[{"month":"01","publication_identifier":{"eissn":["1420-9020"],"issn":["1022-1824"]},"quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1007/s00029-023-00914-2","article_number":"20","publication_status":"epub_ahead","publisher":"Springer Nature","department":[{"_id":"TaHa"}],"year":"2024","acknowledgement":"Special thanks go to Christof Geiss, Bernard Leclerc and Jan Schröer for explaining their work but also for sharing some unpublished results with us. We also thank the referee for many useful suggestions. We would like to thank Tommaso Scognamiglio for pointing out a mistake in the proof of Proposition 5.17 in an earlier version of the paper. We would like also to thank Alexander Beilinson, Bill Crawley-Boevey, Joel Kamnitzer, and Peng Shan for useful discussions.","date_updated":"2024-02-05T12:58:21Z","date_created":"2024-02-04T23:00:53Z","volume":30,"author":[{"last_name":"Hausel","first_name":"Tamás","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","full_name":"Hausel, Tamás"},{"full_name":"Letellier, Emmanuel","last_name":"Letellier","first_name":"Emmanuel"},{"first_name":"Fernando","last_name":"Rodriguez-Villegas","full_name":"Rodriguez-Villegas, Fernando"}],"scopus_import":"1","day":"27","article_processing_charge":"No","article_type":"original","publication":"Selecta Mathematica","citation":{"ama":"Hausel T, Letellier E, Rodriguez-Villegas F. Locally free representations of quivers over commutative Frobenius algebras. Selecta Mathematica. 2024;30(2). doi:10.1007/s00029-023-00914-2","apa":"Hausel, T., Letellier, E., & Rodriguez-Villegas, F. (2024). Locally free representations of quivers over commutative Frobenius algebras. Selecta Mathematica. Springer Nature. https://doi.org/10.1007/s00029-023-00914-2","ieee":"T. Hausel, E. Letellier, and F. Rodriguez-Villegas, “Locally free representations of quivers over commutative Frobenius algebras,” Selecta Mathematica, vol. 30, no. 2. Springer Nature, 2024.","ista":"Hausel T, Letellier E, Rodriguez-Villegas F. 2024. Locally free representations of quivers over commutative Frobenius algebras. Selecta Mathematica. 30(2), 20.","short":"T. Hausel, E. Letellier, F. Rodriguez-Villegas, Selecta Mathematica 30 (2024).","mla":"Hausel, Tamás, et al. “Locally Free Representations of Quivers over Commutative Frobenius Algebras.” Selecta Mathematica, vol. 30, no. 2, 20, Springer Nature, 2024, doi:10.1007/s00029-023-00914-2.","chicago":"Hausel, Tamás, Emmanuel Letellier, and Fernando Rodriguez-Villegas. “Locally Free Representations of Quivers over Commutative Frobenius Algebras.” Selecta Mathematica. Springer Nature, 2024. https://doi.org/10.1007/s00029-023-00914-2."},"date_published":"2024-01-27T00:00:00Z","type":"journal_article","abstract":[{"text":"In this paper we investigate locally free representations of a quiver Q over a commutative Frobenius algebra R by arithmetic Fourier transform. When the base field is finite we prove that the number of isomorphism classes of absolutely indecomposable locally free representations of fixed rank is independent of the orientation of Q. We also prove that the number of isomorphism classes of locally free absolutely indecomposable representations of the preprojective algebra of Q over R equals the number of isomorphism classes of locally free absolutely indecomposable representations of Q over R[t]/(t2). Using these results together with results of Geiss, Leclerc and Schröer we give, when k is algebraically closed, a classification of pairs (Q, R) such that the set of isomorphism classes of indecomposable locally free representations of Q over R is finite. Finally when the representation is free of rank 1 at each vertex of Q, we study the function that counts the number of isomorphism classes of absolutely indecomposable locally free representations of Q over the Frobenius algebra Fq[t]/(tr). We prove that they are polynomial in q and their generating function is rational and satisfies a functional equation.","lang":"eng"}],"issue":"2","title":"Locally free representations of quivers over commutative Frobenius algebras","status":"public","intvolume":" 30","_id":"14930","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None"},{"issue":"2","abstract":[{"lang":"eng","text":"The near-surface boundary layer can mediate the response of mountain glaciers to external climate, cooling the overlying air and promoting a density-driven glacier wind. The fundamental processes are conceptually well understood, though the magnitudes of cooling and presence of glacier winds are poorly quantified in space and time, increasing the forcing uncertainty for melt models. We utilize a new data set of on-glacier meteorological measurements on three neighboring glaciers in the Swiss Alps to explore their distinct response to regional climate under the extreme 2022 summer. We find that synoptic wind origins and local terrain modifications, not only glacier size, play an important role in the ability of a glacier to cool the near-surface air. Warm air intrusions from valley or synoptically-driven winds onto the glacier can occur between ∼19% and 64% of the time and contribute between 3% and 81% of the total sensible heat flux to the surface during warm afternoon hours, depending on the fetch of the glacier flowline and its susceptibility to boundary layer erosion. In the context of extreme summer warmth, indicative of future conditions, the boundary layer cooling (up to 6.5°C cooler than its surroundings) and resultant katabatic wind flow are highly heterogeneous between the study glaciers, highlighting the complex and likely non-linear response of glaciers to an uncertain future."}],"type":"journal_article","oa_version":"Published Version","file":[{"success":1,"checksum":"cad5b93caadb40c14e5faedc34f7bba7","date_updated":"2024-02-06T08:38:27Z","date_created":"2024-02-06T08:38:27Z","file_id":"14943","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":7481087,"access_level":"open_access","file_name":"2024_JGRAtmospheres_Shaw.pdf"}],"intvolume":" 129","title":"Local controls on near-surface glacier cooling under warm atmospheric conditions","ddc":["550"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14885","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"28","scopus_import":"1","date_published":"2024-01-28T00:00:00Z","article_type":"original","citation":{"chicago":"Shaw, Thomas, Pascal Buri, Michael McCarthy, Evan S. Miles, and Francesca Pellicciotti. “Local Controls on Near-Surface Glacier Cooling under Warm Atmospheric Conditions.” Journal of Geophysical Research: Atmospheres. Wiley, 2024. https://doi.org/10.1029/2023JD040214.","short":"T. Shaw, P. Buri, M. McCarthy, E.S. Miles, F. Pellicciotti, Journal of Geophysical Research: Atmospheres 129 (2024).","mla":"Shaw, Thomas, et al. “Local Controls on Near-Surface Glacier Cooling under Warm Atmospheric Conditions.” Journal of Geophysical Research: Atmospheres, vol. 129, no. 2, e2023JD040214, Wiley, 2024, doi:10.1029/2023JD040214.","ieee":"T. Shaw, P. Buri, M. McCarthy, E. S. Miles, and F. Pellicciotti, “Local controls on near-surface glacier cooling under warm atmospheric conditions,” Journal of Geophysical Research: Atmospheres, vol. 129, no. 2. Wiley, 2024.","apa":"Shaw, T., Buri, P., McCarthy, M., Miles, E. S., & Pellicciotti, F. (2024). Local controls on near-surface glacier cooling under warm atmospheric conditions. Journal of Geophysical Research: Atmospheres. Wiley. https://doi.org/10.1029/2023JD040214","ista":"Shaw T, Buri P, McCarthy M, Miles ES, Pellicciotti F. 2024. Local controls on near-surface glacier cooling under warm atmospheric conditions. Journal of Geophysical Research: Atmospheres. 129(2), e2023JD040214.","ama":"Shaw T, Buri P, McCarthy M, Miles ES, Pellicciotti F. Local controls on near-surface glacier cooling under warm atmospheric conditions. Journal of Geophysical Research: Atmospheres. 2024;129(2). doi:10.1029/2023JD040214"},"publication":"Journal of Geophysical Research: Atmospheres","file_date_updated":"2024-02-06T08:38:27Z","article_number":"e2023JD040214","volume":129,"date_created":"2024-01-28T23:01:42Z","date_updated":"2024-02-06T08:44:02Z","related_material":{"record":[{"id":"14919","relation":"research_data","status":"public"}]},"author":[{"first_name":"Thomas","last_name":"Shaw","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","orcid":"0000-0001-7640-6152","full_name":"Shaw, Thomas"},{"full_name":"Buri, Pascal","first_name":"Pascal","last_name":"Buri","id":"317987aa-9421-11ee-ac5a-b941b041abba"},{"full_name":"Mccarthy, Michael","id":"22a2674a-61ce-11ee-94b5-d18813baf16f","last_name":"Mccarthy","first_name":"Michael"},{"last_name":"Miles","first_name":"Evan S.","full_name":"Miles, Evan S."},{"orcid":"0000-0002-5554-8087","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti","first_name":"Francesca","full_name":"Pellicciotti, Francesca"}],"publisher":"Wiley","department":[{"_id":"FrPe"}],"publication_status":"published","year":"2024","acknowledgement":"This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 101026058. The authors acknowledge the invaluable field assistance of Marta Corrà, Achille Jouberton, Marin Kneib, Stefan Fugger, Celine Ducret and Alexander Groos. The authors would also like to thank Luca Carturan for advice regarding AWS setup and maintenance and Simone Fatichi for provision and support in the use of the Tethys-Chloris model. Open access funding provided by ETH-Bereich Forschungsanstalten.","publication_identifier":{"eissn":["2169-8996"],"issn":["2169-897X"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1029/2023JD040214","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"}},{"type":"journal_article","abstract":[{"text":"High elevation headwater catchments are complex hydrological systems that seasonally buffer water and release it in the form of snow and ice melt, modulating downstream runoff regimes and water availability. In High Mountain Asia (HMA), where a wide range of climates from semi-arid to monsoonal exist, the importance of the cryospheric contributions to the water budget varies with the amount and seasonal distribution of precipitation. Losses due to evapotranspiration and sublimation are to date largely unquantified components of the water budget in such catchments, although they can be comparable in magnitude to glacier melt contributions to streamflow. 
Here, we simulate the hydrology of three high elevation headwater catchments in distinct climates in HMA over 10 years using an ecohydrological model geared towards high-mountain areas including snow and glaciers, forced with reanalysis data. 
Our results show that evapotranspiration and sublimation together are most important at the semi-arid site, Kyzylsu, on the northernmost slopes of the Pamir mountain range. Here, the evaporative loss amounts to 28% of the water throughput, which we define as the total water added to, or removed from the water balance within a year. In comparison, evaporative losses are 19% at the Central Himalayan site Langtang and 13% at the wettest site, 24K, on the Southeastern Tibetan Plateau. At the three sites, respectively, sublimation removes 15%, 13% and 6% of snowfall, while evapotranspiration removes the equivalent of 76%, 28% and 19% of rainfall. In absolute terms, and across a comparable elevation range, the highest ET flux is 413 mm yr-1 at 24K, while the highest sublimation flux is 91 mm yr-1 at Kyzylsu. During warm and dry years, glacier melt was found to only partially compensate for the annual supply deficit.","lang":"eng"}],"_id":"14938","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["550"],"status":"public","title":"Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia","oa_version":"Published Version","keyword":["Public Health","Environmental and Occupational Health","General Environmental Science","Renewable Energy","Sustainability and the Environment"],"day":"02","has_accepted_license":"1","article_processing_charge":"Yes","publication":"Environmental Research Letters","citation":{"ista":"Fugger S, Shaw T, Jouberton A, Miles E, Buri P, McCarthy M, Fyffe CL, Fatichi S, Kneib M, Molnar P, Pellicciotti F. Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia. Environmental Research Letters.","apa":"Fugger, S., Shaw, T., Jouberton, A., Miles, E., Buri, P., McCarthy, M., … Pellicciotti, F. (n.d.). Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia. Environmental Research Letters. IOP Publishing. https://doi.org/10.1088/1748-9326/ad25a0","ieee":"S. Fugger et al., “Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia,” Environmental Research Letters. IOP Publishing.","ama":"Fugger S, Shaw T, Jouberton A, et al. Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia. Environmental Research Letters. doi:10.1088/1748-9326/ad25a0","chicago":"Fugger, Stefan, Thomas Shaw, Achille Jouberton, Evan Miles, Pascal Buri, Michael McCarthy, Catriona Louise Fyffe, et al. “Hydrological Regimes and Evaporative Flux Partitioning at the Climatic Ends of High Mountain Asia.” Environmental Research Letters. IOP Publishing, n.d. https://doi.org/10.1088/1748-9326/ad25a0.","mla":"Fugger, Stefan, et al. “Hydrological Regimes and Evaporative Flux Partitioning at the Climatic Ends of High Mountain Asia.” Environmental Research Letters, IOP Publishing, doi:10.1088/1748-9326/ad25a0.","short":"S. Fugger, T. Shaw, A. Jouberton, E. Miles, P. Buri, M. McCarthy, C.L. Fyffe, S. Fatichi, M. Kneib, P. Molnar, F. Pellicciotti, Environmental Research Letters (n.d.)."},"article_type":"original","date_published":"2024-02-02T00:00:00Z","year":"2024","publication_status":"accepted","publisher":"IOP Publishing","department":[{"_id":"FrPe"}],"author":[{"id":"86698d64-c4c6-11ee-af02-cdf1e6a7d31f","last_name":"Fugger","first_name":"Stefan","full_name":"Fugger, Stefan"},{"first_name":"Thomas","last_name":"Shaw","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","orcid":"0000-0001-7640-6152","full_name":"Shaw, Thomas"},{"last_name":"Jouberton","first_name":"Achille","full_name":"Jouberton, Achille"},{"last_name":"Miles","first_name":"Evan","full_name":"Miles, Evan"},{"first_name":"Pascal","last_name":"Buri","id":"317987aa-9421-11ee-ac5a-b941b041abba","full_name":"Buri, Pascal"},{"full_name":"McCarthy, Michael","id":"22a2674a-61ce-11ee-94b5-d18813baf16f","last_name":"McCarthy","first_name":"Michael"},{"first_name":"Catriona Louise","last_name":"Fyffe","id":"001b0422-8d15-11ed-bc51-cab6c037a228","full_name":"Fyffe, Catriona Louise"},{"full_name":"Fatichi, Simone","first_name":"Simone","last_name":"Fatichi"},{"full_name":"Kneib, Marin","last_name":"Kneib","first_name":"Marin"},{"full_name":"Molnar, Peter","last_name":"Molnar","first_name":"Peter"},{"first_name":"Francesca","last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","orcid":"0000-0002-5554-8087","full_name":"Pellicciotti, Francesca"}],"date_updated":"2024-02-06T08:35:39Z","date_created":"2024-02-05T09:01:11Z","month":"02","publication_identifier":{"issn":["1748-9326"]},"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":[{"url":"https://doi.org/10.1088/1748-9326/ad25a0","open_access":"1"}],"quality_controlled":"1","doi":"10.1088/1748-9326/ad25a0","language":[{"iso":"eng"}]},{"day":"03","month":"01","article_processing_charge":"No","has_accepted_license":"1","language":[{"iso":"eng"}],"conference":{"end_date":"2024-01-03","start_date":"2024-01-03","location":"Hong Kong, China","name":"CPAL: Conference on Parsimony and Learning"},"date_published":"2024-01-03T00:00:00Z","quality_controlled":"1","publication":"1st Conference on Parsimony and Learning","external_id":{"arxiv":["2304.01430"]},"citation":{"mla":"Lao, Dong, et al. “Divided Attention: Unsupervised Multi-Object Discovery with Contextually Separated Slots.” 1st Conference on Parsimony and Learning, 2024.","short":"D. Lao, Z. Hu, F. Locatello, Y. Yang, S. Soatto, in:, 1st Conference on Parsimony and Learning, 2024.","chicago":"Lao, Dong, Zhengyang Hu, Francesco Locatello, Yanchao Yang, and Stefano Soatto. “Divided Attention: Unsupervised Multi-Object Discovery with Contextually Separated Slots.” In 1st Conference on Parsimony and Learning, 2024.","ama":"Lao D, Hu Z, Locatello F, Yang Y, Soatto S. Divided attention: Unsupervised multi-object discovery with contextually separated slots. In: 1st Conference on Parsimony and Learning. ; 2024.","ista":"Lao D, Hu Z, Locatello F, Yang Y, Soatto S. 2024. Divided attention: Unsupervised multi-object discovery with contextually separated slots. 1st Conference on Parsimony and Learning. CPAL: Conference on Parsimony and Learning.","apa":"Lao, D., Hu, Z., Locatello, F., Yang, Y., & Soatto, S. (2024). Divided attention: Unsupervised multi-object discovery with contextually separated slots. In 1st Conference on Parsimony and Learning. Hong Kong, China.","ieee":"D. Lao, Z. Hu, F. Locatello, Y. Yang, and S. Soatto, “Divided attention: Unsupervised multi-object discovery with contextually separated slots,” in 1st Conference on Parsimony and Learning, Hong Kong, China, 2024."},"oa":1,"file_date_updated":"2024-02-12T08:40:36Z","abstract":[{"lang":"eng","text":"We introduce a method to segment the visual field into independently moving regions, trained with no ground truth or supervision. It consists of an adversarial conditional encoder-decoder architecture based on Slot Attention, modified to use the image as context to decode optical flow without attempting to reconstruct the image itself. In the resulting multi-modal representation, one modality (flow) feeds the encoder to produce separate latent codes (slots), whereas the other modality (image) conditions the decoder to generate the first (flow) from the slots. This design frees the representation from having to encode complex nuisance variability in the image due to, for instance, illumination and reflectance properties of the scene. Since customary autoencoding based on minimizing the reconstruction error does not preclude the entire flow from being encoded into a single slot, we modify the loss to an adversarial criterion based on Contextual Information Separation. The resulting min-max optimization fosters the separation of objects and their assignment to different attention slots, leading to Divided Attention, or DivA. DivA outperforms recent unsupervised multi-object motion segmentation methods while tripling run-time speed up to 104FPS and reducing the performance gap from supervised methods to 12% or less. DivA can handle different numbers of objects and different image sizes at training and test time, is invariant to permutation of object labels, and does not require explicit regularization."}],"type":"conference","date_created":"2023-08-22T14:19:59Z","date_updated":"2024-02-12T08:56:23Z","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":8038511,"file_name":"2024_CPAL_Lao.pdf","access_level":"open_access","date_updated":"2024-02-12T08:40:36Z","date_created":"2024-02-12T08:40:36Z","success":1,"checksum":"8fad894c34f1b3d5a14fb8ffb12f7277","file_id":"14978","relation":"main_file"}],"author":[{"first_name":"Dong","last_name":"Lao","full_name":"Lao, Dong"},{"full_name":"Hu, Zhengyang","last_name":"Hu","first_name":"Zhengyang"},{"last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco"},{"full_name":"Yang, Yanchao","last_name":"Yang","first_name":"Yanchao"},{"full_name":"Soatto, Stefano","last_name":"Soatto","first_name":"Stefano"}],"title":"Divided attention: Unsupervised multi-object discovery with contextually separated slots","ddc":["000"],"publication_status":"published","status":"public","department":[{"_id":"FrLo"}],"_id":"14213","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024"},{"quality_controlled":"1","project":[{"grant_number":"101087907","_id":"bdb2a702-d553-11ed-ba76-f12e3e5a3bc6","name":"A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational quantum mechanics"}],"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":["2306.12804"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/physrevresearch.6.013141","month":"02","publication_identifier":{"eissn":["2643-1564"]},"publication_status":"published","department":[{"_id":"OnHo"}],"publisher":"American Physical Society","acknowledgement":"We thank Pere Rosselló for his contributions to the initial modeling of the presented sensing technique. This work was supported by Institute of Science and Technology Austria, and\r\nthe European Research Council under Grant No. 101087907 (ERC CoG QuHAMP).","year":"2024","date_updated":"2024-02-12T11:49:06Z","date_created":"2024-02-12T11:42:18Z","volume":6,"author":[{"last_name":"Agafonova","first_name":"Sofya","orcid":"0000-0003-0582-2946","id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80","full_name":"Agafonova, Sofya"},{"full_name":"Mishra, Umang","first_name":"Umang","last_name":"Mishra","id":"4328fa4c-f128-11eb-9611-c107b0fe4d51"},{"orcid":"0000-0002-4947-8924","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87","last_name":"Diorico","first_name":"Fritz R","full_name":"Diorico, Fritz R"},{"first_name":"Onur","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X","full_name":"Hosten, Onur"}],"article_number":"013141","file_date_updated":"2024-02-12T11:46:50Z","article_type":"original","publication":"Physical Review Research","citation":{"mla":"Agafonova, Sofya, et al. “Zigzag Optical Cavity for Sensing and Controlling Torsional Motion.” Physical Review Research, vol. 6, no. 1, 013141, American Physical Society, 2024, doi:10.1103/physrevresearch.6.013141.","short":"S. Agafonova, U. Mishra, F.R. Diorico, O. Hosten, Physical Review Research 6 (2024).","chicago":"Agafonova, Sofya, Umang Mishra, Fritz R Diorico, and Onur Hosten. “Zigzag Optical Cavity for Sensing and Controlling Torsional Motion.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/physrevresearch.6.013141.","ama":"Agafonova S, Mishra U, Diorico FR, Hosten O. Zigzag optical cavity for sensing and controlling torsional motion. Physical Review Research. 2024;6(1). doi:10.1103/physrevresearch.6.013141","ista":"Agafonova S, Mishra U, Diorico FR, Hosten O. 2024. Zigzag optical cavity for sensing and controlling torsional motion. Physical Review Research. 6(1), 013141.","apa":"Agafonova, S., Mishra, U., Diorico, F. R., & Hosten, O. (2024). Zigzag optical cavity for sensing and controlling torsional motion. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.6.013141","ieee":"S. Agafonova, U. Mishra, F. R. Diorico, and O. Hosten, “Zigzag optical cavity for sensing and controlling torsional motion,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024."},"date_published":"2024-02-05T00:00:00Z","day":"05","has_accepted_license":"1","article_processing_charge":"Yes","ddc":["530"],"title":"Zigzag optical cavity for sensing and controlling torsional motion","status":"public","intvolume":" 6","_id":"14980","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","file_id":"14981","date_created":"2024-02-12T11:46:50Z","date_updated":"2024-02-12T11:46:50Z","checksum":"3a39ebffb24c1cc1dd0b547a726dc52d","success":1,"file_name":"2024_PhysicalRevResearch_Agafonova.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1437167,"creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Precision sensing and manipulation of milligram-scale mechanical oscillators has attracted growing interest in the fields of table-top explorations of gravity and tests of quantum mechanics at macroscopic scales. Torsional oscillators present an opportunity in this regard due to their remarked isolation from environmental noise. For torsional motion, an effective employment of optical cavities to enhance optomechanical interactions—as already established for linear oscillators—so far faced certain challenges. Here, we propose a concept for sensing and manipulating torsional motion, where exclusively the torsional rotations of a pendulum are mapped onto the path length of a single two-mirror optical cavity. The concept inherently alleviates many limitations of previous approaches. A proof-of-principle experiment is conducted with a rigidly controlled pendulum to explore the sensing aspects of the concept and to identify practical limitations in a potential state-of-the art setup. Based on this study, we anticipate development of precision torque sensors utilizing torsional pendulums that can support sensitivities below 10−19Nm/√Hz, while the motion of the pendulums are dominated by quantum radiation pressure noise at sub-microwatts of incoming laser power. These developments will provide horizons for experiments at the interface of quantum mechanics and gravity."}],"issue":"1"},{"file_date_updated":"2024-01-23T12:18:07Z","author":[{"first_name":"Volker","last_name":"Karle","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","orcid":"0000-0002-6963-0129","full_name":"Karle, Volker"},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"volume":55,"date_updated":"2024-02-15T14:29:04Z","date_created":"2024-01-22T08:19:36Z","year":"2024","publisher":"Wiley","department":[{"_id":"MiLe"}],"publication_status":"published","publication_identifier":{"issn":["0031-9252"],"eissn":["1521-3943"]},"month":"01","doi":"10.1002/piuz.202301690","language":[{"iso":"ger"}],"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","issue":"1","abstract":[{"text":"Die Quantenrotation ist ein spannendes Phänomen, das in vielen verschiedenen Systemen auftritt, von Molekülen und Atomen bis hin zu subatomaren Teilchen wie Neutronen und Protonen. Durch den Einsatz von starken Laserpulsen ist es möglich, die mathematisch anspruchsvolle Topologie der Rotation von Molekülen aufzudecken und topologisch geschützte Zustände zu erzeugen, die unerwartetes Verhalten zeigen. Diese Entdeckungen könnten Auswirkungen auf die Molekülphysik und physikalische Chemie haben und die Entwicklung neuer Technologien ermöglichen. Die Verbindung von Quantenrotation und Topologie stellt ein aufregendes, interdisziplinäres Forschungsfeld dar und bietet neue Wege zur Kontrolle und Nutzung von quantenmechanischen Phänomenen.","lang":"ger"}],"type":"journal_article","file":[{"file_name":"2024_PhysikZeit_Karle.pdf","access_level":"open_access","file_size":1155244,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"14878","date_created":"2024-01-23T12:18:07Z","date_updated":"2024-01-23T12:18:07Z","checksum":"3051dadcf9bc57da97e36b647c596ab1","success":1}],"oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"14851","intvolume":" 55","ddc":["530"],"title":"Die faszinierende Topologie rotierender Quanten","status":"public","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","keyword":["General Earth and Planetary Sciences","General Environmental Science"],"date_published":"2024-01-01T00:00:00Z","citation":{"ama":"Karle V, Lemeshko M. Die faszinierende Topologie rotierender Quanten. Physik in unserer Zeit. 2024;55(1):28-33. doi:10.1002/piuz.202301690","apa":"Karle, V., & Lemeshko, M. (2024). Die faszinierende Topologie rotierender Quanten. Physik in unserer Zeit. Wiley. https://doi.org/10.1002/piuz.202301690","ieee":"V. Karle and M. Lemeshko, “Die faszinierende Topologie rotierender Quanten,” Physik in unserer Zeit, vol. 55, no. 1. Wiley, pp. 28–33, 2024.","ista":"Karle V, Lemeshko M. 2024. Die faszinierende Topologie rotierender Quanten. Physik in unserer Zeit. 55(1), 28–33.","short":"V. Karle, M. Lemeshko, Physik in unserer Zeit 55 (2024) 28–33.","mla":"Karle, Volker, and Mikhail Lemeshko. “Die faszinierende Topologie rotierender Quanten.” Physik in unserer Zeit, vol. 55, no. 1, Wiley, 2024, pp. 28–33, doi:10.1002/piuz.202301690.","chicago":"Karle, Volker, and Mikhail Lemeshko. “Die faszinierende Topologie rotierender Quanten.” Physik in unserer Zeit. Wiley, 2024. https://doi.org/10.1002/piuz.202301690."},"publication":"Physik in unserer Zeit","page":"28-33","article_type":"original"},{"article_processing_charge":"Yes (via OA deal)","day":"05","keyword":["General Mathematics"],"date_published":"2024-02-05T00:00:00Z","article_type":"original","citation":{"ama":"Shen S. Tamely ramified geometric Langlands correspondence in positive characteristic. International Mathematics Research Notices. 2024. doi:10.1093/imrn/rnae005","apa":"Shen, S. (2024). Tamely ramified geometric Langlands correspondence in positive characteristic. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnae005","ieee":"S. Shen, “Tamely ramified geometric Langlands correspondence in positive characteristic,” International Mathematics Research Notices. Oxford University Press, 2024.","ista":"Shen S. 2024. Tamely ramified geometric Langlands correspondence in positive characteristic. International Mathematics Research Notices.","short":"S. Shen, International Mathematics Research Notices (2024).","mla":"Shen, Shiyu. “Tamely Ramified Geometric Langlands Correspondence in Positive Characteristic.” International Mathematics Research Notices, Oxford University Press, 2024, doi:10.1093/imrn/rnae005.","chicago":"Shen, Shiyu. “Tamely Ramified Geometric Langlands Correspondence in Positive Characteristic.” International Mathematics Research Notices. Oxford University Press, 2024. https://doi.org/10.1093/imrn/rnae005."},"publication":"International Mathematics Research Notices","abstract":[{"text":"We prove a version of the tamely ramified geometric Langlands correspondence in positive characteristic for GLn(k). Let k be an algebraically closed field of characteristic p>n. Let X be a smooth projective curve over k with marked points, and fix a parabolic subgroup of GLn(k) at each marked point. We denote by Bunn,P the moduli stack of (quasi-)parabolic vector bundles on X, and by Locn,P the moduli stack of parabolic flat connections such that the residue is nilpotent with respect to the parabolic reduction at each marked point. We construct an equivalence between the bounded derived category Db(Qcoh(Loc0n,P)) of quasi-coherent sheaves on an open substack Loc0n,P⊂Locn,P, and the bounded derived category Db(D0Bunn,P-mod) of D0Bunn,P-modules, where D0Bunn,P is a localization of DBunn,P the sheaf of crystalline differential operators on Bunn,P. Thus we extend the work of Bezrukavnikov-Braverman to the tamely ramified case. We also prove a correspondence between flat connections on X with regular singularities and meromorphic Higgs bundles on the Frobenius twist X(1) of X with first order poles .","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","status":"public","title":"Tamely ramified geometric Langlands correspondence in positive characteristic","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14986","publication_identifier":{"eissn":["1687-0247"],"issn":["1073-7928"]},"month":"02","language":[{"iso":"eng"}],"doi":"10.1093/imrn/rnae005","project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1810.12491"]},"main_file_link":[{"url":"https://doi.org/10.1093/imrn/rnae005","open_access":"1"}],"ec_funded":1,"date_created":"2024-02-14T12:16:17Z","date_updated":"2024-02-19T10:22:44Z","author":[{"last_name":"Shen","first_name":"Shiyu","id":"544cccd3-9005-11ec-87bc-94aef1c5b814","full_name":"Shen, Shiyu"}],"publisher":"Oxford University Press","department":[{"_id":"TaHa"}],"publication_status":"epub_ahead","year":"2024","acknowledgement":"This work was supported by the NSF [DMS-1502125to S.S.]; and the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement [101034413 to S.S.].\r\nI would like to thank my advisor Tom Nevins for many helpful discussions on this subject and for his comments on this paper. I would like to thank Christopher Dodd, Michael Groechenig, and Tamas Hausel for helpful conversations. I would like to thank Tsao-Hsien Chen for useful comments on an earlier version of this paper."},{"abstract":[{"text":"The development, evolution, and function of the vertebrate central nervous system (CNS) can be best studied using diverse model organisms. Amphibians, with their unique phylogenetic position at the transition between aquatic and terrestrial lifestyles, are valuable for understanding the origin and evolution of the tetrapod brain and spinal cord. Their metamorphic developmental transitions and unique regenerative abilities also facilitate the discovery of mechanisms for neural circuit remodeling and replacement. The genetic toolkit for amphibians, however, remains limited, with only a few species having sequenced genomes and a small number of transgenic lines available. In mammals, recombinant adeno-associated viral vectors (AAVs) have become a powerful alternative to genome modification for visualizing and perturbing the nervous system. AAVs are DNA viruses that enable neuronal transduction in both developing and adult animals with low toxicity and spatial, temporal, and cell-type specificity. However, AAVs have never been shown to transduce amphibian cells efficiently. To bridge this gap, we established a simple, scalable, and robust strategy to screen AAV serotypes in three distantly-related amphibian species: the frogs Xenopus laevis and Pelophylax bedriagae, and the salamander Pleurodeles waltl, in both developing larval tadpoles and post-metamorphic animals. For each species, we successfully identified at least two AAV serotypes capable of infecting the CNS; however, no pan-amphibian serotype was identified, indicating rapid evolution of AAV tropism. In addition, we developed an AAV-based strategy that targets isochronic cohorts of developing neurons – a critical tool for parsing neural circuit assembly. Finally, to enable visualization and manipulation of neural circuits, we identified AAV variants for retrograde tracing of neuronal projections in adult animals. Our findings expand the toolkit for amphibians to include AAVs, establish a generalizable workflow for AAV screening in non-canonical research organisms, generate testable hypotheses for the evolution of AAV tropism, and lay the foundation for modern cross-species comparisons of vertebrate CNS development, function, and evolution. ","lang":"eng"}],"type":"preprint","oa_version":"Preprint","date_created":"2024-02-20T09:20:32Z","date_updated":"2024-02-20T09:34:25Z","author":[{"first_name":"Eliza C.B.","last_name":"Jaeger","full_name":"Jaeger, Eliza C.B."},{"full_name":"Vijatovic, David","id":"cf391e77-ec3c-11ea-a124-d69323410b58","last_name":"Vijatovic","first_name":"David"},{"last_name":"Deryckere","first_name":"Astrid","full_name":"Deryckere, Astrid"},{"last_name":"Zorin","first_name":"Nikol","full_name":"Zorin, Nikol"},{"last_name":"Nguyen","first_name":"Akemi L.","full_name":"Nguyen, Akemi L."},{"full_name":"Ivanian, Georgiy","last_name":"Ivanian","first_name":"Georgiy","id":"eaf2b366-cfd1-11ee-bbdf-c8790f800a05"},{"full_name":"Woych, Jamie","last_name":"Woych","first_name":"Jamie"},{"full_name":"Arnold, Rebecca C","id":"d6cce458-14c9-11ed-a755-c1c8fc6fde6f","first_name":"Rebecca C","last_name":"Arnold"},{"first_name":"Alonso","last_name":"Ortega Gurrola","full_name":"Ortega Gurrola, Alonso"},{"first_name":"Arik","last_name":"Shvartsman","full_name":"Shvartsman, Arik"},{"id":"a9492887-8972-11ed-ae7b-bfae10998254","last_name":"Barbieri","first_name":"Francesca","full_name":"Barbieri, Francesca"},{"first_name":"Florina-Alexandra","last_name":"Toma","id":"85dd99f2-15b2-11ec-abd3-d1ae4d57f3b5","full_name":"Toma, Florina-Alexandra"},{"last_name":"Gorbsky","first_name":"Gary J.","full_name":"Gorbsky, Gary J."},{"last_name":"Horb","first_name":"Marko E.","full_name":"Horb, Marko E."},{"full_name":"Cline, Hollis T.","first_name":"Hollis T.","last_name":"Cline"},{"full_name":"Shay, Timothy F.","first_name":"Timothy F.","last_name":"Shay"},{"full_name":"Kelley, Darcy B.","last_name":"Kelley","first_name":"Darcy B."},{"first_name":"Ayako","last_name":"Yamaguchi","full_name":"Yamaguchi, Ayako"},{"full_name":"Shein-Idelson, Mark","last_name":"Shein-Idelson","first_name":"Mark"},{"first_name":"Maria Antonietta","last_name":"Tosches","full_name":"Tosches, Maria Antonietta"},{"id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","orcid":"0000-0001-9242-5601","first_name":"Lora Beatrice Jaeger","last_name":"Sweeney","full_name":"Sweeney, Lora Beatrice Jaeger"}],"department":[{"_id":"LoSw"},{"_id":"MaDe"},{"_id":"GaNo"}],"title":"Adeno-associated viral tools to trace neural development and connectivity across amphibians","publication_status":"submitted","status":"public","_id":"15016","year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We would like to extend our thanks to members of the Sweeney, Tosches, Shein-Idelson,\r\nYamaguchi, Kelley, and Cline Labs for their contributions to this project, discussion and support.