity correlates to the keto-enamine tautomer isomerism. This allows switching between high charge-carrier mobility and persistent, localized charge-separated species depending on the nodes, a tool to tailor the materials for specific reactions. Moreover, nickel-loaded COFs are recyclable and catalyze cross-couplings even using red light irradiation."}],"issue":"4","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1002/chem.202202967","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1002/chem.202202967","open_access":"1"}],"oa":1,"month":"01","publication_identifier":{"eissn":["1521-3765"],"issn":["0947-6539"]},"date_created":"2023-05-08T08:25:34Z","date_updated":"2023-05-15T08:39:24Z","volume":29,"author":[{"full_name":"Traxler, Michael","first_name":"Michael","last_name":"Traxler"},{"last_name":"Reischauer","first_name":"Susanne","full_name":"Reischauer, Susanne"},{"first_name":"Sarah","last_name":"Vogl","full_name":"Vogl, Sarah"},{"last_name":"Roeser","first_name":"Jérôme","full_name":"Roeser, Jérôme"},{"full_name":"Rabeah, Jabor","first_name":"Jabor","last_name":"Rabeah"},{"full_name":"Penschke, Christopher","first_name":"Christopher","last_name":"Penschke"},{"full_name":"Saalfrank, Peter","first_name":"Peter","last_name":"Saalfrank"},{"orcid":"0000-0001-8689-388X","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","last_name":"Pieber","first_name":"Bartholomäus","full_name":"Pieber, Bartholomäus"},{"last_name":"Thomas","first_name":"Arne","full_name":"Thomas, Arne"}],"publication_status":"published","publisher":"Wiley","year":"2023","extern":"1","article_number":"e202202967"},{"type":"journal_article","issue":"7","abstract":[{"text":"Visible-light photocatalysis provides numerous useful methodologies for synthetic organic chemistry. However, the mechanisms of these reactions are often not fully understood. Common mechanistic experiments mainly aim to characterize excited state properties of photocatalysts and their interaction with other species. Recently, in situ reaction monitoring using dedicated techniques was shown to be well-suited for the identification of intermediates and to obtain kinetic insights, thereby providing more holistic pictures of the reactions of interest. This minireview surveys these technologies and discusses selected examples where reaction monitoring was used to elucidate the mechanism of photocatalytic reactions.","lang":"eng"}],"intvolume":" 15","status":"public","title":"In situ reaction monitoring in photocatalytic organic synthesis","_id":"12921","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","keyword":["Inorganic Chemistry","Organic Chemistry","Physical and Theoretical Chemistry","Catalysis"],"scopus_import":"1","article_processing_charge":"No","day":"06","article_type":"original","citation":{"ama":"Madani A, Pieber B. In situ reaction monitoring in photocatalytic organic synthesis. ChemCatChem. 2023;15(7). doi:10.1002/cctc.202201583","ista":"Madani A, Pieber B. 2023. In situ reaction monitoring in photocatalytic organic synthesis. ChemCatChem. 15(7), e202201583.","ieee":"A. Madani and B. Pieber, “In situ reaction monitoring in photocatalytic organic synthesis,” ChemCatChem, vol. 15, no. 7. Wiley, 2023.","apa":"Madani, A., & Pieber, B. (2023). In situ reaction monitoring in photocatalytic organic synthesis. ChemCatChem. Wiley. https://doi.org/10.1002/cctc.202201583","mla":"Madani, Amiera, and Bartholomäus Pieber. “In Situ Reaction Monitoring in Photocatalytic Organic Synthesis.” ChemCatChem, vol. 15, no. 7, e202201583, Wiley, 2023, doi:10.1002/cctc.202201583.","short":"A. Madani, B. Pieber, ChemCatChem 15 (2023).","chicago":"Madani, Amiera, and Bartholomäus Pieber. “In Situ Reaction Monitoring in Photocatalytic Organic Synthesis.” ChemCatChem. Wiley, 2023. https://doi.org/10.1002/cctc.202201583."},"publication":"ChemCatChem","date_published":"2023-04-06T00:00:00Z","article_number":"e202201583","extern":"1","publisher":"Wiley","publication_status":"published","year":"2023","volume":15,"date_created":"2023-05-08T08:25:55Z","date_updated":"2023-05-15T08:35:48Z","author":[{"full_name":"Madani, Amiera","first_name":"Amiera","last_name":"Madani"},{"full_name":"Pieber, Bartholomäus","orcid":"0000-0001-8689-388X","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","last_name":"Pieber","first_name":"Bartholomäus"}],"publication_identifier":{"eissn":["1867-3899"],"issn":["1867-3880"]},"month":"04","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/cctc.202201583"}],"language":[{"iso":"eng"}],"doi":"10.1002/cctc.202201583"},{"publication_status":"published","publisher":"Georg Thieme Verlag","year":"2023","date_updated":"2023-05-15T08:43:50Z","date_created":"2023-05-08T08:25:08Z","volume":55,"author":[{"full_name":"Murakami, Sho","last_name":"Murakami","first_name":"Sho"},{"first_name":"Cosima","last_name":"Brudy","full_name":"Brudy, Cosima"},{"last_name":"Bachmann","first_name":"Moritz","full_name":"Bachmann, Moritz"},{"first_name":"Yoshiji","last_name":"Takemoto","full_name":"Takemoto, Yoshiji"},{"id":"93e5e5b2-0da6-11ed-8a41-af589a024726","orcid":"0000-0001-8689-388X","first_name":"Bartholomäus","last_name":"Pieber","full_name":"Pieber, Bartholomäus"}],"extern":"1","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1055/a-1979-5933","month":"05","publication_identifier":{"eissn":["1437-210X"],"issn":["0039-7881"]},"status":"public","title":"Photocatalytic cleavage of trityl protected thiols and alcohols","intvolume":" 55","_id":"12919","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"We report the visible light photocatalytic cleavage of trityl thioethers or ethers under pH-neutral conditions. The method results in the formation of the respective symmetrical disulfides and alcohols in moderate to excellent yield. The protocol only requires the addition of a suitable photocatalyst and light rendering it orthogonal to several functionalities, including acid labile protective groups. The same conditions can be used to directly convert trityl-protected thiols into unsymmetrical disulfides or selenosulfides, and to cleave trityl resins in solid phase organic synthesis."}],"issue":"09","article_type":"original","page":"1367-1374","publication":"Synthesis","citation":{"chicago":"Murakami, Sho, Cosima Brudy, Moritz Bachmann, Yoshiji Takemoto, and Bartholomäus Pieber. “Photocatalytic Cleavage of Trityl Protected Thiols and Alcohols.” Synthesis. Georg Thieme Verlag, 2023. https://doi.org/10.1055/a-1979-5933.","mla":"Murakami, Sho, et al. “Photocatalytic Cleavage of Trityl Protected Thiols and Alcohols.” Synthesis, vol. 55, no. 09, Georg Thieme Verlag, 2023, pp. 1367–74, doi:10.1055/a-1979-5933.","short":"S. Murakami, C. Brudy, M. Bachmann, Y. Takemoto, B. Pieber, Synthesis 55 (2023) 1367–1374.","ista":"Murakami S, Brudy C, Bachmann M, Takemoto Y, Pieber B. 2023. Photocatalytic cleavage of trityl protected thiols and alcohols. Synthesis. 55(09), 1367–1374.","ieee":"S. Murakami, C. Brudy, M. Bachmann, Y. Takemoto, and B. Pieber, “Photocatalytic cleavage of trityl protected thiols and alcohols,” Synthesis, vol. 55, no. 09. Georg Thieme Verlag, pp. 1367–1374, 2023.","apa":"Murakami, S., Brudy, C., Bachmann, M., Takemoto, Y., & Pieber, B. (2023). Photocatalytic cleavage of trityl protected thiols and alcohols. Synthesis. Georg Thieme Verlag. https://doi.org/10.1055/a-1979-5933","ama":"Murakami S, Brudy C, Bachmann M, Takemoto Y, Pieber B. Photocatalytic cleavage of trityl protected thiols and alcohols. Synthesis. 2023;55(09):1367-1374. doi:10.1055/a-1979-5933"},"date_published":"2023-05-01T00:00:00Z","keyword":["Organic Chemistry","Catalysis"],"scopus_import":"1","day":"01","article_processing_charge":"No"},{"language":[{"iso":"eng"}],"conference":{"name":"STOC: Symposium on Theory of Computing","end_date":"2023-06-23","start_date":"2023-06-20","location":"Orlando, FL, United States"},"doi":"10.1145/3564246.3585113","quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","grant_number":"M03073","name":"Learning and triangulating manifolds via collapses"}],"main_file_link":[{"url":"https://arxiv.org/abs/2303.04014","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2303.04014"]},"month":"06","publication_identifier":{"isbn":["9781450399135"]},"date_created":"2023-05-22T08:02:02Z","date_updated":"2023-05-22T08:15:19Z","author":[{"first_name":"André","last_name":"Lieutier","full_name":"Lieutier, André"},{"id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220","first_name":"Mathijs","last_name":"Wintraecken","full_name":"Wintraecken, Mathijs"}],"publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"HeEd"}],"year":"2023","acknowledgement":"We are greatly indebted to Erin Chambers for posing a number of questions that eventually led to this paper. We would also like to thank the other organizers of the workshop on ‘Algorithms\r\nfor the medial axis’. We are also indebted to Tatiana Ezubova for helping with the search for and translation of Russian literature. The second author thanks all members of the Edelsbrunner and Datashape groups for the atmosphere in which the research was conducted.\r\nThe research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement No. 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions). Supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411. The Austrian science fund (FWF) M-3073.","ec_funded":1,"date_published":"2023-06-02T00:00:00Z","page":"1768-1776","publication":"Proceedings of the 55th Annual ACM Symposium on Theory of Computing","citation":{"chicago":"Lieutier, André, and Mathijs Wintraecken. “Hausdorff and Gromov-Hausdorff Stable Subsets of the Medial Axis.” In Proceedings of the 55th Annual ACM Symposium on Theory of Computing, 1768–76. Association for Computing Machinery, 2023. https://doi.org/10.1145/3564246.3585113.","short":"A. Lieutier, M. Wintraecken, in:, Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2023, pp. 1768–1776.","mla":"Lieutier, André, and Mathijs Wintraecken. “Hausdorff and Gromov-Hausdorff Stable Subsets of the Medial Axis.” Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2023, pp. 1768–76, doi:10.1145/3564246.3585113.","ieee":"A. Lieutier and M. Wintraecken, “Hausdorff and Gromov-Hausdorff stable subsets of the medial axis,” in Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Orlando, FL, United States, 2023, pp. 1768–1776.","apa":"Lieutier, A., & Wintraecken, M. (2023). Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. In Proceedings of the 55th Annual ACM Symposium on Theory of Computing (pp. 1768–1776). Orlando, FL, United States: Association for Computing Machinery. https://doi.org/10.1145/3564246.3585113","ista":"Lieutier A, Wintraecken M. 2023. Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. Proceedings of the 55th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 1768–1776.","ama":"Lieutier A, Wintraecken M. Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. In: Proceedings of the 55th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2023:1768-1776. doi:10.1145/3564246.3585113"},"day":"02","article_processing_charge":"No","oa_version":"Preprint","status":"public","title":"Hausdorff and Gromov-Hausdorff stable subsets of the medial axis","_id":"13048","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"In this paper we introduce a pruning of the medial axis called the (λ,α)-medial axis (axλα). We prove that the (λ,α)-medial axis of a set K is stable in a Gromov-Hausdorff sense under weak assumptions. More formally we prove that if K and K′ are close in the Hausdorff (dH) sense then the (λ,α)-medial axes of K and K′ are close as metric spaces, that is the Gromov-Hausdorff distance (dGH) between the two is 1/4-Hölder in the sense that dGH (axλα(K),axλα(K′)) ≲ dH(K,K′)1/4. The Hausdorff distance between the two medial axes is also bounded, by dH (axλα(K),λα(K′)) ≲ dH(K,K′)1/2. These quantified stability results provide guarantees for practical computations of medial axes from approximations. Moreover, they provide key ingredients for studying the computability of the medial axis in the context of computable analysis.","lang":"eng"}],"type":"conference"},{"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"date_published":"2023-05-01T00:00:00Z","conference":{"location":"Kigali, Rwanda ","start_date":"2023-05-01","end_date":"2023-05-05","name":"ICLR: International Conference on Learning Representations"},"project":[{"call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://openreview.net/pdf?id=_eTZBs-yedr","open_access":"1"}],"external_id":{"arxiv":["2207.14200"]},"citation":{"ieee":"E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, and D.-A. Alistarh, “CrAM: A Compression-Aware Minimizer,” in 11th International Conference on Learning Representations , Kigali, Rwanda .","apa":"Peste, E.-A., Vladu, A., Kurtic, E., Lampert, C., & Alistarh, D.-A. (n.d.). CrAM: A Compression-Aware Minimizer. In 11th International Conference on Learning Representations . Kigali, Rwanda .","ista":"Peste E-A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. 11th International Conference on Learning Representations . ICLR: International Conference on Learning Representations.","ama":"Peste E-A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. In: 11th International Conference on Learning Representations .","chicago":"Peste, Elena-Alexandra, Adrian Vladu, Eldar Kurtic, Christoph Lampert, and Dan-Adrian Alistarh. “CrAM: A Compression-Aware Minimizer.” In 11th International Conference on Learning Representations , n.d.","short":"E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, D.-A. Alistarh, in:, 11th International Conference on Learning Representations , n.d.","mla":"Peste, Elena-Alexandra, et al. “CrAM: A Compression-Aware Minimizer.” 