[{"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"},{"call_identifier":"H2020","name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate","_id":"629205d8-2b32-11ec-9570-e1356ff73576","grant_number":"805041"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1029/2023gl106523","publication_identifier":{"issn":["0094-8276"],"eissn":["1944-8007"]},"month":"03","publisher":"American Geophysical Union","department":[{"_id":"CaMu"}],"publication_status":"published","year":"2024","acknowledgement":"YLH is supported by funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant 101034413. CM gratefully acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant 805041). The authors warmly thank Steven Sherwood, Jiawei Bao, Bidyut Goswami, and Martin Janssens for stimulating and helpful discussions. They also thank Christopher Holloway and an anonymous reviewer for providing helpful feedback that greatly improved this manuscript.\r\n","volume":51,"date_updated":"2024-03-25T11:32:06Z","date_created":"2024-03-25T10:27:30Z","author":[{"first_name":"Yi-Ling","last_name":"Hwong","id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22","orcid":"0000-0001-9281-3479","full_name":"Hwong, Yi-Ling"},{"full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","first_name":"Caroline J"}],"article_number":" e2023GL106523","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"file_date_updated":"2024-03-25T11:28:25Z","article_type":"original","citation":{"chicago":"Hwong, Yi-Ling, and Caroline J Muller. “The Unreasonable Efficiency of Total Rain Evaporation Removal in Triggering Convective Self‐aggregation.” Geophysical Research Letters. American Geophysical Union, 2024. https://doi.org/10.1029/2023gl106523.","mla":"Hwong, Yi-Ling, and Caroline J. Muller. “The Unreasonable Efficiency of Total Rain Evaporation Removal in Triggering Convective Self‐aggregation.” Geophysical Research Letters, vol. 51, no. 6, e2023GL106523, American Geophysical Union, 2024, doi:10.1029/2023gl106523.","short":"Y.-L. Hwong, C.J. Muller, Geophysical Research Letters 51 (2024).","ista":"Hwong Y-L, Muller CJ. 2024. The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation. Geophysical Research Letters. 51(6), e2023GL106523.","apa":"Hwong, Y.-L., & Muller, C. J. (2024). The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation. Geophysical Research Letters. American Geophysical Union. https://doi.org/10.1029/2023gl106523","ieee":"Y.-L. Hwong and C. J. Muller, “The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation,” Geophysical Research Letters, vol. 51, no. 6. American Geophysical Union, 2024.","ama":"Hwong Y-L, Muller CJ. The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation. Geophysical Research Letters. 2024;51(6). doi:10.1029/2023gl106523"},"publication":"Geophysical Research Letters","date_published":"2024-03-19T00:00:00Z","keyword":["General Earth and Planetary Sciences","Geophysics"],"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"19","intvolume":" 51","status":"public","title":"The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation","ddc":["550"],"_id":"15186","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"checksum":"eacb011091a503b9e7b748fef639ba4c","success":1,"date_updated":"2024-03-25T11:28:25Z","date_created":"2024-03-25T11:28:25Z","relation":"main_file","file_id":"15187","content_type":"application/pdf","file_size":1280108,"creator":"dernst","access_level":"open_access","file_name":"2024_GeophysResLetters_Hwong.pdf"}],"type":"journal_article","issue":"6","abstract":[{"text":"The elimination of rain evaporation in the planetary boundary layer (PBL) has been found to lead to convective self‐aggregation (CSA) even without radiative feedback, but the precise mechanisms underlying this phenomenon remain unclear. We conducted cloud‐resolving simulations with two domain sizes and progressively reduced rain evaporation in the PBL. Surprisingly, CSA only occurred when rain evaporation was almost completely removed. The additional convective heating resulting from the reduction of evaporative cooling in the moist patch was found to be the trigger, thereafter a dry subsidence intrusion into the PBL in the dry patch takes over and sets CSA in motion. Temperature and moisture anomalies oppose each other in their buoyancy effects, hence explaining the need for almost total rain evaporation removal. We also found radiative cooling and not cold pools to be the leading cause for the comparative ease of CSA to take place in the larger domain.","lang":"eng"}]},{"article_number":"013257","ec_funded":1,"file_date_updated":"2024-03-25T09:24:55Z","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","acknowledgement":"This work has been funded by the Cluster of Excellence “Advanced Imaging of Matter” of the Deutsche Forschungsgemeinschaft (DFG) - EXC 2056 - Project ID 390715994.\r\nG.M.K. gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","year":"2024","volume":6,"date_updated":"2024-03-25T09:27:37Z","date_created":"2024-03-25T08:57:07Z","author":[{"first_name":"A.","last_name":"Becker","full_name":"Becker, A."},{"full_name":"Koutentakis, Georgios","last_name":"Koutentakis","first_name":"Georgios","id":"d7b23d3a-9e21-11ec-b482-f76739596b95"},{"full_name":"Schmelcher, P.","first_name":"P.","last_name":"Schmelcher"}],"publication_identifier":{"issn":["2643-1564"]},"month":"03","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"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"},"external_id":{"arxiv":["2310.17995"]},"language":[{"iso":"eng"}],"doi":"10.1103/physrevresearch.6.013257","type":"journal_article","issue":"1","abstract":[{"text":"We demonstrate the failure of the adiabatic Born-Oppenheimer approximation to describe the ground state of a quantum impurity within an ultracold Fermi gas despite substantial mass differences between the bath and impurity species. Increasing repulsion leads to the appearance of nonadiabatic couplings between the fast bath and slow impurity degrees of freedom, which reduce the parity symmetry of the latter according to the pseudo Jahn-Teller effect. The presence of this mechanism is associated to a conical intersection involving the impurity position and the inverse of the interaction strength, which acts as a synthetic dimension. We elucidate the presence of these effects via a detailed ground-state