\r\nWe additionally thank the Beckman Institute Clover Center and Viviana Gradinaru (Caltech),\r\nKimberly Ritola (UNC NeuroTools), Flavia Gama Gomez Leite (ISTA Viral Core), and Hüseyin\r\nCihan Önal (Shigemoto Group, ISTA) for their consultation and assistance regarding AAVs, as\r\nwell as Andras Simon and Alberto Joven for feedback and discussions on AAVs in Pleurodeles.\r\nTo do these experiments, we have also benefited from the tremendous support of our animal care and imaging facilities at our respective institutions, as well as the amphibian stock centers\r\n(National Xenopus Resource Center, European Xenopus Resource Center, Xenopus Express)\r\nand our funding sources: U.S. National Science Foundation (NSF) Grant Number IOS 2110086\r\n(D.B.K., L.B.S., M.A.T., A.Y., and H.T.C.); United States-Israel Binational Science Foundation\r\n(BSF) Grant Number 2020702 (M.S.-I.); NSF Award Number 1645105 (G.J.G., M.E.H.); FTI\r\nStrategy Lower Austria Dissertation Grant Number FTI21-D-046 (D.V.); Horizon Europe ERC\r\nStarting Grant Number 101041551 (L.B.S.); NIH grant number R35GM146973 (M.A.T.); Rita Allen\r\nFoundation award number GA_032522_FE (M.A.T.); European Molecular Biology Organization\r\nLong-Term Fellowship ALTF 874-2021 (A.D.); National Science Foundation Graduate Research\r\nFellowship DGE 2036197 (E.C.J.B.); NIH grant number P40OD010997 (M.E.H).","article_processing_charge":"No","day":"16","month":"02","language":[{"iso":"eng"}],"doi":"10.1101/2024.02.15.580289","date_published":"2024-02-16T00:00:00Z","project":[{"name":"Entwicklung und Funktion der V1 Interneuronen vom Schwimmen zum Laufen während der Metamorphose von Xenopus","grant_number":"FTI21-D-046","_id":"bd73af52-d553-11ed-ba76-912049f0ac7a"},{"name":"Development and Evolution of Tetrapod Motor Circuits","_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae","grant_number":"101041551"}],"citation":{"apa":"Jaeger, E. C. B., Vijatovic, D., Deryckere, A., Zorin, N., Nguyen, A. L., Ivanian, G., … Sweeney, L. B. (n.d.). Adeno-associated viral tools to trace neural development and connectivity across amphibians. bioRxiv. https://doi.org/10.1101/2024.02.15.580289","ieee":"E. C. B. Jaeger et al., “Adeno-associated viral tools to trace neural development and connectivity across amphibians,” bioRxiv. .","ista":"Jaeger ECB, Vijatovic D, Deryckere A, Zorin N, Nguyen AL, Ivanian G, Woych J, Arnold RC, Ortega Gurrola A, Shvartsman A, Barbieri F, Toma F-A, Gorbsky GJ, Horb ME, Cline HT, Shay TF, Kelley DB, Yamaguchi A, Shein-Idelson M, Tosches MA, Sweeney LB. Adeno-associated viral tools to trace neural development and connectivity across amphibians. bioRxiv, 10.1101/2024.02.15.580289.","ama":"Jaeger ECB, Vijatovic D, Deryckere A, et al. Adeno-associated viral tools to trace neural development and connectivity across amphibians. bioRxiv. doi:10.1101/2024.02.15.580289","chicago":"Jaeger, Eliza C.B., David Vijatovic, Astrid Deryckere, Nikol Zorin, Akemi L. Nguyen, Georgiy Ivanian, Jamie Woych, et al. “Adeno-Associated Viral Tools to Trace Neural Development and Connectivity across Amphibians.” BioRxiv, n.d. https://doi.org/10.1101/2024.02.15.580289.","short":"E.C.B. Jaeger, D. Vijatovic, A. Deryckere, N. Zorin, A.L. Nguyen, G. Ivanian, J. Woych, R.C. Arnold, A. Ortega Gurrola, A. Shvartsman, F. Barbieri, F.-A. Toma, G.J. Gorbsky, M.E. Horb, H.T. Cline, T.F. Shay, D.B. Kelley, A. Yamaguchi, M. Shein-Idelson, M.A. Tosches, L.B. Sweeney, BioRxiv (n.d.).","mla":"Jaeger, Eliza C. B., et al. “Adeno-Associated Viral Tools to Trace Neural Development and Connectivity across Amphibians.” BioRxiv, doi:10.1101/2024.02.15.580289."},"main_file_link":[{"url":"https://doi.org/10.1101/2024.02.15.580289","open_access":"1"}],"oa":1,"publication":"bioRxiv"},{"date_published":"2024-01-01T00:00:00Z","page":"339-346","publication":"31st International Symposium on Graph Drawing and Network Visualization","citation":{"short":"J. Pach, M. Saghafian, P. Schnider, in:, 31st International Symposium on Graph Drawing and Network Visualization, Springer Nature, 2024, pp. 339–346.","mla":"Pach, János, et al. “Decomposition of Geometric Graphs into Star-Forests.” 31st International Symposium on Graph Drawing and Network Visualization, vol. 14465, Springer Nature, 2024, pp. 339–46, doi:10.1007/978-3-031-49272-3_23.","chicago":"Pach, János, Morteza Saghafian, and Patrick Schnider. “Decomposition of Geometric Graphs into Star-Forests.” In 31st International Symposium on Graph Drawing and Network Visualization, 14465:339–46. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-49272-3_23.","ama":"Pach J, Saghafian M, Schnider P. Decomposition of geometric graphs into star-forests. In: 31st International Symposium on Graph Drawing and Network Visualization. Vol 14465. Springer Nature; 2024:339-346. doi:10.1007/978-3-031-49272-3_23","ieee":"J. Pach, M. Saghafian, and P. Schnider, “Decomposition of geometric graphs into star-forests,” in 31st International Symposium on Graph Drawing and Network Visualization, Isola delle Femmine, Palermo, Italy, 2024, vol. 14465, pp. 339–346.","apa":"Pach, J., Saghafian, M., & Schnider, P. (2024). Decomposition of geometric graphs into star-forests. In 31st International Symposium on Graph Drawing and Network Visualization (Vol. 14465, pp. 339–346). Isola delle Femmine, Palermo, Italy: Springer Nature. https://doi.org/10.1007/978-3-031-49272-3_23","ista":"Pach J, Saghafian M, Schnider P. 2024. Decomposition of geometric graphs into star-forests. 31st International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LNCS, vol. 14465, 339–346."},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","title":"Decomposition of geometric graphs into star-forests","status":"public","intvolume":" 14465","_id":"15012","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We solve a problem of Dujmović and Wood (2007) by showing that a complete convex geometric graph on n vertices cannot be decomposed into fewer than n-1 star-forests, each consisting of noncrossing edges. This bound is clearly tight. We also discuss similar questions for abstract graphs.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"conference":{"name":"GD: Graph Drawing and Network Visualization","location":"Isola delle Femmine, Palermo, Italy","start_date":"2023-09-20","end_date":"2023-09-22"},"doi":"10.1007/978-3-031-49272-3_23","quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2306.13201","open_access":"1"}],"external_id":{"arxiv":["2306.13201"]},"month":"01","publication_identifier":{"issn":["03029743"],"isbn":["9783031492716"],"eissn":["16113349"]},"date_created":"2024-02-18T23:01:03Z","date_updated":"2024-02-20T09:13:07Z","volume":14465,"author":[{"last_name":"Pach","first_name":"János","id":"E62E3130-B088-11EA-B919-BF823C25FEA4","full_name":"Pach, János"},{"full_name":"Saghafian, Morteza","first_name":"Morteza","last_name":"Saghafian","id":"f86f7148-b140-11ec-9577-95435b8df824"},{"last_name":"Schnider","first_name":"Patrick","full_name":"Schnider, Patrick"}],"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","acknowledgement":"János Pach’s Research partially supported by European Research Council (ERC), grant “GeoScape” No. 882971 and by the Hungarian Science Foundation (NKFIH), grant K-131529. Work by Morteza Saghafian is partially supported by the European Research Council (ERC), grant No. 788183, and by the Wittgenstein Prize, Austrian Science Fund (FWF), grant No. Z 342-N31.","year":"2024","ec_funded":1},{"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"18","citation":{"apa":"Hirvonen, J., Schmid, L., Chatterjee, K., & Schmid, S. (2024). On the convergence time in graphical games: A locality-sensitive approach. In 27th International Conference on Principles of Distributed Systems (Vol. 286). Tokyo, Japan: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.OPODIS.2023.11","ieee":"J. Hirvonen, L. Schmid, K. Chatterjee, and S. Schmid, “On the convergence time in graphical games: A locality-sensitive approach,” in 27th International Conference on Principles of Distributed Systems, Tokyo, Japan, 2024, vol. 286.","ista":"Hirvonen J, Schmid L, Chatterjee K, Schmid S. 2024. On the convergence time in graphical games: A locality-sensitive approach. 27th International Conference on Principles of Distributed Systems. OPODIS: Conference on Principles of Distributed Systems, LIPIcs, vol. 286, 11.","ama":"Hirvonen J, Schmid L, Chatterjee K, Schmid S. On the convergence time in graphical games: A locality-sensitive approach. In: 27th International Conference on Principles of Distributed Systems. Vol 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.OPODIS.2023.11","chicago":"Hirvonen, Juho, Laura Schmid, Krishnendu Chatterjee, and Stefan Schmid. “On the Convergence Time in Graphical Games: A Locality-Sensitive Approach.” In 27th International Conference on Principles of Distributed Systems, Vol. 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.OPODIS.2023.11.","short":"J. Hirvonen, L. Schmid, K. Chatterjee, S. Schmid, in:, 27th International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","mla":"Hirvonen, Juho, et al. “On the Convergence Time in Graphical Games: A Locality-Sensitive Approach.” 27th International Conference on Principles of Distributed Systems, vol. 286, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.OPODIS.2023.11."},"publication":"27th International Conference on Principles of Distributed Systems","date_published":"2024-01-18T00:00:00Z","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"Graphical games are a useful framework for modeling the interactions of (selfish) agents who are connected via an underlying topology and whose behaviors influence each other. They have wide applications ranging from computer science to economics and biology. Yet, even though an agent’s payoff only depends on the actions of their direct neighbors in graphical games, computing the Nash equilibria and making statements about the convergence time of \"natural\" local dynamics in particular can be highly challenging. In this work, we present a novel approach for classifying complexity of Nash equilibria in graphical games by establishing a connection to local graph algorithms, a subfield of distributed computing. In particular, we make the observation that the equilibria of graphical games are equivalent to locally verifiable labelings (LVL) in graphs; vertex labelings which are verifiable with constant-round local algorithms. This connection allows us to derive novel lower bounds on the convergence time to equilibrium of best-response dynamics in graphical games. Since we establish that distributed convergence can sometimes be provably slow, we also introduce and give bounds on an intuitive notion of \"time-constrained\" inefficiency of best responses. We exemplify how our results can be used in the implementation of mechanisms that ensure convergence of best responses to a Nash equilibrium. Our results thus also give insight into the convergence of strategy-proof algorithms for graphical games, which is still not well understood.","lang":"eng"}],"intvolume":" 286","ddc":["000"],"title":"On the convergence time in graphical games: A locality-sensitive approach","status":"public","_id":"15006","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","file_name":"2024_LIPICs_Hirvonen.pdf","creator":"dernst","content_type":"application/pdf","file_size":867363,"file_id":"15028","relation":"main_file","success":1,"checksum":"4fc7eea6e4ba140b904781fc7df868ec","date_created":"2024-02-26T09:04:58Z","date_updated":"2024-02-26T09:04:58Z"}],"oa_version":"Published Version","publication_identifier":{"issn":["18688969"],"isbn":["9783959773089"]},"month":"01","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"quality_controlled":"1","external_id":{"arxiv":["2102.13457"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.OPODIS.2023.11","conference":{"location":"Tokyo, Japan","start_date":"2023-12-06","end_date":"2023-12-08","name":"OPODIS: Conference on Principles of Distributed Systems"},"article_number":"11","ec_funded":1,"file_date_updated":"2024-02-26T09:04:58Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"}],"publication_status":"published","acknowledgement":"This work was partially funded by the Academy of Finland, grant 314888, the European Research Council CoG 863818 (ForM-SMArt), and the Austrian Science Fund (FWF) project I 4800-N (ADVISE). LS was supported by the Stochastic Analysis and Application Research Center (SAARC) under National Research Foundation of Korea grant NRF-2019R1A5A1028324.","year":"2024","volume":286,"date_created":"2024-02-18T23:01:01Z","date_updated":"2024-02-26T09:16:12Z","author":[{"last_name":"Hirvonen","first_name":"Juho","full_name":"Hirvonen, Juho"},{"full_name":"Schmid, Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6978-7329","first_name":"Laura","last_name":"Schmid"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Stefan","last_name":"Schmid","full_name":"Schmid, Stefan"}]},{"article_number":"e2220075121","ec_funded":1,"file_date_updated":"2024-02-26T08:20:00Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","pmid":1,"year":"2024","acknowledgement":"We acknowledge support from the Erasmus programme and the University College London Institute for the Physics of Living Systems (S.C., T.C.T.M., A.Š.), the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Engineering and Physical Sciences Research Council (D.F.), the European Research Council (T.P.J.K., S.L., D.F., and A.Š.), the Frances and Augustus Newman Foundation (T.P.J.K.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (S.C. and A.Š.).","department":[{"_id":"AnSa"}],"publisher":"Proceedings of the National Academy of Sciences","publication_status":"published","related_material":{"record":[{"status":"public","relation":"research_data","id":"15027"}]},"author":[{"id":"031eff0d-d481-11ee-8508-cd12a7a86e5b","orcid":"0000-0001-6160-9766","first_name":"Samo","last_name":"Curk","full_name":"Curk, Samo"},{"full_name":"Krausser, Johannes","last_name":"Krausser","first_name":"Johannes"},{"full_name":"Meisl, Georg","last_name":"Meisl","first_name":"Georg"},{"full_name":"Frenkel, Daan","first_name":"Daan","last_name":"Frenkel"},{"first_name":"Sara","last_name":"Linse","full_name":"Linse, Sara"},{"full_name":"Michaels, Thomas C.T.","first_name":"Thomas C.T.","last_name":"Michaels"},{"last_name":"Knowles","first_name":"Tuomas P.J.","full_name":"Knowles, Tuomas P.J."},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela"}],"volume":121,"date_updated":"2024-02-26T08:45:56Z","date_created":"2024-02-18T23:01:00Z","publication_identifier":{"eissn":["1091-6490"]},"month":"02","external_id":{"pmid":["38335256"]},"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,"project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"quality_controlled":"1","doi":"10.1073/pnas.2220075121","language":[{"iso":"eng"}],"type":"journal_article","issue":"7","abstract":[{"text":"Self-replication of amyloid fibrils via secondary nucleation is an intriguing physicochemical phenomenon in which existing fibrils catalyze the formation of their own copies. The molecular events behind this fibril surface-mediated process remain largely inaccessible to current structural and imaging techniques. Using statistical mechanics, computer modeling, and chemical kinetics, we show that the catalytic structure of the fibril surface can be inferred from the aggregation behavior in the presence and absence of a fibril-binding inhibitor. We apply our approach to the case of Alzheimer’s A\r\n amyloid fibrils formed in the presence of proSP-C Brichos inhibitors. We find that self-replication of A\r\n fibrils occurs on small catalytic sites on the fibril surface, which are far apart from each other, and each of which can be covered by a single Brichos inhibitor.","lang":"eng"}],"_id":"15001","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 121","title":"Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites","status":"public","ddc":["570"],"oa_version":"Published Version","file":[{"success":1,"checksum":"5aeb65bcc0dd829b1f9ab307c5031d4b","date_updated":"2024-02-26T08:20:00Z","date_created":"2024-02-26T08:20:00Z","file_id":"15026","relation":"main_file","creator":"dernst","file_size":7699487,"content_type":"application/pdf","access_level":"open_access","file_name":"2024_PNAS_Curk.pdf"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"13","citation":{"chicago":"Curk, Samo, Johannes Krausser, Georg Meisl, Daan Frenkel, Sara Linse, Thomas C.T. Michaels, Tuomas P.J. Knowles, and Anđela Šarić. “Self-Replication of Aβ42 Aggregates Occurs on Small and Isolated Fibril Sites.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2220075121.","mla":"Curk, Samo, et al. “Self-Replication of Aβ42 Aggregates Occurs on Small and Isolated Fibril Sites.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 7, e2220075121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2220075121.","short":"S. Curk, J. Krausser, G. Meisl, D. Frenkel, S. Linse, T.C.T. Michaels, T.P.J. Knowles, A. Šarić, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ista":"Curk S, Krausser J, Meisl G, Frenkel D, Linse S, Michaels TCT, Knowles TPJ, Šarić A. 2024. Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. Proceedings of the National Academy of Sciences of the United States of America. 121(7), e2220075121.","ieee":"S. Curk et al., “Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 7. Proceedings of the National Academy of Sciences, 2024.","apa":"Curk, S., Krausser, J., Meisl, G., Frenkel, D., Linse, S., Michaels, T. C. T., … Šarić, A. (2024). Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2220075121","ama":"Curk S, Krausser J, Meisl G, et al. Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(7). doi:10.1073/pnas.2220075121"},"publication":"Proceedings of the National Academy of Sciences of the United States of America","article_type":"original","date_published":"2024-02-13T00:00:00Z"},{"article_number":"050401","acknowledgement":"We thank A. Bargov, I. Khaymovich, and V. Tiunova for fruitful discussions and for useful comments. M. C. B. thanks S. Kühn for discussions about the phase structure of the model. A. K. F. thanks V. Gritsev and A. Garkun for insightful comments. E. V. P., E. S. T., and A. K. F. are\r\nsupported by the RSF Grant No. 20-42-05002 (studying the fractal Ansatz) and the Roadmap on Quantum Computing (Contract No. 868-1.3-15/15-2021, October 5, 2021; calculating on GS energies). A. K. F. thanks the Priority 2030 program at the NIST “MISIS” under the project No. K1-2022-027. M. C. B. was partly funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2111–390814868.","year":"2024","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","publication_status":"published","author":[{"full_name":"Petrova, Elena","id":"0ac84990-897b-11ed-a09c-f5abb56a4ede","first_name":"Elena","last_name":"Petrova"},{"full_name":"Tiunov, Egor S.","first_name":"Egor S.","last_name":"Tiunov"},{"full_name":"Bañuls, Mari Carmen","first_name":"Mari Carmen","last_name":"Bañuls"},{"full_name":"Fedorov, Aleksey K.","first_name":"Aleksey K.","last_name":"Fedorov"}],"volume":132,"date_updated":"2024-02-26T08:03:31Z","date_created":"2024-02-18T23:01:00Z","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"month":"01","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2201.10220","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2201.10220"]},"quality_controlled":"1","doi":"10.1103/PhysRevLett.132.050401","language":[{"iso":"eng"}],"type":"journal_article","issue":"5","abstract":[{"text":"The lattice Schwinger model, the discrete version of QED in \r\n1\r\n+\r\n1\r\n dimensions, is a well-studied test bench for lattice gauge theories. Here, we study the fractal properties of this model. We reveal the self-similarity of the ground state, which allows us to develop a recurrent procedure for finding the ground-state wave functions and predicting ground-state energies. We present the results of recurrently calculating ground-state wave functions using the fractal Ansatz and automized software package for fractal image processing. In certain parameter regimes, just a few terms are enough for our recurrent procedure to predict ground-state energies close to the exact ones for several hundreds of sites. Our findings pave the way to understanding the complexity of calculating many-body wave functions in terms of their fractal properties as well as finding new links between condensed matter and high-energy lattice models.","lang":"eng"}],"_id":"15002","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 132","status":"public","title":"Fractal states of the Schwinger model","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"30","citation":{"ama":"Petrova E, Tiunov ES, Bañuls MC, Fedorov AK. Fractal states of the Schwinger model. Physical Review Letters. 2024;132(5). doi:10.1103/PhysRevLett.132.050401","ieee":"E. Petrova, E. S. Tiunov, M. C. Bañuls, and A. K. Fedorov, “Fractal states of the Schwinger model,” Physical Review Letters, vol. 132, no. 5. American Physical Society, 2024.","apa":"Petrova, E., Tiunov, E. S., Bañuls, M. C., & Fedorov, A. K. (2024). Fractal states of the Schwinger model. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.132.050401","ista":"Petrova E, Tiunov ES, Bañuls MC, Fedorov AK. 2024. Fractal states of the Schwinger model. Physical Review Letters. 132(5), 050401.","short":"E. Petrova, E.S. Tiunov, M.C. Bañuls, A.K. Fedorov, Physical Review Letters 132 (2024).","mla":"Petrova, Elena, et al. “Fractal States of the Schwinger Model.” Physical Review Letters, vol. 132, no. 5, 050401, American Physical Society, 2024, doi:10.1103/PhysRevLett.132.050401.","chicago":"Petrova, Elena, Egor S. Tiunov, Mari Carmen Bañuls, and Aleksey K. Fedorov. “Fractal States of the Schwinger Model.” Physical Review Letters. American Physical Society, 2024. https://doi.org/10.1103/PhysRevLett.132.050401."},"publication":"Physical Review Letters","article_type":"original","date_published":"2024-01-30T00:00:00Z"},{"ec_funded":1,"department":[{"_id":"JuFi"}],"publisher":"Springer Nature","publication_status":"epub_ahead","year":"2024","acknowledgement":"The first author has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819) . The second author is supported by the VICI subsidy VI.C.212.027 of the Netherlands Organisation for Scientific Research (NWO).","date_updated":"2024-02-26T09:39:07Z","date_created":"2023-02-02T10:45:15Z","author":[{"full_name":"Agresti, Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","orcid":"0000-0002-9573-2962","first_name":"Antonio","last_name":"Agresti"},{"last_name":"Veraar","first_name":"Mark","full_name":"Veraar, Mark"}],"publication_identifier":{"issn":["0178-8051"],"eissn":["1432-2064"]},"month":"02","project":[{"grant_number":"948819","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","name":"Bridging Scales in Random Materials","call_identifier":"H2020"}],"quality_controlled":"1","external_id":{"arxiv":["2206.00230"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1007/s00440-023-01249-x","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1007/s00440-023-01249-x","type":"journal_article","abstract":[{"text":"In this paper we introduce the critical variational setting for parabolic stochastic evolution equations of quasi- or semi-linear type. Our results improve many of the abstract results in the classical variational setting. In particular, we are able to replace the usual weak or local monotonicity condition by a more flexible local Lipschitz condition. Moreover, the usual growth conditions on the multiplicative noise are weakened considerably. Our new setting provides general conditions under which local and global existence and uniqueness hold. Moreover, we prove continuous dependence on the initial data. We show that many classical SPDEs, which could not be covered by the classical variational setting, do fit in the critical variational setting. In particular, this is the case for the Cahn-Hilliard equations, tamed Navier-Stokes equations, and Allen-Cahn equation.","lang":"eng"}],"status":"public","title":"The critical variational setting for stochastic evolution equations","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12485","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"02","article_type":"original","citation":{"ista":"Agresti A, Veraar M. 2024. The critical variational setting for stochastic evolution equations. Probability Theory and Related Fields.","ieee":"A. Agresti and M. Veraar, “The critical variational setting for stochastic evolution equations,” Probability Theory and Related Fields. Springer Nature, 2024.","apa":"Agresti, A., & Veraar, M. (2024). The critical variational setting for stochastic evolution equations. Probability Theory and Related Fields. Springer Nature. https://doi.org/10.1007/s00440-023-01249-x","ama":"Agresti A, Veraar M. The critical variational setting for stochastic evolution equations. Probability Theory and Related Fields. 2024. doi:10.1007/s00440-023-01249-x","chicago":"Agresti, Antonio, and Mark Veraar. “The Critical Variational Setting for Stochastic Evolution Equations.” Probability Theory and Related Fields. Springer Nature, 2024. https://doi.org/10.1007/s00440-023-01249-x.","mla":"Agresti, Antonio, and Mark Veraar. “The Critical Variational Setting for Stochastic Evolution Equations.” Probability Theory and Related Fields, Springer Nature, 2024, doi:10.1007/s00440-023-01249-x.","short":"A. Agresti, M. Veraar, Probability Theory and Related Fields (2024)."},"publication":"Probability Theory and Related Fields","date_published":"2024-02-02T00:00:00Z"},{"quality_controlled":"1","project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564","call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures"},{"_id":"34def286-11ca-11ed-8bc3-da5948e1613c","grant_number":"Z00422","name":"Wittgenstein Award - Monika Henzinger"},{"grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","name":"Static and Dynamic Hierarchical Graph Decompositions"},{"grant_number":"P33775 ","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer"}],"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":["2303.02491"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2024-02-02","location":"Berkeley, CA, United States","start_date":"2024-01-30","name":"ITCS: Innovations in Theoretical Computer Science Conference"},"doi":"10.4230/LIPIcs.ITCS.2024.55","month":"01","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773096"]},"publication_status":"published","department":[{"_id":"MoHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","acknowledgement":"Monika Henzinger and A. R. Sricharan: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation\r\nprogramme (Grant agreement No. 101019564) and the Austrian Science Fund (FWF) project Z\r\n422-N, project I 5982-N, and project P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nHarald Räcke: Research supported by German Research Foundation (DFG), grant 470029389\r\n(FlexNets), 2021-2024.\r\nSushant Sachdeva: SS’s work is supported by an Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant RGPIN-2018-06398 and a Sloan Research Fellowship.","year":"2024","date_updated":"2024-02-26T10:12:19Z","date_created":"2024-02-18T23:01:02Z","volume":287,"author":[{"last_name":"Goranci","first_name":"Gramoz","full_name":"Goranci, Gramoz"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H"},{"first_name":"Harald","last_name":"Räcke","full_name":"Räcke, Harald"},{"first_name":"Sushant","last_name":"Sachdeva","full_name":"Sachdeva, Sushant"},{"first_name":"A. R.","last_name":"Sricharan","full_name":"Sricharan, A. R."}],"article_number":"55","file_date_updated":"2024-02-26T10:10:48Z","ec_funded":1,"publication":"15th Innovations in Theoretical Computer Science Conference","citation":{"chicago":"Goranci, Gramoz, Monika H Henzinger, Harald Räcke, Sushant Sachdeva, and A. R. Sricharan. “Electrical Flows for Polylogarithmic Competitive Oblivious Routing.” In 15th Innovations in Theoretical Computer Science Conference, Vol. 287. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.ITCS.2024.55.","mla":"Goranci, Gramoz, et al. “Electrical Flows for Polylogarithmic Competitive Oblivious Routing.” 15th Innovations in Theoretical Computer Science Conference, vol. 287, 55, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.ITCS.2024.55.","short":"G. Goranci, M.H. Henzinger, H. Räcke, S. Sachdeva, A.R. Sricharan, in:, 15th Innovations in Theoretical Computer Science Conference, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","ista":"Goranci G, Henzinger MH, Räcke H, Sachdeva S, Sricharan AR. 2024. Electrical flows for polylogarithmic competitive oblivious routing. 15th Innovations in Theoretical Computer Science Conference. ITCS: Innovations in Theoretical Computer Science Conference, LIPIcs, vol. 287, 55.","apa":"Goranci, G., Henzinger, M. H., Räcke, H., Sachdeva, S., & Sricharan, A. R. (2024). Electrical flows for polylogarithmic competitive oblivious routing. In 15th Innovations in Theoretical Computer Science Conference (Vol. 287). Berkeley, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITCS.2024.55","ieee":"G. Goranci, M. H. Henzinger, H. Räcke, S. Sachdeva, and A. R. Sricharan, “Electrical flows for polylogarithmic competitive oblivious routing,” in 15th Innovations in Theoretical Computer Science Conference, Berkeley, CA, United States, 2024, vol. 287.","ama":"Goranci G, Henzinger MH, Räcke H, Sachdeva S, Sricharan AR. Electrical flows for polylogarithmic competitive oblivious routing. In: 15th Innovations in Theoretical Computer Science Conference. Vol 287. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.ITCS.2024.55"},"date_published":"2024-01-24T00:00:00Z","scopus_import":"1","day":"24","has_accepted_license":"1","article_processing_charge":"No","status":"public","ddc":["000"],"title":"Electrical flows for polylogarithmic competitive oblivious routing","intvolume":" 287","_id":"15008","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2024_LIPICs_Goranci.pdf","content_type":"application/pdf","file_size":1054754,"creator":"dernst","relation":"main_file","file_id":"15030","checksum":"b89716aae6a5599f187897e39de1e53a","success":1,"date_created":"2024-02-26T10:10:48Z","date_updated":"2024-02-26T10:10:48Z"}],"alternative_title":["LIPIcs"],"type":"conference","abstract":[{"lang":"eng","text":"Oblivious routing is a well-studied paradigm that uses static precomputed routing tables for selecting routing paths within a network. Existing oblivious routing schemes with polylogarithmic competitive ratio for general networks are tree-based, in the sense that routing is performed according to a convex combination of trees. However, this restriction to trees leads to a construction that has time quadratic in the size of the network and does not parallelize well. \r\nIn this paper we study oblivious routing schemes based on electrical routing. In particular, we show that general networks with n vertices and m edges admit a routing scheme that has competitive ratio O(log² n) and consists of a convex combination of only O(√m) electrical routings. This immediately leads to an improved construction algorithm with time Õ(m^{3/2}) that can also be implemented in parallel with Õ(√m) depth."}]},{"alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"Traditional blockchains grant the miner of a block full control not only over which transactions but also their order. This constitutes a major flaw discovered with the introduction of decentralized finance and allows miners to perform MEV attacks. In this paper, we address the issue of sandwich attacks by providing a construction that takes as input a blockchain protocol and outputs a new blockchain protocol with the same security but in which sandwich attacks are not profitable. Furthermore, our protocol is fully decentralized with no trusted third parties or heavy cryptography primitives and carries a linear increase in latency and minimum computation overhead.","lang":"eng"}],"ddc":["000"],"status":"public","title":"Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks","intvolume":" 286","_id":"15007","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"checksum":"2993e810a45e8c8056106834b07aea92","success":1,"date_created":"2024-02-26T10:16:57Z","date_updated":"2024-02-26T10:16:57Z","relation":"main_file","file_id":"15031","content_type":"application/pdf","file_size":1505994,"creator":"dernst","access_level":"open_access","file_name":"2024_LIPICs_Alpos.pdf"}],"scopus_import":"1","day":"18","article_processing_charge":"No","has_accepted_license":"1","publication":"27th International Conference on Principles of Distributed Systems","citation":{"ama":"Alpos O, Amores-Sesar I, Cachin C, Yeo MX. Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks. In: 27th International Conference on Principles of Distributed Systems. Vol 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.OPODIS.2023.12","ista":"Alpos O, Amores-Sesar I, Cachin C, Yeo MX. 2024. Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks. 27th International Conference on Principles of Distributed Systems. OPODIS: Conference on Principles of Distributed Systems, LIPIcs, vol. 286, 12.","apa":"Alpos, O., Amores-Sesar, I., Cachin, C., & Yeo, M. X. (2024). Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks. In 27th International Conference on Principles of Distributed Systems (Vol. 286). Tokyo, Japan: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.OPODIS.2023.12","ieee":"O. Alpos, I. Amores-Sesar, C. Cachin, and M. X. Yeo, “Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks,” in 27th International Conference on Principles of Distributed Systems, Tokyo, Japan, 2024, vol. 286.","mla":"Alpos, Orestis, et al. “Eating Sandwiches: Modular and Lightweight Elimination of Transaction Reordering Attacks.” 27th International Conference on Principles of Distributed Systems, vol. 286, 12, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.OPODIS.2023.12.","short":"O. Alpos, I. Amores-Sesar, C. Cachin, M.X. Yeo, in:, 27th International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","chicago":"Alpos, Orestis, Ignacio Amores-Sesar, Christian Cachin, and Michelle X Yeo. “Eating Sandwiches: Modular and Lightweight Elimination of Transaction Reordering Attacks.” In 27th International Conference on Principles of Distributed Systems, Vol. 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.OPODIS.2023.12."},"date_published":"2024-01-18T00:00:00Z","article_number":"12","file_date_updated":"2024-02-26T10:16:57Z","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrPi"}],"acknowledgement":"We would like to thank Krzysztof Pietrzak and Jovana Mićić for useful discussions. This work has been funded by the Swiss National Science Foundation (SNSF) under grant agreement Nr. 200021_188443 (Advanced Consensus Protocols).\r\n","year":"2024","date_updated":"2024-02-26T10:18:18Z","date_created":"2024-02-18T23:01:02Z","volume":286,"author":[{"full_name":"Alpos, Orestis","last_name":"Alpos","first_name":"Orestis"},{"first_name":"Ignacio","last_name":"Amores-Sesar","full_name":"Amores-Sesar, Ignacio"},{"first_name":"Christian","last_name":"Cachin","full_name":"Cachin, Christian"},{"full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","last_name":"Yeo","first_name":"Michelle X"}],"month":"01","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773089"]},"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,"external_id":{"arxiv":["2307.02954"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2023-12-08","location":"Tokyo, Japan","start_date":"2023-12-06","name":"OPODIS: Conference on Principles of Distributed Systems"},"doi":"10.4230/LIPIcs.OPODIS.2023.12"},{"oa_version":"Preprint","title":"Experimental evaluation of fully dynamic k-means via coresets","status":"public","_id":"14769","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"For a set of points in Rd, the Euclidean k-means problems consists of finding k centers such that the sum of distances squared from each data point to its closest center is minimized. Coresets are one the main tools developed recently to solve this problem in a big data context. They allow to compress the initial dataset while preserving its structure: running any algorithm on the coreset provides a guarantee almost equivalent to running it on the full data. In this work, we study coresets in a fully-dynamic setting: points are added and deleted with the goal to efficiently maintain a coreset with which a k-means solution can be computed. Based on an algorithm from Henzinger and Kale [ESA'20], we present an efficient and practical implementation of a fully dynamic coreset algorithm, that improves the running time by up to a factor of 20 compared to our non-optimized implementation of the algorithm by Henzinger and Kale, without sacrificing more than 7% on the quality of the k-means solution."