11th International Conference on Learning Representations ."},"publication":"11th International Conference on Learning Representations ","article_processing_charge":"No","month":"05","oa_version":"Preprint","date_updated":"2023-06-01T12:54:45Z","date_created":"2023-05-23T11:36:18Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"13074"}]},"author":[{"first_name":"Elena-Alexandra","last_name":"Peste","id":"32D78294-F248-11E8-B48F-1D18A9856A87","full_name":"Peste, Elena-Alexandra"},{"full_name":"Vladu, Adrian","first_name":"Adrian","last_name":"Vladu"},{"full_name":"Kurtic, Eldar","last_name":"Kurtic","first_name":"Eldar","id":"47beb3a5-07b5-11eb-9b87-b108ec578218"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph"},{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"publication_status":"accepted","title":"CrAM: A Compression-Aware Minimizer","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13053","year":"2023","acknowledgement":"AP, EK, DA received funding from the European Research Council (ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). AV acknowledges the support of the French Agence Nationale de la Recherche (ANR), under grant ANR-21-CE48-0016 (project COMCOPT). We further acknowledge the support from the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp)-","ec_funded":1,"abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) often have to be compressed, via pruning and/or quantization, before they can be deployed in practical settings. In this work we propose a new compression-aware minimizer dubbed CrAM that modifies the optimization step in a principled way, in order to produce models whose local loss behavior is stable under compression operations such as pruning. Thus, dense models trained via CrAM should be compressible post-training, in a single step, without significant accuracy loss. Experimental results on standard benchmarks, such as residual networks for ImageNet classification and BERT models for language modelling, show that CrAM produces dense models that can be more accurate than the standard SGD/Adam-based baselines, but which are stable under weight pruning: specifically, we can prune models in one-shot to 70-80% sparsity with almost no accuracy loss, and to 90% with reasonable (∼1%) accuracy loss, which is competitive with gradual compression methods. Additionally, CrAM can produce sparse models which perform well for transfer learning, and it also works for semi-structured 2:4 pruning patterns supported by GPU hardware. The code for reproducing the results is available at this https URL ."}],"type":"conference"},{"alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"GIMPS and PrimeGrid are large-scale distributed projects dedicated to searching giant prime numbers, usually of special forms like Mersenne and Proth primes. The numbers in the current search-space are millions of digits large and the participating volunteers need to run resource-consuming primality tests. Once a candidate prime N has been found, the only way for another party to independently verify the primality of N used to be by repeating the expensive primality test. To avoid the need for second recomputation of each primality test, these projects have recently adopted certifying mechanisms that enable efficient verification of performed tests. However, the mechanisms presently in place only detect benign errors and there is no guarantee against adversarial behavior: a malicious volunteer can mislead the project to reject a giant prime as being non-prime.\r\nIn this paper, we propose a practical, cryptographically-sound mechanism for certifying the non-primality of Proth numbers. That is, a volunteer can – parallel to running the primality test for N – generate an efficiently verifiable proof at a little extra cost certifying that N is not prime. The interactive protocol has statistical soundness and can be made non-interactive using the Fiat-Shamir heuristic.\r\nOur approach is based on a cryptographic primitive called Proof of Exponentiation (PoE) which, for a group G, certifies that a tuple (x,y,T)∈G2×N satisfies x2T=y (Pietrzak, ITCS 2019 and Wesolowski, J. Cryptol. 2020). In particular, we show how to adapt Pietrzak’s PoE at a moderate additional cost to make it a cryptographically-sound certificate of non-primality.","lang":"eng"}],"status":"public","title":"Certifying giant nonprimes","intvolume":" 13940","_id":"13143","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","scopus_import":"1","day":"02","article_processing_charge":"No","page":"530-553","publication":"Public-Key Cryptography - PKC 2023","citation":{"ista":"Hoffmann C, Hubáček P, Kamath C, Pietrzak KZ. 2023. Certifying giant nonprimes. Public-Key Cryptography - PKC 2023. PKC: Public-Key Cryptography, LNCS, vol. 13940, 530–553.","apa":"Hoffmann, C., Hubáček, P., Kamath, C., & Pietrzak, K. Z. (2023). Certifying giant nonprimes. In Public-Key Cryptography - PKC 2023 (Vol. 13940, pp. 530–553). Atlanta, GA, United States: Springer Nature. https://doi.org/10.1007/978-3-031-31368-4_19","ieee":"C. Hoffmann, P. Hubáček, C. Kamath, and K. Z. Pietrzak, “Certifying giant nonprimes,” in Public-Key Cryptography - PKC 2023, Atlanta, GA, United States, 2023, vol. 13940, pp. 530–553.","ama":"Hoffmann C, Hubáček P, Kamath C, Pietrzak KZ. Certifying giant nonprimes. In: Public-Key Cryptography - PKC 2023. Vol 13940. Springer Nature; 2023:530-553. doi:10.1007/978-3-031-31368-4_19","chicago":"Hoffmann, Charlotte, Pavel Hubáček, Chethan Kamath, and Krzysztof Z Pietrzak. “Certifying Giant Nonprimes.” In Public-Key Cryptography - PKC 2023, 13940:530–53. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-31368-4_19.","mla":"Hoffmann, Charlotte, et al. “Certifying Giant Nonprimes.” Public-Key Cryptography - PKC 2023, vol. 13940, Springer Nature, 2023, pp. 530–53, doi:10.1007/978-3-031-31368-4_19.","short":"C. Hoffmann, P. Hubáček, C. Kamath, K.Z. Pietrzak, in:, Public-Key Cryptography - PKC 2023, Springer Nature, 2023, pp. 530–553."},"date_published":"2023-05-02T00:00:00Z","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer Nature","acknowledgement":"We are grateful to Pavel Atnashev for clarifying via e-mail several aspects of the primality tests implementated in the PrimeGrid project. Pavel Hubáček is supported by the Czech Academy of Sciences (RVO 67985840), the Grant Agency of the Czech Republic under the grant agreement no. 19-27871X, and by the Charles University project UNCE/SCI/004. Chethan Kamath is supported by Azrieli International Postdoctoral Fellowship, ISF grants 484/18 and 1789/19, and ERC StG project SPP: Secrecy Preserving Proofs.","year":"2023","date_updated":"2023-06-19T08:03:37Z","date_created":"2023-06-18T22:00:47Z","volume":13940,"author":[{"full_name":"Hoffmann, Charlotte","last_name":"Hoffmann","first_name":"Charlotte","id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7"},{"last_name":"Hubáček","first_name":"Pavel","full_name":"Hubáček, Pavel"},{"full_name":"Kamath, Chethan","last_name":"Kamath","first_name":"Chethan"},{"last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"}],"month":"05","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031313677"]},"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2023/238"}],"language":[{"iso":"eng"}],"conference":{"end_date":"2023-05-10","start_date":"2023-05-07","location":"Atlanta, GA, United States","name":"PKC: Public-Key Cryptography"},"doi":"10.1007/978-3-031-31368-4_19"},{"page":"3-25","publication":"Tools and Algorithms for the Construction and Analysis of Systems ","citation":{"mla":"Chatterjee, Krishnendu, et al. “A Learner-Verifier Framework for Neural Network Controllers and Certificates of Stochastic Systems.” Tools and Algorithms for the Construction and Analysis of Systems , vol. 13993, Springer Nature, 2023, pp. 3–25, doi:10.1007/978-3-031-30823-9_1.","short":"K. Chatterjee, T.A. Henzinger, M. Lechner, D. Zikelic, in:, Tools and Algorithms for the Construction and Analysis of Systems , Springer Nature, 2023, pp. 3–25.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Mathias Lechner, and Dorde Zikelic. “A Learner-Verifier Framework for Neural Network Controllers and Certificates of Stochastic Systems.” In Tools and Algorithms for the Construction and Analysis of Systems , 13993:3–25. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30823-9_1.","ama":"Chatterjee K, Henzinger TA, Lechner M, Zikelic D. A learner-verifier framework for neural network controllers and certificates of stochastic systems. In: Tools and Algorithms for the Construction and Analysis of Systems . Vol 13993. Springer Nature; 2023:3-25. doi:10.1007/978-3-031-30823-9_1","ista":"Chatterjee K, Henzinger TA, Lechner M, Zikelic D. 2023. A learner-verifier framework for neural network controllers and certificates of stochastic systems. Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13993, 3–25.","apa":"Chatterjee, K., Henzinger, T. A., Lechner, M., & Zikelic, D. (2023). A learner-verifier framework for neural network controllers and certificates of stochastic systems. In Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13993, pp. 3–25). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30823-9_1","ieee":"K. Chatterjee, T. A. Henzinger, M. Lechner, and D. Zikelic, “A learner-verifier framework for neural network controllers and certificates of stochastic systems,” in Tools and Algorithms for the Construction and Analysis of Systems , Paris, France, 2023, vol. 13993, pp. 3–25."},"date_published":"2023-04-22T00:00:00Z","scopus_import":"1","day":"22","article_processing_charge":"No","has_accepted_license":"1","status":"public","title":"A learner-verifier framework for neural network controllers and certificates of stochastic systems","ddc":["000"],"intvolume":" 13993","_id":"13142","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":528455,"creator":"dernst","access_level":"open_access","file_name":"2023_LNCS_Chatterjee.pdf","checksum":"3d8a8bb24d211bc83360dfc2fd744307","success":1,"date_created":"2023-06-19T08:29:30Z","date_updated":"2023-06-19T08:29:30Z","relation":"main_file","file_id":"13150"}],"alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Reinforcement learning has received much attention for learning controllers of deterministic systems. We consider a learner-verifier framework for stochastic control systems and survey recent methods that formally guarantee a conjunction of reachability and safety properties. Given a property and a lower bound on the probability of the property being satisfied, our framework jointly learns a control policy and a formal certificate to ensure the satisfaction of the property with a desired probability threshold. Both the control policy and the formal certificate are continuous functions from states to reals, which are learned as parameterized neural networks. While in the deterministic case, the certificates are invariant and barrier functions for safety, or Lyapunov and ranking functions for liveness, in the stochastic case the certificates are supermartingales. For certificate verification, we use interval arithmetic abstract interpretation to bound the expected values of neural network functions."}],"quality_controlled":"1","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2023-04-27","location":"Paris, France","start_date":"2023-04-22"},"doi":"10.1007/978-3-031-30823-9_1","month":"04","publication_identifier":{"isbn":["9783031308222"],"eissn":["1611-3349"],"issn":["0302-9743"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"year":"2023","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","date_updated":"2023-06-19T08:30:54Z","date_created":"2023-06-18T22:00:47Z","volume":13993,"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"},{"full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner"},{"full_name":"Zikelic, Dorde","first_name":"Dorde","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2023-06-19T08:29:30Z","ec_funded":1},{"page":"211-228","citation":{"short":"A. Anand, K. Mallik, S.P. Nayak, A.K. Schmuck, in:, TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 211–228.","mla":"Anand, Ashwani, et al. “Computing Adequately Permissive Assumptions for Synthesis.” TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, vol. 13994, Springer Nature, 2023, pp. 211–28, doi:10.1007/978-3-031-30820-8_15.","chicago":"Anand, Ashwani, Kaushik Mallik, Satya Prakash Nayak, and Anne Kathrin Schmuck. “Computing Adequately Permissive Assumptions for Synthesis.” In TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, 13994:211–28. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30820-8_15.","ama":"Anand A, Mallik K, Nayak SP, Schmuck AK. Computing adequately permissive assumptions for synthesis. In: TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems. Vol 13994. Springer Nature; 2023:211-228. doi:10.1007/978-3-031-30820-8_15","apa":"Anand, A., Mallik, K., Nayak, S. P., & Schmuck, A. K. (2023). Computing adequately permissive assumptions for synthesis. In TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13994, pp. 211–228). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30820-8_15","ieee":"A. Anand, K. Mallik, S. P. Nayak, and A. K. Schmuck, “Computing adequately permissive assumptions for synthesis,” in TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Paris, France, 2023, vol. 13994, pp. 211–228.","ista":"Anand A, Mallik K, Nayak SP, Schmuck AK. 2023. Computing adequately permissive assumptions for synthesis. TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994, 211–228."