analysis involving the comparison of ab initio fully correlated simulations with effective models. Our study suggests ultracold atomic ensembles as potent emulators of complex molecular phenomena.","lang":"eng"}],"intvolume":" 6","status":"public","title":"Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions","ddc":["530"],"_id":"15181","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","file_id":"15183","checksum":"4e0e58d1f58386fb016284c84db2a300","success":1,"date_created":"2024-03-25T09:24:55Z","date_updated":"2024-03-25T09:24:55Z","access_level":"open_access","file_name":"2024_PhysicalReviewResearch_Becker.pdf","content_type":"application/pdf","file_size":2207067,"creator":"dernst"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"01","article_type":"original","citation":{"chicago":"Becker, A., Georgios Koutentakis, and P. Schmelcher. “Synthetic Dimension-Induced Pseudo Jahn-Teller Effect in One-Dimensional Confined Fermions.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/physrevresearch.6.013257.","mla":"Becker, A., et al. “Synthetic Dimension-Induced Pseudo Jahn-Teller Effect in One-Dimensional Confined Fermions.” Physical Review Research, vol. 6, no. 1, 013257, American Physical Society, 2024, doi:10.1103/physrevresearch.6.013257.","short":"A. Becker, G. Koutentakis, P. Schmelcher, Physical Review Research 6 (2024).","ista":"Becker A, Koutentakis G, Schmelcher P. 2024. Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions. Physical Review Research. 6(1), 013257.","ieee":"A. Becker, G. Koutentakis, and P. Schmelcher, “Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.","apa":"Becker, A., Koutentakis, G., & Schmelcher, P. (2024). Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.6.013257","ama":"Becker A, Koutentakis G, Schmelcher P. Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions. Physical Review Research. 2024;6(1). doi:10.1103/physrevresearch.6.013257"},"publication":"Physical Review Research","date_published":"2024-03-01T00:00:00Z"},{"day":"13","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2024-03-13T00:00:00Z","publication":"Advanced Energy Materials","citation":{"short":"T. Kleinhanns, F. Milillo, M. Calcabrini, C. Fiedler, S. Horta, D. Balazs, M.J. Strumolo, R. Hasler, J. Llorca, M. Tkadletz, R.L. Brutchey, M. Ibáñez, Advanced Energy Materials (2024).","mla":"Kleinhanns, Tobias, et al. “A Route to High Thermoelectric Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.” Advanced Energy Materials, 2400408, Wiley, 2024, doi:10.1002/aenm.202400408.","chicago":"Kleinhanns, Tobias, Francesco Milillo, Mariano Calcabrini, Christine Fiedler, Sharona Horta, Daniel Balazs, Marissa J. Strumolo, et al. “A Route to High Thermoelectric Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.” Advanced Energy Materials. Wiley, 2024. https://doi.org/10.1002/aenm.202400408.","ama":"Kleinhanns T, Milillo F, Calcabrini M, et al. A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials. 2024. doi:10.1002/aenm.202400408","apa":"Kleinhanns, T., Milillo, F., Calcabrini, M., Fiedler, C., Horta, S., Balazs, D., … Ibáñez, M. (2024). A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials. Wiley. https://doi.org/10.1002/aenm.202400408","ieee":"T. Kleinhanns et al., “A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se,” Advanced Energy Materials. Wiley, 2024.","ista":"Kleinhanns T, Milillo F, Calcabrini M, Fiedler C, Horta S, Balazs D, Strumolo MJ, Hasler R, Llorca J, Tkadletz M, Brutchey RL, Ibáñez M. 2024. A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials., 2400408."},"article_type":"original","abstract":[{"lang":"eng","text":"Thermoelectric materials convert heat into electricity, with a broad range of applications near room temperature (RT). However, the library of RT high-performance materials is limited. Traditional high-temperature synthetic methods constrain the range of materials achievable, hindering the ability to surpass crystal structure limitations and engineer defects. Here, a solution-based synthetic approach is introduced, enabling RT synthesis of powders and exploration of densification at lower temperatures to influence the material's microstructure. The approach is exemplified by Ag2Se, an n-type alternative to bismuth telluride. It is demonstrated that the concentration of Ag interstitials, grain boundaries, and dislocations are directly correlated to the sintering temperature, and achieve a figure of merit of 1.1 from RT to 100 °C after optimization. Moreover, insights into and resolve Ag2Se's challenges are provided, including stoichiometry issues leading to irreproducible performances. This work highlights the potential of RT solution synthesis in expanding the repertoire of high-performance thermoelectric materials for practical applications."}],"type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15182","title":"A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se","status":"public","month":"03","publication_identifier":{"eissn":["1614-6840"],"issn":["1614-6832"]},"doi":"10.1002/aenm.202400408","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/aenm.202400408"}],"oa":1,"quality_controlled":"1","project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"article_number":"2400408","author":[{"id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias","last_name":"Kleinhanns","full_name":"Kleinhanns, Tobias"},{"full_name":"Milillo, Francesco","last_name":"Milillo","first_name":"Francesco","id":"38b830db-ea88-11ee-bf9b-929beaf79054"},{"full_name":"Calcabrini, Mariano","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4566-5877","first_name":"Mariano","last_name":"Calcabrini"},{"full_name":"Fiedler, Christine","first_name":"Christine","last_name":"Fiedler","id":"bd3fceba-dc74-11ea-a0a7-c17f71817366"},{"last_name":"Horta","first_name":"Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","full_name":"Horta, Sharona"},{"first_name":"Daniel","last_name":"Balazs","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel"},{"first_name":"Marissa J.","last_name":"Strumolo","full_name":"Strumolo, Marissa J."},{"full_name":"Hasler, Roger","last_name":"Hasler","first_name":"Roger"},{"last_name":"Llorca","first_name":"Jordi","full_name":"Llorca, Jordi"},{"full_name":"Tkadletz, Michael","last_name":"Tkadletz","first_name":"Michael"},{"full_name":"Brutchey, Richard L.","last_name":"Brutchey","first_name":"Richard L."