}],"type":"conference","date_published":"2024-01-04T00:00:00Z","page":"220-233","publication":"2024 Proceedings of the Symposium on Algorithm Engineering and Experiments","citation":{"mla":"Henzinger, Monika H., et al. “Experimental Evaluation of Fully Dynamic K-Means via Coresets.” 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, Society for Industrial & Applied Mathematics, 2024, pp. 220–33, doi:10.1137/1.9781611977929.17.","short":"M.H. Henzinger, D. Saulpic, L. Sidl, in:, 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, Society for Industrial & Applied Mathematics, 2024, pp. 220–233.","chicago":"Henzinger, Monika H, David Saulpic, and Leonhard Sidl. “Experimental Evaluation of Fully Dynamic K-Means via Coresets.” In 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, 220–33. Society for Industrial & Applied Mathematics, 2024. https://doi.org/10.1137/1.9781611977929.17.","ama":"Henzinger MH, Saulpic D, Sidl L. Experimental evaluation of fully dynamic k-means via coresets. In: 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments. Society for Industrial & Applied Mathematics; 2024:220-233. doi:10.1137/1.9781611977929.17","ista":"Henzinger MH, Saulpic D, Sidl L. 2024. Experimental evaluation of fully dynamic k-means via coresets. 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments. ALENEX: Workshop on Algorithm Engineering and Experiments, 220–233.","apa":"Henzinger, M. H., Saulpic, D., & Sidl, L. (2024). Experimental evaluation of fully dynamic k-means via coresets. In 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments (pp. 220–233). Alexandria, VA, United States: Society for Industrial & Applied Mathematics. https://doi.org/10.1137/1.9781611977929.17","ieee":"M. H. Henzinger, D. Saulpic, and L. Sidl, “Experimental evaluation of fully dynamic k-means via coresets,” in 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, Alexandria, VA, United States, 2024, pp. 220–233."},"day":"04","article_processing_charge":"No","scopus_import":"1","date_created":"2024-01-09T16:22:47Z","date_updated":"2024-02-26T09:51:31Z","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":"Saulpic","first_name":"David","id":"f8e48cf0-b0ff-11ed-b0e9-b4c35598f964","full_name":"Saulpic, David"},{"full_name":"Sidl, Leonhard","id":"8b563fd0-b441-11ee-9101-a3891c61efa6","first_name":"Leonhard","last_name":"Sidl"}],"publication_status":"published","department":[{"_id":"MoHe"}],"publisher":"Society for Industrial & Applied Mathematics","acknowledgement":"This project has received funding from the Euro-pean Research Council (ERC) under the EuropeanUnion’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564 “The De-sign of Modern Fully Dynamic Data Structures (Mo-DynStruct)” and the Austrian Science Fund (FWF)project Z 422-N, project “Static and Dynamic Hierar-chical Graph Decompositions”, I 5982-N, and project“Fast Algorithms for a Reactive Network Layer (Re-actNet)”, P 33775-N, with additional funding from thenetidee SCIENCE Stiftung, 2020–2024.D. Sauplic has received funding from the Euro-pean Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreementNo 101034413.","year":"2024","ec_funded":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2024-01-08","location":"Alexandria, VA, United States","start_date":"2024-01-07","name":"ALENEX: Workshop on Algorithm Engineering and Experiments"},"doi":"10.1137/1.9781611977929.17","quality_controlled":"1","project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564","call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures"},{"grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Wittgenstein Award - Monika Henzinger"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982"},{"grant_number":"P33775 ","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer"},{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"oa":1,"external_id":{"arxiv":["2310.18034"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2310.18034"}],"month":"01","publication_identifier":{"eisbn":["9781611977929"]}},{"type":"journal_article","abstract":[{"lang":"eng","text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, is still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of A. franciscana (Kellogg 1906), from the Great Salt Lake, United States. The genome is 1 GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species."}],"issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15009","ddc":["570"],"title":"Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation","status":"public","intvolume":" 16","file":[{"access_level":"open_access","file_name":"2024_GBE_Bett.pdf","creator":"dernst","file_size":5213306,"content_type":"application/pdf","file_id":"15029","relation":"main_file","success":1,"checksum":"106a40f10443b2e7ba66749844ebbdf1","date_created":"2024-02-26T09:54:59Z","date_updated":"2024-02-26T09:54:59Z"}],"oa_version":"Published Version","scopus_import":"1","day":"20","has_accepted_license":"1","article_processing_charge":"Yes","publication":"Genome Biology and Evolution","citation":{"ama":"Bett VK, Macon A, Vicoso B, Elkrewi MN. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. 2024;16(1). doi:10.1093/gbe/evae006","apa":"Bett, V. K., Macon, A., Vicoso, B., & Elkrewi, M. N. (2024). Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evae006","ieee":"V. K. Bett, A. Macon, B. Vicoso, and M. N. Elkrewi, “Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation,” Genome Biology and Evolution, vol. 16, no. 1. Oxford University Press, 2024.","ista":"Bett VK, Macon A, Vicoso B, Elkrewi MN. 2024. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. 16(1), evae006.","short":"V.K. Bett, A. Macon, B. Vicoso, M.N. Elkrewi, Genome Biology and Evolution 16 (2024).","mla":"Bett, Vincent K., et al. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” Genome Biology and Evolution, vol. 16, no. 1, evae006, Oxford University Press, 2024, doi:10.1093/gbe/evae006.","chicago":"Bett, Vincent K, Ariana Macon, Beatriz Vicoso, and Marwan N Elkrewi. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” Genome Biology and Evolution. Oxford University Press, 2024. https://doi.org/10.1093/gbe/evae006."},"article_type":"original","date_published":"2024-01-20T00:00:00Z","article_number":"evae006","file_date_updated":"2024-02-26T09:54:59Z","year":"2024","pmid":1,"publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"BeVi"}],"author":[{"full_name":"Bett, Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","last_name":"Bett","first_name":"Vincent K"},{"full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","last_name":"Macon"},{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"},{"full_name":"Elkrewi, Marwan N","first_name":"Marwan N","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"14705"}]},"date_created":"2024-02-18T23:01:02Z","date_updated":"2024-02-26T09:59:30Z","volume":16,"month":"01","publication_identifier":{"eissn":["1759-6653"]},"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":["38245839"]},"quality_controlled":"1","doi":"10.1093/gbe/evae006","language":[{"iso":"eng"}]},{"type":"journal_article","abstract":[{"lang":"eng","text":"The impulsive limit (the “sudden approximation”) has been widely employed to describe the interaction between molecules and short, far-off-resonant laser pulses. This approximation assumes that the timescale of the laser-molecule interaction is significantly shorter than the internal rotational period of the molecule, resulting in the rotational motion being instantaneously “frozen” during the interaction. This simplified description of the laser-molecule interaction is incorporated in various theoretical models predicting rotational dynamics of molecules driven by short laser pulses. In this theoretical work, we develop an effective theory for ultrashort laser pulses by examining the full time-evolution operator and solving the time-dependent Schrödinger equation at the operator level. Our findings reveal a critical angular momentum, lcrit, at which the impulsive limit breaks down. In other words, the validity of the sudden approximation depends not only on the pulse duration but also on its intensity, since the latter determines how many angular momentum states are populated. We explore both ultrashort multicycle (Gaussian) pulses and the somewhat less studied half-cycle pulses, which produce distinct effective potentials. We discuss the limitations of the impulsive limit and propose a method that rescales the effective matrix elements, enabling an improved and more accurate description of laser-molecule interactions."}],"issue":"2","status":"public","title":"Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics","intvolume":" 109","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15004","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","publication":"Physical Review A","citation":{"ista":"Karle V, Lemeshko M. 2024. Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics. Physical Review A. 109(2), 023101.","apa":"Karle, V., & Lemeshko, M. (2024). Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.109.023101","ieee":"V. Karle and M. Lemeshko, “Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics,” Physical Review A, vol. 109, no. 2. American Physical Society, 2024.","ama":"Karle V, Lemeshko M. Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics. Physical Review A. 2024;109(2). doi:10.1103/PhysRevA.109.023101","chicago":"Karle, Volker, and Mikhail Lemeshko. “Modeling Laser Pulses as δ Kicks: Reevaluating the Impulsive Limit in Molecular Rotational Dynamics.” Physical Review A. American Physical Society, 2024. https://doi.org/10.1103/PhysRevA.109.023101.","mla":"Karle, Volker, and Mikhail Lemeshko. “Modeling Laser Pulses as δ Kicks: Reevaluating the Impulsive Limit in Molecular Rotational Dynamics.” Physical Review A, vol. 109, no. 2, 023101, American Physical Society, 2024, doi:10.1103/PhysRevA.109.023101.","short":"V. Karle, M. Lemeshko, Physical Review A 109 (2024)."},"date_published":"2024-02-01T00:00:00Z","article_number":"023101","ec_funded":1,"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"acknowledgement":"We thank Bretislav Friedrich, Marjan Mirahmadi, Artem Volosniev, and Burkhard Schmidt for insightful discussions. M.L. acknowledges support by the European Research Council (ERC) under Starting Grant No. 801770 (ANGULON).","year":"2024","date_updated":"2024-02-26T09:45:20Z","date_created":"2024-02-18T23:01:01Z","volume":109,"author":[{"full_name":"Karle, Volker","orcid":"0000-0002-6963-0129","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","last_name":"Karle","first_name":"Volker"},{"first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"}],"month":"02","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"quality_controlled":"1","project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"}],"external_id":{"arxiv":["2307.07256"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2307.07256"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.109.023101"},{"month":"01","day":"02","has_accepted_license":"1","article_processing_charge":"No","keyword":["sex chromosome evolution","genome assembly","dosage compensation"],"doi":"10.15479/AT:ISTA:14705","date_published":"2024-01-02T00:00:00Z","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"},"citation":{"apa":"Elkrewi, M. 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Elkrewi, (2024).","mla":"Elkrewi, Marwan N. Data from “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:14705."},"project":[{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"}],"file_date_updated":"2023-12-22T14:14:06Z","abstract":[{"lang":"eng","text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake, USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species."}],"type":"research_data","author":[{"full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","first_name":"Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"15009"}]},"contributor":[{"first_name":"Vincent K","contributor_type":"researcher","last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","contributor_type":"project_member","last_name":"Macon"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","contributor_type":"supervisor","first_name":"Beatriz"},{"orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","contributor_type":"researcher","last_name":"Elkrewi","first_name":"Marwan N"}],"date_updated":"2024-02-26T09:59:29Z","date_created":"2023-12-22T13:40:48Z","file":[{"file_id":"14707","relation":"main_file","date_updated":"2023-12-22T13:54:21Z","date_created":"2023-12-22T13:54:21Z","success":1,"checksum":"bdaf1392867786634ec5466d528c36ca","file_name":"readme.txt.txt","access_level":"open_access","creator":"melkrewi","file_size":847,"content_type":"text/plain"},{"date_updated":"2023-12-22T14:14:06Z","date_created":"2023-12-22T14:14:06Z","checksum":"973e1cbdab923a71709782177980829f","success":1,"relation":"main_file","file_id":"14708","content_type":"application/x-zip-compressed","file_size":343632753,"creator":"melkrewi","file_name":"data_artemia_franciscana_genome.zip","access_level":"open_access"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14705","year":"2024","title":"Data from \"Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation\"","ddc":["576"],"status":"public","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"publisher":"Institute of Science and Technology Austria"},{"article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2024-02-01T00:00:00Z","article_type":"original","citation":{"chicago":"Franco, D. G., R. Avalos, D. Hafner, Kimberly A Modic, Yu Prots, O. Stockert, A. Hoser, et al. “Frustrated Magnetism in Octahedra-Based Ce6 Ni6 P17.” Physical Review B. American Physical Society, 2024. https://doi.org/10.1103/PhysRevB.109.054405.","mla":"Franco, D. G., et al. “Frustrated Magnetism in Octahedra-Based Ce6 Ni6 P17.” Physical Review B, vol. 109, no. 5, 054405, American Physical Society, 2024, doi:10.1103/PhysRevB.109.054405.","short":"D.G. Franco, R. Avalos, D. Hafner, K.A. Modic, Y. Prots, O. Stockert, A. Hoser, P.J.W. Moll, M. Brando, A.A. Aligia, C. Geibel, Physical Review B 109 (2024).","ista":"Franco DG, Avalos R, Hafner D, Modic KA, Prots Y, Stockert O, Hoser A, Moll PJW, Brando M, Aligia AA, Geibel C. 2024. Frustrated magnetism in octahedra-based Ce6 Ni6 P17. Physical Review B. 109(5), 054405.","apa":"Franco, D. G., Avalos, R., Hafner, D., Modic, K. A., Prots, Y., Stockert, O., … Geibel, C. (2024). Frustrated magnetism in octahedra-based Ce6 Ni6 P17. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.109.054405","ieee":"D. G. Franco et al., “Frustrated magnetism in octahedra-based Ce6 Ni6 P17,” Physical Review B, vol. 109, no. 5. American Physical Society, 2024.","ama":"Franco DG, Avalos R, Hafner D, et al. Frustrated magnetism in octahedra-based Ce6 Ni6 P17. Physical Review B. 2024;109(5). doi:10.1103/PhysRevB.109.054405"},"publication":"Physical Review B","issue":"5","abstract":[{"text":"Magnetic frustration allows to access novel and intriguing properties of magnetic systems and has been explored mainly in planar triangular-like arrays of magnetic ions. In this work, we describe the phosphide Ce6Ni6P17, where the Ce+3 ions accommodate in a body-centered cubic lattice of Ce6 regular octahedra. From measurements of magnetization, specific heat, and resistivity, we determine a rich phase diagram as a function of temperature and magnetic field in which different magnetic phases are found. Besides clear evidence of magnetic frustration is obtained from entropy analysis. At zero field, a second-order antiferromagnetic transition occurs at TN1≈1 K followed by a first-order transition at TN2≈0.45 K. With magnetic field new magnetic phases appear, including a weakly first-order transition which ends in a classical critical point and a third magnetic phase. We also study the exact solution of the spin-1/2 Heisenberg model in an octahedron which allows us a qualitative understanding of the phase diagram and compare with the experimental results.","lang":"eng"}],"type":"journal_article","oa_version":"None","intvolume":" 109","status":"public","title":"Frustrated magnetism in octahedra-based Ce6 Ni6 P17","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15003","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"02","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.109.054405","quality_controlled":"1","article_number":"054405","volume":109,"date_updated":"2024-02-26T09:50:10Z","date_created":"2024-02-18T23:01:01Z","author":[{"last_name":"Franco","first_name":"D. G.","full_name":"Franco, D. G."},{"full_name":"Avalos, R.","first_name":"R.","last_name":"Avalos"},{"first_name":"D.","last_name":"Hafner","full_name":"Hafner, D."},{"full_name":"Modic, Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","orcid":"0000-0001-9760-3147","first_name":"Kimberly A","last_name":"Modic"},{"full_name":"Prots, Yu","first_name":"Yu","last_name":"Prots"},{"first_name":"O.","last_name":"Stockert","full_name":"Stockert, O."},{"last_name":"Hoser","first_name":"A.","full_name":"Hoser, A."},{"full_name":"Moll, P. J.W.","first_name":"P. J.W.","last_name":"Moll"},{"full_name":"Brando, M.","last_name":"Brando","first_name":"M."},{"last_name":"Aligia","first_name":"A. A.","full_name":"Aligia, A. A."},{"full_name":"Geibel, C.","last_name":"Geibel","first_name":"C."}],"department":[{"_id":"KiMo"}],"publisher":"American Physical Society","publication_status":"published","acknowledgement":"The authors thank Bernardo Pentke for the SEM micrographs (Departamento Fisicoquímica de Materiales CABCNEA). We are indebted to Julián Sereni for useful discussions. D. G. F. acknowledges financial support provided by Agencia I+D+i, Argentina, Grant No. PICT-2021-I-INVI00852 and Universidad Nacional de Cuyo (SIIP) Grant No. 06/C018-T1. A. A. A. acknowledges financial support provided by PICT 2018-01546 and PICT 2020A-03661 of the\r\nAgencia I+D+i. ","year":"2024"},{"month":"02","publication_identifier":{"issn":["1369-8001"]},"doi":"10.1016/j.mssp.2024.108231","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.mssp.2024.108231"}],"quality_controlled":"1","project":[{"name":"Integrated GermaNIum quanTum tEchnology","grant_number":"101069515","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452"}],"article_number":"108231","author":[{"last_name":"Shimura","first_name":"Yosuke","full_name":"Shimura, Yosuke"},{"first_name":"Clement","last_name":"Godfrin","full_name":"Godfrin, Clement"},{"full_name":"Hikavyy, Andriy","first_name":"Andriy","last_name":"Hikavyy"},{"full_name":"Li, Roy","first_name":"Roy","last_name":"Li"},{"id":"2A67C376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2862-8372","first_name":"Juan L","last_name":"Aguilera Servin","full_name":"Aguilera Servin, Juan L"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros","full_name":"Katsaros, Georgios"},{"last_name":"Favia","first_name":"Paola","full_name":"Favia, Paola"},{"first_name":"Han","last_name":"Han","full_name":"Han, Han"},{"last_name":"Wan","first_name":"Danny","full_name":"Wan, Danny"},{"full_name":"de Greve, Kristiaan","last_name":"de Greve","first_name":"Kristiaan"},{"last_name":"Loo","first_name":"Roger","full_name":"Loo, Roger"}],"date_created":"2024-02-22T14:10:40Z","date_updated":"2024-02-26T10:36:35Z","volume":174,"year":"2024","acknowledgement":"The Ge project received funding from the European Union's Horizon Europe programme under the Grant Agreement 101069515 – IGNITE. Siltronic AG is acknowledged for providing the SRB wafers. This work was supported by Imec's Industrial Affiliation Program on Quantum Computing.","publication_status":"epub_ahead","publisher":"Elsevier","department":[{"_id":"GeKa"},{"_id":"NanoFab"}],"day":"20","has_accepted_license":"1","article_processing_charge":"No","keyword":["Mechanical Engineering","Mechanics of Materials","Condensed Matter Physics","General Materials Science"],"date_published":"2024-02-20T00:00:00Z","publication":"Materials Science in Semiconductor Processing","citation":{"ama":"Shimura Y, Godfrin C, Hikavyy A, et al. Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. 2024;174(5). doi:10.1016/j.mssp.2024.108231","ieee":"Y. Shimura et al., “Compressively strained epitaxial Ge layers for quantum computing applications,” Materials Science in Semiconductor Processing, vol. 174, no. 5. Elsevier, 2024.","apa":"Shimura, Y., Godfrin, C., Hikavyy, A., Li, R., Aguilera Servin, J. L., Katsaros, G., … Loo, R. (2024). Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. Elsevier. https://doi.org/10.1016/j.mssp.2024.108231","ista":"Shimura Y, Godfrin C, Hikavyy A, Li R, Aguilera Servin JL, Katsaros G, Favia P, Han H, Wan D, de Greve K, Loo R. 2024. Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. 174(5), 108231.","short":"Y. Shimura, C. Godfrin, A. Hikavyy, R. Li, J.L. Aguilera Servin, G. Katsaros, P. Favia, H. Han, D. Wan, K. de Greve, R. Loo, Materials Science in Semiconductor Processing 174 (2024).","mla":"Shimura, Yosuke, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” Materials Science in Semiconductor Processing, vol. 174, no. 5, 108231, Elsevier, 2024, doi:10.1016/j.mssp.2024.108231.","chicago":"Shimura, Yosuke, Clement Godfrin, Andriy Hikavyy, Roy Li, Juan L Aguilera Servin, Georgios Katsaros, Paola Favia, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” Materials Science in Semiconductor Processing. Elsevier, 2024. https://doi.org/10.1016/j.mssp.2024.108231."},"article_type":"original","abstract":[{"text":"The epitaxial growth of a strained Ge layer, which is a promising candidate for the channel material of a hole spin qubit, has been demonstrated on 300 mm Si wafers using commercially available Si0.3Ge0.7 strain relaxed buffer (SRB) layers. The assessment of the layer and the interface qualities for a buried strained Ge layer embedded in Si0.3Ge0.7 layers is reported. The XRD reciprocal space mapping confirmed that the reduction of the growth temperature enables the 2-dimensional growth of the Ge layer fully strained with respect to the Si0.3Ge0.7. Nevertheless, dislocations at the top and/or bottom interface of the Ge layer were observed by means of electron channeling contrast imaging, suggesting the importance of the careful dislocation assessment. The interface abruptness does not depend on the selection of the precursor gases, but it is strongly influenced by the growth temperature which affects the coverage of the surface H-passivation. The mobility of 2.7 × 105 cm2/Vs is promising, while the low percolation density of 3 × 1010 /cm2 measured with a Hall-bar device at 7 K illustrates the high quality of the heterostructure thanks to the high Si0.3Ge0.7 SRB quality.","lang":"eng"}],"issue":"5","type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15018","ddc":["530"],"title":"Compressively strained epitaxial Ge layers for quantum computing applications","status":"public","intvolume":" 174"},{"publication_identifier":{"eissn":["2640-3498"]},"month":"01","language":[{"iso":"eng"}],"conference":{"name":"CPAL: Conference on Parsimony and Learning","end_date":"2024-01-06","start_date":"2024-01-03","location":"Hongkong, China"},"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://proceedings.mlr.press/v234/kurtic24a","open_access":"1"}],"external_id":{"arxiv":["2312.13547"]},"volume":234,"date_updated":"2024-02-26T10:30:52Z","date_created":"2024-02-18T23:01:03Z","author":[{"last_name":"Kurtic","first_name":"Eldar","id":"47beb3a5-07b5-11eb-9b87-b108ec578218","full_name":"Kurtic, Eldar"},{"first_name":"Torsten","last_name":"Hoefler","full_name":"Hoefler, Torsten"},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"publisher":"ML Research Press","department":[{"_id":"DaAl"}],"publication_status":"published","year":"2024","article_processing_charge":"No","day":"08","scopus_import":"1","date_published":"2024-01-08T00:00:00Z","page":"542-553","citation":{"apa":"Kurtic, E., Hoefler, T., & Alistarh, D.-A. (2024). How to prune your language model: Recovering accuracy on the “Sparsity May Cry” benchmark. In Proceedings of Machine Learning Research (Vol. 234, pp. 542–553). Hongkong, China: ML Research Press.","ieee":"E. Kurtic, T. Hoefler, and D.-A. Alistarh, “How to prune your language model: Recovering accuracy on the ‘Sparsity May Cry’ benchmark,” in Proceedings of Machine Learning Research, Hongkong, China, 2024, vol. 234, pp. 542–553.","ista":"Kurtic E, Hoefler T, Alistarh D-A. 2024. How to prune your language model: Recovering accuracy on the ‘Sparsity May Cry’ benchmark. Proceedings of Machine Learning Research. CPAL: Conference on Parsimony and Learning, PMLR, vol. 234, 542–553.","ama":"Kurtic E, Hoefler T, Alistarh D-A. How to prune your language model: Recovering accuracy on the “Sparsity May Cry” benchmark. In: Proceedings of Machine Learning Research. Vol 234. ML Research Press; 2024:542-553.","chicago":"Kurtic, Eldar, Torsten Hoefler, and Dan-Adrian Alistarh. “How to Prune Your Language Model: Recovering Accuracy on the ‘Sparsity May Cry’ Benchmark.” In Proceedings of Machine Learning Research, 234:542–53. ML Research Press, 2024.","short":"E. Kurtic, T. Hoefler, D.-A. Alistarh, in:, Proceedings of Machine Learning Research, ML Research Press, 2024, pp. 542–553.","mla":"Kurtic, Eldar, et al. “How to Prune Your Language Model: Recovering Accuracy on the ‘Sparsity May Cry’ Benchmark.” Proceedings of Machine Learning Research, vol. 234, ML Research Press, 2024, pp. 542–53."},"publication":"Proceedings of Machine Learning Research","abstract":[{"lang":"eng","text":"Pruning large language models (LLMs) from the BERT family has emerged as a standard compression benchmark, and several pruning methods have been proposed for this task. The recent “Sparsity May Cry” (SMC) benchmark put into question the validity of all existing methods, exhibiting a more complex setup where many known pruning methods appear to fail. We revisit the question of accurate BERT-pruning during fine-tuning on downstream datasets, and propose a set of general guidelines for successful pruning, even on the challenging SMC benchmark. First, we perform a cost-vs-benefits analysis of pruning model components, such as the embeddings and the classification head; second, we provide a simple-yet-general way of scaling training, sparsification and learning rate schedules relative to the desired target sparsity; finally, we investigate the importance of proper parametrization for Knowledge Distillation in the context of LLMs. Our simple insights lead to state-of-the-art results, both on classic BERT-pruning benchmarks, as well as on the SMC benchmark, showing that even classic gradual magnitude pruning (GMP) can yield competitive results, with the right approach."}],"alternative_title":["PMLR"],"type":"conference","oa_version":"Preprint","intvolume":" 234","title":"How to prune your language model: Recovering accuracy on the \"Sparsity May Cry\" benchmark","status":"public","_id":"15011","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"month":"02","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"language":[{"iso":"eng"}],"doi":"10.1063/5.0188215","quality_controlled":"1","project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"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":["2311.11784"],"pmid":["38349632"]},"oa":1,"file_date_updated":"2024-02-27T08:12:52Z","ec_funded":1,"article_number":"064503","date_created":"2024-02-25T23:00:55Z","date_updated":"2024-02-27T08:16:06Z","volume":160,"author":[{"full_name":"Robin, Paul","last_name":"Robin","first_name":"Paul","orcid":"0000-0002-5728-9189","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d"}],"publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"AIP Publishing","year":"2024","acknowledgement":"The author thanks Lydéric Bocquet, Baptiste Coquinot, and Mathieu Lizée for fruitful discussions. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","pmid":1,"day":"14","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","date_published":"2024-02-14T00:00:00Z","article_type":"original","publication":"Journal of Chemical Physics","citation":{"apa":"Robin, P. (2024). Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0188215","ieee":"P. Robin, “Correlation-induced viscous dissipation in concentrated electrolytes,” Journal of Chemical Physics, vol. 160, no. 6. AIP Publishing, 2024.","ista":"Robin P. 2024. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 160(6), 064503.","ama":"Robin P. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 2024;160(6). doi:10.1063/5.0188215","chicago":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” Journal of Chemical Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0188215.","short":"P. Robin, Journal of Chemical Physics 160 (2024).","mla":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” Journal of Chemical Physics, vol. 160, no. 6, 064503, AIP Publishing, 2024, doi:10.1063/5.0188215."},"abstract":[{"lang":"eng","text":"Electrostatic correlations between ions dissolved in water are known to impact their transport properties in numerous ways, from conductivity to ion selectivity. The effects of these correlations on the solvent itself remain, however, much less clear. In particular, the addition of salt has been consistently reported to affect the solution’s viscosity, but most modeling attempts fail to reproduce experimental data even at moderate salt concentrations. Here, we use an approach based on stochastic density functional theory, which accurately captures charge fluctuations and correlations. We derive a simple analytical expression for the viscosity correction in concentrated electrolytes, by directly linking it to the liquid’s structure factor. Our prediction compares quantitatively to experimental data at all temperatures and all salt concentrations up to the saturation limit. This universal link between the microscopic structure and viscosity allows us to shed light on the nanoscale dynamics of water and ions under highly concentrated and correlated conditions."}],"issue":"6","type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2024_JourChemicalPhysics_Robin.pdf","access_level":"open_access","file_size":5452738,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"15034","date_created":"2024-02-27T08:12:52Z","date_updated":"2024-02-27T08:12:52Z","checksum":"0a5e0ae70849bce674466fc054390ec0","success":1}],"status":"public","ddc":["540"],"title":"Correlation-induced viscous dissipation in concentrated electrolytes","intvolume":" 160","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15024"},{"page":"1623-1662","article_type":"original","citation":{"mla":"Erdös, László, and Benjamin McKenna. “Extremal Statistics of Quadratic Forms of GOE/GUE Eigenvectors.” Annals of Applied Probability, vol. 34, no. 1B, Institute of Mathematical Statistics, 2024, pp. 1623–62, doi:10.1214/23-AAP2000.","short":"L. Erdös, B. McKenna, Annals of Applied Probability 34 (2024) 1623–1662.","chicago":"Erdös, László, and Benjamin McKenna. “Extremal Statistics of Quadratic Forms of GOE/GUE Eigenvectors.” Annals of Applied Probability. Institute of Mathematical Statistics, 2024. https://doi.org/10.1214/23-AAP2000.","ama":"Erdös L, McKenna B. Extremal statistics of quadratic forms of GOE/GUE eigenvectors. Annals of Applied Probability. 2024;34(1B):1623-1662. doi:10.1214/23-AAP2000","ista":"Erdös L, McKenna B. 2024. Extremal statistics of quadratic forms of GOE/GUE eigenvectors. Annals of Applied Probability. 34(1B), 1623–1662.","ieee":"L. Erdös and B. McKenna, “Extremal statistics of quadratic forms of GOE/GUE eigenvectors,” Annals of Applied Probability, vol. 34, no. 1B. Institute of Mathematical Statistics, pp. 1623–1662, 2024.","apa":"Erdös, L., & McKenna, B. (2024). Extremal statistics of quadratic forms of GOE/GUE eigenvectors. Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/23-AAP2000"},"publication":"Annals of Applied Probability","date_published":"2024-02-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 34","status":"public","title":"Extremal statistics of quadratic forms of GOE/GUE eigenvectors","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15025","oa_version":"Preprint","type":"journal_article","issue":"1B","abstract":[{"text":"We consider quadratic forms of deterministic matrices A evaluated at the random eigenvectors of a large N×N GOE or GUE matrix, or equivalently evaluated at the columns of a Haar-orthogonal or Haar-unitary random matrix. We prove that, as long as the deterministic matrix has rank much smaller than √N, the distributions of the extrema of these quadratic forms are asymptotically the same as if the eigenvectors were independent Gaussians. This reduces the problem to Gaussian computations, which we carry out in several cases to illustrate our result, finding Gumbel or Weibull limiting distributions depending on the signature of A. Our result also naturally applies to the eigenvectors of any invariant ensemble.","lang":"eng"}],"project":[{"grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020"}],"quality_controlled":"1","external_id":{"arxiv":["2208.12206"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2208.12206"}],"language":[{"iso":"eng"}],"doi":"10.1214/23-AAP2000","publication_identifier":{"issn":["1050-5164"]},"month":"02","publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"publication_status":"published","acknowledgement":"The first author was supported by the ERC Advanced Grant “RMTBeyond” No. 101020331. The second author was supported by Fulbright Austria and the Austrian Marshall Plan Foundation.","year":"2024","volume":34,"date_updated":"2024-02-27T08:29:05Z","date_created":"2024-02-25T23:00:56Z","author":[{"full_name":"Erdös, László","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"id":"b0cc634c-d549-11ee-96c8-87338c7ad808","orcid":"0000-0003-2625-495X","first_name":"Benjamin","last_name":"McKenna","full_name":"McKenna, Benjamin"}],"ec_funded":1},{"article_type":"original","citation":{"apa":"Adamowski, M., Matijevic, I., & Friml, J. (2024). Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.68993","ieee":"M. Adamowski, I. Matijevic, and J. Friml, “Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery,” eLife, vol. 13. eLife Sciences Publications, 2024.","ista":"Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.","ama":"Adamowski M, Matijevic I, Friml J. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 2024;13. doi:10.7554/elife.68993","chicago":"Adamowski, Maciek, Ivana Matijevic, and Jiří Friml. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” ELife. eLife Sciences Publications, 2024. https://doi.org/10.7554/elife.68993.","short":"M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024).","mla":"Adamowski, Maciek, et al. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” ELife, vol. 13, eLife Sciences Publications, 2024, doi:10.7554/elife.68993."},"publication":"eLife","date_published":"2024-02-21T00:00:00Z","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"has_accepted_license":"1","article_processing_charge":"Yes","day":"21","intvolume":" 13","ddc":["580"],"title":"Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15033","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF) is among the best studied trafficking regulators in plants, playing crucial and unique developmental roles in patterning and polarity. The current models place GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis (CME). The mechanistic basis of the developmental function of GN, distinct from the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains elusive. Insights from this study largely extend the current notions of GN function. We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures distinct from clathrin-coated pits, while CME and secretion proceed normally in gn knockouts. The functional GN mutant variant GNfewerroots, absent from the GA, suggests that the cell periphery is the major site of GN action responsible for its developmental function. Following inhibition by Brefeldin A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting selective molecular associations en route to the cell periphery. A study of GN-GNL1 chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN function in a partially redundant manner. Together, this study offers significant steps toward the elucidation of the mechanism underlying unique cellular and development functions of GNOM."