},"publication":"TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems","date_published":"2023-04-20T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"20","intvolume":" 13994","title":"Computing adequately permissive assumptions for synthesis","status":"public","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13141","oa_version":"Published Version","file":[{"file_id":"13151","relation":"main_file","success":1,"checksum":"60dcafc1b4f6f070be43bad3fe877974","date_created":"2023-06-19T08:43:21Z","date_updated":"2023-06-19T08:43:21Z","access_level":"open_access","file_name":"2023_LNCS_Anand.pdf","creator":"dernst","content_type":"application/pdf","file_size":521425}],"alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"We automatically compute a new class of environment assumptions in two-player turn-based finite graph games which characterize an “adequate cooperation” needed from the environment to allow the system player to win. Given an ω-regular winning condition Φ for the system player, we compute an ω-regular assumption Ψ for the environment player, such that (i) every environment strategy compliant with Ψ allows the system to fulfill Φ (sufficiency), (ii) Ψ\r\n can be fulfilled by the environment for every strategy of the system (implementability), and (iii) Ψ does not prevent any cooperative strategy choice (permissiveness).\r\nFor parity games, which are canonical representations of ω-regular games, we present a polynomial-time algorithm for the symbolic computation of adequately permissive assumptions and show that our algorithm runs faster and produces better assumptions than existing approaches—both theoretically and empirically. To the best of our knowledge, for ω\r\n-regular games, we provide the first algorithm to compute sufficient and implementable environment assumptions that are also permissive."}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-30820-8_15","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2023-04-27","location":"Paris, France","start_date":"2023-04-22"},"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031308192"]},"month":"04","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2023","volume":13994,"date_updated":"2023-06-19T08:49:46Z","date_created":"2023-06-18T22:00:47Z","author":[{"first_name":"Ashwani","last_name":"Anand","full_name":"Anand, Ashwani"},{"orcid":"0000-0001-9864-7475","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","last_name":"Mallik","first_name":"Kaushik","full_name":"Mallik, Kaushik"},{"last_name":"Nayak","first_name":"Satya Prakash","full_name":"Nayak, Satya Prakash"},{"last_name":"Schmuck","first_name":"Anne Kathrin","full_name":"Schmuck, Anne Kathrin"}],"file_date_updated":"2023-06-19T08:43:21Z"},{"supervisor":[{"first_name":"Maximilian A","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12826","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"04","publication_identifier":{"issn":["2663 - 337X"]},"date_updated":"2023-06-23T09:47:36Z","date_created":"2023-04-14T14:56:04Z","author":[{"full_name":"Pokusaeva, Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7660-444X","first_name":"Victoria","last_name":"Pokusaeva"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"MaJö"},{"_id":"GradSch"}],"year":"2023","file_date_updated":"2023-04-20T09:26:51Z","ec_funded":1,"date_published":"2023-04-18T00:00:00Z","page":"106","citation":{"ama":"Pokusaeva V. Neural control of optic flow-based navigation in Drosophila melanogaster. 2023. doi:10.15479/at:ista:12826","ista":"Pokusaeva V. 2023. Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria.","apa":"Pokusaeva, V. (2023). Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12826","ieee":"V. Pokusaeva, “Neural control of optic flow-based navigation in Drosophila melanogaster,” Institute of Science and Technology Austria, 2023.","mla":"Pokusaeva, Victoria. Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12826.","short":"V. Pokusaeva, Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster, Institute of Science and Technology Austria, 2023.","chicago":"Pokusaeva, Victoria. “Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12826."},"day":"18","has_accepted_license":"1","article_processing_charge":"No","oa_version":"Published Version","file":[{"file_id":"12857","relation":"source_file","checksum":"5f589a9af025f7eeebfd0c186209913e","date_created":"2023-04-20T09:14:38Z","date_updated":"2023-04-20T09:26:51Z","access_level":"closed","file_name":"Thesis_Pokusaeva.docx","creator":"vpokusae","file_size":14507243,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"relation":"main_file","file_id":"12858","date_created":"2023-04-20T09:14:44Z","date_updated":"2023-04-20T09:14:44Z","checksum":"bbeed76db45a996b4c91a9abe12ce0ec","success":1,"file_name":"Thesis_Pokusaeva.pdf","access_level":"open_access","content_type":"application/pdf","file_size":10090711,"creator":"vpokusae"}],"ddc":["570","571"],"status":"public","title":"Neural control of optic flow-based navigation in Drosophila melanogaster","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12826","abstract":[{"lang":"eng","text":"During navigation, animals can infer the structure of the environment by computing the optic flow cues elicited by their own movements, and subsequently use this information to instruct proper locomotor actions. These computations require a panoramic assessment of the visual environment in order to disambiguate similar sensory experiences that may require distinct behavioral responses. The estimation of the global motion patterns is therefore essential for successful navigation. Yet, our understanding of the algorithms and implementations that enable coherent panoramic visual perception remains scarce. Here I pursue this problem by dissecting the functional aspects of interneuronal communication in the lobula plate tangential cell network in Drosophila melanogaster. The results presented in the thesis demonstrate that the basis for effective interpretation of the optic flow in this circuit are stereotyped synaptic connections that mediate the formation of distinct subnetworks, each extracting a particular pattern of global motion. \r\nFirstly, I show that gap junctions are essential for a correct interpretation of binocular motion cues by horizontal motion-sensitive cells. HS cells form electrical synapses with contralateral H2 neurons that are involved in detecting yaw rotation and translation. I developed an FlpStop-mediated mutant of a gap junction protein ShakB that disrupts these electrical synapses. While the loss of electrical synapses does not affect the tuning of the direction selectivity in HS neurons, it severely alters their sensitivity to horizontal motion in the contralateral side. These physiological changes result in an inappropriate integration of binocular motion cues in walking animals. While wild-type flies form a binocular perception of visual motion by non-linear integration of monocular optic flow cues, the mutant flies sum the monocular inputs linearly. These results indicate that rather than averaging signals in neighboring neurons, gap-junctions operate in conjunction with chemical synapses to mediate complex non-linear optic flow computations.\r\nSecondly, I show that stochastic manipulation of neuronal activity in the lobula plate tangential cell network is a powerful approach to study the neuronal implementation of optic flow-based navigation in flies. Tangential neurons form multiple subnetworks, each mediating course-stabilizing response to a particular global pattern of visual motion. Application of genetic mosaic techniques can provide sparse optogenetic activation of HS cells in numerous combinations. These distinct combinations of activated neurons drive an array of distinct behavioral responses, providing important insights into how visuomotor transformation is performed in the lobula plate tangential cell network. This approach can be complemented by stochastic silencing of tangential neurons, enabling direct assessment of the functional role of individual tangential neurons in the processing of specific visual motion patterns.\r\n\tTaken together, the findings presented in this thesis suggest that establishing specific activity patterns of tangential cells via stereotyped synaptic connectivity is a key to efficient optic flow-based navigation in Drosophila melanogaster."}],"alternative_title":["ISTA Thesis"],"type":"dissertation"},{"doi":"10.1007/s00453-022-01027-6","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000846967100001"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"month":"01","publication_identifier":{"eissn":["1432-0541"],"issn":["0178-4617"]},"author":[{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"full_name":"Osang, Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang","first_name":"Georg F"}],"date_updated":"2023-06-27T12:53:43Z","date_created":"2022-09-11T22:01:57Z","volume":85,"acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.","year":"2023","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","file_date_updated":"2023-01-20T10:02:48Z","ec_funded":1,"date_published":"2023-01-01T00:00:00Z","publication":"Algorithmica","citation":{"ista":"Edelsbrunner H, Osang GF. 2023. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 85, 277–295.","apa":"Edelsbrunner, H., & Osang, G. F. (2023). A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. Springer Nature. https://doi.org/10.1007/s00453-022-01027-6","ieee":"H. Edelsbrunner and G. F. Osang, “A simple algorithm for higher-order Delaunay mosaics and alpha shapes,” Algorithmica, vol. 85. Springer Nature, pp. 277–295, 2023.","ama":"Edelsbrunner H, Osang GF. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 2023;85:277-295. doi:10.1007/s00453-022-01027-6","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica. Springer Nature, 2023. https://doi.org/10.1007/s00453-022-01027-6.","mla":"Edelsbrunner, Herbert, and Georg F. Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica, vol. 85, Springer Nature, 2023, pp. 277–95, doi:10.1007/s00453-022-01027-6.","short":"H. Edelsbrunner, G.F. Osang, Algorithmica 85 (2023) 277–295."},"article_type":"original","page":"277-295","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"file_id":"12322","relation":"main_file","date_updated":"2023-01-20T10:02:48Z","date_created":"2023-01-20T10:02:48Z","success":1,"checksum":"71685ca5121f4c837f40c3f8eb50c915","file_name":"2023_Algorithmica_Edelsbrunner.pdf","access_level":"open_access","creator":"dernst","file_size":911017,"content_type":"application/pdf"}],"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","_id":"12086","status":"public","ddc":["510"],"title":"A simple algorithm for higher-order Delaunay mosaics and alpha shapes","intvolume":" 85","abstract":[{"lang":"eng","text":"We present a simple algorithm for computing higher-order Delaunay mosaics that works in Euclidean spaces of any finite dimensions. The algorithm selects the vertices of the order-k mosaic from incrementally constructed lower-order mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box to construct the order-k mosaic from its vertices. Beyond this black-box, the algorithm uses only combinatorial operations, thus facilitating easy implementation. We extend this algorithm to compute higher-order α-shapes and provide open-source implementations. We present experimental results for properties of higher-order Delaunay mosaics of random point sets."}],"type":"journal_article"},{"date_published":"2023-01-01T00:00:00Z","publication":"Journal of Evolution Equations","citation":{"chicago":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” Journal of Evolution Equations. Springer Nature, 2023. https://doi.org/10.1007/s00028-022-00859-7.","short":"L. Dello Schiavo, M. Wirth, Journal of Evolution Equations 23 (2023).","mla":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” Journal of Evolution Equations, vol. 23, no. 1, 9, Springer Nature, 2023, doi:10.1007/s00028-022-00859-7.","apa":"Dello Schiavo, L., & Wirth, M. (2023). Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. Springer Nature. https://doi.org/10.1007/s00028-022-00859-7","ieee":"L. Dello Schiavo and M. Wirth, “Ergodic decompositions of Dirichlet forms under order isomorphisms,” Journal of Evolution Equations, vol. 23, no. 1. Springer Nature, 2023.","ista":"Dello Schiavo L, Wirth M. 2023. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 23(1), 9.","ama":"Dello Schiavo L, Wirth M. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 2023;23(1). doi:10.1007/s00028-022-00859-7"},"article_type":"original","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","file":[{"file_name":"2023_JourEvolutionEquations_DelloSchiavo.pdf","access_level":"open_access","content_type":"application/pdf","file_size":422612,"creator":"dernst","relation":"main_file","file_id":"12325","date_created":"2023-01-20T10:45:06Z","date_updated":"2023-01-20T10:45:06Z","checksum":"1f34f3e2cb521033de6154f274ea3a4e","success":1}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12104","status":"public","title":"Ergodic decompositions of Dirichlet forms under order isomorphisms","ddc":["510"],"intvolume":" 23","abstract":[{"text":"We study ergodic decompositions of Dirichlet spaces under intertwining via unitary order isomorphisms. We show that the ergodic decomposition of a quasi-regular Dirichlet space is unique up to a unique isomorphism of the indexing space. Furthermore, every unitary order isomorphism intertwining two quasi-regular Dirichlet spaces is decomposable over their ergodic decompositions up to conjugation via an isomorphism of the corresponding indexing spaces.","lang":"eng"}],"issue":"1","type":"journal_article","doi":"10.1007/s00028-022-00859-7","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000906214600004"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"},{"grant_number":"E208","_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","name":"Configuration Spaces over Non-Smooth Spaces"},{"name":"Gradient flow techniques for quantum Markov semigroups","grant_number":"ESP156_N","_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833"}],"month":"01","publication_identifier":{"eissn":["1424-3202"],"issn":["1424-3199"]},"author":[{"orcid":"0000-0002-9881-6870","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","last_name":"Dello Schiavo","first_name":"Lorenzo","full_name":"Dello Schiavo, Lorenzo"},{"full_name":"Wirth, Melchior","last_name":"Wirth","first_name":"Melchior","orcid":"0000-0002-0519-4241","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E"}],"date_created":"2023-01-08T23:00:53Z","date_updated":"2023-06-28T11:54:35Z","volume":23,"year":"2023","acknowledgement":"Research supported by the Austrian Science Fund (FWF) grant F65 at the Institute of Science and Technology Austria and by the European Research Council (ERC) (Grant agreement No. 716117 awarded to Prof. Dr. Jan Maas). L.D.S. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 208). M.W. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 156).","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JaMa"}],"file_date_updated":"2023-01-20T10:45:06Z","ec_funded":1,"article_number":"9"},{"month":"01","publication_identifier":{"eissn":["1432-0894"],"issn":["0930-7575"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00382-022-06337-7","quality_controlled":"1","isi":1,"external_id":{"isi":["000803119400002"]},"date_created":"2022-06-05T22:01:50Z","date_updated":"2023-06-28T11:49:58Z","volume":60,"author":[{"id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","first_name":"Bidyut B","last_name":"Goswami","full_name":"Goswami, Bidyut B"}],"related_material":{"link":[{"url":" https://doi.org/10.1007/s00382-022-06401-2","relation":"erratum"}]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"CaMu"}],"acknowledgement":"This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (NRF-2018R1A5A1024958). Model simulation and data transfer were supported by the National Supercomputing Center with supercomputing resources including technical support (KSC-2019-CHA-0005), the National Center for Meteorological Supercomputer of Korea Meteorological Administration, and by the Korea Research Environment Open NETwork (KREONET), respectively. The authors declare no conflicts of interest.","year":"2023","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2023-01-01T00:00:00Z","article_type":"original","page":"427-442","publication":"Climate Dynamics","citation":{"ama":"GOSWAMI BB. Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. 2023;60:427-442. doi:10.1007/s00382-022-06337-7","ista":"GOSWAMI BB. 2023. Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. 60, 427–442.","ieee":"B. B. GOSWAMI, “Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend,” Climate Dynamics, vol. 60. Springer Nature, pp. 427–442, 2023.","apa":"GOSWAMI, B. B. (2023). Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. Springer Nature. https://doi.org/10.1007/s00382-022-06337-7","mla":"GOSWAMI, BIDYUT B. “Role of the Eastern Equatorial Indian Ocean Warming in the Indian Summer Monsoon Rainfall Trend.” Climate Dynamics, vol. 60, Springer Nature, 2023, pp. 427–42, doi:10.1007/s00382-022-06337-7.","short":"B.B. GOSWAMI, Climate Dynamics 60 (2023) 427–442.","chicago":"GOSWAMI, BIDYUT B. “Role of the Eastern Equatorial Indian Ocean Warming in the Indian Summer Monsoon Rainfall Trend.” Climate Dynamics. Springer Nature, 2023. https://doi.org/10.1007/s00382-022-06337-7."},"abstract":[{"lang":"eng","text":"The Indian summer monsoon rainfall (ISMR) has been declining since the 1950s. However, since 2002 it is reported to have revived. For these observed changes in the ISMR, several explanations have been reported. Among these explanations, however, the role of the eastern equatorial Indian Ocean (EEIO) is missing despite being one of the warmest regions in the Indian Ocean, and monotonously warming. A recent study reported that EEIO warming impacts the rainfall over northern India. Here we report that warming in the EEIO weakens the low-level Indian summer monsoon circulation and reduces ISMR. A warm EEIO drives easterly winds in the Indo–Pacific sector as a Gill response. The warm EEIO also enhances nocturnal convection offshore the western coast of Sumatra. The latent heating associated with the increased convection augments the Gill response and the resultant circulation opposes the monsoon low-level circulation and weakens the seasonal rainfall."}],"type":"journal_article","oa_version":"None","title":"Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend","status":"public","intvolume":" 60","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11434"},{"date_published":"2023-04-21T00:00:00Z","page":"349-370","citation":{"ama":"Henzinger TA, Mazzocchi NA, Sarac NE. Quantitative safety and liveness. In: 26th International Conference Foundations of Software Science and Computation Structures. Vol 13992. Springer Nature; 2023:349-370. doi:10.1007/978-3-031-30829-1_17","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.","ieee":"T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Quantitative safety and liveness,” in 26th International Conference Foundations of Software Science and Computation Structures, Paris, France, 2023, vol. 13992, pp. 349–370.","apa":"Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2023). Quantitative safety and liveness. In 26th International Conference Foundations of Software Science and Computation Structures (Vol. 13992, pp. 349–370). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30829-1_17","mla":"Henzinger, Thomas A., et al. “Quantitative Safety and Liveness.” 26th International Conference Foundations of Software Science and Computation Structures, vol. 13992, Springer Nature, 2023, pp. 349–70, doi:10.1007/978-3-031-30829-1_17.","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.","chicago":"Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Quantitative Safety and Liveness.” In 26th International Conference Foundations of Software Science and Computation Structures, 13992:349–70. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30829-1_17."},"publication":"26th International Conference Foundations of Software Science and Computation Structures","has_accepted_license":"1","article_processing_charge":"No","day":"21","scopus_import":"1","file":[{"creator":"esarac","content_type":"application/pdf","file_size":449027,"file_name":"qsl.pdf","access_level":"open_access","date_created":"2023-01-31T07:22:21Z","date_updated":"2023-01-31T07:22:21Z","success":1,"checksum":"981025aed580b6b27c426cb8856cf63e","file_id":"12468","relation":"main_file"},{"relation":"main_file","file_id":"13153","checksum":"f16e2af1e0eb243158ab0f0fe74e7d5a","success":1,"date_updated":"2023-06-19T10:28:09Z","date_created":"2023-06-19T10:28:09Z","access_level":"open_access","file_name":"2023_LNCS_HenzingerT.pdf","content_type":"application/pdf","file_size":1048171,"creator":"dernst"}],"oa_version":"Published Version","intvolume":" 13992","ddc":["000"],"title":"Quantitative safety and liveness","status":"public","_id":"12467","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","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."}],"alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-30829-1_17","conference":{"name":"FOSSACS: Foundations of Software Science and Computation Structures","end_date":"2023-04-27","location":"Paris, France","start_date":"2023-04-22"},"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2301.11175"]},"oa":1,"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031308284"]},"month":"04","volume":13992,"date_updated":"2023-07-14T11:20:27Z","date_created":"2023-01-31T07:23:56Z","author":[{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"id":"b26baa86-3308-11ec-87b0-8990f34baa85","first_name":"Nicolas Adrien","last_name":"Mazzocchi","full_name":"Mazzocchi, Nicolas Adrien"},{"last_name":"Sarac","first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","full_name":"Sarac, Naci E"}],"publisher":"Springer Nature","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"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.","year":"2023","ec_funded":1,"file_date_updated":"2023-06-19T10:28:09Z"},{"language":[{"iso":"eng"}],"doi":"10.1145/3591230","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"06","publication_identifier":{"eissn":["2475-1421"]},"date_created":"2023-07-02T22:00:43Z","date_updated":"2023-07-17T08:43:19Z","volume":7,"author":[{"full_name":"Koval, Nikita","first_name":"Nikita","last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dmitry","last_name":"Khalanskiy","full_name":"Khalanskiy, Dmitry"},{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"}],"publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"Association for Computing Machinery ","year":"2023","file_date_updated":"2023-07-03T13:09:39Z","article_number":"116","date_published":"2023-06-06T00:00:00Z","article_type":"original","publication":"Proceedings of the ACM on Programming Languages","citation":{"ama":"Koval N, Khalanskiy D, Alistarh D-A. CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. 2023;7. doi:10.1145/3591230","ieee":"N. Koval, D. Khalanskiy, and D.-A. Alistarh, “CQS: A formally-verified framework for fair and abortable synchronization,” Proceedings of the ACM on Programming Languages, vol. 7. Association for Computing Machinery , 2023.","apa":"Koval, N., Khalanskiy, D., & Alistarh, D.-A. (2023). CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. Association for Computing Machinery . https://doi.org/10.1145/3591230","ista":"Koval N, Khalanskiy D, Alistarh D-A. 2023. CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. 7, 116.","short":"N. Koval, D. Khalanskiy, D.-A. Alistarh, Proceedings of the ACM on Programming Languages 7 (2023).","mla":"Koval, Nikita, et al. “CQS: A Formally-Verified Framework for Fair and Abortable Synchronization.” Proceedings of the ACM on Programming Languages, vol. 7, 116, Association for Computing Machinery , 2023, doi:10.1145/3591230.","chicago":"Koval, Nikita, Dmitry Khalanskiy, and Dan-Adrian Alistarh. “CQS: A Formally-Verified Framework for Fair and Abortable Synchronization.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery , 2023. https://doi.org/10.1145/3591230."},"day":"06","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"creator":"alisjak","content_type":"application/pdf","file_size":1266773,"access_level":"open_access","file_name":"2023_ACMProgram.Lang._Koval.pdf","success":1,"checksum":"5dba6e73f0ed79adbdae14d165bc2f68","date_updated":"2023-07-03T13:09:39Z","date_created":"2023-07-03T13:09:39Z","file_id":"13187","relation":"main_file"}],"status":"public","ddc":["000"],"title":"CQS: A formally-verified framework for fair and abortable synchronization","intvolume":" 7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13179","abstract":[{"lang":"eng","text":"Writing concurrent code that is both correct and efficient is notoriously difficult. Thus, programmers often prefer to use synchronization abstractions, which render code simpler and easier to reason about. Despite a wealth of work on this topic, there is still a gap between the rich semantics provided by synchronization abstractions in modern programming languages—specifically, fair FIFO ordering of synchronization requests and support for abortable operations—and frameworks for implementing it correctly and efficiently. Supporting such semantics is critical given the rising popularity of constructs for asynchronous programming, such as coroutines, which abort frequently and are cheaper to suspend and resume compared to native threads.\r\n\r\nThis paper introduces a new framework called CancellableQueueSynchronizer (CQS), which enables simple yet efficient implementations of a wide range of fair and abortable synchronization primitives: mutexes, semaphores, barriers, count-down latches, and blocking pools. Our main contribution is algorithmic, as implementing both fairness and abortability efficiently at this level of generality is non-trivial. Importantly, all our algorithms, including the CQS framework and the primitives built on top of it, come with formal proofs in the Iris framework for Coq for many of their properties. These proofs are modular, so it is easy to show correctness for new primitives implemented on top of CQS. From a practical perspective, implementation of CQS for native threads on the JVM improves throughput by up to two orders of magnitude over Java’s AbstractQueuedSynchronizer, the only practical abstraction offering similar semantics. Further, we successfully integrated CQS as a core component of the popular Kotlin Coroutines library, validating the framework’s practical impact and expressiveness in a real-world environment. In sum, CancellableQueueSynchronizer is the first framework to combine expressiveness with formal guarantees and solid practical performance. Our approach should be extensible to other languages and families of synchronization primitives."