},{"full_name":"Ibáñez, Maria","first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843"}],"date_updated":"2024-03-25T09:21:05Z","date_created":"2024-03-25T08:57:40Z","year":"2024","acknowledgement":"This work was supported by the Scientific Service Units (SSU) of ISTA through resources provided by the Electron Microscopy Facility (EMF), the Lab Support Facility (LSF), and the Nanofabrication Facility (NNF). This work was financially supported by ISTA and the Werner Siemens Foundation. The USTEM Service Unit of the Technical University of Vienna is acknowledged for EBSD sample preparation and analysis. R.L.B. acknowledges the National Science Foundation for funding the mass spectrometry analysis under award DMR 1904719. J.L. is a Serra Húnter Fellow and is grateful to the ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and GC 2021 SGR 01061.","publication_status":"epub_ahead","publisher":"Wiley","department":[{"_id":"MaIb"},{"_id":"LifeSc"}]},{"article_number":"e2023GL106569","ec_funded":1,"file_date_updated":"2024-03-25T08:36:00Z","publisher":"Wiley","department":[{"_id":"CaMu"}],"publication_status":"published","acknowledgement":"The author gratefully acknowledges ISTA for supporting this research through funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Project CLUSTER, grant agreement No. 805041).","year":"2024","volume":51,"date_updated":"2024-03-25T10:00:57Z","date_created":"2024-03-24T23:00:58Z","author":[{"orcid":"0000-0001-8602-3083","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","last_name":"Goswami","first_name":"Bidyut B","full_name":"Goswami, Bidyut B"}],"publication_identifier":{"eissn":["1944-8007"],"issn":["0094-8276"]},"month":"03","project":[{"name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate","call_identifier":"H2020","grant_number":"805041","_id":"629205d8-2b32-11ec-9570-e1356ff73576"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1029/2023GL106569","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"Current knowledge suggests a drought Indian monsoon (perhaps a severe one) when the El Nino Southern Oscillation and Pacific Decadal Oscillation each exhibit positive phases (a joint positive phase). For the monsoons, which are exceptions in this regard, we found northeast India often gets excess pre-monsoon rainfall. Further investigation reveals that this excess pre-monsoon rainfall is produced by the interaction of the large-scale circulation associated with the joint phase with the mountains in northeast India. We posit that a warmer troposphere, a consequence of excess rainfall over northeast India, drives a stronger monsoon circulation and enhances monsoon rainfall over central India. Hence, we argue that pre-monsoon rainfall over northeast India can be used for seasonal monsoon rainfall prediction over central India. Most importantly, its predictive value is at its peak when the Pacific Ocean exhibits a joint positive phase and the threat of extreme drought monsoon looms over India."}],"intvolume":" 51","status":"public","title":"A pre-monsoon signal of false alarms of Indian monsoon droughts","ddc":["550"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15165","file":[{"content_type":"application/pdf","file_size":2887134,"creator":"dernst","access_level":"open_access","file_name":"2024_GeophysResLetters_Goswami.pdf","checksum":"243bd966aca968ec7d9e474af8639f8d","success":1,"date_created":"2024-03-25T08:36:00Z","date_updated":"2024-03-25T08:36:00Z","relation":"main_file","file_id":"15178"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"16","article_type":"original","citation":{"ama":"GOSWAMI BB. A pre-monsoon signal of false alarms of Indian monsoon droughts. Geophysical Research Letters. 2024;51(5). doi:10.1029/2023GL106569","ista":"GOSWAMI BB. 2024. A pre-monsoon signal of false alarms of Indian monsoon droughts. Geophysical Research Letters. 51(5), e2023GL106569.","ieee":"B. B. GOSWAMI, “A pre-monsoon signal of false alarms of Indian monsoon droughts,” Geophysical Research Letters, vol. 51, no. 5. Wiley, 2024.","apa":"GOSWAMI, B. B. (2024). A pre-monsoon signal of false alarms of Indian monsoon droughts. Geophysical Research Letters. Wiley. https://doi.org/10.1029/2023GL106569","mla":"GOSWAMI, BIDYUT B. “A Pre-Monsoon Signal of False Alarms of Indian Monsoon Droughts.” Geophysical Research Letters, vol. 51, no. 5, e2023GL106569, Wiley, 2024, doi:10.1029/2023GL106569.","short":"B.B. GOSWAMI, Geophysical Research Letters 51 (2024).","chicago":"GOSWAMI, BIDYUT B. “A Pre-Monsoon Signal of False Alarms of Indian Monsoon Droughts.” Geophysical Research Letters. Wiley, 2024. https://doi.org/10.1029/2023GL106569."},"publication":"Geophysical Research Letters","date_published":"2024-03-16T00:00:00Z"},{"issue":"6688","abstract":[{"lang":"eng","text":"Reducing defects boosts room-temperature performance of a thermoelectric device"}],"type":"journal_article","oa_version":"None","intvolume":" 383","status":"public","title":"Electron highways are cooler","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15166","article_processing_charge":"No","day":"14","scopus_import":"1","date_published":"2024-03-14T00:00:00Z","page":"1184","article_type":"letter_note","citation":{"chicago":"Jakhar, Navita, and Maria Ibáñez. “Electron Highways Are Cooler.” Science. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/science.ado4077.","mla":"Jakhar, Navita, and Maria Ibáñez. “Electron Highways Are Cooler.” Science, vol. 383, no. 6688, American Association for the Advancement of Science, 2024, p. 1184, doi:10.1126/science.ado4077.","short":"N. Jakhar, M. Ibáñez, Science 383 (2024) 1184.","ista":"Jakhar N, Ibáñez M. 2024. Electron highways are cooler. Science. 383(6688), 1184.","ieee":"N. Jakhar and M. Ibáñez, “Electron highways are cooler,” Science, vol. 383, no. 6688. American Association for the Advancement of Science, p. 1184, 2024.","apa":"Jakhar, N., & Ibáñez, M. (2024). Electron highways are cooler. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.ado4077","ama":"Jakhar N, Ibáñez M. Electron highways are cooler. Science. 