}],"project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"}],"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"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.7554/eLife.68993"}],"language":[{"iso":"eng"}],"doi":"10.7554/elife.68993","publication_identifier":{"issn":["2050-084X"]},"month":"02","publisher":"eLife Sciences Publications","department":[{"_id":"JiFr"}],"publication_status":"epub_ahead","year":"2024","acknowledgement":"The authors would like to gratefully acknowledge Dr Xixi Zhang for cloning the GNL1/pDONR221 construct and for useful discussions.H2020 European Research\r\nCouncil Advanced Grant ETAP742985 to Jiří Friml, Austrian Science Fund I 3630-B25 to Jiří Friml","volume":13,"date_updated":"2024-02-28T12:29:43Z","date_created":"2024-02-27T07:10:11Z","author":[{"orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","first_name":"Maciek","full_name":"Adamowski, Maciek"},{"first_name":"Ivana","last_name":"Matijevic","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","full_name":"Matijevic, Ivana"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1},{"doi":"10.1016/j.cub.2024.01.017","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["38307022"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.10.26.564092"}],"quality_controlled":"1","month":"02","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"author":[{"first_name":"Eniko","last_name":"Csata","full_name":"Csata, Eniko"},{"full_name":"Perez-Escudero, Alfonso","last_name":"Perez-Escudero","first_name":"Alfonso"},{"first_name":"Emmanuel","last_name":"Laury","full_name":"Laury, Emmanuel"},{"id":"8fc5c6f6-5903-11ec-abad-c83f046253e7","last_name":"Leitner","first_name":"Hanna","full_name":"Leitner, Hanna"},{"last_name":"Latil","first_name":"Gerard","full_name":"Latil, Gerard"},{"last_name":"Heinze","first_name":"Juerge","full_name":"Heinze, Juerge"},{"first_name":"Stephen","last_name":"Simpson","full_name":"Simpson, Stephen"},{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer"},{"full_name":"Dussutour, Audrey","last_name":"Dussutour","first_name":"Audrey"}],"date_created":"2023-10-31T13:30:20Z","date_updated":"2024-03-04T07:14:41Z","volume":34,"acknowledgement":"We are sincerely grateful to the referees for their valuable comments and suggestions, which helped us to improve the paper. We are thankful to Jorgen Eilenberg and Nicolai V. Meyling for the fungal strain, to Simon Tragust, Abel Bernadou, and Brian Lazarro for insightful discussions, to Iago Sanmartín-Villar, Léa Briard, Céline Maitrel, and Nolwenn Rissen for their help with the experiments. Furthermore, we thank Anna V. Grasse for help with the immune gene expression analyses. We thank Sergio Ibarra for creating the graphical abstract. E.C. was supported by a Fyssen Foundation grant and the Alexander von Humboldt Foundation. A.D. was supported by the CNRS.","year":"2024","pmid":1,"publication_status":"published","department":[{"_id":"SyCr"}],"publisher":"Elsevier","date_published":"2024-02-26T00:00:00Z","publication":"Current Biology","citation":{"chicago":"Csata, Eniko, Alfonso Perez-Escudero, Emmanuel Laury, Hanna Leitner, Gerard Latil, Juerge Heinze, Stephen Simpson, Sylvia Cremer, and Audrey Dussutour. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” Current Biology. Elsevier, 2024. https://doi.org/10.1016/j.cub.2024.01.017.","mla":"Csata, Eniko, et al. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” Current Biology, vol. 34, no. 4, Elsevier, 2024, p. 902–909.e6, doi:10.1016/j.cub.2024.01.017.","short":"E. Csata, A. Perez-Escudero, E. Laury, H. Leitner, G. Latil, J. Heinze, S. Simpson, S. Cremer, A. Dussutour, Current Biology 34 (2024) 902–909.e6.","ista":"Csata E, Perez-Escudero A, Laury E, Leitner H, Latil G, Heinze J, Simpson S, Cremer S, Dussutour A. 2024. Fungal infection alters collective nutritional intake of ant colonies. Current Biology. 34(4), 902–909.e6.","ieee":"E. Csata et al., “Fungal infection alters collective nutritional intake of ant colonies,” Current Biology, vol. 34, no. 4. Elsevier, p. 902–909.e6, 2024.","apa":"Csata, E., Perez-Escudero, A., Laury, E., Leitner, H., Latil, G., Heinze, J., … Dussutour, A. (2024). Fungal infection alters collective nutritional intake of ant colonies. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2024.01.017","ama":"Csata E, Perez-Escudero A, Laury E, et al. Fungal infection alters collective nutritional intake of ant colonies. Current Biology. 2024;34(4):902-909.e6. doi:10.1016/j.cub.2024.01.017"},"article_type":"original","page":"902-909.e6","day":"26","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","_id":"14479","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Fungal infection alters collective nutritional intake of ant colonies","status":"public","intvolume":" 34","abstract":[{"lang":"eng","text":"In animals, parasitic infections impose significant fitness costs.1,2,3,4,5,6 Infected animals can alter their feeding behavior to resist infection,7,8,9,10,11,12 but parasites can manipulate animal foraging behavior to their own benefits.13,14,15,16 How nutrition influences host-parasite interactions is not well understood, as studies have mainly focused on the host and less on the parasite.9,12,17,18,19,20,21,22,23 We used the nutritional geometry framework24 to investigate the role of amino acids (AA) and carbohydrates (C) in a host-parasite system: the Argentine ant, Linepithema humile, and the entomopathogenic fungus, Metarhizium brunneum. First, using 18 diets varying in AA:C composition, we established that the fungus performed best on the high-amino-acid diet 1:4. Second, we found that the fungus reached this optimal diet when given various diet pairings, revealing its ability to cope with nutritional challenges. Third, we showed that the optimal fungal diet reduced the lifespan of healthy ants when compared with a high-carbohydrate diet but had no effect on infected ants. Fourth, we revealed that infected ant colonies, given a choice between the optimal fungal diet and a high-carbohydrate diet, chose the optimal fungal diet, whereas healthy colonies avoided it. Lastly, by disentangling fungal infection from host immune response, we demonstrated that infected ants foraged on the optimal fungal diet in response to immune activation and not as a result of parasite manipulation. Therefore, we revealed that infected ant colonies chose a diet that is costly for survival in the long term but beneficial in the short term—a form of collective self-medication."}],"issue":"4","type":"journal_article"},{"article_type":"original","citation":{"ista":"Varshney A, Ghazaryan A, Volosniev A. 2024. Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. 65, 12.","apa":"Varshney, A., Ghazaryan, A., & Volosniev, A. (2024). Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. Springer Nature. https://doi.org/10.1007/s00601-024-01880-x","ieee":"A. Varshney, A. Ghazaryan, and A. Volosniev, “Classical ‘spin’ filtering with two degrees of freedom and dissipation,” Few-Body Systems, vol. 65. Springer Nature, 2024.","ama":"Varshney A, Ghazaryan A, Volosniev A. Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. 2024;65. doi:10.1007/s00601-024-01880-x","chicago":"Varshney, Atul, Areg Ghazaryan, and Artem Volosniev. “Classical ‘Spin’ Filtering with Two Degrees of Freedom and Dissipation.” Few-Body Systems. Springer Nature, 2024. https://doi.org/10.1007/s00601-024-01880-x.","mla":"Varshney, Atul, et al. “Classical ‘Spin’ Filtering with Two Degrees of Freedom and Dissipation.” Few-Body Systems, vol. 65, 12, Springer Nature, 2024, doi:10.1007/s00601-024-01880-x.","short":"A. Varshney, A. Ghazaryan, A. Volosniev, Few-Body Systems 65 (2024)."},"publication":"Few-Body Systems","date_published":"2024-02-17T00:00:00Z","keyword":["Atomic and Molecular Physics","and Optics"],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"17","intvolume":" 65","ddc":["530"],"title":"Classical ‘spin’ filtering with two degrees of freedom and dissipation","status":"public","_id":"15045","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","file_name":"2024_FewBodySys_Varshney.pdf","content_type":"application/pdf","file_size":436712,"creator":"dernst","relation":"main_file","file_id":"15049","checksum":"c4e08cc7bc756da69b1b36fda7bb92fb","success":1,"date_updated":"2024-03-04T07:07:10Z","date_created":"2024-03-04T07:07:10Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Coupling of orbital motion to a spin degree of freedom gives rise to various transport phenomena in quantum systems that are beyond the standard paradigms of classical physics. Here, we discuss features of spin-orbit dynamics that can be visualized using a classical model with two coupled angular degrees of freedom. Specifically, we demonstrate classical ‘spin’ filtering through our model and show that the interplay between angular degrees of freedom and dissipation can lead to asymmetric ‘spin’ transport.","lang":"eng"}],"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":["2401.08454"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00601-024-01880-x","publication_identifier":{"issn":["1432-5411"]},"month":"02","department":[{"_id":"MiLe"}],"publisher":"Springer Nature","publication_status":"published","year":"2024","acknowledgement":"We thank Mikhail Lemeshko and members of his group for many inspiring discussions; Alberto Cappellaro for comments on the manuscript.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","volume":65,"date_created":"2024-03-01T11:39:33Z","date_updated":"2024-03-04T07:08:16Z","author":[{"orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","last_name":"Varshney","first_name":"Atul","full_name":"Varshney, Atul"},{"full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","first_name":"Areg"},{"full_name":"Volosniev, Artem","first_name":"Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525"}],"article_number":"12","file_date_updated":"2024-03-04T07:07:10Z"},{"article_processing_charge":"Yes","has_accepted_license":"1","day":"13","keyword":["General Physics and Astronomy"],"scopus_import":"1","date_published":"2024-02-13T00:00:00Z","article_type":"original","citation":{"ama":"Jin S, Dai K, Verstraten J, et al. Multipurpose platform for analog quantum simulation. Physical Review Research. 2024;6(1). doi:10.1103/physrevresearch.6.013158","ista":"Jin S, Dai K, Verstraten J, Dixmerias M, Al Hyder R, Salomon C, Peaudecerf B, de Jongh T, Yefsah T. 2024. Multipurpose platform for analog quantum simulation. Physical Review Research. 6(1), 013158.","apa":"Jin, S., Dai, K., Verstraten, J., Dixmerias, M., Al Hyder, R., Salomon, C., … Yefsah, T. (2024). Multipurpose platform for analog quantum simulation. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.6.013158","ieee":"S. Jin et al., “Multipurpose platform for analog quantum simulation,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.","mla":"Jin, Shuwei, et al. “Multipurpose Platform for Analog Quantum Simulation.” Physical Review Research, vol. 6, no. 1, 013158, American Physical Society, 2024, doi:10.1103/physrevresearch.6.013158.","short":"S. Jin, K. Dai, J. Verstraten, M. Dixmerias, R. Al Hyder, C. Salomon, B. Peaudecerf, T. de Jongh, T. Yefsah, Physical Review Research 6 (2024).","chicago":"Jin, Shuwei, Kunlun Dai, Joris Verstraten, Maxime Dixmerias, Ragheed Al Hyder, Christophe Salomon, Bruno Peaudecerf, Tim de Jongh, and Tarik Yefsah. “Multipurpose Platform for Analog Quantum Simulation.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/physrevresearch.6.013158."},"publication":"Physical Review Research","issue":"1","abstract":[{"lang":"eng","text":"Atom-based quantum simulators have had many successes in tackling challenging quantum many-body problems, owing to the precise and dynamical control that they provide over the systems' parameters. They are, however, often optimized to address a specific type of problem. Here, we present the design and implementation of a 6Li-based quantum gas platform that provides wide-ranging capabilities and is able to address a variety of quantum many-body problems. Our two-chamber architecture relies on a robust combination of gray molasses and optical transport from a laser-cooling chamber to a glass cell with excellent optical access. There, we first create unitary Fermi superfluids in a three-dimensional axially symmetric harmonic trap and characterize them using in situ thermometry, reaching temperatures below 20 nK. This allows us to enter the deep superfluid regime with samples of extreme diluteness, where the interparticle spacing is sufficiently large for direct single-atom imaging. Second, we generate optical lattice potentials with triangular and honeycomb geometry in which we study diffraction of molecular Bose-Einstein condensates, and show how going beyond the Kapitza-Dirac regime allows us to unambiguously distinguish between the two geometries. With the ability to probe quantum many-body physics in both discrete and continuous space, and its suitability for bulk and single-atom imaging, our setup represents an important step towards achieving a wide-scope quantum simulator."}],"type":"journal_article","file":[{"file_id":"15054","relation":"main_file","success":1,"checksum":"ba2ae3e3a011f8897d3803c9366a67e2","date_updated":"2024-03-04T07:53:08Z","date_created":"2024-03-04T07:53:08Z","access_level":"open_access","file_name":"2024_PhysicalReviewResearch_Jin.pdf","creator":"dernst","file_size":4025988,"content_type":"application/pdf"}],"oa_version":"Published Version","intvolume":" 6","status":"public","ddc":["530"],"title":"Multipurpose platform for analog quantum simulation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15053","publication_identifier":{"issn":["2643-1564"]},"month":"02","language":[{"iso":"eng"}],"doi":"10.1103/physrevresearch.6.013158","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":["2304.08433"]},"file_date_updated":"2024-03-04T07:53:08Z","article_number":"013158","volume":6,"date_updated":"2024-03-04T07:55:29Z","date_created":"2024-03-04T07:42:52Z","author":[{"full_name":"Jin, Shuwei","last_name":"Jin","first_name":"Shuwei"},{"first_name":"Kunlun","last_name":"Dai","full_name":"Dai, Kunlun"},{"last_name":"Verstraten","first_name":"Joris","full_name":"Verstraten, Joris"},{"full_name":"Dixmerias, Maxime","first_name":"Maxime","last_name":"Dixmerias"},{"full_name":"Al Hyder, Ragheed","last_name":"Al Hyder","first_name":"Ragheed","id":"d1c405be-ae15-11ed-8510-ccf53278162e"},{"full_name":"Salomon, Christophe","last_name":"Salomon","first_name":"Christophe"},{"full_name":"Peaudecerf, Bruno","last_name":"Peaudecerf","first_name":"Bruno"},{"full_name":"de Jongh, Tim","first_name":"Tim","last_name":"de Jongh"},{"full_name":"Yefsah, Tarik","first_name":"Tarik","last_name":"Yefsah"}],"department":[{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","year":"2024","acknowledgement":"We thank Clara Bachorz, Darby Bates, Markus Bohlen, Valentin Crépel, Yann Kiefer, Joanna Lis, Mihail Rabinovic, and Julian Struck for experimental assistance in the early stages of this project, and Sebastian Will for a critical reading of the manuscript. This work has been supported by Agence Nationale de la Recherche (Grant No. ANR-21-CE30-0021), the European Research Council (Grant No. ERC-2016-ADG-743159), CNRS (Tremplin@INP 2020), and Région Ile-de-France in the framework of DIM SIRTEQ (Super2D and SISCo) and DIM QuanTiP."},{"ec_funded":1,"file_date_updated":"2024-03-04T07:24:43Z","volume":151,"date_created":"2024-03-03T23:00:50Z","date_updated":"2024-03-04T07:28:25Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"14926"}]},"author":[{"orcid":"0000-0001-7659-9142","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","last_name":"Schauer","first_name":"Alexandra","full_name":"Schauer, Alexandra"},{"first_name":"Kornelija","last_name":"Pranjic-Ferscha","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","full_name":"Pranjic-Ferscha, Kornelija"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"publisher":"The Company of Biologists","department":[{"_id":"CaHe"},{"_id":"Bio"}],"publication_status":"published","year":"2024","acknowledgement":"We thank Patrick Müller for sharing the chordintt250 mutant zebrafish line as well as the plasmid for chrd-GFP, Katherine Rogers for sharing the bmp2b plasmid and Andrea Pauli for sharing the draculin plasmid. Diana Pinheiro generated the MZlefty1,2;Tg(sebox::EGFP) line. We are grateful to Patrick Müller, Diana Pinheiro and Katherine Rogers and members of the Heisenberg lab for discussions, technical advice and feedback on the manuscript. We also thank Anna Kicheva and Edouard Hannezo for discussions. We thank the Imaging and Optics Facility as well as the Life Science facility at IST Austria for support with microscopy and fish maintenance.\r\nThis work was supported by a European Research Council Advanced Grant\r\n(MECSPEC 742573 to C.-P.H.). A.S. is a recipient of a DOC Fellowship of the Austrian\r\nAcademy of Sciences at IST Austria. Open Access funding provided by Institute of\r\nScience and Technology Austria. ","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"month":"02","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.1242/dev.202316","project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"},{"name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"}],"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"},"issue":"4","abstract":[{"lang":"eng","text":"Embryogenesis results from the coordinated activities of different signaling pathways controlling cell fate specification and morphogenesis. In vertebrate gastrulation, both Nodal and BMP signaling play key roles in germ layer specification and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis is still insufficiently understood. Here, we took a reductionist approach using zebrafish embryonic explants to study the coordination of Nodal and BMP signaling for embryo patterning and morphogenesis. We show that Nodal signaling triggers explant elongation by inducing mesendodermal progenitors but also suppressing BMP signaling activity at the site of mesendoderm induction. Consistent with this, ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm intercalations, key processes during explant elongation. Translating these ex vivo observations to the intact embryo showed that, similar to explants, Nodal signaling suppresses the effect of BMP signaling on cell intercalations in the dorsal domain, thus allowing robust embryonic axis elongation. These findings suggest a dual function of Nodal signaling in embryonic axis elongation by both inducing mesendoderm and suppressing BMP effects in the dorsal portion of the mesendoderm."}],"type":"journal_article","file":[{"file_id":"15050","relation":"main_file","date_updated":"2024-03-04T07:24:43Z","date_created":"2024-03-04T07:24:43Z","success":1,"checksum":"6961ea10012bf0d266681f9628bb8f13","file_name":"2024_Development_Schauer.pdf","access_level":"open_access","creator":"dernst","file_size":14839986,"content_type":"application/pdf"}],"oa_version":"Published Version","intvolume":" 151","title":"Robust axis elongation by Nodal-dependent restriction of BMP signaling","ddc":["570"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15048","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2024-02-01T00:00:00Z","page":"1-18","article_type":"original","citation":{"short":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, C.-P.J. Heisenberg, Development 151 (2024) 1–18.","mla":"Schauer, Alexandra, et al. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” Development, vol. 151, no. 4, The Company of Biologists, 2024, pp. 1–18, doi:10.1242/dev.202316.","chicago":"Schauer, Alexandra, Kornelija Pranjic-Ferscha, Robert Hauschild, and Carl-Philipp J Heisenberg. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” Development. The Company of Biologists, 2024. https://doi.org/10.1242/dev.202316.","ama":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 2024;151(4):1-18. doi:10.1242/dev.202316","apa":"Schauer, A., Pranjic-Ferscha, K., Hauschild, R., & Heisenberg, C.-P. J. (2024). Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. The Company of Biologists. https://doi.org/10.1242/dev.202316","ieee":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, and C.-P. J. Heisenberg, “Robust axis elongation by Nodal-dependent restriction of BMP signaling,” Development, vol. 151, no. 4. The Company of Biologists, pp. 1–18, 2024.","ista":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. 2024. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 151(4), 1–18."},"publication":"Development"},{"issue":"5","abstract":[{"lang":"eng","text":"Substrate induces mechanical strain on perovskite devices, which can result in alterations to its lattice dynamics and thermal transport. Herein, we have performed a theoretical investigation on the anharmonic lattice dynamics and thermal property of perovskite Rb2SnBr6 and Cs2SnBr6 under strains using perturbation theory up to the fourth-order terms and the unified thermal transport theory. We demonstrate a pronounced hardening of low-frequency optical phonons as temperature increases, indicating strong lattice anharmonicity and the necessity of adopting temperature-dependent interatomic force constants in the lattice thermal conductivity (\r\nκL) calculations. It is found that the low-lying optical phonon modes of Rb2SnBr6 are extremely soft and their phonon energies are almost strain independent, which ultimately lead to a lower \r\nκL and a weaker strain dependence than Cs2SnBr6. We further reveal that the strain dependence of these phonon modes in the A2XB6-type perovskites weakens as their ibrational frequency decreases. This study deepens the understanding of lattice thermal transport in perovskites A2XB6 and provides a perspective on the selection of materials that meet the expected thermal behaviors in practical applications."}],"type":"journal_article","oa_version":"None","intvolume":" 109","status":"public","title":"Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15052","article_processing_charge":"No","day":"14","scopus_import":"1","date_published":"2024-02-14T00:00:00Z","article_type":"original","citation":{"ama":"Cheng R, Zeng Z, Wang C, Ouyang N, Chen Y. Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. Physical Review B. 2024;109(5). doi:10.1103/physrevb.109.054305","ista":"Cheng R, Zeng Z, Wang C, Ouyang N, Chen Y. 2024. Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. Physical Review B. 109(5), 054305.","ieee":"R. Cheng, Z. Zeng, C. Wang, N. Ouyang, and Y. Chen, “Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites,” Physical Review B, vol. 109, no. 5. American Physical Society, 2024.","apa":"Cheng, R., Zeng, Z., Wang, C., Ouyang, N., & Chen, Y. (2024). Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.109.054305","mla":"Cheng, Ruihuan, et al. “Impact of Strain-Insensitive Low-Frequency Phonon Modes on Lattice Thermal Transport in AxXB6-Type Perovskites.” Physical Review B, vol. 109, no. 5, 054305, American Physical Society, 2024, doi:10.1103/physrevb.109.054305.","short":"R. Cheng, Z. Zeng, C. Wang, N. Ouyang, Y. Chen, Physical Review B 109 (2024).","chicago":"Cheng, Ruihuan, Zezhu Zeng, Chen Wang, Niuchang Ouyang, and Yue Chen. “Impact of Strain-Insensitive Low-Frequency Phonon Modes on Lattice Thermal Transport in AxXB6-Type Perovskites.” Physical Review B. American Physical Society, 2024. https://doi.org/10.1103/physrevb.109.054305."},"publication":"Physical Review B","ec_funded":1,"article_number":"054305","volume":109,"date_updated":"2024-03-04T07:48:55Z","date_created":"2024-03-04T07:41:23Z","author":[{"full_name":"Cheng, Ruihuan","last_name":"Cheng","first_name":"Ruihuan"},{"id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","first_name":"Zezhu","last_name":"Zeng","full_name":"Zeng, Zezhu"},{"last_name":"Wang","first_name":"Chen","full_name":"Wang, Chen"},{"first_name":"Niuchang","last_name":"Ouyang","full_name":"Ouyang, Niuchang"},{"full_name":"Chen, Yue","first_name":"Yue","last_name":"Chen"}],"publisher":"American Physical Society","department":[{"_id":"BiCh"}],"publication_status":"published","acknowledgement":"This work is supported by the Research Grants Council of Hong Kong (C7002-22Y and 17318122). The authors are grateful for the research computing facilities offered by\r\nITS, HKU. Z.Z. acknowledges the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","year":"2024","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"month":"02","language":[{"iso":"eng"}],"doi":"10.1103/physrevb.109.054305","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"quality_controlled":"1"},{"article_type":"original","publication":"Science Advances","citation":{"mla":"Bao, Jiawei, et al. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” Science Advances, vol. 10, no. 8, eadj6801, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adj6801.","short":"J. Bao, B. Stevens, L. Kluft, C.J. Muller, Science Advances 10 (2024).","chicago":"Bao, Jiawei, Bjorn Stevens, Lukas Kluft, and Caroline J Muller. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” Science Advances. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adj6801.","ama":"Bao J, Stevens B, Kluft L, Muller CJ. Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. 2024;10(8). doi:10.1126/sciadv.adj6801","ista":"Bao J, Stevens B, Kluft L, Muller CJ. 2024. Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. 10(8), eadj6801.","ieee":"J. Bao, B. Stevens, L. Kluft, and C. J. Muller, “Intensification of daily tropical precipitation extremes from more organized convection,” Science Advances, vol. 10, no. 8. American Association for the Advancement of Science, 2024.","apa":"Bao, J., Stevens, B., Kluft, L., & Muller, C. J. (2024). Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adj6801"},"date_published":"2024-02-23T00:00:00Z","scopus_import":"1","day":"23","has_accepted_license":"1","article_processing_charge":"Yes","status":"public","ddc":["550"],"title":"Intensification of daily tropical precipitation extremes from more organized convection","intvolume":" 10","_id":"15047","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2024-03-04T07:34:00Z","date_created":"2024-03-04T07:34:00Z","success":1,"checksum":"d4ec4f05a6d14745057e14d1b8bf45ae","file_id":"15051","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":800926,"file_name":"2024_ScienceAdv_Bao.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Tropical precipitation extremes and their changes with surface warming are investigated using global storm resolving simulations and high-resolution observations. The simulations demonstrate that the mesoscale organization of convection, a process that cannot be physically represented by conventional global climate models, is important for the variations of tropical daily accumulated precipitation extremes. In both the simulations and observations, daily precipitation extremes increase in a more organized state, in association with larger, but less frequent, storms. Repeating the simulations for a warmer climate results in a robust increase in monthly-mean daily precipitation extremes. Higher precipitation percentiles have a greater sensitivity to convective organization, which is predicted to increase with warming. Without changes in organization, the strongest daily precipitation extremes over the tropical oceans increase at a rate close to Clausius-Clapeyron (CC) scaling. Thus, in a future warmer state with increased organization, the strongest daily precipitation extremes over oceans increase at a faster rate than CC scaling.","lang":"eng"}],"issue":"8","quality_controlled":"1","project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"},{"grant_number":"805041","_id":"629205d8-2b32-11ec-9570-e1356ff73576","call_identifier":"H2020","name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate"}],"external_id":{"pmid":["38394192"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1126/sciadv.adj6801","month":"02","publication_identifier":{"eissn":["2375-2548"]},"publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"CaMu"}],"year":"2024","acknowledgement":"This work is supported by the Max-Planck-Gesellschaft (MPG). We greatly appreciate computational resources from Deutsches Klimarechenzentrum (DKRZ) and the Jülich Supercomputing Centre (JSC). ICONA/O simulations are funded through the NextGEMS project by the EU’s Horizon 2020 programme (grant agreement no. 101003470). ICONA simulations are funded through the MONSOON-2.0 project (grant agreement no. 01LP1927A) which is supported from German Federal Ministry of Education and Research (BMBF). J.B. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant (grant agreement no. 101034413). B.S. acknowledges funding from the EU’s Horizon 2020 programme (grant agreement no. 101003470). C.M. gratefully acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Project CLUSTER, grant agreement no. 805041).","pmid":1,"date_updated":"2024-03-05T09:26:47Z","date_created":"2024-03-03T23:00:50Z","volume":10,"author":[{"full_name":"Bao, Jiawei","id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160","first_name":"Jiawei","last_name":"Bao"},{"last_name":"Stevens","first_name":"Bjorn","full_name":"Stevens, Bjorn"},{"last_name":"Kluft","first_name":"Lukas","full_name":"Kluft, Lukas"},{"orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","first_name":"Caroline J","full_name":"Muller, Caroline J"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/cloud-clustering-causes-more-extreme-rain/","relation":"press_release","description":"News on ISTA Website"}]},"article_number":"eadj6801","file_date_updated":"2024-03-04T07:34:00Z","ec_funded":1},{"scopus_import":"1","day":"17","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","article_type":"original","page":"230-246.e11","publication":"Neuron","citation":{"mla":"Cheung, Giselle T., et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” Neuron, vol. 112, no. 2, Elsevier, 2024, p. 230–246.e11, doi:10.1016/j.neuron.2023.11.009.","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, T. Krausgruber, C. Streicher, M. Schrammel, N.Y. Özgen, A. Ivec, C. Bock, R. Shigemoto, S. Hippenmeyer, Neuron 112 (2024) 230–246.e11.","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, Thomas Krausgruber, Carmen Streicher, Martin Schrammel, Natalie Y Özgen, et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” Neuron. Elsevier, 2024. https://doi.org/10.1016/j.neuron.2023.11.009.","ama":"Cheung GT, Pauler F, Koppensteiner P, et al. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 2024;112(2):230-246.e11. doi:10.1016/j.neuron.2023.11.009","ista":"Cheung GT, Pauler F, Koppensteiner P, Krausgruber T, Streicher C, Schrammel M, Özgen NY, Ivec A, Bock C, Shigemoto R, Hippenmeyer S. 2024. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 112(2), 230–246.e11.","ieee":"G. T. Cheung et al., “Multipotent progenitors instruct ontogeny of the superior colliculus,” Neuron, vol. 112, no. 2. Elsevier, p. 230–246.e11, 2024.","apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., Krausgruber, T., Streicher, C., Schrammel, M., … Hippenmeyer, S. (2024). Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.11.009"},"date_published":"2024-01-17T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny."}],"issue":"2","status":"public","title":"Multipotent progenitors instruct ontogeny of the superior colliculus","ddc":["570"],"intvolume":" 112","_id":"12875","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"2024_Neuron_Cheung.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":5942467,"file_id":"14944","relation":"main_file","date_created":"2024-02-06T13:56:15Z","date_updated":"2024-02-06T13:56:15Z","success":1,"checksum":"32b3788f7085cf44a84108d8faaff3ce"}],"oa_version":"Published Version","month":"01","publication_identifier":{"issn":["0896-6273"]},"quality_controlled":"1","project":[{"grant_number":"F07805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression"}],"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":{"pmid":["38096816"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2023.11.009","file_date_updated":"2024-02-06T13:56:15Z","publication_status":"published","publisher":"Elsevier","department":[{"_id":"SiHi"},{"_id":"RySh"}],"year":"2024","acknowledgement":"We thank Liqun Luo for his continued support, for providing essential resources for generating Fzd10-CreER mice which were generated in his laboratory, and for comments on the manuscript; W. Zhong for providing Nestin-Cre transgenic mouse line for this study; A. Heger for mouse colony management; R. Beattie and T. Asenov for designing and producing components of acute slice recovery chamber for MADM-CloneSeq experiments; and K. Leopold, J. Rodarte and N. Amberg for initial experiments, technical support and/or assistance. This study was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging & Optics Facility (IOF), Laboratory Support Facility (LSF), Miba Machine Shop, and Pre-clinical Facility (PCF). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional\r\nfunds; the Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H. ","pmid":1,"date_created":"2023-04-27T09:41:48Z","date_updated":"2024-03-05T09:43:02Z","volume":112,"author":[{"full_name":"Cheung, Giselle T","first_name":"Giselle T","last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572"},{"first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian"},{"full_name":"Koppensteiner, Peter","first_name":"Peter","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948"},{"full_name":"Krausgruber, Thomas","last_name":"Krausgruber","first_name":"Thomas"},{"full_name":"Streicher, Carmen","last_name":"Streicher","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schrammel, Martin","id":"f13e7cae-e8bd-11ed-841a-96dedf69f46d","last_name":"Schrammel","first_name":"Martin"},{"last_name":"Özgen","first_name":"Natalie Y","id":"e68ece33-f6e0-11ea-865d-ae1031dcc090","full_name":"Özgen, Natalie Y"},{"id":"1d144691-e8be-11ed-9b33-bdd3077fad4c","first_name":"Alexis","last_name":"Ivec","full_name":"Ivec, Alexis"},{"full_name":"Bock, Christoph","last_name":"Bock","first_name":"Christoph"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/the-pedigree-of-brain-cells/","relation":"press_release","description":"News on ISTA Website"}]}},{"acknowledgement":"We thank A. Bergthaler (Research Center for Molecular Medicine of the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel and other members of the Schur group for support and helpful discussions. We also thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S. also received support from the Austrian Science Fund (FWF) grant P31445. This publication has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis research was also supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of COSMIC45 and Colabfold46.","year":"2024","pmid":1,"publication_status":"epub_ahead","publisher":"Springer Nature","department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"author":[{"full_name":"Datler, Julia","orcid":"0000-0002-3616-8580","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler","first_name":"Julia"},{"full_name":"Hansen, Jesse","last_name":"Hansen","first_name":"Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63"},{"full_name":"Thader, Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Thader"},{"full_name":"Schlögl, Alois","first_name":"Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100"},{"last_name":"Bauer","first_name":"Lukas W","id":"0c894dcf-897b-11ed-a09c-8186353224b0","full_name":"Bauer, Lukas W"},{"first_name":"Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin"},{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/","relation":"press_release","description":"News on ISTA Website"}]},"date_updated":"2024-03-05T09:27:47Z","date_created":"2024-02-12T09:59:45Z","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"},"main_file_link":[{"url":"https://doi.org/10.1038/s41594-023-01201-6","open_access":"1"}],"external_id":{"pmid":["38316877"]},"quality_controlled":"1","project":[{"name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"doi":"10.1038/s41594-023-01201-6","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"month":"02","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"_id":"14979","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","status":"public","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses."}],"publication":"Nature Structural & Molecular Biology","citation":{"apa":"Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., & Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-023-01201-6","ieee":"J. Datler et al., “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” Nature Structural & Molecular Biology. Springer Nature, 2024.","ista":"Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology.","ama":"Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. 2024. doi:10.1038/s41594-023-01201-6","chicago":"Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-023-01201-6.","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural & Molecular Biology (2024).","mla":"Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology, Springer Nature, 2024, doi:10.1038/s41594-023-01201-6."},"article_type":"original","date_published":"2024-02-05T00:00:00Z","keyword":["Molecular Biology","Structural Biology"],"day":"05","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)"},{"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14846","status":"public","title":"Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization","abstract":[{"lang":"eng","text":"Contraction and flow of the actin cell cortex have emerged as a common principle by which cells reorganize their cytoplasm and take shape. However, how these cortical flows interact with adjacent cytoplasmic components, changing their form and localization, and how this affects cytoplasmic organization and cell shape remains unclear. Here we show that in ascidian oocytes, the cooperative activities of cortical actomyosin flows and deformation of the adjacent mitochondria-rich myoplasm drive oocyte cytoplasmic reorganization and shape changes following fertilization. We show that vegetal-directed cortical actomyosin flows, established upon oocyte fertilization, lead to both the accumulation of cortical actin at the vegetal pole of the zygote and compression and local buckling of the adjacent elastic solid-like myoplasm layer due to friction forces generated at their interface. Once cortical flows have ceased, the multiple myoplasm buckles resolve into one larger buckle, which again drives the formation of the contraction pole—a protuberance of the zygote’s vegetal pole where maternal mRNAs accumulate. Thus, our findings reveal a mechanism where cortical actomyosin network flows determine cytoplasmic reorganization and cell shape by deforming adjacent cytoplasmic components through friction forces."}],"type":"journal_article","date_published":"2024-01-09T00:00:00Z","publication":"Nature Physics","citation":{"mla":"Caballero Mancebo, Silvia, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” Nature Physics, Springer Nature, 2024, doi:10.1038/s41567-023-02302-1.","short":"S. Caballero Mancebo, R. Shinde, M. Bolger-Munro, M. Peruzzo, G. Szep, I. Steccari, D. Labrousse Arias, V. Zheden, J. Merrin, A. Callan-Jones, R. Voituriez, C.-P.J. Heisenberg, Nature Physics (2024).","chicago":"Caballero Mancebo, Silvia, Rushikesh Shinde, Madison Bolger-Munro, Matilda Peruzzo, Gregory Szep, Irene Steccari, David Labrousse Arias, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-023-02302-1.","ama":"Caballero Mancebo S, Shinde R, Bolger-Munro M, et al. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics. 2024. doi:10.1038/s41567-023-02302-1","ista":"Caballero Mancebo S, Shinde R, Bolger-Munro M, Peruzzo M, Szep G, Steccari I, Labrousse Arias D, Zheden V, Merrin J, Callan-Jones A, Voituriez R, Heisenberg C-PJ. 2024. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics.","ieee":"S. Caballero Mancebo et al., “Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization,” Nature Physics. Springer Nature, 2024.","apa":"Caballero Mancebo, S., Shinde, R., Bolger-Munro, M., Peruzzo, M., Szep, G., Steccari, I., … Heisenberg, C.-P. J. (2024). Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02302-1"},"article_type":"original","day":"09","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","author":[{"full_name":"Caballero Mancebo, Silvia","last_name":"Caballero Mancebo","first_name":"Silvia","orcid":"0000-0002-5223-3346","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Shinde","first_name":"Rushikesh","full_name":"Shinde, Rushikesh"},{"full_name":"Bolger-Munro, Madison","last_name":"Bolger-Munro","first_name":"Madison","orcid":"0000-0002-8176-4824","id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E"},{"full_name":"Peruzzo, Matilda","last_name":"Peruzzo","first_name":"Matilda","orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Szep, Gregory","id":"4BFB7762-F248-11E8-B48F-1D18A9856A87","last_name":"Szep","first_name":"Gregory"},{"first_name":"Irene","last_name":"Steccari","id":"2705C766-9FE2-11EA-B224-C6773DDC885E","full_name":"Steccari, Irene"},{"full_name":"Labrousse Arias, David","id":"CD573DF4-9ED3-11E9-9D77-3223E6697425","first_name":"David","last_name":"Labrousse Arias"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783","first_name":"Vanessa","last_name":"Zheden","full_name":"Zheden, Vanessa"},{"last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"},{"first_name":"Andrew","last_name":"Callan-Jones","full_name":"Callan-Jones, Andrew"},{"first_name":"Raphaël","last_name":"Voituriez","full_name":"Voituriez, Raphaël"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"related_material":{"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/stranger-than-friction-a-force-initiating-life/"}]},"date_updated":"2024-03-05T09:33:38Z","date_created":"2024-01-21T23:00:57Z","acknowledgement":"We would like to thank A. McDougall, E. Hannezo and the Heisenberg lab for fruitful discussions and reagents. We also thank E. Munro for the iMyo-YFP and Bra>iMyo-mScarlet constructs. This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria through resources provided by the Electron Microscopy Facility, Imaging and Optics Facility and the Nanofabrication Facility. This work was supported by a Joint Project Grant from the FWF (I 3601-B27).","year":"2024","publication_status":"epub_ahead","department":[{"_id":"CaHe"},{"_id":"JoFi"},{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"publisher":"Springer Nature","doi":"10.1038/s41567-023-02302-1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://doi.org/10.1038/s41567-023-02302-1","open_access":"1"}],"oa":1,"quality_controlled":"1","project":[{"_id":"2646861A-B435-11E9-9278-68D0E5697425","grant_number":"I03601","call_identifier":"FWF","name":"Control of embryonic cleavage pattern"}],"month":"01","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]}},{"date_published":"2024-01-05T00:00:00Z","publication":"Science","citation":{"mla":"Stankowski, Sean, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science, vol. 383, no. 6678, American Association for the Advancement of Science, 2024, pp. 114–19, doi:10.1126/science.adi2982.","short":"S. Stankowski, Z.B. Zagrodzka, M.D. Garlovsky, A. Pal, D. Shipilina, D.F. Garcia Castillo, H. Lifchitz, A. Le Moan, E. Leder, J. Reeve, K. Johannesson, A.M. Westram, R.K. Butlin, Science 383 (2024) 114–119.","chicago":"Stankowski, Sean, Zuzanna B. Zagrodzka, Martin D. Garlovsky, Arka Pal, Daria Shipilina, Diego Fernando Garcia Castillo, Hila Lifchitz, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/science.adi2982.","ama":"Stankowski S, Zagrodzka ZB, Garlovsky MD, et al. The genetic basis of a recent transition to live-bearing in marine snails. Science. 2024;383(6678):114-119. doi:10.1126/science.adi2982","ista":"Stankowski S, Zagrodzka ZB, Garlovsky MD, Pal A, Shipilina D, Garcia Castillo DF, Lifchitz H, Le Moan A, Leder E, Reeve J, Johannesson K, Westram AM, Butlin RK. 2024. The genetic basis of a recent transition to live-bearing in marine snails. Science. 383(6678), 114–119.","ieee":"S. Stankowski et al., “The genetic basis of a recent transition to live-bearing in marine snails,” Science, vol. 383, no. 6678. American Association for the Advancement of Science, pp. 114–119, 2024.","apa":"Stankowski, S., Zagrodzka, Z. B., Garlovsky, M. D., Pal, A., Shipilina, D., Garcia Castillo, D. F., … Butlin, R. K. (2024). The genetic basis of a recent transition to live-bearing in marine snails. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adi2982"},"article_type":"original","page":"114-119","day":"05","article_processing_charge":"No","scopus_import":"1","oa_version":"None","_id":"14796","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The genetic basis of a recent transition to live-bearing in marine snails","status":"public","intvolume":" 383","abstract":[{"lang":"eng","text":"Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step."}],"issue":"6678","type":"journal_article","doi":"10.1126/science.adi2982","language":[{"iso":"eng"}],"external_id":{"pmid":["38175895"]},"quality_controlled":"1","month":"01","publication_identifier":{"eissn":["1095-9203"]},"author":[{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"full_name":"Zagrodzka, Zuzanna B.","last_name":"Zagrodzka","first_name":"Zuzanna B."},{"last_name":"Garlovsky","first_name":"Martin D.","full_name":"Garlovsky, Martin D."},{"orcid":"0000-0002-4530-8469","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal","first_name":"Arka","full_name":"Pal, Arka"},{"first_name":"Daria","last_name":"Shipilina","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226","full_name":"Shipilina, Daria"},{"full_name":"Garcia Castillo, Diego Fernando","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","first_name":"Diego Fernando","last_name":"Garcia Castillo"},{"first_name":"Hila","last_name":"Lifchitz","id":"d6ab5470-2fb3-11ed-8633-986a9b84edac","full_name":"Lifchitz, Hila"},{"full_name":"Le Moan, Alan","first_name":"Alan","last_name":"Le Moan"},{"first_name":"Erica","last_name":"Leder","full_name":"Leder, Erica"},{"full_name":"Reeve, James","first_name":"James","last_name":"Reeve"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/the-snail-or-the-egg/","relation":"press_release","description":"News on ISTA Website"}],"record":[{"relation":"research_data","status":"public","id":"14812"}]},"date_created":"2024-01-14T23:00:56Z","date_updated":"2024-03-05T09:35:25Z","volume":383,"year":"2024","acknowledgement":"We thank J. Galindo, M. Montaño-Rendón, N. Mikhailova, A. Blakeslee, E. Arnason, and P. Kemppainen for providing samples; R. Turney, G. Sotelo, J. Larsson, T. Broquet, and S. Loisel for help collecting samples; Science Animated for providing the snail cartoons shown in Fig. 1; M. Dunning for help in developing bioinformatic pipelines; R. Faria, H. Morales, and V. Sousa for advice; and M. Hahn, J. Slate, M. Ravinet, J. Raeymaekers, A. Comeault, and N. Barton for feedback on a draft manuscript.\r\nThis work was supported by the Natural Environment Research Council (grant NE/P001610/1 to R.K.B.), the European Research Council (grant ERC-2015-AdG693030-BARRIERS to R.K.B.), the Norwegian Research Council (RCN Project 315287 to A.M.W.), and the Swedish Research Council (grant 2020-05385 to E.L.).","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"publisher":"American Association for the Advancement of Science"},{"author":[{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","last_name":"Hledik","full_name":"Hledik, Michal"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7553"},{"id":"12081","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7606"}]},"date_updated":"2024-03-06T14:22:52Z","date_created":"2024-02-23T14:02:04Z","year":"2024","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2024-02-23T14:20:16Z","ec_funded":1,"doi":"10.15479/at:ista:15020","acknowledged_ssus":[{"_id":"ScienComp"}],"supervisor":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"},{"name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327"}],"month":"02","publication_identifier":{"issn":["2663 - 337X"]},"oa_version":"Published Version","file":[{"date_updated":"2024-02-23T13:50:53Z","date_created":"2024-02-23T13:50:53Z","checksum":"b2d3da47c98d481577a4baf68944fe41","success":1,"relation":"main_file","file_id":"15021","file_size":7102089,"content_type":"application/pdf","creator":"mhledik","file_name":"hledik thesis pdfa 2b.pdf","access_level":"open_access"},{"relation":"source_file","file_id":"15022","date_updated":"2024-02-23T14:20:16Z","date_created":"2024-02-23T13:50:54Z","checksum":"eda9b9430da2610fee7ce1c1419a479a","file_name":"hledik thesis source.zip","access_level":"closed","file_size":14014790,"content_type":"application/zip","creator":"mhledik"}],"_id":"15020","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["576","519"],"title":"Genetic information and biological optimization","status":"public","abstract":[{"lang":"eng","text":"This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.\r\nChapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?\r\nChapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2024-02-23T00:00:00Z","citation":{"ama":"Hledik M. Genetic information and biological optimization. 2024. doi:10.15479/at:ista:15020","apa":"Hledik, M. (2024). Genetic information and biological optimization. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15020","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria.","short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.","mla":"Hledik, Michal. Genetic Information and Biological Optimization. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15020.","chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15020."},"page":"158","day":"23","article_processing_charge":"No","has_accepted_license":"1","keyword":["Theoretical biology","Optimality","Evolution","Information"]},{"year":"2024","publication_status":"published","publisher":"Elsevier","department":[{"_id":"EvBe"}],"author":[{"full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2024-01-21T23:00:56Z","date_updated":"2024-03-12T12:19:12Z","volume":34,"month":"01","publication_identifier":{"eissn":["1879-0445"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2023.11.039"}],"quality_controlled":"1","doi":"10.1016/j.cub.2023.11.039","language":[{"iso":"eng"}],"type":"other_academic_publication","abstract":[{"lang":"eng","text":"Eva Benkova received a PhD in Biophysics at the Institute of Biophysics of the Czech Academy of Sciences in 1998. After working as a postdoc at the Max Planck Institute in Cologne and the Center for Plant Molecular Biology (ZMBP) in Tübingen, she became a group leader at the Plant Systems Biology Department of the Vlaams Instituut voor Biotechnologie (VIB) in Gent. In 2012, she transitioned to an Assistant Professor position at the Institute of Science and Technology Austria (ISTA) where she was later promoted to Professor. Since 2021, she has served as the Dean of the ISTA Graduate School. As a plant developmental biologist, she focuses on unraveling the molecular mechanisms and principles that underlie hormonal interactions in plants. In her current work, she explores the intricate connections between hormones and regulatory pathways that mediate the perception of environmental stimuli, including abiotic stress and nitrate availability."}],"issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14842","status":"public","title":"Eva Benkova","intvolume":" 34","oa_version":"Published Version","day":"08","article_processing_charge":"No","publication":"Current Biology","citation":{"apa":"Benková, E. (2024). Eva Benkova. Current Biology (Vol. 34, pp. R3–R5). Elsevier. https://doi.org/10.1016/j.cub.2023.11.039","ieee":"E. Benková, Eva Benkova, vol. 34, no. 1. Elsevier, 2024, pp. R3–R5.","ista":"Benková E. 2024. Eva Benkova, Elsevier,p.","ama":"Benková E. Eva Benkova. Vol 34. Elsevier; 2024:R3-R5. doi:10.1016/j.cub.2023.11.039","chicago":"Benková, Eva. Eva Benkova. Current Biology. Vol. 34. Elsevier, 2024. https://doi.org/10.1016/j.cub.2023.11.039.","short":"E. Benková, Eva Benkova, Elsevier, 2024.","mla":"Benková, Eva. “Eva Benkova.” Current Biology, vol. 34, no. 1, Elsevier, 2024, pp. R3–5, doi:10.1016/j.cub.2023.11.039."},"page":"R3-R5","date_published":"2024-01-08T00:00:00Z"},{"month":"02","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2301449121","quality_controlled":"1","project":[{"call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"external_id":{"pmid":["38346189"]},"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,"file_date_updated":"2024-03-12T13:42:42Z","ec_funded":1,"article_number":"e2301449121","date_created":"2024-03-05T09:23:55Z","date_updated":"2024-03-12T13:44:18Z","volume":121,"author":[{"orcid":"0000-0002-3509-1948","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","first_name":"Peter","full_name":"Koppensteiner, Peter"},{"orcid":"0000-0003-0863-4481","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","last_name":"Bhandari","first_name":"Pradeep","full_name":"Bhandari, Pradeep"},{"full_name":"Önal, Hüseyin C","id":"4659D740-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2771-2011","first_name":"Hüseyin C","last_name":"Önal"},{"full_name":"Borges Merjane, Carolina","first_name":"Carolina","last_name":"Borges Merjane","id":"4305C450-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0005-401X"},{"first_name":"Elodie","last_name":"Le Monnier","id":"3B59276A-F248-11E8-B48F-1D18A9856A87","full_name":"Le Monnier, Elodie"},{"full_name":"Roy, Utsa","first_name":"Utsa","last_name":"Roy","id":"4d26cf11-5355-11ee-ae5a-eb05e255b9b2"},{"full_name":"Nakamura, Yukihiro","last_name":"Nakamura","first_name":"Yukihiro"},{"full_name":"Sadakata, Tetsushi","last_name":"Sadakata","first_name":"Tetsushi"},{"first_name":"Makoto","last_name":"Sanbo","full_name":"Sanbo, Makoto"},{"last_name":"Hirabayashi","first_name":"Masumi","full_name":"Hirabayashi, Masumi"},{"first_name":"JeongSeop","last_name":"Rhee","full_name":"Rhee, JeongSeop"},{"full_name":"Brose, Nils","last_name":"Brose","first_name":"Nils"},{"full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"13173"}],"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/"}]},"publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"RySh"},{"_id":"PeJo"}],"acknowledgement":"We thank Erwin Neher and Ipe Ninan for critical comments on the manuscript. This project has received funding from the European Research Council (ERC) and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to R.S. and the Marie Skłodowska-Curie grant agreement no. 665385 to C.Ö.). This study was supported by the Cooperative Study Program of Center for Animal Resources and Collaborative Study of NINS. We thank Kohgaku Eguchi for statistical analysis, Yu Kasugai for additional EM imaging, Robert Beattie for the design of the slice recovery chamber for Flash and Freeze experiments, Todor Asenov from the ISTA machine shop for custom part preparations for high-pressure freezing, the ISTA preclinical facility for animal caretaking, and the ISTA EM facilities for technical support.","year":"2024","pmid":1,"day":"20","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","date_published":"2024-02-20T00:00:00Z","article_type":"original","publication":"Proceedings of the National Academy of Sciences","citation":{"short":"P. Koppensteiner, P. Bhandari, C. Önal, C. Borges Merjane, E. Le Monnier, U. Roy, Y. Nakamura, T. Sadakata, M. Sanbo, M. Hirabayashi, J. Rhee, N. Brose, P.M. Jonas, R. Shigemoto, Proceedings of the National Academy of Sciences 121 (2024).","mla":"Koppensteiner, Peter, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences, vol. 121, no. 8, e2301449121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2301449121.","chicago":"Koppensteiner, Peter, Pradeep Bhandari, Cihan Önal, Carolina Borges Merjane, Elodie Le Monnier, Utsa Roy, Yukihiro Nakamura, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2301449121.","ama":"Koppensteiner P, Bhandari P, Önal C, et al. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences. 2024;121(8). doi:10.1073/pnas.2301449121","ieee":"P. Koppensteiner et al., “GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles,” Proceedings of the National Academy of Sciences, vol. 121, no. 8. Proceedings of the National Academy of Sciences, 2024.","apa":"Koppensteiner, P., Bhandari, P., Önal, C., Borges Merjane, C., Le Monnier, E., Roy, U., … Shigemoto, R. (2024). GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2301449121","ista":"Koppensteiner P, Bhandari P, Önal C, Borges Merjane C, Le Monnier E, Roy U, Nakamura Y, Sadakata T, Sanbo M, Hirabayashi M, Rhee J, Brose N, Jonas PM, Shigemoto R. 2024. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences. 121(8), e2301449121."},"abstract":[{"text":"GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca\r\n 2+\r\n -dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the “Flash and Freeze-fracture” method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals.","lang":"eng"}],"issue":"8","type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2024_PNAS_Koppensteiner.pdf","file_size":13648221,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"15110","checksum":"b25b2a057c266ff317a48b0d54d6fc8a","success":1,"date_updated":"2024-03-12T13:42:42Z","date_created":"2024-03-12T13:42:42Z"}],"status":"public","title":"GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles","ddc":["570"],"intvolume":" 121","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15084"},{"type":"journal_article","issue":"10","abstract":[{"lang":"eng","text":"Direct reciprocity is a powerful mechanism for cooperation in social dilemmas. The very logic of reciprocity, however, seems to require that individuals are symmetric, and that everyone has the same means to influence each others’ payoffs. Yet in many applications, individuals are asymmetric. Herein, we study the effect of asymmetry in linear public good games. Individuals may differ in their endowments (their ability to contribute to a public good) and in their productivities (how effective their contributions are). Given the individuals’ productivities, we ask which allocation of endowments is optimal for cooperation. To this end, we consider two notions of optimality. The first notion focuses on the resilience of cooperation. The respective endowment distribution ensures that full cooperation is feasible even under the most adverse conditions. The second notion focuses on efficiency. The corresponding endowment distribution maximizes group welfare. Using analytical methods, we fully characterize these two endowment distributions. This analysis reveals that both optimality notions favor some endowment inequality: More productive players ought to get higher endowments. Yet the two notions disagree on how unequal endowments are supposed to be. A focus on resilience results in less inequality. With additional simulations, we show that the optimal endowment allocation needs to account for both the resilience and the efficiency of cooperation."}],"intvolume":" 121","ddc":["000"],"status":"public","title":"Efficiency and resilience of cooperation in asymmetric social dilemmas","_id":"15083","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"15109","relation":"main_file","success":1,"checksum":"068520e3efd4d008bb9177e8aedb7d22","date_created":"2024-03-12T13:12:22Z","date_updated":"2024-03-12T13:12:22Z","access_level":"open_access","file_name":"2024_PNAS_Huebner.pdf","creator":"dernst","file_size":2203220,"content_type":"application/pdf"}],"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"05","article_type":"original","citation":{"ama":"Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences. 2024;121(10). doi:10.1073/pnas.2315558121","ista":"Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. 2024. Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences. 121(10), e2315558121.","apa":"Hübner, V., Staab, M., Hilbe, C., Chatterjee, K., & Kleshnina, M. (2024). Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2315558121","ieee":"V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, and M. Kleshnina, “Efficiency and resilience of cooperation in asymmetric social dilemmas,” Proceedings of the National Academy of Sciences, vol. 121, no. 10. Proceedings of the National Academy of Sciences, 2024.","mla":"Hübner, Valentin, et al. “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Proceedings of the National Academy of Sciences, vol. 121, no. 10, e2315558121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2315558121.","short":"V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, M. Kleshnina, Proceedings of the National Academy of Sciences 121 (2024).","chicago":"Hübner, Valentin, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina. “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2315558121."},"publication":"Proceedings of the National Academy of Sciences","date_published":"2024-03-05T00:00:00Z","article_number":"e2315558121","ec_funded":1,"file_date_updated":"2024-03-12T13:12:22Z","department":[{"_id":"KrCh"}],"publisher":"Proceedings of the National Academy of Sciences","publication_status":"published","pmid":1,"year":"2024","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement #754411 and the French Agence Nationale de la Recherche (under the Investissement d’Avenir Programme, ANR-17-EURE-0010) (to M.K.).","volume":121,"date_updated":"2024-03-12T13:29:25Z","date_created":"2024-03-05T09:18:49Z","related_material":{"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/what-math-tells-us-about-social-dilemmas/"}],"record":[{"status":"public","relation":"research_data","id":"15108"}]},"author":[{"full_name":"Hübner, Valentin","last_name":"Hübner","first_name":"Valentin","id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910"},{"first_name":"Manuel","last_name":"Staab","full_name":"Staab, Manuel"},{"full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","first_name":"Christian"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Kleshnina, Maria","first_name":"Maria","last_name":"Kleshnina"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"month":"03","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","external_id":{"pmid":["38408249"]},"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":"10.1073/pnas.2315558121"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15108","year":"2024","ddc":["000"],"title":"Computer code for \"Efficiency and resilience of cooperation in asymmetric social dilemmas\"","status":"public","publisher":"Zenodo","department":[{"_id":"KrCh"}],"author":[{"full_name":"Hübner, Valentin","last_name":"Hübner","first_name":"Valentin","id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910"},{"last_name":"Kleshnina","first_name":"Maria","full_name":"Kleshnina, Maria"}],"related_material":{"record":[{"id":"15083","relation":"used_in_publication","status":"public"}]},"date_created":"2024-03-12T13:02:58Z","date_updated":"2024-03-12T13:29:26Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"lang":"eng","text":"in the research article \"Efficiency and resilience of cooperation in asymmetric social dilemmas\" (by Valentin Hübner, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina).\r\n\r\nWe used different implementations for the case of two and three players, both described below."}],"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"},"citation":{"ama":"Hübner V, Kleshnina M. Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” 2024. doi:10.5281/ZENODO.10639167","ista":"Hübner V, Kleshnina M. 2024. Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas’, Zenodo, 10.5281/ZENODO.10639167.","ieee":"V. Hübner and M. Kleshnina, “Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas.’” Zenodo, 2024.","apa":"Hübner, V., & Kleshnina, M. (2024). Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” Zenodo. https://doi.org/10.5281/ZENODO.10639167","mla":"Hübner, Valentin, and Maria Kleshnina. Computer Code for “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Zenodo, 2024, doi:10.5281/ZENODO.10639167.","short":"V. Hübner, M. Kleshnina, (2024).","chicago":"Hübner, Valentin, and Maria Kleshnina. “Computer Code for ‘Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.’” Zenodo, 2024. https://doi.org/10.5281/ZENODO.10639167."},"main_file_link":[{"open_access":"1","url":"https://10.5281/zenodo.10639167"}],"date_published":"2024-02-09T00:00:00Z","doi":"10.5281/ZENODO.10639167","month":"02","day":"09","article_processing_charge":"No","has_accepted_license":"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,"language":[{"iso":"eng"}],"doi":"10.5194/gmd-17-1563-2024","publication_identifier":{"eissn":["1991-9603"],"issn":["1991-959X"]},"month":"02","department":[{"_id":"CaMu"}],"publisher":"European Geosciences Union","publication_status":"published","acknowledgement":"The authors wish to thank Ann Kristin Naumann and three anonymous reviewers for very helpful comments on an earlier version of this paper. We are grateful to René Redler and Karl-Hermann Wieners for useful recommendations regarding running the simulations. We thank Luis Kornblueh for providing an external vertical grid generator and resolving the memory requirements for the very fine vertical grids. We acknowledge Hauke Schulz for providing the radiosonde data. The simulations were run at the German Climate Computing Center (DKRZ), and we thank the DKRZ staff for their support.\r\nHauke Schmidt and Diego Jimenez-de la Cuesta received financial support from the SOCTOC project within the framework of the ROMIC program, funded by the German Ministry of Education and Research (BMBF) (grant no. 01LG1903A).\r\nThe article processing charges for this open-access publication were covered by the Max Planck Society.","year":"2024","volume":17,"date_updated":"2024-03-13T09:01:20Z","date_created":"2024-03-10T23:00:53Z","author":[{"first_name":"Hauke","last_name":"Schmidt","full_name":"Schmidt, Hauke"},{"first_name":"Sebastian","last_name":"Rast","full_name":"Rast, Sebastian"},{"full_name":"Bao, Jiawei","last_name":"Bao","first_name":"Jiawei","id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160"},{"full_name":"Cassim, Amrit","last_name":"Cassim","first_name":"Amrit"},{"full_name":"Fang, Shih Wei","first_name":"Shih Wei","last_name":"Fang"},{"last_name":"Jimenez-De La Cuesta","first_name":"Diego","full_name":"Jimenez-De La Cuesta, Diego"},{"last_name":"Keil","first_name":"Paul","full_name":"Keil, Paul"},{"full_name":"Kluft, Lukas","last_name":"Kluft","first_name":"Lukas"},{"first_name":"Clarissa","last_name":"Kroll","full_name":"Kroll, Clarissa"},{"first_name":"Theresa","last_name":"Lang","full_name":"Lang, Theresa"},{"full_name":"Niemeier, Ulrike","first_name":"Ulrike","last_name":"Niemeier"},{"full_name":"Schneidereit, Andrea","last_name":"Schneidereit","first_name":"Andrea"},{"full_name":"Williams, Andrew I.L.","first_name":"Andrew I.L.","last_name":"Williams"},{"first_name":"Bjorn","last_name":"Stevens","full_name":"Stevens, Bjorn"}],"file_date_updated":"2024-03-13T08:59:21Z","page":"1563-1584","article_type":"original","citation":{"short":"H. Schmidt, S. Rast, J. Bao, A. Cassim, S.W. Fang, D. Jimenez-De La Cuesta, P. Keil, L. Kluft, C. Kroll, T. Lang, U. Niemeier, A. Schneidereit, A.I.L. Williams, B. Stevens, Geoscientific Model Development 17 (2024) 1563–1584.","mla":"Schmidt, Hauke, et al. “Effects of Vertical Grid Spacing on the Climate Simulated in the ICON-Sapphire Global Storm-Resolving Model.” Geoscientific Model Development, vol. 17, no. 4, European Geosciences Union, 2024, pp. 1563–84, doi:10.5194/gmd-17-1563-2024.","chicago":"Schmidt, Hauke, Sebastian Rast, Jiawei Bao, Amrit Cassim, Shih Wei Fang, Diego Jimenez-De La Cuesta, Paul Keil, et al. “Effects of Vertical Grid Spacing on the Climate Simulated in the ICON-Sapphire Global Storm-Resolving Model.” Geoscientific Model Development. European Geosciences Union, 2024. https://doi.org/10.5194/gmd-17-1563-2024.","ama":"Schmidt H, Rast S, Bao J, et al. Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. 2024;17(4):1563-1584. doi:10.5194/gmd-17-1563-2024","ieee":"H. Schmidt et al., “Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model,” Geoscientific Model Development, vol. 17, no. 4. European Geosciences Union, pp. 1563–1584, 2024.","apa":"Schmidt, H., Rast, S., Bao, J., Cassim, A., Fang, S. W., Jimenez-De La Cuesta, D., … Stevens, B. (2024). Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. European Geosciences Union. https://doi.org/10.5194/gmd-17-1563-2024","ista":"Schmidt H, Rast S, Bao J, Cassim A, Fang SW, Jimenez-De La Cuesta D, Keil P, Kluft L, Kroll C, Lang T, Niemeier U, Schneidereit A, Williams AIL, Stevens B. 2024. Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. 17(4), 1563–1584."},"publication":"Geoscientific Model Development","date_published":"2024-02-22T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"22","intvolume":" 17","ddc":["550"],"status":"public","title":"Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15097","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":13364601,"creator":"dernst","file_name":"2024_GeoscientificModelDev_Schmidt.pdf","access_level":"open_access","date_updated":"2024-03-13T08:59:21Z","date_created":"2024-03-13T08:59:21Z","checksum":"270d2340402729b0532f7072ea914cae","success":1,"relation":"main_file","file_id":"15111"}],"type":"journal_article","issue":"4","abstract":[{"text":"Global storm-resolving models (GSRMs) use strongly refined horizontal grids compared with the climate models typically used in the Coupled Model Intercomparison Project (CMIP) but employ comparable vertical grid spacings. Here, we study how changes in the vertical grid spacing and adjustments to the integration time step affect the basic climate quantities simulated by the ICON-Sapphire atmospheric GSRM. Simulations are performed over a 45 d period for five different vertical grids with between 55 and 540 vertical layers and maximum tropospheric vertical grid spacings of between 800 and 50 m, respectively. The effects of changes in the vertical grid spacing are compared with the effects of reducing the horizontal grid spacing from 5 to 2.5 km. For most of the quantities considered, halving the vertical grid spacing has a smaller effect than halving the horizontal grid spacing, but it is not negligible. Each halving of the vertical grid spacing, along with the necessary reductions in time step length, increases cloud liquid water by about 7 %, compared with an approximate 16 % decrease for halving the horizontal grid spacing. The effect is due to both the vertical grid refinement and the time step reduction. There is no tendency toward convergence in the range of grid spacings tested here. The cloud ice amount also increases with a refinement in the vertical grid, but it is hardly affected by the time step length and does show a tendency to converge. While the effect on shortwave radiation is globally dominated by the altered reflection due to the change in the cloud liquid water content, the effect on longwave radiation is more difficult to interpret because changes in the cloud ice concentration and cloud fraction are anticorrelated in some regions. The simulations show that using a maximum tropospheric vertical grid spacing larger than 400 m would increase the truncation error strongly. Computing time investments in a further vertical grid refinement can affect the truncation errors of GSRMs similarly to comparable investments in horizontal refinement, because halving the vertical grid spacing is generally cheaper than halving the horizontal grid spacing. However, convergence of boundary layer cloud properties cannot be expected, even for the smallest maximum tropospheric grid spacing of 50 m used in this study.","lang":"eng"}]},{"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12311","ddc":["510"],"title":"Common valuations of division polynomials","status":"public","abstract":[{"text":"In this note, we prove a formula for the cancellation exponent kv,n between division polynomials ψn and ϕn associated with a sequence {nP}n∈N of points on an elliptic curve E defined over a discrete valuation field K. The formula greatly generalizes the previously known special cases and treats also the case of non-standard Kodaira types for non-perfect residue fields.","lang":"eng"}],"type":"journal_article","date_published":"2024-02-26T00:00:00Z","citation":{"short":"B. Naskręcki, M. Verzobio, Proceedings of the Royal Society of Edinburgh Section A: Mathematics (2024).","mla":"Naskręcki, Bartosz, and Matteo Verzobio. “Common Valuations of Division Polynomials.” Proceedings of the Royal Society of Edinburgh Section A: Mathematics, 2203.02015, Cambridge University Press, 2024, doi:10.1017/prm.2024.7.","chicago":"Naskręcki, Bartosz, and Matteo Verzobio. “Common Valuations of Division Polynomials.” Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press, 2024. https://doi.org/10.1017/prm.2024.7.","ama":"Naskręcki B, Verzobio M. Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics. 2024. doi:10.1017/prm.2024.7","apa":"Naskręcki, B., & Verzobio, M. (2024). Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press. https://doi.org/10.1017/prm.2024.7","ieee":"B. Naskręcki and M. Verzobio, “Common valuations of division polynomials,” Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press, 2024.","ista":"Naskręcki B, Verzobio M. 2024. Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics., 2203.02015."},"publication":"Proceedings of the Royal Society of Edinburgh Section A: Mathematics","article_type":"original","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"26","scopus_import":"1","keyword":["Elliptic curves","Néron models","division polynomials","height functions","discrete valuation rings"],"author":[{"last_name":"Naskręcki","first_name":"Bartosz","full_name":"Naskręcki, Bartosz"},{"last_name":"Verzobio","first_name":"Matteo","orcid":"0000-0002-0854-0306","id":"7aa8f170-131e-11ed-88e1-a9efd01027cb","full_name":"Verzobio, Matteo"}],"date_updated":"2024-03-13T11:55:21Z","date_created":"2023-01-16T11:45:22Z","year":"2024","acknowledgement":"Silverman, and Paul Voutier for the comments on the earlier version of this paper. The first author acknowledges the support by Dioscuri programme initiated by the Max Planck Society, jointly managed with the National Science Centre (Poland), and mutually funded by the Polish Ministry of Science and Higher Education and the German Federal Ministry of Education and Research. The second author has been supported by MIUR (Italy) through PRIN 2017 ‘Geometric, algebraic and analytic methods in arithmetic’ and has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","department":[{"_id":"TiBr"}],"publisher":"Cambridge University Press","publication_status":"epub_ahead","ec_funded":1,"article_number":"2203.02015","doi":"10.1017/prm.2024.7","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2203.02015"]},"main_file_link":[{"url":"https://doi.org/10.1017/prm.2024.7","open_access":"1"}],"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"quality_controlled":"1","publication_identifier":{"issn":["0308-2105"],"eissn":["1473-7124"]},"month":"02"},{"year":"2024","acknowledgement":"KJ, MR, and RKB were supported by grants from the Swedish Research Council (2021-0419, 2021-05243, and 2018-03695, respectively). RKB was also supported by the Leverhulme Trust (RPG-2021-141), RF by FCT- Portuguese Science Foundation (PTDC/BIA-EVL/1614/2021 and 2020.00275.CEECIND), and AMW by Norwegian Research Council RCN (Project number 315287). We thank the members of the Integration of Speciation Research network for stimulating discussions, the Littorina research community for important contributions of data and analyses, and Cynthia Riginos for useful comments on an earlier draft.","pmid":1,"publication_status":"epub_ahead","department":[{"_id":"NiBa"}],"publisher":"Cell Press","author":[{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"last_name":"Le Moan","first_name":"Alan","full_name":"Le Moan, Alan"},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."},{"full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"}],"date_created":"2024-03-10T23:00:54Z","date_updated":"2024-03-13T12:08:57Z","month":"02","publication_identifier":{"eissn":["1362-4555"],"issn":["0168-9525"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.tig.2024.01.002"}],"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":["38395682"]},"quality_controlled":"1","doi":"10.1016/j.tig.2024.01.002","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems.","lang":"eng"}],"_id":"15099","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Diverse pathways to speciation revealed by marine snails","status":"public","ddc":["570"],"oa_version":"Published Version","scopus_import":"1","day":"22","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","publication":"Trends in Genetics","citation":{"ama":"Johannesson K, Faria R, Le Moan A, et al. Diverse pathways to speciation revealed by marine snails. Trends in Genetics. 2024. doi:10.1016/j.tig.2024.01.002","ieee":"K. Johannesson et al., “Diverse pathways to speciation revealed by marine snails,” Trends in Genetics. Cell Press, 2024.","apa":"Johannesson, K., Faria, R., Le Moan, A., Rafajlović, M., Westram, A. M., Butlin, R. K., & Stankowski, S. (2024). Diverse pathways to speciation revealed by marine snails. Trends in Genetics. Cell Press. https://doi.org/10.1016/j.tig.2024.01.002","ista":"Johannesson K, Faria R, Le Moan A, Rafajlović M, Westram AM, Butlin RK, Stankowski S. 2024. Diverse pathways to speciation revealed by marine snails. Trends in Genetics.","short":"K. Johannesson, R. Faria, A. Le Moan, M. Rafajlović, A.M. Westram, R.K. Butlin, S. Stankowski, Trends in Genetics (2024).","mla":"Johannesson, Kerstin, et al. “Diverse Pathways to Speciation Revealed by Marine Snails.” Trends in Genetics, Cell Press, 2024, doi:10.1016/j.tig.2024.01.002.","chicago":"Johannesson, Kerstin, Rui Faria, Alan Le Moan, Marina Rafajlović, Anja M Westram, Roger K. Butlin, and Sean Stankowski. “Diverse Pathways to Speciation Revealed by Marine Snails.” Trends in Genetics. Cell Press, 2024. https://doi.org/10.1016/j.tig.2024.01.002."},"article_type":"review","date_published":"2024-02-22T00:00:00Z"},{"date_published":"2024-02-27T00:00:00Z","citation":{"short":"A. Agresti, E. Luongo, Mathematische Annalen (2024).","mla":"Agresti, Antonio, and Eliseo Luongo. “Global Well-Posedness and Interior Regularity of 2D Navier-Stokes Equations with Stochastic Boundary Conditions.” Mathematische Annalen, Springer Nature, 2024, doi:10.1007/s00208-024-02812-0.","chicago":"Agresti, Antonio, and Eliseo Luongo. “Global Well-Posedness and Interior Regularity of 2D Navier-Stokes Equations with Stochastic Boundary Conditions.” Mathematische Annalen. Springer Nature, 2024. https://doi.org/10.1007/s00208-024-02812-0.","ama":"Agresti A, Luongo E. Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen. 2024. doi:10.1007/s00208-024-02812-0","apa":"Agresti, A., & Luongo, E. (2024). Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen. Springer Nature. https://doi.org/10.1007/s00208-024-02812-0","ieee":"A. Agresti and E. Luongo, “Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions,” Mathematische Annalen. Springer Nature, 2024.","ista":"Agresti A, Luongo E. 2024. Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen."},"publication":"Mathematische Annalen","article_type":"original","article_processing_charge":"Yes (via OA deal)","day":"27","scopus_import":"1","oa_version":"Published Version","_id":"15098","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions","abstract":[{"lang":"eng","text":"The paper is devoted to the analysis of the global well-posedness and the interior regularity of the 2D Navier–Stokes equations with inhomogeneous stochastic boundary conditions. The noise, white in time and coloured in space, can be interpreted as the physical law describing the driving mechanism on the atmosphere–ocean interface, i.e. as a balance of the shear stress of the ocean and the horizontal wind force."}],"type":"journal_article","doi":"10.1007/s00208-024-02812-0","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00208-024-02812-0"}],"external_id":{"arxiv":["2306.11081"]},"oa":1,"project":[{"grant_number":"948819","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020","name":"Bridging Scales in Random Materials"}],"quality_controlled":"1","publication_identifier":{"eissn":["1432-1807"],"issn":["0025-5831"]},"month":"02","author":[{"orcid":"0000-0002-9573-2962","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","last_name":"Agresti","first_name":"Antonio","full_name":"Agresti, Antonio"},{"full_name":"Luongo, Eliseo","first_name":"Eliseo","last_name":"Luongo"}],"date_created":"2024-03-10T23:00:54Z","date_updated":"2024-03-13T12:20:23Z","year":"2024","acknowledgement":"The authors thank Professor Franco Flandoli for useful discussions and valuable insight into the subject. In particular, A.A. would like to thank professor Franco Flandoli for hosting and financially contributing to his research visit at Scuola Normale di Pisa in January 2023, where this work started. E.L. would like to express sincere gratitude to Professor Marco Fuhrman for igniting his interest in this particular field of research. E.L. want to thank Professor Matthias Hieber and Dr. Martin Saal for useful discussions. Finally, the authors thank the anonymous referee for helpful comments which improved the paper from its initial version.Open access funding provided by Scuola Normale Superiore within the CRUI-CARE Agreement. A. Agresti has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 948819).","department":[{"_id":"JuFi"}],"publisher":"Springer Nature","publication_status":"epub_ahead","ec_funded":1},{"oa_version":"None","title":"Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse","status":"public","_id":"14843","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission."}],"type":"journal_article","date_published":"2024-01-11T00:00:00Z","article_type":"original","citation":{"chicago":"Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” Neuron. Elsevier, n.d. https://doi.org/10.1016/j.neuron.2023.12.002.","short":"J. Chen, W. Kaufmann, C. Chen, itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas, Neuron (n.d.).","mla":"Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” Neuron, Elsevier, doi:10.1016/j.neuron.2023.12.002.","apa":"Chen, J., Kaufmann, W., Chen, C., Arai, itaru, Kim, O., Shigemoto, R., & Jonas, P. M. (n.d.). Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.12.002","ieee":"J. Chen et al., “Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse,” Neuron. Elsevier.","ista":"Chen J, Kaufmann W, Chen C, Arai itaru, Kim O, Shigemoto R, Jonas PM. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron.","ama":"Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. doi:10.1016/j.neuron.2023.12.002"},"publication":"Neuron","article_processing_charge":"No","day":"11","scopus_import":"1","date_updated":"2024-03-14T13:14:18Z","date_created":"2024-01-21T23:00:56Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"15101"}],"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/synapses-brought-to-the-point/"}]},"author":[{"last_name":"Chen","first_name":"JingJing","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, JingJing"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter"},{"full_name":"Chen, Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","first_name":"Chong","last_name":"Chen"},{"id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","last_name":"Arai","first_name":"Itaru","full_name":"Arai, Itaru"},{"first_name":"Olena","last_name":"Kim","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","full_name":"Kim, Olena"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M"}],"department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"publisher":"Elsevier","publication_status":"inpress","pmid":1,"acknowledgement":"We thank Drs. David DiGregorio and Erwin Neher for critically reading an earlier version of the manuscript, Ralf Schneggenburger for helpful discussions, Benjamin Suter and Katharina Lichter for support with image analysis, Chris Wojtan for advice on numerical solution of partial differential equations, Maria Reva for help with Ripley analysis, Alois Schlögl for programming, and Akari Hagiwara and Toshihisa Ohtsuka for anti-ELKS antibody. We are grateful to Florian Marr, Christina Altmutter, and Vanessa Zheden for excellent technical assistance and to Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA (Electron Microscopy Facility, Preclinical Facility, and Machine Shop). The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 692692), the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award; P 36232-B), all to P.J., and a DOC fellowship of the Austrian Academy of Sciences to J.-J.C.","year":"2024","ec_funded":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"M-Shop"}],"doi":"10.1016/j.neuron.2023.12.002","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5"},{"name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","_id":"26B66A3E-B435-11E9-9278-68D0E5697425","grant_number":"25383"}],"quality_controlled":"1","external_id":{"pmid":["38215739"]},"publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"month":"01"},{"page":"84","citation":{"chicago":"Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15101.","mla":"Chen, JingJing. Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15101.","short":"J. Chen, Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse, Institute of Science and Technology Austria, 2024.","ista":"Chen J. 2024. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria.","ieee":"J. Chen, “Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse,” Institute of Science and Technology Austria, 2024.","apa":"Chen, J. (2024). Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15101","ama":"Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:10.15479/at:ista:15101"},"date_published":"2024-03-11T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"11","status":"public","title":"Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse","ddc":["570"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"15101","oa_version":"Published Version","file":[{"access_level":"closed","file_name":"Thesis_Jingjing CHEN.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":11271363,"creator":"jchen","relation":"source_file","file_id":"15104","checksum":"db4947474ffa271e66c254b6fe876a55","date_created":"2024-03-11T14:10:58Z","date_updated":"2024-03-12T07:12:17Z"},{"content_type":"application/pdf","file_size":16627311,"creator":"jchen","embargo_to":"open_access","file_name":"Thesis_Jingjing CHEN_merged.pdf","access_level":"closed","date_updated":"2024-03-11T14:11:06Z","date_created":"2024-03-11T14:11:06Z","checksum":"a5eeae8b5702cd540f5d03469bc33dde","relation":"main_file","file_id":"15105","embargo":"2024-04-01"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312"},{"grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits"},{"grant_number":"25383","_id":"26B66A3E-B435-11E9-9278-68D0E5697425","name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse"}],"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"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"EM-Fac"}],"supervisor":[{"first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"}],"doi":"10.15479/at:ista:15101","publication_identifier":{"issn":["2663 - 337X"]},"month":"03","department":[{"_id":"GradSch"},{"_id":"PeJo"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2024","date_updated":"2024-03-14T13:14:19Z","date_created":"2024-03-11T10:09:54Z","related_material":{"record":[{"id":"14843","relation":"part_of_dissertation","status":"public"}]},"author":[{"last_name":"Chen","first_name":"JingJing","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, JingJing"}],"ec_funded":1,"file_date_updated":"2024-03-12T07:12:17Z"},{"doi":"10.1103/PhysRevResearch.6.013223","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2307.14427"]},"quality_controlled":"1","project":[{"name":"Quantum_Quantum Circuits and Software_Variational quantum algorithms on NISQ devices","_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d"}],"month":"03","publication_identifier":{"issn":["2643-1564"]},"author":[{"first_name":"Stefan","last_name":"Sack","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","orcid":"0000-0001-5400-8508","full_name":"Sack, Stefan"},{"full_name":"Egger, Daniel J.","first_name":"Daniel J.","last_name":"Egger"}],"date_created":"2024-03-17T23:00:59Z","date_updated":"2024-03-19T07:24:03Z","volume":6,"year":"2024","acknowledgement":"S.H.S. acknowledges support from the IBM Ph.D. fellowship 2022 in quantum computing. The authors also thank M. Serbyn, R. Kueng, R. A. Medina, and S. Woerner for fruitful discussions.","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"file_date_updated":"2024-03-19T07:16:38Z","article_number":"013223","date_published":"2024-03-01T00:00:00Z","publication":"Physical Review Research","citation":{"ieee":"S. Sack and D. J. Egger, “Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.","apa":"Sack, S., & Egger, D. J. (2024). Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.6.013223","ista":"Sack S, Egger DJ. 2024. Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. Physical Review Research. 6(1), 013223.","ama":"Sack S, Egger DJ. Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. Physical Review Research. 2024;6(1). doi:10.1103/PhysRevResearch.6.013223","chicago":"Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization on Nonplanar Graphs with Machine Learning Noise Mitigation.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/PhysRevResearch.6.013223.","short":"S. Sack, D.J. Egger, Physical Review Research 6 (2024).","mla":"Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization on Nonplanar Graphs with Machine Learning Noise Mitigation.” Physical Review Research, vol. 6, no. 1, 013223, American Physical Society, 2024, doi:10.1103/PhysRevResearch.6.013223."},"article_type":"original","day":"01","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"file_id":"15123","relation":"main_file","date_created":"2024-03-19T07:16:38Z","date_updated":"2024-03-19T07:16:38Z","success":1,"checksum":"274c9f1b15b3547a10a03f39e4ccc582","file_name":"2024_PhysicalReviewResearch_Sack.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":2777593}],"_id":"15122","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"status":"public","title":"Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation","intvolume":" 6","abstract":[{"lang":"eng","text":"Quantum computers are increasing in size and quality but are still very noisy. Error mitigation extends the size of the quantum circuits that noisy devices can meaningfully execute. However, state-of-the-art error mitigation methods are hard to implement and the limited qubit connectivity in superconducting qubit devices restricts most applications to the hardware's native topology. Here we show a quantum approximate optimization algorithm (QAOA) on nonplanar random regular graphs with up to 40 nodes enabled by a machine learning-based error mitigation. We use a swap network with careful decision-variable-to-qubit mapping and a feed-forward neural network to optimize a depth-two QAOA on up to 40 qubits. We observe a meaningful parameter optimization for the largest graph which requires running quantum circuits with 958 two-qubit gates. Our paper emphasizes the need to mitigate samples, and not only expectation values, in quantum approximate optimization. These results are a step towards executing quantum approximate optimization at a scale that is not classically simulable. Reaching such system sizes is key to properly understanding the true potential of heuristic algorithms like QAOA."}],"issue":"1","type":"journal_article"},{"type":"journal_article","issue":"3","abstract":[{"text":"Cell division in all domains of life requires the orchestration of many proteins, but in Archaea most of the machinery remains poorly characterized. Here we investigate the FtsZ-based cell division mechanism in Haloferax volcanii and find proteins containing photosynthetic reaction centre (PRC) barrel domains that play an essential role in archaeal cell division. We rename these proteins cell division protein B 1 (CdpB1) and CdpB2. Depletions and deletions in their respective genes cause severe cell division defects, generating drastically enlarged cells. Fluorescence microscopy of tagged FtsZ1, FtsZ2 and SepF in CdpB1 and CdpB2 mutant strains revealed an unusually disordered divisome that is not organized into a distinct ring-like structure. Biochemical analysis shows that SepF forms a tripartite complex with CdpB1/2 and crystal structures suggest that these two proteins might form filaments, possibly aligning SepF and the FtsZ2 ring during cell division. Overall our results indicate that PRC-domain proteins play essential roles in FtsZ-based cell division in Archaea.","lang":"eng"}],"_id":"15118","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 9","status":"public","title":"Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division","oa_version":"None","scopus_import":"1","article_processing_charge":"No","day":"04","citation":{"short":"P. Nußbaum, D. Kureisaite-Ciziene, D. Bellini, C. Van Der Does, M. Kojic, N. Taib, A. Yeates, M. Tourte, S. Gribaldo, M. Loose, J. Löwe, S.V. Albers, Nature Microbiology 9 (2024) 698–711.","mla":"Nußbaum, Phillip, et al. “Proteins Containing Photosynthetic Reaction Centre Domains Modulate FtsZ-Based Archaeal Cell Division.” Nature Microbiology, vol. 9, no. 3, Springer Nature, 2024, pp. 698–711, doi:10.1038/s41564-024-01600-5.","chicago":"Nußbaum, Phillip, Danguole Kureisaite-Ciziene, Dom Bellini, Chris Van Der Does, Marko Kojic, Najwa Taib, Anna Yeates, et al. “Proteins Containing Photosynthetic Reaction Centre Domains Modulate FtsZ-Based Archaeal Cell Division.” Nature Microbiology. Springer Nature, 2024. https://doi.org/10.1038/s41564-024-01600-5.","ama":"Nußbaum P, Kureisaite-Ciziene D, Bellini D, et al. Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology. 2024;9(3):698-711. doi:10.1038/s41564-024-01600-5","ieee":"P. Nußbaum et al., “Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division,” Nature Microbiology, vol. 9, no. 3. Springer Nature, pp. 698–711, 2024.","apa":"Nußbaum, P., Kureisaite-Ciziene, D., Bellini, D., Van Der Does, C., Kojic, M., Taib, N., … Albers, S. V. (2024). Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-024-01600-5","ista":"Nußbaum P, Kureisaite-Ciziene D, Bellini D, Van Der Does C, Kojic M, Taib N, Yeates A, Tourte M, Gribaldo S, Loose M, Löwe J, Albers SV. 2024. Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology. 9(3), 698–711."},"publication":"Nature Microbiology","page":"698-711","article_type":"original","date_published":"2024-03-04T00:00:00Z","pmid":1,"year":"2024","acknowledgement":"We thank X. Ye (ISTA) for providing the His–SUMO expression plasmid pSVA13429. pCDB302 was a gift from C. Bahl (Addgene plasmid number 113673; http://n2t.net/addgene:113673; RRID Addgene_113673). We thank B. Ahsan, G. Sharov, G. Cannone and S. Chen from the Medical Research Council (MRC) LMB Electron Microscopy Facility for help and support. We thank Scientific Computing at the MRC LMB for their support. We thank L. Trübestein and N. Krasnici of the protein service unit of the ISTA Lab Support Facility for help with the SEC coupled with multi-angle light scattering experiments. We thank D. Grohmann and R. Reichelt from the Archaea Centre at the University of Regensburg for providing the P. furiosus cell material. P.N. and S.-V.A. were supported by a Momentum grant from the Volkswagen (VW) Foundation (grant number 94933). D.K.-C. and D.B. were supported by the VW Stiftung ‘Life?’ programme (to J.L.; grant number Az 96727) and by the MRC, as part of UK Research and Innovation (UKRI), MRC file reference number U105184326 (to J.L.). N.T. and S.G. acknowledge support from the French Government’s Investissement d’Avenir program, Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (grant number ANR-10-LABX-62-IBEID), and the computational and storage services (Maestro cluster) provided by the IT department at Institut Pasteur. M.K. and M.L. were supported by the Austrian Science Fund (FWF) Stand-Alone P34607. For the purpose of open access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any author accepted manuscript version arising.","publisher":"Springer Nature","department":[{"_id":"MaLo"}],"publication_status":"published","author":[{"full_name":"Nußbaum, Phillip","first_name":"Phillip","last_name":"Nußbaum"},{"last_name":"Kureisaite-Ciziene","first_name":"Danguole","full_name":"Kureisaite-Ciziene, Danguole"},{"full_name":"Bellini, Dom","last_name":"Bellini","first_name":"Dom"},{"last_name":"Van Der Does","first_name":"Chris","full_name":"Van Der Does, Chris"},{"full_name":"Kojic, Marko","id":"73e7ecd4-dc85-11ea-9058-88a16394b160","last_name":"Kojic","first_name":"Marko"},{"last_name":"Taib","first_name":"Najwa","full_name":"Taib, Najwa"},{"full_name":"Yeates, Anna","last_name":"Yeates","first_name":"Anna"},{"full_name":"Tourte, Maxime","last_name":"Tourte","first_name":"Maxime"},{"last_name":"Gribaldo","first_name":"Simonetta","full_name":"Gribaldo, Simonetta"},{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","first_name":"Martin","last_name":"Loose"},{"first_name":"Jan","last_name":"Löwe","full_name":"Löwe, Jan"},{"full_name":"Albers, Sonja Verena","last_name":"Albers","first_name":"Sonja Verena"}],"volume":9,"date_updated":"2024-03-19T07:30:53Z","date_created":"2024-03-17T23:00:58Z","publication_identifier":{"eissn":["2058-5276"]},"month":"03","external_id":{"pmid":["38443575"]},"project":[{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607","name":"Understanding bacterial cell division by in vitro\r\nreconstitution"}],"quality_controlled":"1","doi":"10.1038/s41564-024-01600-5","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}]},{"year":"2024","acknowledgement":"The first author has been partially supported by the Nachwuchsring – Network for the promotion of young scientists – at TU Kaiserslautern. The second author is supported by the VIDI subsidy 639.032.427 of the Netherlands Organisation for Scientific Research (NWO). The authors thank the anonymous referees and Max Sauerbrey for careful reading and helpful suggestions.","publication_status":"published","publisher":"Institute of Mathematical Statistics","department":[{"_id":"JuFi"}],"author":[{"id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","orcid":"0000-0002-9573-2962","first_name":"Antonio","last_name":"Agresti","full_name":"Agresti, Antonio"},{"full_name":"Veraar, Mark","first_name":"Mark","last_name":"Veraar"}],"date_created":"2024-03-17T23:00:58Z","date_updated":"2024-03-19T08:14:17Z","volume":60,"month":"02","publication_identifier":{"issn":["0246-0203"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.01274","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2106.01274"]},"quality_controlled":"1","doi":"10.1214/22-AIHP1333","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"In this paper we consider an SPDE where the leading term is a second order operator with periodic boundary conditions, coefficients which are measurable in (t,ω) , and Hölder continuous in space. Assuming stochastic parabolicity conditions, we prove Lp((0,T)×Ω,tκdt;Hσ,q(Td)) -estimates. The main novelty is that we do not require p=q . Moreover, we allow arbitrary σ∈R and weights in time. Such mixed regularity estimates play a crucial role in applications to nonlinear SPDEs which is clear from our previous work. To prove our main results we develop a general perturbation theory for SPDEs. Moreover, we prove a new result on pointwise multiplication in spaces with fractional smoothness."}],"issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15119","status":"public","title":"Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions","intvolume":" 60","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Annales de l'institut Henri Poincare Probability and Statistics","citation":{"ieee":"A. Agresti and M. Veraar, “Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions,” Annales de l’institut Henri Poincare Probability and Statistics, vol. 60, no. 1. Institute of Mathematical Statistics, pp. 413–430, 2024.","apa":"Agresti, A., & Veraar, M. (2024). Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions. Annales de l’institut Henri Poincare Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/22-AIHP1333","ista":"Agresti A, Veraar M. 2024. Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions. Annales de l’institut Henri Poincare Probability and Statistics. 60(1), 413–430.","ama":"Agresti A, Veraar M. Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions. Annales de l’institut Henri Poincare Probability and Statistics. 2024;60(1):413-430. doi:10.1214/22-AIHP1333","chicago":"Agresti, Antonio, and Mark Veraar. “Stochastic Maximal Lp(Lq)-Regularity for Second Order Systems with Periodic Boundary Conditions.” Annales de l’institut Henri Poincare Probability and Statistics. Institute of Mathematical Statistics, 2024. https://doi.org/10.1214/22-AIHP1333.","short":"A. Agresti, M. Veraar, Annales de l’institut Henri Poincare Probability and Statistics 60 (2024) 413–430.","mla":"Agresti, Antonio, and Mark Veraar. “Stochastic Maximal Lp(Lq)-Regularity for Second Order Systems with Periodic Boundary Conditions.” Annales de l’institut Henri Poincare Probability and Statistics, vol. 60, no. 1, Institute of Mathematical Statistics, 2024, pp. 413–30, doi:10.1214/22-AIHP1333."},"article_type":"original","page":"413-430","date_published":"2024-02-01T00:00:00Z"},{"date_published":"2024-03-12T00:00:00Z","article_type":"original","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"mla":"Habig, Michael, et al. “Frequent Horizontal Chromosome Transfer between Asexual Fungal Insect Pathogens.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11, e2316284121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2316284121.","short":"M. Habig, A.V. Grasse, J. Müller, E.H. Stukenbrock, H. Leitner, S. Cremer, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","chicago":"Habig, Michael, Anna V Grasse, Judith Müller, Eva H. Stukenbrock, Hanna Leitner, and Sylvia Cremer. “Frequent Horizontal Chromosome Transfer between Asexual Fungal Insect Pathogens.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2316284121.","ama":"Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(11). doi:10.1073/pnas.2316284121","ista":"Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. 2024. Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. 121(11), e2316284121.","apa":"Habig, M., Grasse, A. V., Müller, J., Stukenbrock, E. H., Leitner, H., & Cremer, S. (2024). Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2316284121","ieee":"M. Habig, A. V. Grasse, J. Müller, E. H. Stukenbrock, H. Leitner, and S. Cremer, “Frequent horizontal chromosome transfer between asexual fungal insect pathogens,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11. Proceedings of the National Academy of Sciences, 2024."},"day":"12","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":5750361,"file_name":"2024_PNAS_Habig.pdf","access_level":"open_access","date_created":"2024-03-19T09:02:57Z","date_updated":"2024-03-19T09:02:57Z","success":1,"checksum":"f5e871db617b682edc71fcd08670dc81","file_id":"15124","relation":"main_file"}],"title":"Frequent horizontal chromosome transfer between asexual fungal insect pathogens","ddc":["570"],"status":"public","intvolume":" 121","_id":"14478","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Entire chromosomes are typically only transmitted vertically from one generation to the next. The horizontal transfer of such chromosomes has long been considered improbable, yet gained recent support in several pathogenic fungi where it may affect the fitness or host specificity. To date, it is unknown how these transfers occur, how common they are and whether they can occur between different species. In this study, we show multiple independent instances of horizontal transfers of the same accessory chromosome between two distinct strains of the asexual entomopathogenic fungusMetarhizium robertsiiduring experimental co-infection of its insect host, the Argentine ant. Notably, only the one chromosome – but no other – was transferred from the donor to the recipient strain. The recipient strain, now harboring the accessory chromosome, exhibited a competitive advantage under certain host conditions. By phylogenetic analysis we further demonstrate that the same accessory chromosome was horizontally transferred in a natural environment betweenM. robertsiiand another congeneric insect pathogen,M. guizhouense. Hence horizontal chromosome transfer is not limited to the observed frequent events within species during experimental infections but also occurs naturally across species. The transferred accessory chromosome contains genes that might be involved in its preferential horizontal transfer, encoding putative histones and histone-modifying enzymes, but also putative virulence factors that may support its establishment. Our study reveals that both intra- and interspecies horizontal transfer of entire chromosomes is more frequent than previously assumed, likely representing a not uncommon mechanism for gene exchange.Significance StatementThe enormous success of bacterial pathogens has been attributed to their ability to exchange genetic material between one another. Similarly, in eukaryotes, horizontal transfer of genetic material allowed the spread of virulence factors across species. The horizontal transfer of whole chromosomes could be an important pathway for such exchange of genetic material, but little is known about the origin of transferable chromosomes and how frequently they are exchanged. Here, we show that the transfer of accessory chromosomes - chromosomes that are non-essential but may provide fitness benefits - is common during fungal co-infections and is even possible between distant pathogenic species, highlighting the importance of horizontal gene transfer via chromosome transfer also for the evolution and function of eukaryotic pathogens."