}],"type":"journal_article"},{"volume":16,"date_created":"2023-07-02T22:00:43Z","date_updated":"2023-07-17T08:39:19Z","author":[{"last_name":"Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D"},{"full_name":"Lyczak, Julian","id":"3572849A-F248-11E8-B48F-1D18A9856A87","last_name":"Lyczak","first_name":"Julian"},{"last_name":"Sarapin","first_name":"Roman","full_name":"Sarapin, Roman"}],"publisher":"Mathematical Sciences Publishers","department":[{"_id":"TiBr"}],"publication_status":"published","year":"2023","language":[{"iso":"eng"}],"doi":"10.2140/involve.2023.16.331","quality_controlled":"1","external_id":{"arxiv":["2203.06881"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2203.06881","open_access":"1"}],"publication_identifier":{"eissn":["1944-4184"],"issn":["1944-4176"]},"month":"05","oa_version":"Preprint","intvolume":" 16","status":"public","title":"Local solubility for a family of quadrics over a split quadric surface","_id":"13180","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"2","abstract":[{"text":"We study the density of everywhere locally soluble diagonal quadric surfaces, parameterised by rational points that lie on a split quadric surface","lang":"eng"}],"type":"journal_article","date_published":"2023-05-26T00:00:00Z","page":"331-342","article_type":"original","citation":{"ama":"Browning TD, Lyczak J, Sarapin R. Local solubility for a family of quadrics over a split quadric surface. Involve. 2023;16(2):331-342. doi:10.2140/involve.2023.16.331","ieee":"T. D. Browning, J. Lyczak, and R. Sarapin, “Local solubility for a family of quadrics over a split quadric surface,” Involve, vol. 16, no. 2. Mathematical Sciences Publishers, pp. 331–342, 2023.","apa":"Browning, T. D., Lyczak, J., & Sarapin, R. (2023). Local solubility for a family of quadrics over a split quadric surface. Involve. Mathematical Sciences Publishers. https://doi.org/10.2140/involve.2023.16.331","ista":"Browning TD, Lyczak J, Sarapin R. 2023. Local solubility for a family of quadrics over a split quadric surface. Involve. 16(2), 331–342.","short":"T.D. Browning, J. Lyczak, R. Sarapin, Involve 16 (2023) 331–342.","mla":"Browning, Timothy D., et al. “Local Solubility for a Family of Quadrics over a Split Quadric Surface.” Involve, vol. 16, no. 2, Mathematical Sciences Publishers, 2023, pp. 331–42, doi:10.2140/involve.2023.16.331.","chicago":"Browning, Timothy D, Julian Lyczak, and Roman Sarapin. “Local Solubility for a Family of Quadrics over a Split Quadric Surface.” Involve. Mathematical Sciences Publishers, 2023. https://doi.org/10.2140/involve.2023.16.331."},"publication":"Involve","article_processing_charge":"No","day":"26","scopus_import":"1"},{"day":"01","month":"07","has_accepted_license":"1","article_processing_charge":"No","quality_controlled":"1","page":"42-42","publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"apa":"Elefante, S., Stadlbauer, S., Alexander, M. F., & Schlögl, A. (n.d.). Cryo-EM software packages: A sys-admins point of view. In ASHPC23 - Austrian-Slovenian HPC Meeting 2023 (pp. 42–42). Maribor, Slovenia: EuroCC.","ieee":"S. Elefante, S. Stadlbauer, M. F. Alexander, and A. Schlögl, “Cryo-EM software packages: A sys-admins point of view,” in ASHPC23 - Austrian-Slovenian HPC Meeting 2023, Maribor, Slovenia, pp. 42–42.","ista":"Elefante S, Stadlbauer S, Alexander MF, Schlögl A. Cryo-EM software packages: A sys-admins point of view. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 42–42.","ama":"Elefante S, Stadlbauer S, Alexander MF, Schlögl A. Cryo-EM software packages: A sys-admins point of view. In: ASHPC23 - Austrian-Slovenian HPC Meeting 2023. EuroCC; :42-42.","chicago":"Elefante, Stefano, Stephan Stadlbauer, Michael F Alexander, and Alois Schlögl. “Cryo-EM Software Packages: A Sys-Admins Point of View.” In ASHPC23 - Austrian-Slovenian HPC Meeting 2023, 42–42. EuroCC, n.d.","short":"S. Elefante, S. Stadlbauer, M.F. Alexander, A. Schlögl, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, n.d., pp. 42–42.","mla":"Elefante, Stefano, et al. “Cryo-EM Software Packages: A Sys-Admins Point of View.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, pp. 42–42."},"oa":1,"language":[{"iso":"eng"}],"conference":{"location":"Maribor, Slovenia","start_date":"2023-06-12","end_date":"2023-06-15","name":"ASHPC: Austrian-Slovenian HPC Meeting"},"date_published":"2023-07-01T00:00:00Z","type":"conference_abstract","file_date_updated":"2023-07-18T09:28:30Z","status":"public","publication_status":"accepted","title":"Cryo-EM software packages: A sys-admins point of view","ddc":["000"],"department":[{"_id":"ScienComp"}],"publisher":"EuroCC","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13162","year":"2023","date_created":"2023-06-23T11:03:18Z","date_updated":"2023-07-18T09:32:16Z","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"2023_ASHPC_Elefante.pdf","creator":"dernst","file_size":380354,"content_type":"application/pdf","file_id":"13250","relation":"main_file","success":1,"checksum":"0ab6173cd5c5634ed773cd37ff012681","date_updated":"2023-07-18T09:28:30Z","date_created":"2023-07-18T09:28:30Z"}],"author":[{"first_name":"Stefano","last_name":"Elefante","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","full_name":"Elefante, Stefano"},{"full_name":"Stadlbauer, Stephan","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","first_name":"Stephan","last_name":"Stadlbauer"},{"full_name":"Alexander, Michael F","last_name":"Alexander","first_name":"Michael F","id":"3A02A8FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","first_name":"Alois"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13161","ddc":["000"],"status":"public","title":"Running Windows-applications on a Linux HPC cluster using WINE","oa_version":"Submitted Version","file":[{"file_id":"13249","relation":"main_file","date_created":"2023-07-18T09:18:55Z","date_updated":"2023-07-18T09:18:55Z","success":1,"checksum":"ec8e4295d54171032cdd1b01423eb4a6","file_name":"2023_ASHPC_Schloegl.pdf","access_level":"open_access","creator":"dernst","file_size":316959,"content_type":"application/pdf"}],"type":"conference_abstract","publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","citation":{"mla":"Schlögl, Alois, et al. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, pp. 59–59.","short":"A. Schlögl, S. Elefante, V.-V. Hodirnau, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, n.d., pp. 59–59.","chicago":"Schlögl, Alois, Stefano Elefante, and Victor-Valentin Hodirnau. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” In ASHPC23 - Austrian-Slovenian HPC Meeting 2023, 59–59. EuroCC, n.d.","ama":"Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. In: ASHPC23 - Austrian-Slovenian HPC Meeting 2023. EuroCC; :59-59.","ista":"Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 59–59.","ieee":"A. Schlögl, S. Elefante, and V.-V. Hodirnau, “Running Windows-applications on a Linux HPC cluster using WINE,” in ASHPC23 - Austrian-Slovenian HPC Meeting 2023, Maribor, Slovenia, pp. 59–59.","apa":"Schlögl, A., Elefante, S., & Hodirnau, V.-V. (n.d.). Running Windows-applications on a Linux HPC cluster using WINE. In ASHPC23 - Austrian-Slovenian HPC Meeting 2023 (pp. 59–59). Maribor, Slovenia: EuroCC."},"page":"59-59","date_published":"2023-07-01T00:00:00Z","day":"01","has_accepted_license":"1","article_processing_charge":"No","acknowledgement":"Thanks to Jesse Hansen for his suggestions on improving the abstract.","year":"2023","publication_status":"inpress","publisher":"EuroCC","department":[{"_id":"ScienComp"},{"_id":"EM-Fac"}],"author":[{"last_name":"Schlögl","first_name":"Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois"},{"full_name":"Elefante, Stefano","first_name":"Stefano","last_name":"Elefante","id":"490F40CE-F248-11E8-B48F-1D18A9856A87"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","first_name":"Victor-Valentin","full_name":"Hodirnau, Victor-Valentin"}],"date_created":"2023-06-23T11:01:23Z","date_updated":"2023-07-18T09:30:54Z","file_date_updated":"2023-07-18T09:18:55Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","conference":{"location":"Maribor, Slovenia","start_date":"2023-06-13","end_date":"2023-06-15","name":"ASHPC: Austrian-Slovenian HPC Meeting"},"language":[{"iso":"eng"}],"month":"07"},{"publication_identifier":{"eissn":["1948-7185"]},"month":"07","external_id":{"arxiv":["2304.14198"],"isi":["001022811500001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","doi":"10.1021/acs.jpclett.3c01158","language":[{"iso":"eng"}],"ec_funded":1,"file_date_updated":"2023-07-19T06:55:39Z","year":"2023","acknowledgement":"We thank Bingqing Cheng and Hong-Zhou Ye for valuable discussions; Y.W.’s work at IST Austria was supported through ISTernship summer internship program funded by OeADGmbH; D.L. and Z.A. acknowledge support by IST Austria (ISTA); M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).\r\nA.A.Z. and O.M.B. acknowledge support by KAUST.","department":[{"_id":"MiLe"},{"_id":"ZhAl"}],"publisher":"American Chemical Society","publication_status":"published","author":[{"full_name":"Wei, Yujing","first_name":"Yujing","last_name":"Wei","id":"0c5ff007-2600-11ee-b896-98bd8d663294","orcid":"0000-0001-8913-9719"},{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev"},{"full_name":"Lorenc, Dusan","first_name":"Dusan","last_name":"Lorenc","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhumekenov, Ayan A.","last_name":"Zhumekenov","first_name":"Ayan A."},{"first_name":"Osman M.","last_name":"Bakr","full_name":"Bakr, Osman M."},{"first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"first_name":"Zhanybek","last_name":"Alpichshev","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7183-5203","full_name":"Alpichshev, Zhanybek"}],"volume":14,"date_updated":"2023-07-19T06:59:19Z","date_created":"2023-07-18T11:13:17Z","keyword":["General Materials Science","Physical and Theoretical Chemistry"],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"05","citation":{"chicago":"Wei, Yujing, Artem Volosniev, Dusan Lorenc, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” The Journal of Physical Chemistry Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpclett.3c01158.","short":"Y. Wei, A. Volosniev, D. Lorenc, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, The Journal of Physical Chemistry Letters 14 (2023) 6309–6314.","mla":"Wei, Yujing, et al. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” The Journal of Physical Chemistry Letters, vol. 14, no. 27, American Chemical Society, 2023, pp. 6309–14, doi:10.1021/acs.jpclett.3c01158.","apa":"Wei, Y., Volosniev, A., Lorenc, D., Zhumekenov, A. A., Bakr, O. M., Lemeshko, M., & Alpichshev, Z. (2023). Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.3c01158","ieee":"Y. Wei et al., “Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites,” The Journal of Physical Chemistry Letters, vol. 14, no. 27. American Chemical Society, pp. 6309–6314, 2023.","ista":"Wei Y, Volosniev A, Lorenc D, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. 14(27), 6309–6314.","ama":"Wei Y, Volosniev A, Lorenc D, et al. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. 2023;14(27):6309-6314. doi:10.1021/acs.jpclett.3c01158"},"publication":"The Journal of Physical Chemistry Letters","page":"6309-6314","article_type":"original","date_published":"2023-07-05T00:00:00Z","type":"journal_article","issue":"27","abstract":[{"text":"A rotating organic cation and a dynamically disordered soft inorganic cage are the hallmark features of organic-inorganic lead-halide perovskites. Understanding the interplay between these two subsystems is a challenging problem, but it is this coupling that is widely conjectured to be responsible for the unique behavior of photocarriers in these materials. In this work, we use the fact that the polarizability of the organic cation strongly depends on the ambient electrostatic environment to put the molecule forward as a sensitive probe of the local crystal fields inside the lattice cell. We measure the average polarizability of the C/N–H bond stretching mode by means of infrared spectroscopy, which allows us to deduce the character of the motion of the cation molecule, find the magnitude of the local crystal field, and place an estimate on the strength of the hydrogen bond between the hydrogen and halide atoms. Our results pave the way for understanding electric fields in lead-halide perovskites using infrared bond spectroscopy.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13251","intvolume":" 14","ddc":["530"],"title":"Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites","status":"public","file":[{"file_id":"13253","relation":"main_file","success":1,"checksum":"c0c040063f06a51b9c463adc504f1a23","date_created":"2023-07-19T06:55:39Z","date_updated":"2023-07-19T06:55:39Z","access_level":"open_access","file_name":"2023_JourPhysChemistry_Wei.pdf","creator":"dernst","content_type":"application/pdf","file_size":2121252}],"oa_version":"Published Version"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13292","ddc":["000"],"status":"public","title":"Regular methods for operator precedence languages","intvolume":" 261","oa_version":"Published Version","file":[{"file_name":"icalp23.pdf","access_level":"open_access","creator":"esarac","content_type":"application/pdf","file_size":859379,"file_id":"13293","relation":"main_file","date_created":"2023-07-24T15:11:05Z","date_updated":"2023-07-24T15:11:05Z","success":1,"checksum":"5d4c8932ef3450615a53b9bb15d92eb2"}],"type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"The operator precedence languages (OPLs) represent the largest known subclass of the context-free languages which enjoys all desirable closure and decidability properties. This includes the decidability of language inclusion, which is the ultimate verification problem. Operator precedence grammars, automata, and logics have been investigated and used, for example, to verify programs with arithmetic expressions and exceptions (both of which are deterministic pushdown but lie outside the scope of the visibly pushdown languages). In this paper, we complete the picture and give, for the first time, an algebraic characterization of the class of OPLs in the form of a syntactic congruence that has finitely many equivalence classes exactly for the operator precedence languages. This is a generalization of the celebrated Myhill-Nerode theorem for the regular languages to OPLs. As one of the consequences, we show that universality and language inclusion for nondeterministic operator precedence automata can be solved by an antichain algorithm. Antichain algorithms avoid determinization and complementation through an explicit subset construction, by leveraging a quasi-order on words, which allows the pruning of the search space for counterexample words without sacrificing completeness. Antichain algorithms can be implemented symbolically, and these implementations are today the best-performing algorithms in practice for the inclusion of finite automata. We give a generic construction of the quasi-order needed for antichain algorithms from a finite syntactic congruence. This yields the first antichain algorithm for OPLs, an algorithm that solves the ExpTime-hard language inclusion problem for OPLs in exponential time."