2024;383(6688):1184. doi:10.1126/science.ado4077"},"publication":"Science","volume":383,"date_updated":"2024-03-25T10:31:20Z","date_created":"2024-03-24T23:00:58Z","author":[{"full_name":"Navita, Navita","first_name":"Navita","last_name":"Navita","id":"6ebe278d-ba0b-11ee-8184-f34cdc671de4"},{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria"}],"publisher":"American Association for the Advancement of Science","department":[{"_id":"MaIb"}],"publication_status":"published","year":"2024","acknowledgement":"The authors thank the Werner-Siemens-Stiftung and the Institute of Science and Technology Austria for financial support.","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1126/science.ado4077","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"quality_controlled":"1"},{"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","title":"Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix","status":"public","ddc":["570"],"intvolume":" 223","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15146","oa_version":"Published Version","file":[{"date_created":"2024-03-25T12:52:04Z","date_updated":"2024-03-25T12:52:04Z","success":1,"checksum":"90d1984a93660735e506c2a304bc3f73","file_id":"15188","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":11907016,"file_name":"2024_JCB_Zens.pdf","access_level":"open_access"}],"scopus_import":"1","day":"20","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","article_type":"original","publication":"Journal of Cell Biology","citation":{"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.","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.","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","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.","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).","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."},"date_published":"2024-03-20T00:00:00Z","article_number":"e202309125","file_date_updated":"2024-03-25T12:52:04Z","ec_funded":1,"publication_status":"published","department":[{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"publisher":"Rockefeller University Press","year":"2024","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).","pmid":1,"date_created":"2024-03-21T06:45:51Z","date_updated":"2024-03-25T13:03:57Z","volume":223,"author":[{"first_name":"Bettina","last_name":"Zens","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","full_name":"Zens, Bettina"},{"first_name":"Florian","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian"},{"full_name":"Hansen, Jesse","first_name":"Jesse","last_name":"Hansen","id":"1063c618-6f9b-11ec-9123-f912fccded63"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"},{"full_name":"Datler, Julia","last_name":"Datler","first_name":"Julia","orcid":"0000-0002-3616-8580","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","first_name":"Victor-Valentin","full_name":"Hodirnau, Victor-Valentin"},{"last_name":"Zheden","first_name":"Vanessa","orcid":"0000-0002-9438-4783","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","full_name":"Zheden, Vanessa"},{"full_name":"Alanko, Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7698-3061","first_name":"Jonna H","last_name":"Alanko"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"},{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM"}],"month":"03","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"quality_controlled":"1","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"},{"_id":"7bd318a1-9f16-11ee-852c-cc9217763180","grant_number":"E435","name":"In Situ Actin Structures via Hybrid Cryo-electron Microscopy"},{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","call_identifier":"H2020","name":"Cellular navigation along spatial gradients"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"21317","_id":"2615199A-B435-11E9-9278-68D0E5697425","name":"Spatiotemporal regulation of chemokine-induced signalling in leukocyte chemotaxis"},{"grant_number":"CZI01","_id":"62909c6f-2b32-11ec-9570-e1476aab5308","name":"CryoMinflux-guided in-situ visual proteomics and structure determination"}],"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"]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"doi":"10.1083/jcb.202309125"},{"ec_funded":1,"article_number":"110320","date_created":"2024-02-04T23:00:53Z","date_updated":"2024-03-28T10:54:02Z","volume":286,"author":[{"last_name":"Lauritsen","first_name":"Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","full_name":"Lauritsen, Asbjørn Bækgaard"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"publication_status":"epub_ahead","publisher":"Elsevier","department":[{"_id":"RoSe"}],"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","month":"01","publication_identifier":{"issn":["0022-1236"],"eissn":["1096--0783"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.jfa.2024.110320","quality_controlled":"1","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020"},{"name":"Mathematical Challenges in BCS Theory of Superconductivity","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","grant_number":"I06427"}],"oa":1,"external_id":{"arxiv":["2301.04894"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.jfa.2024.110320","open_access":"1"}],"abstract":[{"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].","lang":"eng"}],"issue":"7","type":"journal_article","oa_version":"Published Version","title":"Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion","status":"public","intvolume":" 286","_id":"14931","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"24","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2024-01-24T00:00:00Z","article_type":"original","publication":"Journal of Functional Analysis","citation":{"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","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","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).","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."