}],"issue":"11","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1073/pnas.2316284121","quality_controlled":"1","project":[{"grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Epidemics in ant societies on a chip"}],"oa":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"},"external_id":{"pmid":["38442176"]},"month":"03","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"date_created":"2023-10-31T13:30:00Z","date_updated":"2024-03-19T09:07:20Z","volume":121,"author":[{"full_name":"Habig, Michael","last_name":"Habig","first_name":"Michael"},{"full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","first_name":"Anna V"},{"full_name":"Müller, Judith","first_name":"Judith","last_name":"Müller"},{"full_name":"Stukenbrock, Eva H.","first_name":"Eva H.","last_name":"Stukenbrock"},{"first_name":"Hanna","last_name":"Leitner","id":"8fc5c6f6-5903-11ec-abad-c83f046253e7","full_name":"Leitner, Hanna"},{"orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia"}],"publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"SyCr"}],"acknowledgement":"We thank Bernhardt Steinwender, Jorgen Eilenberg, and Nicolai V. Meyling for the fungal strains. We further thank Chengshu Wang for providing the short sequencing reads for M. guizhouense ARESF977 he used for his published genome assembly, and Kristian Ullrich for help in the bioinformatics analysis for methylation pattern in Nanopore reads, and the VBC and the Max Planck Society for the use of their sequencing centers. We thank Barbara Milutinović and Hinrich Schulenburg for discussion, and Tal Dagan and Jens Rolff for comments on a previous version of the manuscript. Fig. 1A was created with BioRender.com. This study received funding by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP) to S.C. and by the German Research Foundation (DFG grant HA9263/1-1) to M.H.","year":"2024","pmid":1,"file_date_updated":"2024-03-19T09:02:57Z","ec_funded":1,"article_number":"e2316284121"},{"year":"2024","acknowledgement":"We thank the anonymous reviewers for their careful reading of our manuscript and their many insightful comments and suggestions. Open access funding provided by Institute of Science and Technology (IST Austria).","publication_status":"epub_ahead","publisher":"Springer Nature","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"author":[{"full_name":"Dvorak, Martin","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","orcid":"0000-0001-5293-214X","first_name":"Martin","last_name":"Dvorak"},{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-03-19T08:20:31Z","date_created":"2021-09-27T10:48:23Z","article_number":"2109.10203","file_date_updated":"2021-09-27T10:54:51Z","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":["2109.10203"]},"oa":1,"quality_controlled":"1","doi":"10.1007/s10107-024-02064-5","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["0025-5610"],"eissn":["1436-4646"]},"_id":"10045","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["004"],"title":"Generalized minimum 0-extension problem and discrete convexity","status":"public","oa_version":"Preprint","file":[{"file_id":"10046","relation":"main_file","success":1,"checksum":"e7e83065f7bc18b9c188bf93b5ca5db6","date_created":"2021-09-27T10:54:51Z","date_updated":"2021-09-27T10:54:51Z","access_level":"open_access","file_name":"Generalized-0-Ext.pdf","creator":"mdvorak","content_type":"application/pdf","file_size":603672}],"type":"journal_article","abstract":[{"lang":"eng","text":"Given a fixed finite metric space (V,μ), the {\\em minimum 0-extension problem}, denoted as 0-Ext[μ], is equivalent to the following optimization problem: minimize function of the form minx∈Vn∑ifi(xi)+∑ijcijμ(xi,xj) where cij,cvi are given nonnegative costs and fi:V→R are functions given by fi(xi)=∑v∈Vcviμ(xi,v). The computational complexity of 0-Ext[μ] has been recently established by Karzanov and by Hirai: if metric μ is {\\em orientable modular} then 0-Ext[μ] can be solved in polynomial time, otherwise 0-Ext[μ] is NP-hard. To prove the tractability part, Hirai developed a theory of discrete convex functions on orientable modular graphs generalizing several known classes of functions in discrete convex analysis, such as L♮-convex functions. We consider a more general version of the problem in which unary functions fi(xi) can additionally have terms of the form cuv;iμ(xi,{u,v}) for {u,v}∈F, where set F⊆(V2) is fixed. We extend the complexity classification above by providing an explicit condition on (μ,F) for the problem to be tractable. In order to prove the tractability part, we generalize Hirai's theory and define a larger class of discrete convex functions. It covers, in particular, another well-known class of functions, namely submodular functions on an integer lattice. Finally, we improve the complexity of Hirai's algorithm for solving 0-Ext on orientable modular graphs.\r\n"}],"publication":"Mathematical Programming","citation":{"apa":"Dvorak, M., & Kolmogorov, V. (2024). Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming. Springer Nature. https://doi.org/10.1007/s10107-024-02064-5","ieee":"M. Dvorak and V. Kolmogorov, “Generalized minimum 0-extension problem and discrete convexity,” Mathematical Programming. Springer Nature, 2024.","ista":"Dvorak M, Kolmogorov V. 2024. Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming., 2109.10203.","ama":"Dvorak M, Kolmogorov V. Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming. 2024. doi:10.1007/s10107-024-02064-5","chicago":"Dvorak, Martin, and Vladimir Kolmogorov. “Generalized Minimum 0-Extension Problem and Discrete Convexity.” Mathematical Programming. Springer Nature, 2024. https://doi.org/10.1007/s10107-024-02064-5.","short":"M. Dvorak, V. Kolmogorov, Mathematical Programming (2024).","mla":"Dvorak, Martin, and Vladimir Kolmogorov. “Generalized Minimum 0-Extension Problem and Discrete Convexity.” Mathematical Programming, 2109.10203, Springer Nature, 2024, doi:10.1007/s10107-024-02064-5."},"article_type":"original","date_published":"2024-03-07T00:00:00Z","scopus_import":"1","keyword":["minimum 0-extension problem","metric labeling problem","discrete metric spaces","metric extensions","computational complexity","valued constraint satisfaction problems","discrete convex analysis","L-convex functions"],"day":"07","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)"},{"ec_funded":1,"date_created":"2024-03-17T23:00:58Z","date_updated":"2024-03-19T08:32:32Z","author":[{"first_name":"Da Wei","last_name":"Zheng","full_name":"Zheng, Da Wei"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"13236"}]},"publication_status":"epub_ahead","department":[{"_id":"MoHe"}],"publisher":"Springer Nature","year":"2024","acknowledgement":"The first author thanks Chandra Chekuri for useful discussions about this paper. This work was done in part at the University of Vienna. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 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.","month":"03","publication_identifier":{"issn":["0025-5610"],"eissn":["1436-4646"]},"language":[{"iso":"eng"}],"doi":"10.1007/s10107-024-02066-3","quality_controlled":"1","project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564","call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures"},{"name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 ","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"external_id":{"arxiv":["2301.09217"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.09217"}],"oa":1,"abstract":[{"lang":"eng","text":"We present an auction algorithm using multiplicative instead of constant weight updates to compute a (1-E)-approximate maximum weight matching (MWM) in a bipartite graph with n vertices and m edges in time 0(mE-1), beating the running time of the fastest known approximation algorithm of Duan and Pettie [JACM ’14] that runs in 0(mE-1 log E-1). Our algorithm is very simple and it can be extended to give a dynamic data structure that maintains a (1-E)-approximate maximum weight matching under (1) one-sided vertex deletions (with incident edges) and (2) one-sided vertex insertions (with incident edges sorted by weight) to the other side. The total time time used is 0(mE-1), where m is the sum of the number of initially existing and inserted edges."}],"type":"journal_article","oa_version":"Preprint","title":"Multiplicative auction algorithm for approximate maximum weight bipartite matching","status":"public","_id":"15121","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"06","article_processing_charge":"No","scopus_import":"1","date_published":"2024-03-06T00:00:00Z","article_type":"original","publication":"Mathematical Programming","citation":{"ieee":"D. W. Zheng and M. H. Henzinger, “Multiplicative auction algorithm for approximate maximum weight bipartite matching,” Mathematical Programming. Springer Nature, 2024.","apa":"Zheng, D. W., & Henzinger, M. H. (2024). Multiplicative auction algorithm for approximate maximum weight bipartite matching. Mathematical Programming. Springer Nature. https://doi.org/10.1007/s10107-024-02066-3","ista":"Zheng DW, Henzinger MH. 2024. Multiplicative auction algorithm for approximate maximum weight bipartite matching. Mathematical Programming.","ama":"Zheng DW, Henzinger MH. Multiplicative auction algorithm for approximate maximum weight bipartite matching. Mathematical Programming. 2024. doi:10.1007/s10107-024-02066-3","chicago":"Zheng, Da Wei, and Monika H Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” Mathematical Programming. Springer Nature, 2024. https://doi.org/10.1007/s10107-024-02066-3.","short":"D.W. Zheng, M.H. Henzinger, Mathematical Programming (2024).","mla":"Zheng, Da Wei, and Monika H. Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” Mathematical Programming, Springer Nature, 2024, doi:10.1007/s10107-024-02066-3."}},{"article_processing_charge":"No","day":"04","scopus_import":"1","date_published":"2024-03-04T00:00:00Z","citation":{"ieee":"Z. Yao, X. Liu, R. Bunting, and J. Wang, “Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling,” Chemical Engineering Science, vol. 291. Elsevier, 2024.","apa":"Yao, Z., Liu, X., Bunting, R., & Wang, J. (2024). Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling. Chemical Engineering Science. Elsevier. https://doi.org/10.1016/j.ces.2024.119959","ista":"Yao Z, Liu X, Bunting R, Wang J. 2024. Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling. Chemical Engineering Science. 291, 119959.","ama":"Yao Z, Liu X, Bunting R, Wang J. Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling. Chemical Engineering Science. 2024;291. doi:10.1016/j.ces.2024.119959","chicago":"Yao, Zihao, Xu Liu, Rhys Bunting, and Jianguo Wang. “Unravelling the Reaction Mechanism for H2 Production via Formic Acid Decomposition over Pd: Coverage-Dependent Microkinetic Modeling.” Chemical Engineering Science. Elsevier, 2024. https://doi.org/10.1016/j.ces.2024.119959.","short":"Z. Yao, X. Liu, R. Bunting, J. Wang, Chemical Engineering Science 291 (2024).","mla":"Yao, Zihao, et al. “Unravelling the Reaction Mechanism for H2 Production via Formic Acid Decomposition over Pd: Coverage-Dependent Microkinetic Modeling.” Chemical Engineering Science, vol. 291, 119959, Elsevier, 2024, doi:10.1016/j.ces.2024.119959."},"publication":"Chemical Engineering Science","article_type":"original","abstract":[{"text":"As a key liquid organic hydrogen carrier, investigating the decomposition of formic acid (HCOOH) on the Pd (1 1 1) transition metal surface is imperative for harnessing hydrogen energy. Despite a multitude of studies, the major mechanisms and key intermediates involved in the dehydrogenation process of formic acid remain a great topic of debate due to ambiguous adsorbate interactions. In this research, we develop an advanced microkinetic model based on first-principles calculations, accounting for adsorbate–adsorbate interactions. Our study unveils a comprehensive mechanism for the Pd (1 1 1) surface, highlighting the significance of coverage effects in formic acid dehydrogenation. Our findings unequivocally demonstrate that H coverage on the Pd (1 1 1) surface renders formic acid more susceptible to decompose into H2 and CO2 through COOH intermediates. Consistent with experimental results, the selectivity of H2 in the decomposition of formic acid on the Pd (1 1 1) surface approaches 100 %. Considering the influence of H coverage, our kinetic analysis aligns perfectly with experimental values at a temperature of 373 K.","lang":"eng"}],"type":"journal_article","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15114","intvolume":" 291","title":"Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling","status":"public","publication_identifier":{"issn":["0009-2509"]},"month":"03","doi":"10.1016/j.ces.2024.119959","language":[{"iso":"eng"}],"quality_controlled":"1","article_number":"119959","author":[{"full_name":"Yao, Zihao","last_name":"Yao","first_name":"Zihao"},{"last_name":"Liu","first_name":"Xu","full_name":"Liu, Xu"},{"last_name":"Bunting","first_name":"Rhys","orcid":"0000-0001-6928-074X","id":"91deeae8-1207-11ec-b130-c194ad5b50c6","full_name":"Bunting, Rhys"},{"first_name":"Jianguo","last_name":"Wang","full_name":"Wang, Jianguo"}],"volume":291,"date_updated":"2024-03-19T08:47:42Z","date_created":"2024-03-17T23:00:57Z","acknowledgement":"The authors acknowledge the financial support from the National Key Research and Development Project of China (2021YFA1500900, 2022YFE0113800), the National Natural Science Foundation of China (22141001, U21A20298), Zhejiang Innovation Team (2017R5203).","year":"2024","publisher":"Elsevier","department":[{"_id":"MaIb"}],"publication_status":"epub_ahead"},{"article_number":"e2313162121","file_date_updated":"2024-03-19T10:22:42Z","publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"AnSa"}],"year":"2024","acknowledgement":"We thank Dr. Steven Roeters (Aarhus University), Dr. Federica Burla, and Prof. Dr. Mischa Bonn (Institute for Polymer Research, Mainz, Germany) for the useful discussions. We thank Dr. Wim Roeterdink and Michiel Hilberts for technical support. G.H.K. acknowledges financial support by the “BaSyC Building a Synthetic Cell” Gravitation grant (024.003.019) of The Netherlands Ministry of Education, Culture and Science (OCW) and The Netherlands Organization for Scientific Research and from NWO grant OCENW.GROOT.2019.022. This work has received support from the National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT, under Grant No. 2022K1A3A1A04062969. This publication is part of the project (with Project Number VI.Veni.212.240) of the research programme NWO Talent Programme Veni 2021, which is financed by the Dutch Research Council (NWO). I.M.I. acknowledges support from the Sectorplan Bèta & Techniek of the Dutch Government and the Dementia Research - Synapsis Foundation Switzerland. A.Š. and K.K. acknowledge support from Royal Society and European Research Council Starting Grant. G. Giubertoni kindly thanks to the Care4Bones community and the Collagen Café community for reminding that we do not own the knowledge we create, but it is, rather, a collective resource intended for the advancement of human progress.","pmid":1,"date_created":"2024-03-17T23:00:57Z","date_updated":"2024-03-19T11:41:32Z","volume":121,"author":[{"last_name":"Giubertoni","first_name":"Giulia","full_name":"Giubertoni, Giulia"},{"full_name":"Feng, Liru","last_name":"Feng","first_name":"Liru"},{"full_name":"Klein, Kevin","first_name":"Kevin","last_name":"Klein"},{"full_name":"Giannetti, Guido","first_name":"Guido","last_name":"Giannetti"},{"full_name":"Rutten, Luco","first_name":"Luco","last_name":"Rutten"},{"last_name":"Choi","first_name":"Yeji","full_name":"Choi, Yeji"},{"full_name":"Van Der Net, Anouk","last_name":"Van Der Net","first_name":"Anouk"},{"full_name":"Castro-Linares, Gerard","first_name":"Gerard","last_name":"Castro-Linares"},{"first_name":"Federico","last_name":"Caporaletti","full_name":"Caporaletti, Federico"},{"last_name":"Micha","first_name":"Dimitra","full_name":"Micha, Dimitra"},{"full_name":"Hunger, Johannes","first_name":"Johannes","last_name":"Hunger"},{"full_name":"Deblais, Antoine","first_name":"Antoine","last_name":"Deblais"},{"full_name":"Bonn, Daniel","first_name":"Daniel","last_name":"Bonn"},{"first_name":"Nico","last_name":"Sommerdijk","full_name":"Sommerdijk, Nico"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela"},{"last_name":"Ilie","first_name":"Ioana M.","full_name":"Ilie, Ioana M."},{"last_name":"Koenderink","first_name":"Gijsje H.","full_name":"Koenderink, Gijsje H."},{"first_name":"Sander","last_name":"Woutersen","full_name":"Woutersen, Sander"}],"related_material":{"record":[{"id":"15126","relation":"research_data","status":"public"}]},"month":"03","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"quality_controlled":"1","external_id":{"pmid":["38451946"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2313162121","type":"journal_article","abstract":[{"text":"Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water–collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H2O/D2O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H2O and D2O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D2O than in H2O, and collagen in D2O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H2O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D2O is less hydrated than in H2O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen–water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly.","lang":"eng"}],"issue":"11","ddc":["550"],"status":"public","title":"Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration","intvolume":" 121","_id":"15116","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"2024_PNAS_Giubertoni.pdf","access_level":"open_access","content_type":"application/pdf","file_size":12952586,"creator":"dernst","relation":"main_file","file_id":"15125","date_updated":"2024-03-19T10:22:42Z","date_created":"2024-03-19T10:22:42Z","checksum":"a3f7fdc29dd9f0a38952ab4e322b3a05","success":1}],"oa_version":"Published Version","scopus_import":"1","day":"12","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","article_type":"original","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"chicago":"Giubertoni, Giulia, Liru Feng, Kevin Klein, Guido Giannetti, Luco Rutten, Yeji Choi, Anouk Van Der Net, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2313162121.","mla":"Giubertoni, Giulia, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11, e2313162121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2313162121.","short":"G. Giubertoni, L. Feng, K. Klein, G. Giannetti, L. Rutten, Y. Choi, A. Van Der Net, G. Castro-Linares, F. Caporaletti, D. Micha, J. Hunger, A. Deblais, D. Bonn, N. Sommerdijk, A. Šarić, I.M. Ilie, G.H. Koenderink, S. Woutersen, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ista":"Giubertoni G, Feng L, Klein K, Giannetti G, Rutten L, Choi Y, Van Der Net A, Castro-Linares G, Caporaletti F, Micha D, Hunger J, Deblais A, Bonn D, Sommerdijk N, Šarić A, Ilie IM, Koenderink GH, Woutersen S. 2024. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. 121(11), e2313162121.","ieee":"G. Giubertoni et al., “Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11. Proceedings of the National Academy of Sciences, 2024.","apa":"Giubertoni, G., Feng, L., Klein, K., Giannetti, G., Rutten, L., Choi, Y., … Woutersen, S. (2024). Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2313162121","ama":"Giubertoni G, Feng L, Klein K, et al. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(11). doi:10.1073/pnas.2313162121"},"date_published":"2024-03-12T00:00:00Z"},{"scopus_import":"1","article_processing_charge":"No","day":"08","citation":{"short":"D.H. Vandael, P.M. Jonas, Science 383 (2024) eadg6757.","mla":"Vandael, David H., and Peter M. Jonas. “Structure, Biophysics, and Circuit Function of a ‘Giant’ Cortical Presynaptic Terminal.” Science, vol. 383, no. 6687, AAAS, 2024, p. eadg6757, doi:10.1126/science.adg6757.","chicago":"Vandael, David H, and Peter M Jonas. “Structure, Biophysics, and Circuit Function of a ‘Giant’ Cortical Presynaptic Terminal.” Science. AAAS, 2024. https://doi.org/10.1126/science.adg6757.","ama":"Vandael DH, Jonas PM. Structure, biophysics, and circuit function of a “giant” cortical presynaptic terminal. Science. 2024;383(6687):eadg6757. doi:10.1126/science.adg6757","apa":"Vandael, D. H., & Jonas, P. M. (2024). Structure, biophysics, and circuit function of a “giant” cortical presynaptic terminal. Science. AAAS. https://doi.org/10.1126/science.adg6757","ieee":"D. H. Vandael and P. M. Jonas, “Structure, biophysics, and circuit function of a ‘giant’ cortical presynaptic terminal,” Science, vol. 383, no. 6687. AAAS, p. eadg6757, 2024.","ista":"Vandael DH, Jonas PM. 2024. Structure, biophysics, and circuit function of a ‘giant’ cortical presynaptic terminal. Science. 383(6687), eadg6757."},"publication":"Science","page":"eadg6757","article_type":"review","date_published":"2024-03-08T00:00:00Z","type":"journal_article","issue":"6687","abstract":[{"lang":"eng","text":"The hippocampal mossy fiber synapse, formed between axons of dentate gyrus granule cells and dendrites of CA3 pyramidal neurons, is a key synapse in the trisynaptic circuitry of the hippocampus. Because of its comparatively large size, this synapse is accessible to direct presynaptic recording, allowing a rigorous investigation of the biophysical mechanisms of synaptic transmission and plasticity. Furthermore, because of its placement in the very center of the hippocampal memory circuit, this synapse seems to be critically involved in several higher network functions, such as learning, memory, pattern separation, and pattern completion. Recent work based on new technologies in both nanoanatomy and nanophysiology, including presynaptic patch-clamp recording, paired recording, super-resolution light microscopy, and freeze-fracture and “flash-and-freeze” electron microscopy, has provided new insights into the structure, biophysics, and network function of this intriguing synapse. This brings us one step closer to answering a fundamental question in neuroscience: how basic synaptic properties shape higher network computations."}],"_id":"15117","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 383","status":"public","title":"Structure, biophysics, and circuit function of a \"giant\" cortical presynaptic terminal","oa_version":"None","publication_identifier":{"eissn":["1095-9203"]},"month":"03","external_id":{"pmid":["38452088"]},"project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312"},{"grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits"}],"quality_controlled":"1","doi":"10.1126/science.adg6757","language":[{"iso":"eng"}],"ec_funded":1,"pmid":1,"acknowledgement":"We thank previous students, postdocs, and collaborators, particularly J. Geiger, and (in alphabetical order) H. Alle, J. Bischofberger, C. Borges-Merjane, D. Engel, M. Frotscher, S. Hallermann, M. Heckmann, S. Jamrichova, O. Kim, L. Li, K. Lichter, P. Lin, J. Lübke, Y. Okamoto, C. Pawlu, C. Schmidt-Hieber, N. Spruston, and N. Vyleta for their outstanding experimental contributions. We also thank P. Castillo, J. Geiger, T. Sakaba, S. Siegert, T. Vogels, and J. Watson for critically reading the manuscript, E. Kralli-Beller for text editing, and J. Malikovic and L. Slomianka for useful discussions. We apologize that, due to space constraints, not all relevant papers could be cited.\r\nThis project was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 692692, AdG “GIANTSYN”) and the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein Award; P 36232-B, stand-alone grant), both to P.J.","year":"2024","department":[{"_id":"PeJo"}],"publisher":"AAAS","publication_status":"published","author":[{"first_name":"David H","last_name":"Vandael","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H"},{"full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"}],"volume":383,"date_updated":"2024-03-20T07:42:52Z","date_created":"2024-03-17T23:00:57Z"},{"publication_identifier":{"issn":["2663 - 337X"]},"month":"03","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"}],"doi":"10.15479/at:ista:15094","project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342"},{"_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","grant_number":"I4887","name":"Discretization in Geometry and Dynamics"},{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ec_funded":1,"file_date_updated":"2024-03-14T14:14:35Z","date_created":"2024-03-08T15:28:10Z","date_updated":"2024-03-20T09:36:57Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11660"},{"status":"public","relation":"part_of_dissertation","id":"11658"},{"relation":"part_of_dissertation","status":"public","id":"13182"},{"id":"15090","relation":"part_of_dissertation","status":"public"},{"id":"15091","relation":"part_of_dissertation","status":"public"},{"id":"15093","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Cultrera di Montesano, Sebastiano","last_name":"Cultrera di Montesano","first_name":"Sebastiano","orcid":"0000-0001-6249-0832","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2024","has_accepted_license":"1","article_processing_charge":"No","day":"08","date_published":"2024-03-08T00:00:00Z","page":"108","citation":{"chicago":"Cultrera di Montesano, Sebastiano. “Persistence and Morse Theory for Discrete Geometric Structures.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15094.","short":"S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric Structures, Institute of Science and Technology Austria, 2024.","mla":"Cultrera di Montesano, Sebastiano. Persistence and Morse Theory for Discrete Geometric Structures. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15094.","ieee":"S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric structures,” Institute of Science and Technology Austria, 2024.","apa":"Cultrera di Montesano, S. (2024). Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15094","ista":"Cultrera di Montesano S. 2024. Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria.","ama":"Cultrera di Montesano S. Persistence and Morse theory for discrete geometric structures. 2024. doi:10.15479/at:ista:15094"},"abstract":[{"text":"Point sets, geometric networks, and arrangements of hyperplanes are fundamental objects in\r\ndiscrete geometry that have captivated mathematicians for centuries, if not millennia. This\r\nthesis seeks to cast new light on these structures by illustrating specific instances where a\r\ntopological perspective, specifically through discrete Morse theory and persistent homology,\r\nprovides valuable insights.\r\n\r\nAt first glance, the topology of these geometric objects might seem uneventful: point sets\r\nessentially lack of topology, arrangements of hyperplanes are a decomposition of Rd, which\r\nis a contractible space, and the topology of a network primarily involves the enumeration\r\nof connected components and cycles within the network. However, beneath this apparent\r\nsimplicity, there lies an array of intriguing structures, a small subset of which will be uncovered\r\nin this thesis.\r\n\r\nFocused on three case studies, each addressing one of the mentioned objects, this work\r\nwill showcase connections that intertwine topology with diverse fields such as combinatorial\r\ngeometry, algorithms and data structures, and emerging applications like spatial biology.\r\n\r\n","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"creator":"scultrer","file_size":4106872,"content_type":"application/pdf","access_level":"open_access","file_name":"Thesis Sebastiano.pdf","success":1,"checksum":"1e468bfa42a7dcf04d89f4dadc621c87","date_created":"2024-03-14T08:55:07Z","date_updated":"2024-03-14T08:55:07Z","file_id":"15112","relation":"main_file"},{"file_size":4746234,"content_type":"application/zip","creator":"scultrer","access_level":"closed","file_name":"Thesis (1).zip","checksum":"bcbd213490f5a7e68855a092bbce93f1","date_created":"2024-03-14T08:56:24Z","date_updated":"2024-03-14T14:14:35Z","relation":"source_file","file_id":"15113"}],"ddc":["514","500","516"],"title":"Persistence and Morse theory for discrete geometric structures","status":"public","_id":"15094","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"_id":"15093","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Dynamically maintaining the persistent homology of time series","status":"public","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"We present a dynamic data structure for maintaining the persistent homology of a time series of real numbers. The data structure supports local operations, including the insertion and deletion of an item and the cutting and concatenating of lists, each in time O(log n + k), in which n counts the critical items and k the changes in the augmented persistence diagram. To achieve this, we design a tailor-made tree structure with an unconventional representation, referred to as banana tree, which may be useful in its own right."}],"publication":"Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA)","citation":{"short":"S. Cultrera di Montesano, H. Edelsbrunner, M.H. Henzinger, L. Ost, in:, D.P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Society for Industrial and Applied Mathematics, 2024, pp. 243–295.","mla":"Cultrera di Montesano, Sebastiano, et al. “Dynamically Maintaining the Persistent Homology of Time Series.” Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), edited by David P. Woodruff, Society for Industrial and Applied Mathematics, 2024, pp. 243–95, doi:10.1137/1.9781611977912.11.","chicago":"Cultrera di Montesano, Sebastiano, Herbert Edelsbrunner, Monika H Henzinger, and Lara Ost. “Dynamically Maintaining the Persistent Homology of Time Series.” In Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), edited by David P. Woodruff, 243–95. Society for Industrial and Applied Mathematics, 2024. https://doi.org/10.1137/1.9781611977912.11.","ama":"Cultrera di Montesano S, Edelsbrunner H, Henzinger MH, Ost L. Dynamically maintaining the persistent homology of time series. In: Woodruff DP, ed. Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). Society for Industrial and Applied Mathematics; 2024:243-295. doi:10.1137/1.9781611977912.11","apa":"Cultrera di Montesano, S., Edelsbrunner, H., Henzinger, M. H., & Ost, L. (2024). Dynamically maintaining the persistent homology of time series. In D. P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA) (pp. 243–295). Alexandria, VA, USA: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977912.11","ieee":"S. Cultrera di Montesano, H. Edelsbrunner, M. H. Henzinger, and L. Ost, “Dynamically maintaining the persistent homology of time series,” in Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Alexandria, VA, USA, 2024, pp. 243–295.","ista":"Cultrera di Montesano S, Edelsbrunner H, Henzinger MH, Ost L. 2024. Dynamically maintaining the persistent homology of time series. Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). SODA: Symposium on Discrete Algorigthms, 243–295."},"page":"243 - 295","date_published":"2024-01-04T00:00:00Z","day":"04","article_processing_charge":"No","acknowledgement":"The first and second authors are funded by the European Research Council under the European Union’s Horizon 2020 research and innovation programme, ERC grant no. 788183,“Alpha Shape Theory Extended (Alpha)”, by the Wittgenstein Prize, FWF grant no. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, FWF grant no. I 02979-N35.The third author received funding by the European Research Council under the European Union’s Horizon 2020research and innovation programme, ERC grant no. 101019564, “The Design of Modern Fully Dynamic DataStructures (MoDynStruct)”, and by the Austrian Science Fund through the Wittgenstein Prize with FWF grant no. Z 422-N, and also by FWF grant no. I 5982-N, and by FWF grant no. P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. The fourth author is funded by the Vienna Graduate School on Computational Optimization, FWF project no. W1260-N35.","year":"2024","publication_status":"published","publisher":"Society for Industrial and Applied Mathematics","editor":[{"last_name":"Woodruff","first_name":"David P.","full_name":"Woodruff, David P."}],"department":[{"_id":"HeEd"},{"_id":"MoHe"}],"author":[{"id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-0832","first_name":"Sebastiano","last_name":"Cultrera di Montesano","full_name":"Cultrera di Montesano, Sebastiano"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H"},{"full_name":"Ost, Lara","first_name":"Lara","last_name":"Ost"}],"related_material":{"record":[{"id":"15094","relation":"dissertation_contains","status":"public"}]},"date_updated":"2024-03-20T09:36:56Z","date_created":"2024-03-08T10:27:39Z","ec_funded":1,"main_file_link":[{"url":"https://arxiv.org/abs/2311.01115","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2311.01115"]},"quality_controlled":"1","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342"},{"call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"name":"Wittgenstein Award - Monika Henzinger","grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775 "}],"conference":{"name":"SODA: Symposium on Discrete Algorigthms","start_date":"2024-01-07","location":"Alexandria, VA, USA","end_date":"2024-01-10"},"doi":"10.1137/1.9781611977912.11","language":[{"iso":"eng"}],"month":"01","publication_identifier":{"eisbn":["9781611977912"]}},{"article_processing_charge":"No","month":"02","day":"07","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"},"main_file_link":[{"url":"https://arxiv.org/abs/2212.03128","open_access":"1"}],"external_id":{"arxiv":["2212.03128"]},"citation":{"ama":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv.","ista":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv, 2212.03128.","apa":"Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., & Saghafian, M. (n.d.). Chromatic alpha complexes. arXiv.","ieee":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “Chromatic alpha complexes,” arXiv. .","mla":"Cultrera di Montesano, Sebastiano, et al. “Chromatic Alpha Complexes.” ArXiv, 2212.03128.","short":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, ArXiv (n.d.).","chicago":"Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “Chromatic Alpha Complexes.” ArXiv, n.d."},"publication":"arXiv","date_published":"2024-02-07T00:00:00Z","language":[{"iso":"eng"}],"type":"preprint","article_number":"2212.03128","abstract":[{"text":"Motivated by applications in the medical sciences, we study finite chromatic\r\nsets in Euclidean space from a topological perspective. Based on the persistent\r\nhomology for images, kernels and cokernels, we design provably stable\r\nhomological quantifiers that describe the geometric micro- and macro-structure\r\nof how the color classes mingle. These can be efficiently computed using\r\nchromatic variants of Delaunay and alpha complexes, and code that does these\r\ncomputations is provided.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"15091","year":"2024","department":[{"_id":"HeEd"}],"publication_status":"submitted","title":"Chromatic alpha complexes","status":"public","related_material":{"record":[{"id":"15094","relation":"dissertation_contains","status":"public"}]},"author":[{"last_name":"Cultrera di Montesano","first_name":"Sebastiano","orcid":"0000-0001-6249-0832","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","full_name":"Cultrera di Montesano, Sebastiano"},{"full_name":"Draganov, Ondrej","first_name":"Ondrej","last_name":"Draganov","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"},{"full_name":"Saghafian, Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824","first_name":"Morteza","last_name":"Saghafian"}],"oa_version":"Preprint","date_updated":"2024-03-20T09:36:56Z","date_created":"2024-03-08T10:13:59Z"},{"article_type":"original","publication":"Nature Neuroscience","citation":{"short":"E.J. Agnes, T.P. Vogels, Nature Neuroscience (2024).","mla":"Agnes, Everton J., and Tim P. Vogels. “Co-Dependent Excitatory and Inhibitory Plasticity Accounts for Quick, Stable and Long-Lasting Memories in Biological Networks.” Nature Neuroscience, Springer Nature, 2024, doi:10.1038/s41593-024-01597-4.","chicago":"Agnes, Everton J., and Tim P Vogels. “Co-Dependent Excitatory and Inhibitory Plasticity Accounts for Quick, Stable and Long-Lasting Memories in Biological Networks.” Nature Neuroscience. Springer Nature, 2024. https://doi.org/10.1038/s41593-024-01597-4.","ama":"Agnes EJ, Vogels TP. Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. Nature Neuroscience. 2024. doi:10.1038/s41593-024-01597-4","apa":"Agnes, E. J., & Vogels, T. P. (2024). Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-024-01597-4","ieee":"E. J. Agnes and T. P. Vogels, “Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks,” Nature Neuroscience. Springer Nature, 2024.","ista":"Agnes EJ, Vogels TP. 2024. Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. Nature Neuroscience."