}],"publication":"50th International Colloquium on Automata, Languages, and Programming","citation":{"chicago":"Henzinger, Thomas A, Pavol Kebis, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Regular Methods for Operator Precedence Languages.” In 50th International Colloquium on Automata, Languages, and Programming, 261:129:1--129:20. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.129.","mla":"Henzinger, Thomas A., et al. “Regular Methods for Operator Precedence Languages.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20, doi:10.4230/LIPIcs.ICALP.2023.129.","short":"T.A. Henzinger, P. Kebis, N.A. Mazzocchi, N.E. Sarac, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20.","ista":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. 2023. Regular methods for operator precedence languages. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 129:1--129:20.","apa":"Henzinger, T. A., Kebis, P., Mazzocchi, N. A., & Sarac, N. E. (2023). Regular methods for operator precedence languages. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261, p. 129:1--129:20). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.129","ieee":"T. A. Henzinger, P. Kebis, N. A. Mazzocchi, and N. E. Sarac, “Regular methods for operator precedence languages,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261, p. 129:1--129:20.","ama":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. Regular methods for operator precedence languages. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023:129:1--129:20. doi:10.4230/LIPIcs.ICALP.2023.129"},"page":"129:1--129:20","date_published":"2023-07-05T00:00:00Z","day":"05","article_processing_charge":"Yes","has_accepted_license":"1","year":"2023","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093.\r\nWe thank Pierre Ganty for early discussions and the anonymous reviewers for their helpful comments.\r\n","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"author":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kebis","first_name":"Pavol","full_name":"Kebis, Pavol"},{"id":"b26baa86-3308-11ec-87b0-8990f34baa85","last_name":"Mazzocchi","first_name":"Nicolas Adrien","full_name":"Mazzocchi, Nicolas Adrien"},{"full_name":"Sarac, Naci E","first_name":"Naci E","last_name":"Sarac","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425"}],"date_updated":"2023-07-31T08:38:38Z","date_created":"2023-07-24T15:11:41Z","volume":261,"file_date_updated":"2023-07-24T15:11:05Z","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2305.03447"]},"oa":1,"quality_controlled":"1","project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","end_date":"2023-07-14","location":"Paderborn, Germany","start_date":"2023-07-10"},"doi":"10.4230/LIPIcs.ICALP.2023.129","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959772785"]}},{"article_type":"original","citation":{"apa":"Tucci, G., De Nicola, S., Wald, S., & Gambassi, A. (2023). Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. SciPost Foundation. https://doi.org/10.21468/scipostphyscore.6.2.029","ieee":"G. Tucci, S. De Nicola, S. Wald, and A. Gambassi, “Stochastic representation of the quantum quartic oscillator,” SciPost Physics Core, vol. 6, no. 2. SciPost Foundation, 2023.","ista":"Tucci G, De Nicola S, Wald S, Gambassi A. 2023. Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. 6(2), 029.","ama":"Tucci G, De Nicola S, Wald S, Gambassi A. Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. 2023;6(2). doi:10.21468/scipostphyscore.6.2.029","chicago":"Tucci, Gennaro, Stefano De Nicola, Sascha Wald, and Andrea Gambassi. “Stochastic Representation of the Quantum Quartic Oscillator.” SciPost Physics Core. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscore.6.2.029.","short":"G. Tucci, S. De Nicola, S. Wald, A. Gambassi, SciPost Physics Core 6 (2023).","mla":"Tucci, Gennaro, et al. “Stochastic Representation of the Quantum Quartic Oscillator.” SciPost Physics Core, vol. 6, no. 2, 029, SciPost Foundation, 2023, doi:10.21468/scipostphyscore.6.2.029."},"publication":"SciPost Physics Core","date_published":"2023-04-14T00:00:00Z","keyword":["Statistical and Nonlinear Physics","Atomic and Molecular Physics","and Optics","Nuclear and High Energy Physics","Condensed Matter Physics"],"article_processing_charge":"No","has_accepted_license":"1","day":"14","intvolume":" 6","status":"public","ddc":["530"],"title":"Stochastic representation of the quantum quartic oscillator","_id":"13277","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_SciPostPhysCore_Tucci.pdf","file_size":523236,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"13329","checksum":"b472bc82108747eda5d52adf9e2ac7f3","success":1,"date_updated":"2023-07-31T09:02:27Z","date_created":"2023-07-31T09:02:27Z"}],"type":"journal_article","issue":"2","abstract":[{"text":"Recent experimental advances have inspired the development of theoretical tools to describe the non-equilibrium dynamics of quantum systems. Among them an exact representation of quantum spin systems in terms of classical stochastic processes has been proposed. Here we provide first steps towards the extension of this stochastic approach to bosonic systems by considering the one-dimensional quantum quartic oscillator. We show how to exactly parameterize the time evolution of this prototypical model via the dynamics of a set of classical variables. We interpret these variables as stochastic processes, which allows us to propose a novel way to numerically simulate the time evolution of the system. We benchmark our findings by considering analytically solvable limits and providing alternative derivations of known results.","lang":"eng"}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2211.01923"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.21468/scipostphyscore.6.2.029","publication_identifier":{"issn":["2666-9366"]},"month":"04","publisher":"SciPost Foundation","department":[{"_id":"MaSe"}],"publication_status":"published","acknowledgement":"S. De Nicola acknowledges funding from the Institute of Science and Technology Austria (ISTA), and from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. S. De Nicola also acknowledges funding from the EPSRC Center for Doctoral Training in Cross-Disciplinary Approaches to NonEquilibrium Systems (CANES) under Grant EP/L015854/1. ","year":"2023","volume":6,"date_created":"2023-07-24T10:47:46Z","date_updated":"2023-07-31T09:03:28Z","author":[{"first_name":"Gennaro","last_name":"Tucci","full_name":"Tucci, Gennaro"},{"full_name":"De Nicola, Stefano","last_name":"De Nicola","first_name":"Stefano","orcid":"0000-0002-4842-6671","id":"42832B76-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sascha","last_name":"Wald","full_name":"Wald, Sascha"},{"full_name":"Gambassi, Andrea","first_name":"Andrea","last_name":"Gambassi"}],"article_number":"029","ec_funded":1,"file_date_updated":"2023-07-31T09:02:27Z"},{"abstract":[{"lang":"eng","text":"We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost."}],"type":"journal_article","file":[{"creator":"dernst","content_type":"application/pdf","file_size":551418,"access_level":"open_access","file_name":"2023_SciPostPhysCodebase_Rammelmueller.pdf","success":1,"checksum":"f583a70fe915d2208c803f5afb426daa","date_created":"2023-07-31T09:09:23Z","date_updated":"2023-07-31T09:09:23Z","file_id":"13330","relation":"main_file"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13276","ddc":["530"],"title":"A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D","status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"19","date_published":"2023-04-19T00:00:00Z","citation":{"ama":"Rammelmüller L, Huber D, Volosniev A. A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases. 2023. doi:10.21468/scipostphyscodeb.12","ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D,” SciPost Physics Codebases. SciPost Foundation, 2023.","apa":"Rammelmüller, L., Huber, D., & Volosniev, A. (2023). A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases. SciPost Foundation. https://doi.org/10.21468/scipostphyscodeb.12","ista":"Rammelmüller L, Huber D, Volosniev A. 2023. A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases., 12.","short":"L. Rammelmüller, D. Huber, A. Volosniev, SciPost Physics Codebases (2023).","mla":"Rammelmüller, Lukas, et al. “A Modular Implementation of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.” SciPost Physics Codebases, 12, SciPost Foundation, 2023, doi:10.21468/scipostphyscodeb.12.","chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “A Modular Implementation of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.” SciPost Physics Codebases. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscodeb.12."},"publication":"SciPost Physics Codebases","article_type":"original","ec_funded":1,"file_date_updated":"2023-07-31T09:09:23Z","article_number":"12","related_material":{"record":[{"relation":"research_data","status":"public","id":"13275"}]},"author":[{"full_name":"Rammelmüller, Lukas","last_name":"Rammelmüller","first_name":"Lukas"},{"full_name":"Huber, David","first_name":"David","last_name":"Huber"},{"full_name":"Volosniev, Artem","first_name":"Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525"}],"date_updated":"2023-07-31T09:16:02Z","date_created":"2023-07-24T10:47:15Z","acknowledgement":"We acknowledge fruitful discussions with Hans-Werner Hammer and thank Gerhard Zürn and\r\nPietro Massignan for sending us their data. We thank Fabian Brauneis for beta-testing the\r\nprovided code-package, and comments on the manuscript.\r\nL.R. is supported by FP7/ERC Consolidator Grant QSIMCORR, No.\r\n771891, and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under\r\nGermany’s Excellence Strategy –EXC–2111–390814868. A.G.V. acknowledges support\r\nby European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411.","year":"2023","department":[{"_id":"MiLe"}],"publisher":"SciPost Foundation","publication_status":"published","publication_identifier":{"issn":["2949-804X"]},"month":"04","doi":"10.21468/scipostphyscodeb.12","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2202.04603"]},"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1"},{"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"13276"}]},"author":[{"full_name":"Rammelmüller, Lukas","last_name":"Rammelmüller","first_name":"Lukas"},{"first_name":"David","last_name":"Huber","full_name":"Huber, David"},{"orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem","full_name":"Volosniev, Artem"}],"oa_version":"Published Version","date_updated":"2023-07-31T09:16:02Z","date_created":"2023-07-24T10:46:23Z","_id":"13275","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MiLe"}],"publisher":"SciPost Foundation","ddc":["530"],"status":"public","title":"Codebase release 1.0 for FermiFCI","ec_funded":1,"abstract":[{"text":"We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost.","lang":"eng"}],"type":"research_data_reference","doi":"10.21468/scipostphyscodeb.12-r1.0","date_published":"2023-04-19T00:00:00Z","oa":1,"citation":{"chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “Codebase Release 1.0 for FermiFCI.” SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscodeb.12-r1.0.","short":"L. Rammelmüller, D. Huber, A. Volosniev, (2023).","mla":"Rammelmüller, Lukas, et al. Codebase Release 1.0 for FermiFCI. SciPost Foundation, 2023, doi:10.21468/scipostphyscodeb.12-r1.0.","apa":"Rammelmüller, L., Huber, D., & Volosniev, A. (2023). Codebase release 1.0 for FermiFCI. SciPost Foundation. https://doi.org/10.21468/scipostphyscodeb.12-r1.0","ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “Codebase release 1.0 for FermiFCI.” SciPost Foundation, 2023.","ista":"Rammelmüller L, Huber D, Volosniev A. 2023. Codebase release 1.0 for FermiFCI, SciPost Foundation, 10.21468/scipostphyscodeb.12-r1.0.","ama":"Rammelmüller L, Huber D, Volosniev A. Codebase release 1.0 for FermiFCI. 