}},{"month":"01","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"language":[{"iso":"eng"}],"doi":"10.1093/mnras/stae012","quality_controlled":"1","main_file_link":[{"url":"https://academic.oup.com/mnras/article/528/1/676/7511123","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":["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","last_name":"Galiullin","first_name":"Ilkham"},{"full_name":"Rodriguez, Antonio C","last_name":"Rodriguez","first_name":"Antonio C"},{"last_name":"Kulkarni","first_name":"Shrinivas R","full_name":"Kulkarni, Shrinivas R"},{"first_name":"Rashid","last_name":"Sunyaev","full_name":"Sunyaev, Rashid"},{"full_name":"Gilfanov, Marat","last_name":"Gilfanov","first_name":"Marat"},{"first_name":"Ilfan","last_name":"Bikmaev","full_name":"Bikmaev, Ilfan"},{"last_name":"Yungelson","first_name":"Lev","full_name":"Yungelson, Lev"},{"full_name":"van Roestel, Jan","last_name":"van Roestel","first_name":"Jan"},{"first_name":"Boris T","last_name":"Gänsicke","full_name":"Gänsicke, Boris T"},{"full_name":"Khamitov, Irek","first_name":"Irek","last_name":"Khamitov"},{"first_name":"Paula","last_name":"Szkody","full_name":"Szkody, Paula"},{"last_name":"El-Badry","first_name":"Kareem","full_name":"El-Badry, Kareem"},{"last_name":"Suslikov","first_name":"Mikhail","full_name":"Suslikov, Mikhail"},{"full_name":"Prince, Thomas A","last_name":"Prince","first_name":"Thomas A"},{"full_name":"Buntov, Mikhail","last_name":"Buntov","first_name":"Mikhail"},{"full_name":"Caiazzo, Ilaria","first_name":"Ilaria","last_name":"Caiazzo","id":"8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d","orcid":"0000-0002-4770-5388"},{"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"},{"last_name":"Laher","first_name":"Russ R","full_name":"Laher, Russ R"},{"first_name":"Pavel","last_name":"Medvedev","full_name":"Medvedev, Pavel"},{"full_name":"Riddle, Reed","last_name":"Riddle","first_name":"Reed"},{"full_name":"Rusholme, Ben","last_name":"Rusholme","first_name":"Ben"},{"first_name":"Nail","last_name":"Sakhibullin","full_name":"Sakhibullin, Nail"},{"last_name":"Sklyanov","first_name":"Alexander","full_name":"Sklyanov, Alexander"},{"last_name":"Vanderbosch","first_name":"Zachary P","full_name":"Vanderbosch, Zachary P"}],"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":{"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","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.","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","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.","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.","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."},"abstract":[{"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.","lang":"eng"}],"issue":"1","type":"journal_article","oa_version":"Published Version","title":"A joint SRG/eROSITA + ZTF search: Discovery of a 97-min period eclipsing cataclysmic variable with evidence of a brown dwarf secondary","status":"public","intvolume":" 528","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"15189"},{"article_type":"original","publication":"The Astrophysical Journal","citation":{"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.","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","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.","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."},"date_published":"2024-01-22T00:00:00Z","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"scopus_import":"1","day":"22","article_processing_charge":"No","title":"Exploring the chemistry and mass function of the globular cluster 47 Tucanae with new theoretical color–magnitude diagrams","status":"public","intvolume":" 961","_id":"15191","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","type":"journal_article","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."}],"issue":"1","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,"main_file_link":[{"open_access":"1","url":"https://iopscience.iop.org/article/10.3847/1538-4357/ad08bf"}],"external_id":{"arxiv":["2310.11800"]},"language":[{"iso":"eng"}],"doi":"10.3847/1538-4357/ad08bf","month":"01","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"publication_status":"published","publisher":"American Astronomical Society","year":"2024","date_updated":"2024-03-29T10:06:31Z","date_created":"2024-03-26T09:44:50Z","volume":961,"author":[{"full_name":"Gerasimov, Roman","last_name":"Gerasimov","first_name":"Roman"},{"full_name":"Burgasser, Adam J.","last_name":"Burgasser","first_name":"Adam J."},{"full_name":"Caiazzo, Ilaria","first_name":"Ilaria","last_name":"Caiazzo","id":"8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d","orcid":"0000-0002-4770-5388"},{"full_name":"Homeier, Derek","last_name":"Homeier","first_name":"Derek"},{"full_name":"Richer, Harvey B.","last_name":"Richer","first_name":"Harvey B."},{"full_name":"Correnti, Matteo","first_name":"Matteo","last_name":"Correnti"},{"full_name":"Heyl, Jeremy","last_name":"Heyl","first_name":"Jeremy"}],"article_number":"139","extern":"1"},{"file_date_updated":"2023-02-03T10:56:39Z","pmid":1,"year":"2023","editor":[{"last_name":"Margadant","first_name":"Coert","full_name":"Margadant, Coert"}],"department":[{"_id":"EdHa"}],"publisher":"Springer Nature","publication_status":"published","author":[{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"full_name":"Scheele, Colinda L.G.J.","last_name":"Scheele","first_name":"Colinda L.G.J."}],"volume":2608,"date_updated":"2023-02-03T10:58:56Z","date_created":"2023-01-29T23:00:58Z","publication_identifier":{"eisbn":["9781071628874"],"eissn":["1940-6029"],"isbn":["9781071628867"]},"month":"01","external_id":{"pmid":["36653709"]},"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","doi":"10.1007/978-1-0716-2887-4_12","language":[{"iso":"eng"}],"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","title":"A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland","status":"public","ddc":["570"],"oa_version":"Published Version","file":[{"file_id":"12500","relation":"main_file","success":1,"checksum":"aec1b8d3ba938ddf9d8fcb777f3c38ee","date_updated":"2023-02-03T10:56:39Z","date_created":"2023-02-03T10:56:39Z","access_level":"open_access","file_name":"2023_MIMB_Hannezo.pdf","creator":"dernst","file_size":826598,"content_type":"application/pdf"}],"scopus_import":"1","series_title":"MIMB","article_processing_charge":"No","has_accepted_license":"1","day":"19","citation":{"short":"E.B. Hannezo, C.L.G.J. Scheele, in:, C. Margadant (Ed.), Cell Migration in Three Dimensions, Springer Nature, 2023, pp. 183–205.","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.","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.","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","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","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.","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."},"publication":"Cell Migration in Three Dimensions","page":"183-205","date_published":"2023-01-19T00:00:00Z"},{"intvolume":" 5","title":"Dissipative dynamics of an impurity with spin-orbit coupling","ddc":["530"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12534","oa_version":"Published Version","file":[{"checksum":"6068b62874c0099628a108bb9c5c6bd2","success":1,"date_created":"2023-02-13T10:38:10Z","date_updated":"2023-02-13T10:38:10Z","relation":"main_file","file_id":"12546","content_type":"application/pdf","file_size":865150,"creator":"dernst","access_level":"open_access","file_name":"2023_PhysicalReviewResearch_Ghazaryan.pdf"}],"type":"journal_article","issue":"1","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."}],"article_type":"original","citation":{"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.","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","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.","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.","short":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, A. Volosniev, Physical Review Research 5 (2023).","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."},"publication":"Physical Review Research","date_published":"2023-01-20T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"20","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","year":"2023","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).","volume":5,"date_created":"2023-02-10T09:02:26Z","date_updated":"2023-02-20T07:02:00Z","author":[{"full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg","last_name":"Ghazaryan"},{"full_name":"Cappellaro, Alberto","last_name":"Cappellaro","first_name":"Alberto","orcid":"0000-0001-6110-2359","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail"},{"first_name":"Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem"}],"article_number":"013029","ec_funded":1,"file_date_updated":"2023-02-13T10:38:10Z","project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"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"},"language":[{"iso":"eng"}],"doi":"10.1103/physrevresearch.5.013029","publication_identifier":{"issn":["2643-1564"]},"month":"01"},{"publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"month":"02","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"},"file_date_updated":"2023-02-27T07:46:45Z","volume":55,"date_updated":"2023-02-27T07:48:24Z","date_created":"2023-01-12T12:09:09Z","author":[{"first_name":"Peter","last_name":"Zeller","full_name":"Zeller, Peter"},{"full_name":"Yeung, Jake","id":"123012b2-db30-11eb-b4d8-a35840c0551b","orcid":"0000-0003-1732-1559","first_name":"Jake","last_name":"Yeung"},{"last_name":"Viñas Gaza","first_name":"Helena","full_name":"Viñas Gaza, Helena"},{"last_name":"de Barbanson","first_name":"Buys Anton","full_name":"de Barbanson, Buys Anton"},{"full_name":"Bhardwaj, Vivek","first_name":"Vivek","last_name":"Bhardwaj"},{"last_name":"Florescu","first_name":"Maria","full_name":"Florescu, Maria"},{"full_name":"van der Linden, Reinier","last_name":"van der Linden","first_name":"Reinier"},{"first_name":"Alexander","last_name":"van Oudenaarden","full_name":"van Oudenaarden, Alexander"}],"publisher":"Springer Nature","department":[{"_id":"ScienComp"}],"publication_status":"published","year":"2023","acknowledgement":"We thank A. Giladi for sharing mRNA abundance tables of cell types together with J. van den Berg for critical reading of the manuscript. We thank M. Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973). Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström under CC-BY-SA 3.0 license. This work was supported by European Research Council Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991), HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z. The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF (ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","has_accepted_license":"1","article_processing_charge":"No","day":"01","keyword":["Genetics"],"scopus_import":"1","date_published":"2023-02-01T00:00:00Z","page":"333-345","article_type":"review","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.","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.","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.","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.","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.","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"},"publication":"Nature Genetics","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","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":21484855,"creator":"dernst","file_name":"2023_NatureGenetics_Zeller.pdf","access_level":"open_access","date_updated":"2023-02-27T07:46:45Z","date_created":"2023-02-27T07:46:45Z","checksum":"6fdb8e34fbeea63edd0f2c6c2cc5823e","success":1,"relation":"main_file","file_id":"12688"}],"intvolume":" 55","status":"public","title":"Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis","ddc":["570","000"],"_id":"12158","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_published":"2023-02-01T00:00:00Z","citation":{"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.","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.","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.","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","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.","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"},"publication":"Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms","page":"4590-4605","article_processing_charge":"No","day":"01","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":[{"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.","lang":"eng"}],"type":"conference","doi":"10.1137/1.9781611977554.ch173","conference":{"end_date":"2023-01-25","location":"Florence, Italy","start_date":"2023-01-22","name":"SODA: Symposium on Discrete Algorithms"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1137/1.9781611977554.ch173","open_access":"1"}],"oa":1,"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"quality_controlled":"1","publication_identifier":{"isbn":["9781611977554"]},"month":"02","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","first_name":"Tobias","last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias"},{"id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","orcid":"0000-0001-5103-038X","first_name":"Raimundo J","last_name":"Saona Urmeneta","full_name":"Saona Urmeneta, Raimundo J"},{"full_name":"Svoboda, Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub","last_name":"Svoboda"}],"date_created":"2023-02-24T12:20:47Z","date_updated":"2023-02-27T09:01:16Z","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant.","year":"2023","publisher":"Society for Industrial and Applied Mathematics","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publication_status":"published","ec_funded":1},{"date_published":"2023-03-01T00:00:00Z","page":"33-44","publication":"DNA Manipulation and Analysis","citation":{"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.","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.","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","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."