2023. doi:10.21468/scipostphyscodeb.12-r1.0"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.21468/SciPostPhysCodeb.12-r1.0"}],"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"article_processing_charge":"No","day":"19","month":"04"},{"language":[{"iso":"eng"}],"doi":"10.1145/3558481.3591082","conference":{"location":"Orlando, FL, United States","start_date":"2023-06-17","end_date":"2023-06-19","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"quality_controlled":"1","external_id":{"arxiv":["2304.09331"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"isbn":["9781450395458"]},"month":"06","date_updated":"2023-07-31T10:54:32Z","date_created":"2023-07-23T22:01:12Z","author":[{"full_name":"Fedorov, Alexander","first_name":"Alexander","last_name":"Fedorov","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6"},{"first_name":"Diba","last_name":"Hashemi","id":"ed9595ea-2f8f-11ee-ba95-d2b546540783","full_name":"Hashemi, Diba"},{"id":"3279A00C-F248-11E8-B48F-1D18A9856A87","last_name":"Nadiradze","first_name":"Giorgi","full_name":"Nadiradze, Giorgi"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"}],"publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"publication_status":"published","year":"2023","file_date_updated":"2023-07-31T10:53:08Z","date_published":"2023-06-17T00:00:00Z","page":"261-271","citation":{"short":"A. Fedorov, D. Hashemi, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–271.","mla":"Fedorov, Alexander, et al. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–71, doi:10.1145/3558481.3591082.","chicago":"Fedorov, Alexander, Diba Hashemi, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” In Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, 261–71. Association for Computing Machinery, 2023. https://doi.org/10.1145/3558481.3591082.","ama":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. Provably-efficient and internally-deterministic parallel Union-Find. In: Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. Association for Computing Machinery; 2023:261-271. doi:10.1145/3558481.3591082","apa":"Fedorov, A., Hashemi, D., Nadiradze, G., & Alistarh, D.-A. (2023). Provably-efficient and internally-deterministic parallel Union-Find. In Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures (pp. 261–271). Orlando, FL, United States: Association for Computing Machinery. https://doi.org/10.1145/3558481.3591082","ieee":"A. Fedorov, D. Hashemi, G. Nadiradze, and D.-A. Alistarh, “Provably-efficient and internally-deterministic parallel Union-Find,” in Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Orlando, FL, United States, 2023, pp. 261–271.","ista":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. 2023. Provably-efficient and internally-deterministic parallel Union-Find. Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 261–271."},"publication":"Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"17","scopus_import":"1","file":[{"content_type":"application/pdf","file_size":2087937,"creator":"dernst","file_name":"2023_SPAA_Fedorov.pdf","access_level":"open_access","date_updated":"2023-07-31T10:53:08Z","date_created":"2023-07-31T10:53:08Z","checksum":"72e312aabf0c5248c99b5cd3a88e4c88","success":1,"relation":"main_file","file_id":"13334"}],"oa_version":"Published Version","ddc":["000"],"status":"public","title":"Provably-efficient and internally-deterministic parallel Union-Find","_id":"13262","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Determining the degree of inherent parallelism in classical sequential algorithms and leveraging it for fast parallel execution is a key topic in parallel computing, and detailed analyses are known for a wide range of classical algorithms. In this paper, we perform the first such analysis for the fundamental Union-Find problem, in which we are given a graph as a sequence of edges, and must maintain its connectivity structure under edge additions. We prove that classic sequential algorithms for this problem are well-parallelizable under reasonable assumptions, addressing a conjecture by [Blelloch, 2017]. More precisely, we show via a new potential argument that, under uniform random edge ordering, parallel union-find operations are unlikely to interfere: T concurrent threads processing the graph in parallel will encounter memory contention O(T2 · log |V| · log |E|) times in expectation, where |E| and |V| are the number of edges and nodes in the graph, respectively. We leverage this result to design a new parallel Union-Find algorithm that is both internally deterministic, i.e., its results are guaranteed to match those of a sequential execution, but also work-efficient and scalable, as long as the number of threads T is O(|E|1 over 3 - ε), for an arbitrarily small constant ε > 0, which holds for most large real-world graphs. We present lower bounds which show that our analysis is close to optimal, and experimental results suggesting that the performance cost of internal determinism is limited."}],"type":"conference"},{"date_published":"2023-02-01T00:00:00Z","page":"542-559","article_type":"original","citation":{"ama":"De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 2023;16(2):542-559. doi:10.1111/eva.13428","ieee":"A. De Jode et al., “Ten years of demographic modelling of divergence and speciation in the sea,” Evolutionary Applications, vol. 16, no. 2. Wiley, pp. 542–559, 2023.","apa":"De Jode, A., Le Moan, A., Johannesson, K., Faria, R., Stankowski, S., Westram, A. M., … Fraisse, C. (2023). Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. Wiley. https://doi.org/10.1111/eva.13428","ista":"De Jode A, Le Moan A, Johannesson K, Faria R, Stankowski S, Westram AM, Butlin RK, Rafajlović M, Fraisse C. 2023. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 16(2), 542–559.","short":"A. De Jode, A. Le Moan, K. Johannesson, R. Faria, S. Stankowski, A.M. Westram, R.K. Butlin, M. Rafajlović, C. Fraisse, Evolutionary Applications 16 (2023) 542–559.","mla":"De Jode, Aurélien, et al. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications, vol. 16, no. 2, Wiley, 2023, pp. 542–59, doi:10.1111/eva.13428.","chicago":"De Jode, Aurélien, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski, Anja M Westram, Roger K. Butlin, Marina Rafajlović, and Christelle Fraisse. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications. Wiley, 2023. https://doi.org/10.1111/eva.13428."},"publication":"Evolutionary Applications","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","file":[{"access_level":"open_access","file_name":"2023_EvolutionaryApplications_DeJode.pdf","creator":"dernst","content_type":"application/pdf","file_size":2269822,"file_id":"12685","relation":"main_file","success":1,"checksum":"d4d6fa9ddf36643af994a6a757919afb","date_updated":"2023-02-27T07:10:17Z","date_created":"2023-02-27T07:10:17Z"}],"oa_version":"Published Version","intvolume":" 16","ddc":["576"],"status":"public","title":"Ten years of demographic modelling of divergence and speciation in the sea","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11479","issue":"2","abstract":[{"text":"Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1111/eva.13428","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000815663700001"]},"publication_identifier":{"eissn":["1752-4571"]},"month":"02","volume":16,"date_updated":"2023-08-01T12:25:44Z","date_created":"2022-07-03T22:01:33Z","author":[{"last_name":"De Jode","first_name":"Aurélien","full_name":"De Jode, Aurélien"},{"last_name":"Le Moan","first_name":"Alan","full_name":"Le Moan, Alan"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean","full_name":"Stankowski, Sean"},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle"}],"department":[{"_id":"NiBa"},{"_id":"BeVi"}],"publisher":"Wiley","publication_status":"published","year":"2023","acknowledgement":"We greatly thank all the corresponding authors of the studies that were included in our synthesis for the sharing of additional data: Thomas Broquet, Dmitry Filatov, Quentin Rougemont, Paolo Momigliano, Pierre-Alexandre Gagnaire, Carlos Prada, Ahmed Souissi, Michael Møller Hansen, Sylvie Lapègue, Joseph Di Battista, Michael Hellberg and Carlos Prada. RKB and ADJ were supported by the European Research Council. MR was supported by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243; to MR) and Formas (grant number 2019-00882; to KJ and MR), and by additional grants from the European Research Council (to RKB) and Vetenskapsrådet (to KJ) through the Centre for Marine Evolutionary Biology (https://www.gu.se/en/cemeb-marine-evolutionary-biology).","file_date_updated":"2023-02-27T07:10:17Z"},{"month":"01","publication_identifier":{"eissn":["2045-2322"]},"doi":"10.1038/s41598-022-19827-9","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001003345000051"]},"isi":1,"quality_controlled":"1","file_date_updated":"2023-01-23T07:53:23Z","article_number":"468","author":[{"first_name":"Arturo","last_name":"Gómez","full_name":"Gómez, Arturo"},{"last_name":"Oliveira","first_name":"Goncalo","id":"58abbde8-f455-11eb-a497-98c8fd71b905","full_name":"Oliveira, Goncalo"}],"date_updated":"2023-08-01T12:31:40Z","date_created":"2023-01-22T23:00:55Z","volume":13,"year":"2023","acknowledgement":"Gonçalo Oliveira is supported by the NOMIS Foundation, Fundação Serrapilheira 1812-27395, by CNPq grants 428959/2018-0 and 307475/2018-2, and by FAPERJ through the grant Jovem Cientista do Nosso Estado E-26/202.793/2019.","publication_status":"published","department":[{"_id":"TaHa"}],"publisher":"Springer Nature","day":"10","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2023-01-10T00:00:00Z","publication":"Scientific Reports","citation":{"ama":"Gómez A, Oliveira G. New approaches to epidemic modeling on networks. Scientific Reports. 2023;13. doi:10.1038/s41598-022-19827-9","apa":"Gómez, A., & Oliveira, G. (2023). New approaches to epidemic modeling on networks. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-19827-9","ieee":"A. Gómez and G. Oliveira, “New approaches to epidemic modeling on networks,” Scientific Reports, vol. 13. Springer Nature, 2023.","ista":"Gómez A, Oliveira G. 2023. New approaches to epidemic modeling on networks. Scientific Reports. 13, 468.","short":"A. Gómez, G. Oliveira, Scientific Reports 13 (2023).","mla":"Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling on Networks.” Scientific Reports, vol. 13, 468, Springer Nature, 2023, doi:10.1038/s41598-022-19827-9.","chicago":"Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling on Networks.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-022-19827-9."},"article_type":"original","abstract":[{"text":"In this article, we develop two independent and new approaches to model epidemic spread in a network. Contrary to the most studied models, those developed here allow for contacts with different probabilities of transmitting the disease (transmissibilities). We then examine each of these models using some mean field type approximations. The first model looks at the late-stage effects of an epidemic outbreak and allows for the computation of the probability that a given vertex was infected. This computation is based on a mean field approximation and only depends on the number of contacts and their transmissibilities. This approach shares many similarities with percolation models in networks. The second model we develop is a dynamic model which we analyze using a mean field approximation which highly reduces the dimensionality of the system. In particular, the original system which individually analyses each vertex of the network is reduced to one with as many equations as different transmissibilities. Perhaps the greatest contribution of this article is the observation that, in both these models, the existence and size of an epidemic outbreak are linked to the properties of a matrix which we call the R-matrix. This is a generalization of the basic reproduction number which more precisely characterizes the main routes of infection.","lang":"eng"}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2023_ScientificReports_Gomez.pdf","file_size":2167792,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"12336","checksum":"a8b83739f4a951e83e0b2a778f03b327","success":1,"date_updated":"2023-01-23T07:53:23Z","date_created":"2023-01-23T07:53:23Z"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12329","status":"public","title":"New approaches to epidemic modeling on networks","ddc":["510"],"intvolume":" 13"},{"year":"2023","acknowledgement":"This work was supported by the German Academic Exchange Service. Parts of this article were prepared at the Institut de Mathémathiques de Jussieu—Paris Rive Gauche. I wish to thank Antoine Chambert-Loir for his remarks and the institute for its hospitality, as well as the anonymous referee for several useful remarks and suggestions for improvements.","department":[{"_id":"TiBr"}],"publisher":"Oxford Academic","publication_status":"published","author":[{"full_name":"Wilsch, Florian Alexander","orcid":"0000-0001-7302-8256","id":"560601DA-8D36-11E9-A136-7AC1E5697425","last_name":"Wilsch","first_name":"Florian Alexander"}],"volume":2023,"date_updated":"2023-08-01T12:23:55Z","date_created":"2021-01-22T09:31:09Z","publication_identifier":{"issn":["1073-7928"],"eissn":["1687-0247"]},"month":"04","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.08503"}],"external_id":{"arxiv":["1901.08503"],"isi":["000773116000001"]},"isi":1,"quality_controlled":"1","doi":"10.1093/imrn/rnac048","language":[{"iso":"eng"}],"type":"journal_article","issue":"8","abstract":[{"lang":"eng","text":"We determine an asymptotic formula for the number of integral points of bounded height on a blow-up of P3 outside certain planes using universal torsors."}],"_id":"9034","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 2023","status":"public","title":"Integral points of bounded height on a log Fano threefold","oa_version":"Preprint","article_processing_charge":"No","day":"01","citation":{"short":"F.A. Wilsch, International Mathematics Research Notices 2023 (2023) 6780–6808.","mla":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices, vol. 2023, no. 8, Oxford Academic, 2023, pp. 6780–808, doi:10.1093/imrn/rnac048.","chicago":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices. Oxford Academic, 2023. https://doi.org/10.1093/imrn/rnac048.","ama":"Wilsch FA. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023;2023(8):6780-6808. doi:10.1093/imrn/rnac048","apa":"Wilsch, F. A. (2023). Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. Oxford Academic. https://doi.org/10.1093/imrn/rnac048","ieee":"F. A. Wilsch, “Integral points of bounded height on a log Fano threefold,” International Mathematics Research Notices, vol. 2023, no. 8. Oxford Academic, pp. 6780–6808, 2023.","ista":"Wilsch FA. 2023. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023(8), 6780–6808."},"publication":"International Mathematics Research Notices","page":"6780-6808","article_type":"original","date_published":"2023-04-01T00:00:00Z"},{"isi":1,"quality_controlled":"1","project":[{"name":"Viral pathogens and social immunity in ants","call_identifier":"FWF","_id":"25DF61D8-B435-11E9-9278-68D0E5697425","grant_number":"M02076"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["PPR559293 "],"isi":["000961542100001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3389/fmicb.2023.1119002","month":"03","publication_identifier":{"eissn":["1664-302X"]},"publication_status":"published","department":[{"_id":"SyCr"}],"publisher":"Frontiers","year":"2023","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). ","pmid":1,"date_created":"2023-01-31T08:13:40Z","date_updated":"2023-08-01T12:39:58Z","volume":14,"author":[{"full_name":"Viljakainen, Lumi","last_name":"Viljakainen","first_name":"Lumi"},{"full_name":"Fürst, Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3712-925X","first_name":"Matthias","last_name":"Fürst"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse","full_name":"Grasse, Anna V"},{"first_name":"Jaana","last_name":"Jurvansuu","full_name":"Jurvansuu, Jaana"},{"full_name":"Oh, Jinook","orcid":"0000-0001-7425-2372","id":"403169A4-080F-11EA-9993-BF3F3DDC885E","last_name":"Oh","first_name":"Jinook"},{"full_name":"Tolonen, Lassi","last_name":"Tolonen","first_name":"Lassi"},{"full_name":"Eder, Thomas","last_name":"Eder","first_name":"Thomas"},{"full_name":"Rattei, Thomas","first_name":"Thomas","last_name":"Rattei"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia"}],"article_number":"1119002","file_date_updated":"2023-04-17T07:49:09Z","article_type":"original","publication":"Frontiers in Microbiology","citation":{"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.","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. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2023.1119002","ieee":"L. Viljakainen et al., “Antiviral immune response reveals host-specific virus infections in natural ant populations,” Frontiers in Microbiology, vol. 14. Frontiers, 2023.","ama":"Viljakainen L, Fürst M, Grasse AV, et al. Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. 2023;14. doi:10.3389/fmicb.2023.1119002","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.” Frontiers in Microbiology. Frontiers, 2023. https://doi.org/10.3389/fmicb.2023.1119002.","mla":"Viljakainen, Lumi, et al. “Antiviral Immune Response Reveals Host-Specific Virus Infections in Natural Ant Populations.” Frontiers in Microbiology, vol. 14, 1119002, Frontiers, 2023, doi:10.3389/fmicb.2023.1119002.","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)."},"date_published":"2023-03-16T00:00:00Z","scopus_import":"1","day":"16","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","title":"Antiviral immune response reveals host-specific virus infections in natural ant populations","ddc":["570"],"status":"public","intvolume":" 14","_id":"12469","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","content_type":"application/pdf","file_size":4866332,"access_level":"open_access","file_name":"2023_FrontMicrobiology_Viljakainen.pdf","success":1,"checksum":"cd52292963acce1111634d9fac08c699","date_updated":"2023-04-17T07:49:09Z","date_created":"2023-04-17T07:49:09Z","file_id":"12843","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"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.","lang":"eng"}]},{"article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","keyword":["Computational Theory and Mathematics","Discrete Mathematics and Combinatorics","Geometry and Topology","Theoretical Computer Science"],"date_published":"2023-01-01T00:00:00Z","citation":{"ista":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. 2023. Local criteria for triangulating general manifolds. Discrete & Computational Geometry. 69, 156–191.","apa":"Boissonnat, J.-D., Dyer, R., Ghosh, A., & Wintraecken, M. (2023). Local criteria for triangulating general manifolds. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00431-7","ieee":"J.-D. Boissonnat, R. Dyer, A. Ghosh, and M. Wintraecken, “Local criteria for triangulating general manifolds,” Discrete & Computational Geometry, vol. 69. Springer Nature, pp. 156–191, 2023.","ama":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. Local criteria for triangulating general manifolds. Discrete & Computational Geometry. 2023;69:156-191. doi:10.1007/s00454-022-00431-7","chicago":"Boissonnat, Jean-Daniel, Ramsay Dyer, Arijit Ghosh, and Mathijs Wintraecken. “Local Criteria for Triangulating General Manifolds.” Discrete & Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00431-7.","mla":"Boissonnat, Jean-Daniel, et al. “Local Criteria for Triangulating General Manifolds.” Discrete & Computational Geometry, vol. 69, Springer Nature, 2023, pp. 156–91, doi:10.1007/s00454-022-00431-7.","short":"J.-D. Boissonnat, R. Dyer, A. Ghosh, M. Wintraecken, Discrete & Computational Geometry 69 (2023) 156–191."},"publication":"Discrete & Computational Geometry","page":"156-191","article_type":"original","abstract":[{"lang":"eng","text":"We present criteria for establishing a triangulation of a manifold. Given a manifold M, a simplicial complex A, and a map H from the underlying space of A to M, our criteria are presented in local coordinate charts for M, and ensure that H is a homeomorphism. These criteria do not require a differentiable structure, or even an explicit metric on M. No Delaunay property of A is assumed. The result provides a triangulation guarantee for algorithms that construct a simplicial complex by working in local coordinate patches. Because the criteria are easily verified in such a setting, they are expected to be of general use."}],"type":"journal_article","file":[{"file_name":"2023_DiscreteCompGeometry_Boissonnat.pdf","access_level":"open_access","file_size":582850,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"12488","date_updated":"2023-02-02T11:01:10Z","date_created":"2023-02-02T11:01:10Z","checksum":"46352e0ee71e460848f88685ca852681","success":1}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12287","intvolume":" 69","ddc":["510"],"status":"public","title":"Local criteria for triangulating general manifolds","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"month":"01","doi":"10.1007/s00454-022-00431-7","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000862193600001"]},"oa":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"grant_number":"M03073","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","name":"Learning and triangulating manifolds via collapses"}],"isi":1,"quality_controlled":"1","ec_funded":1,"file_date_updated":"2023-02-02T11:01:10Z","author":[{"full_name":"Boissonnat, Jean-Daniel","last_name":"Boissonnat","first_name":"Jean-Daniel"},{"last_name":"Dyer","first_name":"Ramsay","full_name":"Dyer, Ramsay"},{"last_name":"Ghosh","first_name":"Arijit","full_name":"Ghosh, Arijit"},{"full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken","first_name":"Mathijs"}],"volume":69,"date_created":"2023-01-16T10:04:06Z","date_updated":"2023-08-01T12:47:32Z","acknowledgement":"This work has been funded by the European Research Council under the European Union’s ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). Arijit Ghosh is supported by Ramanujan Fellowship (No. SB/S2/RJN-064/2015). Part of this work was done when Arijit Ghosh was a Researcher at Max-Planck-Institute for Informatics, Germany, supported by the IndoGerman Max Planck Center for Computer Science (IMPECS). Mathijs Wintraecken also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411 and the Austrian Science Fund (FWF): M-3073. A part of the results described in this paper were presented at SoCG 2018 and in [3]. \r\nOpen access funding provided by the Austrian Science Fund (FWF).","year":"2023","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","publication_status":"published"},{"department":[{"_id":"BjHo"}],"publisher":"Springer Nature","publication_status":"published","year":"2023","volume":5,"date_updated":"2023-08-01T12:50:48Z","date_created":"2023-01-12T12:10:18Z","author":[{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn"}],"publication_identifier":{"eissn":["2522-5820"]},"month":"01","isi":1,"quality_controlled":"1","external_id":{"isi":["000890148700002"]},"language":[{"iso":"eng"}],"doi":"10.1038/s42254-022-00539-y","type":"journal_article","abstract":[{"lang":"eng","text":"It may come as a surprise that a phenomenon as ubiquitous and prominent as the transition from laminar to turbulent flow has resisted combined efforts by physicists, engineers and mathematicians, and remained unresolved for almost one and a half centuries. In recent years, various studies have proposed analogies to directed percolation, a well-known universality class in statistical mechanics, which describes a non-equilibrium phase transition from a fluctuating active phase into an absorbing state. It is this unlikely relation between the multiscale, high-dimensional dynamics that signify the transition process in virtually all flows of practical relevance, and the arguably most basic non-equilibrium phase transition, that so far has mainly been the subject of model studies, which I review in this Perspective."}],"intvolume":" 5","title":"Directed percolation and the transition to turbulence","status":"public","_id":"12165","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"None","keyword":["General Physics and Astronomy"],"scopus_import":"1","article_processing_charge":"No","day":"01","page":"62-72","article_type":"original","citation":{"mla":"Hof, Björn. “Directed Percolation and the Transition to Turbulence.” Nature Reviews Physics, vol. 5, Springer Nature, 2023, pp. 62–72, doi:10.1038/s42254-022-00539-y.","short":"B. Hof, Nature Reviews Physics 5 (2023) 62–72.","chicago":"Hof, Björn. “Directed Percolation and the Transition to Turbulence.” Nature Reviews Physics. Springer Nature, 2023. https://doi.org/10.1038/s42254-022-00539-y.","ama":"Hof B. Directed percolation and the transition to turbulence. Nature Reviews Physics. 2023;5:62-72. doi:10.1038/s42254-022-00539-y","ista":"Hof B. 2023. Directed percolation and the transition to turbulence. Nature Reviews Physics. 5, 62–72.","ieee":"B. Hof, “Directed percolation and the transition to turbulence,” Nature Reviews Physics, vol. 5. Springer Nature, pp. 62–72, 2023.","apa":"Hof, B. (2023). Directed percolation and the transition to turbulence. Nature Reviews Physics. Springer Nature. https://doi.org/10.1038/s42254-022-00539-y"},"publication":"Nature Reviews Physics","date_published":"2023-01-01T00:00:00Z"},{"type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"1","_id":"12421","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"title":"Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM","status":"public","intvolume":" 51","file":[{"access_level":"open_access","file_name":"2023_BioChemicalSocietyTransactions_Faessler.pdf","file_size":10045006,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"12728","checksum":"4e7069845e3dad22bb44fb71ec624c60","success":1,"date_created":"2023-03-16T07:58:16Z","date_updated":"2023-03-16T07:58:16Z"}],"oa_version":"Published Version","scopus_import":"1","keyword":["Biochemistry"],"day":"01","article_processing_charge":"No","has_accepted_license":"1","publication":"Biochemical Society Transactions","citation":{"ama":"Fäßler F, Javoor M, Schur FK. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. 2023;51(1):87-99. doi:10.1042/bst20220221","apa":"Fäßler, F., Javoor, M., & Schur, F. K. (2023). Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. Portland Press. https://doi.org/10.1042/bst20220221","ieee":"F. Fäßler, M. Javoor, and F. K. Schur, “Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM,” Biochemical Society Transactions, 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.","mla":"Fäßler, Florian, et al. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” Biochemical Society Transactions, vol. 51, no. 1, Portland Press, 2023, pp. 87–99, doi:10.1042/bst20220221.","chicago":"Fäßler, Florian, Manjunath Javoor, and Florian KM Schur. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” Biochemical Society Transactions. Portland Press, 2023. https://doi.org/10.1042/bst20220221."},"article_type":"original","page":"87-99","date_published":"2023-02-01T00:00:00Z","file_date_updated":"2023-03-16T07:58:16Z","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.","year":"2023","publication_status":"published","publisher":"Portland Press","department":[{"_id":"FlSc"}],"author":[{"last_name":"Fäßler","first_name":"Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian"},{"full_name":"Javoor, Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","first_name":"Manjunath","last_name":"Javoor"},{"full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur"}],"date_updated":"2023-08-01T12:55:32Z","date_created":"2023-01-27T10:08:19Z","volume":51,"month":"02","publication_identifier":{"eissn":["1470-8752"],"issn":["0300-5127"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000926043100001"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"doi":"10.1042/bst20220221","language":[{"iso":"eng"}]}]