},"day":"01","article_processing_charge":"No","series_title":"MIMB","scopus_import":"1","oa_version":"None","title":"Molecular Cloning Using In Vivo DNA Assembly","status":"public","intvolume":" 2633","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12720","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"}],"alternative_title":["Methods in Molecular Biology"],"type":"book_chapter","language":[{"iso":"eng"}],"doi":"10.1007/978-1-0716-3004-4_3","quality_controlled":"1","external_id":{"pmid":["36853454"]},"month":"03","publication_identifier":{"issn":["1064-3745"],"eisbn":["978-1-0716-3004-4"],"eissn":["1940-6029"],"isbn":["978-1-0716-3003-7"]},"date_updated":"2023-03-16T08:34:24Z","date_created":"2023-03-12T23:01:02Z","volume":2633,"author":[{"first_name":"Sandra","last_name":"Arroyo-Urea","full_name":"Arroyo-Urea, Sandra"},{"orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson","first_name":"Jake","full_name":"Watson, Jake"},{"full_name":"García-Nafría, Javier","last_name":"García-Nafría","first_name":"Javier"}],"publication_status":"published","editor":[{"full_name":"Scarlett, Garry","last_name":"Scarlett","first_name":"Garry"}],"department":[{"_id":"PeJo"}],"publisher":"Springer Nature","year":"2023","pmid":1,"place":"New York, NY, United States"},{"publication_status":"published","status":"public","title":"Fast and scalable channels in Kotlin Coroutines","publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"}],"year":"2023","_id":"12735","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-03-20T07:29:28Z","date_created":"2023-03-19T23:00:58Z","oa_version":"Preprint","author":[{"first_name":"Nikita","last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita"},{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Roman","last_name":"Elizarov","full_name":"Elizarov, Roman"}],"type":"conference","abstract":[{"lang":"eng","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."}],"quality_controlled":"1","page":"107-118","publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","citation":{"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","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.","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.","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."},"external_id":{"arxiv":["2211.04986"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.04986","open_access":"1"}],"language":[{"iso":"eng"}],"conference":{"end_date":"2023-03-01","start_date":"2023-02-25","location":"Montreal, QC, Canada","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"doi":"10.1145/3572848.3577481","date_published":"2023-02-25T00:00:00Z","scopus_import":"1","day":"25","month":"02","article_processing_charge":"No","publication_identifier":{"isbn":["9798400700156"]}},{"publication_identifier":{"isbn":["9798400700156"]},"article_processing_charge":"No","day":"25","month":"02","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3572848.3577512"}],"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,"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","page":"438-440","quality_controlled":"1","date_published":"2023-02-25T00:00:00Z","doi":"10.1145/3572848.3577512","conference":{"name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming","end_date":"2023-03-01","location":"Montreal, QB, Canada","start_date":"2023-02-25"},"language":[{"iso":"eng"}],"type":"conference_poster","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"}],"_id":"12736","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.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"title":"Unexpected scaling in path copying trees","publication_status":"published","status":"public","author":[{"last_name":"Aksenov","first_name":"Vitaly","full_name":"Aksenov, Vitaly"},{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","first_name":"Trevor A","full_name":"Brown, Trevor A"},{"full_name":"Fedorov, Alexander","first_name":"Alexander","last_name":"Fedorov","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6"},{"full_name":"Kokorin, Ilya","first_name":"Ilya","last_name":"Kokorin"}],"oa_version":"Published Version","date_created":"2023-03-19T23:00:58Z","date_updated":"2023-03-20T07:57:27Z"},{"article_number":"36","file_date_updated":"2023-03-27T06:37:22Z","department":[{"_id":"MoHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","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","volume":254,"date_created":"2023-03-26T22:01:07Z","date_updated":"2023-03-27T06:46:27Z","author":[{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H"},{"last_name":"Neumann","first_name":"Stefan","full_name":"Neumann, Stefan"},{"full_name":"Räcke, Harald","last_name":"Räcke","first_name":"Harald"},{"last_name":"Schmid","first_name":"Stefan","full_name":"Schmid, Stefan"}],"publication_identifier":{"isbn":["9783959772662"],"issn":["1868-8969"]},"month":"03","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":["2301.01744"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.STACS.2023.36","conference":{"location":"Hamburg, Germany","start_date":"2023-03-07","end_date":"2023-03-09","name":"STACS: Symposium on Theoretical Aspects of Computer Science"},"alternative_title":["LIPIcs"],"type":"conference","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"}],"intvolume":" 254","status":"public","title":"Dynamic maintenance of monotone dynamic programs and applications","ddc":["000"],"_id":"12760","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"22141ab8bc55188e2dfff665e5daecbd","success":1,"date_updated":"2023-03-27T06:37:22Z","date_created":"2023-03-27T06:37:22Z","relation":"main_file","file_id":"12769","file_size":872706,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_LIPICS_HenzingerM.pdf"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","citation":{"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","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.","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.","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.","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.","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."},"publication":"40th International Symposium on Theoretical Aspects of Computer Science","date_published":"2023-03-01T00:00:00Z"},{"file_date_updated":"2023-03-08T15:08:46Z","ec_funded":1,"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"year":"2023","date_created":"2023-03-08T15:19:45Z","date_updated":"2023-04-05T10:59:04Z","author":[{"id":"3B717F68-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8937-410X","first_name":"Laura","last_name":"Burnett","full_name":"Burnett, Laura"}],"month":"03","publication_identifier":{"issn":["2663-337X"]},"project":[{"grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Circuits of Visual Attention"}],"oa":1,"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"degree_awarded":"PhD","supervisor":[{"last_name":"Jösch","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12716","alternative_title":["ISTA Thesis"],"type":"dissertation","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."}],"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","ddc":["599","573"],"status":"public","_id":"12716","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"file_id":"12717","relation":"source_file","date_created":"2023-03-08T15:08:46Z","date_updated":"2023-03-08T15:08:46Z","checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332","file_name":"Burnett_Thesis_2023.docx","access_level":"closed","creator":"lburnett","file_size":23029260,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"file_id":"12718","relation":"main_file","date_created":"2023-03-08T15:08:46Z","date_updated":"2023-03-08T15:08:46Z","success":1,"checksum":"cebc77705288bf4382db9b3541483cd0","file_name":"Burnett_Thesis_2023_pdfA.pdf","access_level":"open_access","creator":"lburnett","file_size":11959869,"content_type":"application/pdf"}],"oa_version":"Published Version","day":"10","has_accepted_license":"1","article_processing_charge":"No","page":"178","citation":{"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","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.","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.","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.","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.","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."},"date_published":"2023-03-10T00:00:00Z"},{"_id":"12854","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 13994","title":"Bubaak: Runtime monitoring of program verifiers","status":"public","ddc":["000"],"file":[{"file_id":"12864","relation":"main_file","success":1,"checksum":"120d2c2a38384058ad0630fdf8288312","date_created":"2023-04-25T06:58:36Z","date_updated":"2023-04-25T06:58:36Z","access_level":"open_access","file_name":"2023_LNCS_Chalupa.pdf","creator":"dernst","file_size":16096413,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"conference","alternative_title":["LNCS"],"abstract":[{"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.","lang":"eng"}],"citation":{"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.","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","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","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.","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.","short":"M. Chalupa, T.A. Henzinger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 535–540."},"publication":"Tools and Algorithms for the Construction and Analysis of Systems","page":"535-540","date_published":"2023-04-20T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"20","acknowledgement":"This work was supported by the ERC-2020-AdG 10102009 grant.","year":"2023","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"publication_status":"published","author":[{"full_name":"Chalupa, Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","last_name":"Chalupa","first_name":"Marek"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"}],"volume":13994,"date_created":"2023-04-20T08:22:53Z","date_updated":"2023-04-25T07:02:43Z","ec_funded":1,"file_date_updated":"2023-04-25T06:58:36Z","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":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"quality_controlled":"1","doi":"10.1007/978-3-031-30820-8_32","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"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0302-9743"],"eisbn":["9783031308208"],"isbn":["9783031308192"],"eissn":["1611-3349"]},"month":"04"},{"article_processing_charge":"No","month":"03","day":"25","language":[{"iso":"eng"}],"date_published":"2023-03-25T00:00:00Z","doi":"10.48550/arXiv.2303.14555","project":[{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"external_id":{"arxiv":["2303.14555"]},"citation":{"chicago":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2303.14555.","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.","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.","ama":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv. doi:10.48550/arXiv.2303.14555"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2303.14555"}],"oa":1,"publication":"arXiv","abstract":[{"lang":"eng","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."}],"type":"preprint","article_number":"2303.14555","oa_version":"Preprint","date_updated":"2023-04-25T06:51:21Z","date_created":"2023-04-18T19:16:06Z","author":[{"full_name":"Chern, Albert","first_name":"Albert","last_name":"Chern"},{"full_name":"Ishida, Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","last_name":"Ishida","first_name":"Sadashige"}],"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"status":"public","publication_status":"submitted","title":"Area formula for spherical polygons via prequantization","_id":"12846","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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).","year":"2023"}]