},"date_published":"2024-03-20T00:00:00Z","scopus_import":"1","day":"20","article_processing_charge":"Yes (via OA deal)","status":"public","title":"Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15171","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"The brain’s functionality is developed and maintained through synaptic plasticity. As synapses undergo plasticity, they also affect each other. The nature of such ‘co-dependency’ is difficult to disentangle experimentally, because multiple synapses must be monitored simultaneously. To help understand the experimentally observed phenomena, we introduce a framework that formalizes synaptic co-dependency between different connection types. The resulting model explains how inhibition can gate excitatory plasticity while neighboring excitatory–excitatory interactions determine the strength of long-term potentiation. Furthermore, we show how the interplay between excitatory and inhibitory synapses can account for the quick rise and long-term stability of a variety of synaptic weight profiles, such as orientation tuning and dendritic clustering of co-active synapses. In recurrent neuronal networks, co-dependent plasticity produces rich and stable motor cortex-like dynamics with high input sensitivity. Our results suggest an essential role for the neighborly synaptic interaction during learning, connecting micro-level physiology with network-wide phenomena.","lang":"eng"}],"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","grant_number":"819603"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.1038/s41593-024-01597-4","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41593-024-01597-4","month":"03","publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"publication_status":"epub_ahead","department":[{"_id":"TiVo"}],"publisher":"Springer Nature","year":"2024","acknowledgement":"We thank C. Currin, B. Podlaski and the members of the Vogels group for fruitful discussions. E.J.A. and T.P.V. were supported by a Research Project Grant from the Leverhulme Trust (RPG-2016-446; TPV), a Sir Henry Dale Fellowship from the Wellcome Trust and the Royal Society (WT100000; T.P.V.), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z; T.P.V.) and a European Research Council Consolidator Grant (SYNAPSEEK, 819603; T.P.V.). For the purpose of open access, the authors have applied a CC BY public copyright license to any author accepted manuscript version arising from this submission. Open access funding provided by University of Basel.","date_created":"2024-03-24T23:01:00Z","date_updated":"2024-03-25T07:04:05Z","author":[{"first_name":"Everton J.","last_name":"Agnes","full_name":"Agnes, Everton J."},{"full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","first_name":"Tim P"}],"ec_funded":1},{"external_id":{"arxiv":["2303.07245"]},"citation":{"chicago":"Esposito, Amedeo Roberto, and Marco Mondelli. “Concentration without Independence via Information Measures.” IEEE Transactions on Information Theory. IEEE, n.d. https://doi.org/10.1109/TIT.2024.3367767.","short":"A.R. Esposito, M. Mondelli, IEEE Transactions on Information Theory (n.d.).","mla":"Esposito, Amedeo Roberto, and Marco Mondelli. “Concentration without Independence via Information Measures.” IEEE Transactions on Information Theory, IEEE, doi:10.1109/TIT.2024.3367767.","ieee":"A. R. Esposito and M. Mondelli, “Concentration without independence via information measures,” IEEE Transactions on Information Theory. IEEE.","apa":"Esposito, A. R., & Mondelli, M. (n.d.). Concentration without independence via information measures. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2024.3367767","ista":"Esposito AR, Mondelli M. Concentration without independence via information measures. IEEE Transactions on Information Theory.","ama":"Esposito AR, Mondelli M. Concentration without independence via information measures. IEEE Transactions on Information Theory. doi:10.1109/TIT.2024.3367767"},"publication":"IEEE Transactions on Information Theory","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"article_type":"original","quality_controlled":"1","date_published":"2024-02-20T00:00:00Z","doi":"10.1109/TIT.2024.3367767","language":[{"iso":"eng"}],"scopus_import":"1","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"article_processing_charge":"No","day":"20","month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15172","year":"2024","department":[{"_id":"MaMo"}],"publisher":"IEEE","status":"public","publication_status":"inpress","title":"Concentration without independence via information measures","related_material":{"record":[{"id":"14922","status":"public","relation":"earlier_version"}]},"author":[{"full_name":"Esposito, Amedeo Roberto","id":"9583e921-e1ad-11ec-9862-cef099626dc9","last_name":"Esposito","first_name":"Amedeo Roberto"},{"last_name":"Mondelli","first_name":"Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco"}],"oa_version":"None","date_created":"2024-03-24T23:01:00Z","date_updated":"2024-03-25T07:15:51Z","type":"journal_article","abstract":[{"text":"We propose a novel approach to concentration for non-independent random variables. The main idea is to “pretend” that the random variables are independent and pay a multiplicative price measuring how far they are from actually being independent. This price is encapsulated in the Hellinger integral between the joint and the product of the marginals, which is then upper bounded leveraging tensorisation properties. Our bounds represent a natural generalisation of concentration inequalities in the presence of dependence: we recover exactly the classical bounds (McDiarmid’s inequality) when the random variables are independent. Furthermore, in a “large deviations” regime, we obtain the same decay in the probability as for the independent case, even when the random variables display non-trivial dependencies. To show this, we consider a number of applications of interest. First, we provide a bound for Markov chains with finite state space. Then, we consider the Simple Symmetric Random Walk, which is a non-contracting Markov chain, and a non-Markovian setting in which the stochastic process depends on its entire past. To conclude, we propose an application to Markov Chain Monte Carlo methods, where our approach leads to an improved lower bound on the minimum burn-in period required to reach a certain accuracy. In all of these settings, we provide a regime of parameters in which our bound fares better than what the state of the art can provide.","lang":"eng"}]},{"file":[{"file_name":"2024_AstrophysicalJourn_Greene.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":2700137,"file_id":"15176","relation":"main_file","date_updated":"2024-03-25T08:02:43Z","date_created":"2024-03-25T08:02:43Z","success":1,"checksum":"389a880e176799d5c062ea7cb82d08c9"}],"oa_version":"Published Version","_id":"15170","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 964","ddc":["550"],"status":"public","title":"UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5","abstract":[{"text":"The James Webb Space Telescope is revealing a new population of dust-reddened broad-line active galactic nuclei (AGN) at redshifts z ≳ 5. Here we present deep NIRSpec/Prism spectroscopy from the Cycle 1 Treasury program Ultradeep NIRSpec and NIRCam ObserVations before the Epoch of Reionization (UNCOVER) of 15 AGN candidates selected to be compact, with red continua in the rest-frame optical but with blue slopes in the UV. From NIRCam photometry alone, they could have been dominated by dusty star formation or an AGN. Here we show that the majority of the compact red sources in UNCOVER are dust-reddened AGN: 60% show definitive evidence for broad-line Hα with a FWHM > 2000 km s −1, 20% of the current data are inconclusive, and 20% are brown dwarf stars. We propose an updated photometric criterion to select red z > 5 AGN that excludes brown dwarfs and is expected to yield >80% AGN. Remarkably, among all zphot > 5 galaxies with F277W – F444W > 1 in UNCOVER at least 33% are AGN regardless of compactness, climbing to at least 80% AGN for sources with F277W – F444W > 1.6. The confirmed AGN have black hole masses of 107–109M⊙. While their UV luminosities (−16 > MUV > −20 AB mag) are low compared to UV-selected AGN at these epochs, consistent with percent-level scattered AGN light or low levels of unobscured star formation, the inferred bolometric luminosities are typical of 107–109M⊙ black holes radiating at ∼10%–40% the Eddington limit. The number densities are surprisingly high at ∼10−5 Mpc−3 mag−1, 100 times more common than the faintest UV-selected quasars, while accounting for ∼1% of the UV-selected galaxies. While their UV faintness suggests they may not contribute strongly to reionization, their ubiquity poses challenges to models of black hole growth.","lang":"eng"}],"type":"journal_article","date_published":"2024-03-01T00:00:00Z","citation":{"mla":"Greene, Jenny E., et al. “UNCOVER Spectroscopy Confirms the Surprising Ubiquity of Active Galactic Nuclei in Red Sources at z > 5.” Astrophysical Journal, vol. 964, 39, IOP Publishing, 2024, doi:10.3847/1538-4357/ad1e5f.","short":"J.E. Greene, I. Labbe, A.D. Goulding, L.J. Furtak, I. Chemerynska, V. Kokorev, P. Dayal, M. Volonteri, C.C. Williams, B. Wang, D.J. Setton, A.J. Burgasser, R. Bezanson, H. Atek, G. Brammer, S.E. Cutler, R. Feldmann, S. Fujimoto, K. Glazebrook, A. De Graaff, G. Khullar, J. Leja, D. Marchesini, M.V. Maseda, J.J. Matthee, T.B. Miller, R.P. Naidu, T. Nanayakkara, P.A. Oesch, R. Pan, C. Papovich, S.H. Price, P. Van Dokkum, J.R. Weaver, K.E. Whitaker, A. Zitrin, Astrophysical Journal 964 (2024).","chicago":"Greene, Jenny E., Ivo Labbe, Andy D. Goulding, Lukas J. Furtak, Iryna Chemerynska, Vasily Kokorev, Pratika Dayal, et al. “UNCOVER Spectroscopy Confirms the Surprising Ubiquity of Active Galactic Nuclei in Red Sources at z > 5.” Astrophysical Journal. IOP Publishing, 2024. https://doi.org/10.3847/1538-4357/ad1e5f.","ama":"Greene JE, Labbe I, Goulding AD, et al. UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5. Astrophysical Journal. 2024;964. doi:10.3847/1538-4357/ad1e5f","ista":"Greene JE, Labbe I, Goulding AD, Furtak LJ, Chemerynska I, Kokorev V, Dayal P, Volonteri M, Williams CC, Wang B, Setton DJ, Burgasser AJ, Bezanson R, Atek H, Brammer G, Cutler SE, Feldmann R, Fujimoto S, Glazebrook K, De Graaff A, Khullar G, Leja J, Marchesini D, Maseda MV, Matthee JJ, Miller TB, Naidu RP, Nanayakkara T, Oesch PA, Pan R, Papovich C, Price SH, Van Dokkum P, Weaver JR, Whitaker KE, Zitrin A. 2024. UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5. Astrophysical Journal. 964, 39.","apa":"Greene, J. E., Labbe, I., Goulding, A. D., Furtak, L. J., Chemerynska, I., Kokorev, V., … Zitrin, A. (2024). UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5. Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ad1e5f","ieee":"J. E. Greene et al., “UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5,” Astrophysical Journal, vol. 964. IOP Publishing, 2024."},"publication":"Astrophysical Journal","article_type":"original","article_processing_charge":"Yes","has_accepted_license":"1","day":"01","scopus_import":"1","author":[{"full_name":"Greene, Jenny E.","first_name":"Jenny E.","last_name":"Greene"},{"full_name":"Labbe, Ivo","last_name":"Labbe","first_name":"Ivo"},{"full_name":"Goulding, Andy D.","last_name":"Goulding","first_name":"Andy D."},{"full_name":"Furtak, Lukas J.","last_name":"Furtak","first_name":"Lukas J."},{"full_name":"Chemerynska, Iryna","first_name":"Iryna","last_name":"Chemerynska"},{"first_name":"Vasily","last_name":"Kokorev","full_name":"Kokorev, Vasily"},{"full_name":"Dayal, Pratika","first_name":"Pratika","last_name":"Dayal"},{"first_name":"Marta","last_name":"Volonteri","full_name":"Volonteri, Marta"},{"full_name":"Williams, Christina C.","first_name":"Christina C.","last_name":"Williams"},{"full_name":"Wang, Bingjie","first_name":"Bingjie","last_name":"Wang"},{"last_name":"Setton","first_name":"David J.","full_name":"Setton, David J."},{"last_name":"Burgasser","first_name":"Adam J.","full_name":"Burgasser, Adam J."},{"last_name":"Bezanson","first_name":"Rachel","full_name":"Bezanson, Rachel"},{"first_name":"Hakim","last_name":"Atek","full_name":"Atek, Hakim"},{"full_name":"Brammer, Gabriel","last_name":"Brammer","first_name":"Gabriel"},{"last_name":"Cutler","first_name":"Sam E.","full_name":"Cutler, Sam E."},{"full_name":"Feldmann, Robert","first_name":"Robert","last_name":"Feldmann"},{"full_name":"Fujimoto, Seiji","last_name":"Fujimoto","first_name":"Seiji"},{"full_name":"Glazebrook, Karl","first_name":"Karl","last_name":"Glazebrook"},{"last_name":"De Graaff","first_name":"Anna","full_name":"De Graaff, Anna"},{"last_name":"Khullar","first_name":"Gourav","full_name":"Khullar, Gourav"},{"first_name":"Joel","last_name":"Leja","full_name":"Leja, Joel"},{"full_name":"Marchesini, Danilo","last_name":"Marchesini","first_name":"Danilo"},{"first_name":"Michael V.","last_name":"Maseda","full_name":"Maseda, Michael V."},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","first_name":"Jorryt J","last_name":"Matthee","full_name":"Matthee, Jorryt J"},{"full_name":"Miller, Tim B.","first_name":"Tim B.","last_name":"Miller"},{"first_name":"Rohan P.","last_name":"Naidu","full_name":"Naidu, Rohan P."},{"last_name":"Nanayakkara","first_name":"Themiya","full_name":"Nanayakkara, Themiya"},{"first_name":"Pascal A.","last_name":"Oesch","full_name":"Oesch, Pascal A."},{"full_name":"Pan, Richard","first_name":"Richard","last_name":"Pan"},{"last_name":"Papovich","first_name":"Casey","full_name":"Papovich, Casey"},{"full_name":"Price, Sedona H.","first_name":"Sedona H.","last_name":"Price"},{"last_name":"Van Dokkum","first_name":"Pieter","full_name":"Van Dokkum, Pieter"},{"first_name":"John R.","last_name":"Weaver","full_name":"Weaver, John R."},{"full_name":"Whitaker, Katherine E.","last_name":"Whitaker","first_name":"Katherine E."},{"first_name":"Adi","last_name":"Zitrin","full_name":"Zitrin, Adi"}],"volume":964,"date_updated":"2024-03-25T08:04:13Z","date_created":"2024-03-24T23:00:59Z","year":"2024","acknowledgement":"J.E.G. and A.D.G acknowledge support from NSF/AAG grant No. 1007094, and J.E.G. also acknowledges support from NSF/AAG grant No. 1007052. A.Z. acknowledges support by grant No. 2020750 from the United States-Israel Binational Science Foundation (BSF) and grant No. 2109066 from the United States National Science Foundation (NSF), and by the Ministry of Science & Technology of Israel. The Cosmic Dawn Center is funded by the Danish National Research Foundation (DNRF) under grant No. 140. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. P.D. acknowledges support from the NWO grant 016.VIDI.189.162 (\"ODIN\") and from the European Commission's and University of Groningen's CO-FUND Rosalind Franklin program. K.G. and T.N. acknowledge support from Australian Research Council Laureate Fellowship FL180100060. H.A. and I.C. acknowledge support from CNES, focused on the JWST mission, and the Programme National Cosmology and Galaxies (PNCG) of CNRS/INSU with INP and IN2P3, cofunded by CEA and CNES. R.P.N. acknowledges funding from JWST programs GO-1933 and GO-2279. Support for this work was provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. The research of C.C.W. is supported by NOIRLab, which is managed by the Association of Universities for Research in Astronomy (AURA) under a cooperative agreement with the National Science Foundation. B.W. acknowledges support from JWST-GO-02561.022-A. A.J.B. acknowledges funding support from NASA/ADAP grant 21-ADAP21-0187. Support for this work was provided by The Brinson Foundation through a Brinson Prize Fellowship grant. R.P.N. acknowledges support for this work provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. C.P. thanks Marsha and Ralph Schilling for the generous support of this research.","department":[{"_id":"JoMa"}],"publisher":"IOP Publishing","publication_status":"published","file_date_updated":"2024-03-25T08:02:43Z","article_number":"39","doi":"10.3847/1538-4357/ad1e5f","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2309.05714"]},"quality_controlled":"1","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"month":"03"},{"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","citation":{"ista":"Filakovský M, Nakajima TV, Opršal J, Tasinato G, Wagner U. 2024. Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. 41st International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 289, 34.","apa":"Filakovský, M., Nakajima, T. V., Opršal, J., Tasinato, G., & Wagner, U. (2024). Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. In 41st International Symposium on Theoretical Aspects of Computer Science (Vol. 289). Clermont-Ferrand, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2024.34","ieee":"M. Filakovský, T. V. Nakajima, J. Opršal, G. Tasinato, and U. Wagner, “Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs,” in 41st International Symposium on Theoretical Aspects of Computer Science, Clermont-Ferrand, France, 2024, vol. 289.","ama":"Filakovský M, Nakajima TV, Opršal J, Tasinato G, Wagner U. Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. In: 41st International Symposium on Theoretical Aspects of Computer Science. Vol 289. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.STACS.2024.34","chicago":"Filakovský, Marek, Tamio Vesa Nakajima, Jakub Opršal, Gianluca Tasinato, and Uli Wagner. “Hardness of Linearly Ordered 4-Colouring of 3-Colourable 3-Uniform Hypergraphs.” In 41st International Symposium on Theoretical Aspects of Computer Science, Vol. 289. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.STACS.2024.34.","mla":"Filakovský, Marek, et al. “Hardness of Linearly Ordered 4-Colouring of 3-Colourable 3-Uniform Hypergraphs.” 41st International Symposium on Theoretical Aspects of Computer Science, vol. 289, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.STACS.2024.34.","short":"M. Filakovský, T.V. Nakajima, J. Opršal, G. Tasinato, U. Wagner, in:, 41st International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024."},"publication":"41st International Symposium on Theoretical Aspects of Computer Science","date_published":"2024-03-01T00:00:00Z","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"A linearly ordered (LO) k-colouring of a hypergraph is a colouring of its vertices with colours 1, … , k such that each edge contains a unique maximal colour. Deciding whether an input hypergraph admits LO k-colouring with a fixed number of colours is NP-complete (and in the special case of graphs, LO colouring coincides with the usual graph colouring). Here, we investigate the complexity of approximating the \"linearly ordered chromatic number\" of a hypergraph. We prove that the following promise problem is NP-complete: Given a 3-uniform hypergraph, distinguish between the case that it is LO 3-colourable, and the case that it is not even LO 4-colourable. We prove this result by a combination of algebraic, topological, and combinatorial methods, building on and extending a topological approach for studying approximate graph colouring introduced by Krokhin, Opršal, Wrochna, and Živný (2023).","lang":"eng"}],"intvolume":" 289","status":"public","ddc":["510"],"title":"Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs","_id":"15168","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"15175","relation":"main_file","success":1,"checksum":"0524d4189fd1ed08989546511343edf3","date_created":"2024-03-25T07:44:30Z","date_updated":"2024-03-25T07:44:30Z","access_level":"open_access","file_name":"2024_LIPICs_Filakovsky.pdf","creator":"dernst","content_type":"application/pdf","file_size":927290}],"oa_version":"Published Version","publication_identifier":{"isbn":["9783959773119"],"eissn":["1868-8969"]},"month":"03","project":[{"call_identifier":"FWF","name":"Algorithms for Embeddings and Homotopy Theory","grant_number":"P31312","_id":"26611F5C-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"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":["2312.12981"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.STACS.2024.34","conference":{"end_date":"2024-03-14","start_date":"2024-03-12","location":"Clermont-Ferrand, France","name":"STACS: Symposium on Theoretical Aspects of Computer Science"},"article_number":"34","ec_funded":1,"file_date_updated":"2024-03-25T07:44:30Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"publication_status":"published","acknowledgement":"Marek Filakovský: This research was supported by Charles University (project PRIMUS/\r\n21/SCI/014), the Austrian Science Fund (FWF project P31312-N35), and MSCAfellow5_MUNI\r\n(CZ.02.01.01/00/22_010/0003229). Tamio-Vesa Nakajima: This research was funded by UKRI EP/X024431/1 and by a Clarendon Fund Scholarship. All data is provided in full in the results section of this paper. Jakub Opršal: This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No 101034413. Uli Wagner: This research was supported by the Austrian Science Fund (FWF project P31312-N35).","year":"2024","volume":289,"date_created":"2024-03-24T23:00:59Z","date_updated":"2024-03-25T07:45:54Z","author":[{"last_name":"Filakovský","first_name":"Marek","id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87","full_name":"Filakovský, Marek"},{"first_name":"Tamio Vesa","last_name":"Nakajima","full_name":"Nakajima, Tamio Vesa"},{"id":"ec596741-c539-11ec-b829-c79322a91242","orcid":"0000-0003-1245-3456","first_name":"Jakub","last_name":"Opršal","full_name":"Opršal, Jakub"},{"full_name":"Tasinato, Gianluca","last_name":"Tasinato","first_name":"Gianluca","id":"0433290C-AF8F-11E9-A4C7-F729E6697425"},{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli"}]},{"date_published":"2024-03-14T00:00:00Z","citation":{"ama":"Chintaluri C, Bejtka M, Sredniawa W, et al. kCSD-python, reliable current source density estimation with quality control. PLoS Computational Biology. 2024;20(3). doi:10.1371/journal.pcbi.1011941","ista":"Chintaluri C, Bejtka M, Sredniawa W, Czerwinski M, Dzik JM, Jedrzejewska-Szmek J, Wojciki DK. 2024. kCSD-python, reliable current source density estimation with quality control. PLoS Computational Biology. 20(3), e1011941.","apa":"Chintaluri, C., Bejtka, M., Sredniawa, W., Czerwinski, M., Dzik, J. M., Jedrzejewska-Szmek, J., & Wojciki, D. K. (2024). kCSD-python, reliable current source density estimation with quality control. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1011941","ieee":"C. Chintaluri et al., “kCSD-python, reliable current source density estimation with quality control,” PLoS Computational Biology, vol. 20, no. 3. Public Library of Science, 2024.","mla":"Chintaluri, Chaitanya, et al. “KCSD-Python, Reliable Current Source Density Estimation with Quality Control.” PLoS Computational Biology, vol. 20, no. 3, e1011941, Public Library of Science, 2024, doi:10.1371/journal.pcbi.1011941.","short":"C. Chintaluri, M. Bejtka, W. Sredniawa, M. Czerwinski, J.M. Dzik, J. Jedrzejewska-Szmek, D.K. Wojciki, PLoS Computational Biology 20 (2024).","chicago":"Chintaluri, Chaitanya, Marta Bejtka, Wladyslaw Sredniawa, Michal Czerwinski, Jakub M. Dzik, Joanna Jedrzejewska-Szmek, and Daniel K. Wojciki. “KCSD-Python, Reliable Current Source Density Estimation with Quality Control.” PLoS Computational Biology. Public Library of Science, 2024. https://doi.org/10.1371/journal.pcbi.1011941."},"publication":"PLoS Computational Biology","article_type":"original","article_processing_charge":"Yes","day":"14","scopus_import":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15169","intvolume":" 20","title":"kCSD-python, reliable current source density estimation with quality control","status":"public","issue":"3","abstract":[{"lang":"eng","text":"Interpretation of extracellular recordings can be challenging due to the long range of electric field. This challenge can be mitigated by estimating the current source density (CSD). Here we introduce kCSD-python, an open Python package implementing Kernel Current Source Density (kCSD) method and related tools to facilitate CSD analysis of experimental data and the interpretation of results. We show how to counter the limitations imposed by noise and assumptions in the method itself. kCSD-python allows CSD estimation for an arbitrary distribution of electrodes in 1D, 2D, and 3D, assuming distributions of sources in tissue, a slice, or in a single cell, and includes a range of diagnostic aids. We demonstrate its features in a Jupyter Notebook tutorial which illustrates a typical analytical workflow and main functionalities useful in validating analysis results."}],"type":"journal_article","doi":"10.1371/journal.pcbi.1011941","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"month":"03","related_material":{"link":[{"relation":"software","url":"https://github.com/Neuroinflab/kCSD-python"}]},"author":[{"last_name":"Chintaluri","first_name":"Chaitanya","id":"E4EDB536-3485-11EA-98D2-20AF3DDC885E","full_name":"Chintaluri, Chaitanya"},{"full_name":"Bejtka, Marta","first_name":"Marta","last_name":"Bejtka"},{"full_name":"Sredniawa, Wladyslaw","first_name":"Wladyslaw","last_name":"Sredniawa"},{"first_name":"Michal","last_name":"Czerwinski","full_name":"Czerwinski, Michal"},{"full_name":"Dzik, Jakub M.","last_name":"Dzik","first_name":"Jakub M."},{"last_name":"Jedrzejewska-Szmek","first_name":"Joanna","full_name":"Jedrzejewska-Szmek, Joanna"},{"full_name":"Wojciki, Daniel K.","last_name":"Wojciki","first_name":"Daniel K."}],"volume":20,"date_created":"2024-03-24T23:00:59Z","date_updated":"2024-03-25T07:54:23Z","year":"2024","acknowledgement":"The Python implementation of kCSD was started by Grzegorz Parka during Google Summer of Code project through the International Neuroinformatics Coordinating Facility. Jan Mąka implemented the first Python version of skCSD class. This work was supported by the Polish National Science Centre (2013/08/W/NZ4/00691 to DKW; 2015/17/B/ST7/04123 to DKW). ","publisher":"Public Library of Science","department":[{"_id":"TiVo"}],"publication_status":"published","article_number":"e1011941"},{"date_updated":"2024-03-25T07:36:55Z","date_created":"2024-03-24T23:00:59Z","volume":109,"author":[{"first_name":"Ragheed","last_name":"Al Hyder","id":"d1c405be-ae15-11ed-8510-ccf53278162e","full_name":"Al Hyder, Ragheed"},{"first_name":"F.","last_name":"Chevy","full_name":"Chevy, F."},{"full_name":"Leyronas, X.","first_name":"X.","last_name":"Leyronas"}],"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"year":"2024","acknowledgement":"We thank Félix Werner and Kris Van Houcke for interesting discussions.","article_number":"033315","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.109.033315","quality_controlled":"1","oa":1,"external_id":{"arxiv":["2311.14536"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2311.14536"}],"month":"03","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"oa_version":"Preprint","status":"public","title":"Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy","intvolume":" 109","_id":"15167","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We perform a diagrammatic analysis of the energy of a mobile impurity immersed in a strongly interacting two-component Fermi gas to second order in the impurity-bath interaction. These corrections demonstrate divergent behavior in the limit of large impurity momentum. We show the fundamental processes responsible for these logarithmically divergent terms. We study the problem in the general case without any assumptions regarding the fermion-fermion interactions in the bath. We show that the divergent term can be summed up to all orders in the Fermi-Fermi interaction and that the resulting expression is equivalent to the one obtained in the few-body calculation. Finally, we provide a perturbative calculation to the second order in the Fermi-Fermi interaction, and we show the diagrams responsible for these terms.","lang":"eng"}],"issue":"3","type":"journal_article","date_published":"2024-03-19T00:00:00Z","article_type":"original","publication":"Physical Review A","citation":{"ieee":"R. Al Hyder, F. Chevy, and X. Leyronas, “Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy,” Physical Review A, vol. 109, no. 3. American Physical Society, 2024.","apa":"Al Hyder, R., Chevy, F., & Leyronas, X. (2024). Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.109.033315","ista":"Al Hyder R, Chevy F, Leyronas X. 2024. Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy. Physical Review A. 109(3), 033315.","ama":"Al Hyder R, Chevy F, Leyronas X. Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy. Physical Review A. 2024;109(3). doi:10.1103/PhysRevA.109.033315","chicago":"Al Hyder, Ragheed, F. Chevy, and X. Leyronas. “Exploring Beyond-Mean-Field Logarithmic Divergences in Fermi-Polaron Energy.” Physical Review A. American Physical Society, 2024. https://doi.org/10.1103/PhysRevA.109.033315.","short":"R. Al Hyder, F. Chevy, X. Leyronas, Physical Review A 109 (2024).","mla":"Al Hyder, Ragheed, et al. “Exploring Beyond-Mean-Field Logarithmic Divergences in Fermi-Polaron Energy.” Physical Review A, vol. 109, no. 3, 033315, American Physical Society, 2024, doi:10.1103/PhysRevA.109.033315."},"day":"19","article_processing_charge":"No","scopus_import":"1"},{"_id":"15163","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Decompositions into two linear forests of bounded lengths","intvolume":" 347","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"For some k∈Z≥0∪{∞}, we call a linear forest k-bounded if each of its components has at most k edges. We will say a (k,ℓ)-bounded linear forest decomposition of a graph G is a partition of E(G) into the edge sets of two linear forests Fk,Fℓ where Fk is k-bounded and Fℓ is ℓ-bounded. We show that the problem of deciding whether a given graph has such a decomposition is NP-complete if both k and ℓ are at least 2, NP-complete if k≥9 and ℓ=1, and is in P for (k,ℓ)=(2,1). Before this, the only known NP-complete cases were the (2,2) and (3,3) cases. Our hardness result answers a question of Bermond et al. from 1984. We also show that planar graphs of girth at least nine decompose into a linear forest and a matching, which in particular is stronger than 3-edge-colouring such graphs.","lang":"eng"}],"issue":"6","publication":"Discrete Mathematics","citation":{"ista":"Campbell R, Hörsch F, Moore B. 2024. Decompositions into two linear forests of bounded lengths. Discrete Mathematics. 347(6), 113962.","ieee":"R. Campbell, F. Hörsch, and B. Moore, “Decompositions into two linear forests of bounded lengths,” Discrete Mathematics, vol. 347, no. 6. Elsevier, 2024.","apa":"Campbell, R., Hörsch, F., & Moore, B. (2024). Decompositions into two linear forests of bounded lengths. Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.disc.2024.113962","ama":"Campbell R, Hörsch F, Moore B. Decompositions into two linear forests of bounded lengths. Discrete Mathematics. 2024;347(6). doi:10.1016/j.disc.2024.113962","chicago":"Campbell, Rutger, Florian Hörsch, and Benjamin Moore. “Decompositions into Two Linear Forests of Bounded Lengths.” Discrete Mathematics. Elsevier, 2024. https://doi.org/10.1016/j.disc.2024.113962.","mla":"Campbell, Rutger, et al. “Decompositions into Two Linear Forests of Bounded Lengths.” Discrete Mathematics, vol. 347, no. 6, 113962, Elsevier, 2024, doi:10.1016/j.disc.2024.113962.","short":"R. Campbell, F. Hörsch, B. Moore, Discrete Mathematics 347 (2024)."},"article_type":"original","date_published":"2024-03-19T00:00:00Z","scopus_import":"1","day":"19","article_processing_charge":"No","year":"2024","acknowledgement":"We wish to thank Dániel Marx and András Sebő for making us aware of the results in [8] and some clarifications on them.","publication_status":"epub_ahead","department":[{"_id":"MaKw"}],"publisher":"Elsevier","author":[{"full_name":"Campbell, Rutger","first_name":"Rutger","last_name":"Campbell"},{"full_name":"Hörsch, Florian","last_name":"Hörsch","first_name":"Florian"},{"last_name":"Moore","first_name":"Benjamin","id":"6dc1a1be-bf1c-11ed-8d2b-d044840f49d6","full_name":"Moore, Benjamin"}],"date_updated":"2024-03-25T08:09:43Z","date_created":"2024-03-24T23:00:58Z","volume":347,"article_number":"113962","external_id":{"arxiv":["2301.11615"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.11615"}],"oa":1,"quality_controlled":"1","doi":"10.1016/j.disc.2024.113962","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["0012-365X"]}},{"date_published":"2024-03-07T00:00:00Z","citation":{"ama":"Matthee JJ, Naidu RP, Brammer G, et al. Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys. The Astrophysical Journal. 2024;963(2). doi:10.3847/1538-4357/ad2345","ista":"Matthee JJ, Naidu RP, Brammer G, Chisholm J, Eilers A-C, Goulding A, Greene J, Kashino D, Labbe I, Lilly SJ, Mackenzie R, Oesch PA, Weibel A, Wuyts S, Xiao M, Bordoloi R, Bouwens R, van Dokkum P, Illingworth G, Kramarenko I, Maseda MV, Mason C, Meyer RA, Nelson EJ, Reddy NA, Shivaei I, Simcoe RA, Yue M. 2024. Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys. The Astrophysical Journal. 963(2), 129.","apa":"Matthee, J. J., Naidu, R. P., Brammer, G., Chisholm, J., Eilers, A.-C., Goulding, A., … Yue, M. (2024). Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/ad2345","ieee":"J. J. Matthee et al., “Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys,” The Astrophysical Journal, vol. 963, no. 2. American Astronomical Society, 2024.","mla":"Matthee, Jorryt J., et al. “Little Red Dots: An Abundant Population of Faint Active Galactic Nuclei at z ∼ 5 Revealed by the EIGER and FRESCO JWST Surveys.” The Astrophysical Journal, vol. 963, no. 2, 129, American Astronomical Society, 2024, doi:10.3847/1538-4357/ad2345.","short":"J.J. Matthee, R.P. Naidu, G. Brammer, J. Chisholm, A.-C. Eilers, A. Goulding, J. Greene, D. Kashino, I. Labbe, S.J. Lilly, R. Mackenzie, P.A. Oesch, A. Weibel, S. Wuyts, M. Xiao, R. Bordoloi, R. Bouwens, P. van Dokkum, G. Illingworth, I. Kramarenko, M.V. Maseda, C. Mason, R.A. Meyer, E.J. Nelson, N.A. Reddy, I. Shivaei, R.A. Simcoe, M. Yue, The Astrophysical Journal 963 (2024).","chicago":"Matthee, Jorryt J, Rohan P. Naidu, Gabriel Brammer, John Chisholm, Anna-Christina Eilers, Andy Goulding, Jenny Greene, et al. “Little Red Dots: An Abundant Population of Faint Active Galactic Nuclei at z ∼ 5 Revealed by the EIGER and FRESCO JWST Surveys.” The Astrophysical Journal. American Astronomical Society, 2024. https://doi.org/10.3847/1538-4357/ad2345."},"publication":"The Astrophysical Journal","article_type":"original","article_processing_charge":"Yes","has_accepted_license":"1","day":"07","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"file":[{"file_id":"15184","relation":"main_file","date_created":"2024-03-25T09:31:58Z","date_updated":"2024-03-25T09:31:58Z","success":1,"checksum":"dc7af4694f9f94a551417ab49fa43edf","file_name":"2024_AstrophysicalJourn_Matthee.pdf","access_level":"open_access","creator":"dernst","file_size":6047536,"content_type":"application/pdf"}],"oa_version":"Published Version","_id":"15180","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 963","ddc":["550"],"title":"Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys","status":"public","issue":"2","abstract":[{"lang":"eng","text":"Characterizing the prevalence and properties of faint active galactic nuclei (AGNs) in the early Universe is key for understanding the formation of supermassive black holes (SMBHs) and determining their role in cosmic reionization. We perform a spectroscopic search for broad Hα emitters at z ≈ 4–6 using deep JWST/NIRCam imaging and wide field slitless spectroscopy from the EIGER and FRESCO surveys. We identify 20 Hα lines at z = 4.2–5.5 that have broad components with line widths from ∼1200–3700 km s−1, contributing ∼30%–90% of the total line flux. We interpret these broad components as being powered by accretion onto SMBHs with implied masses ∼107–8M⊙. In the UV luminosity range MUV,AGN+host = −21 to −18, we measure number densities of ≈10−5 cMpc−3. This is an order of magnitude higher than expected from extrapolating quasar UV luminosity functions (LFs). Yet, such AGN are found in only <1% of star-forming galaxies at z ∼ 5. The number density discrepancy is much lower when compared to the broad Hα LF. The SMBH mass function agrees with large cosmological simulations. In two objects, we detect complex Hα profiles that we tentatively interpret as caused by absorption signatures from dense gas fueling SMBH growth and outflows. We may be witnessing early AGN feedback that will clear dust-free pathways through which more massive blue quasars are seen. We uncover a strong correlation between reddening and the fraction of total galaxy luminosity arising from faint AGN. This implies that early SMBH growth is highly obscured and that faint AGN are only minor contributors to cosmic reionization."}],"type":"journal_article","doi":"10.3847/1538-4357/ad2345","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"Young galaxies as tracers and agents of cosmic reionization","_id":"bd9b2118-d553-11ed-ba76-db24564edfea","grant_number":"101076224"}],"quality_controlled":"1","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"month":"03","author":[{"first_name":"Jorryt J","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J"},{"first_name":"Rohan P.","last_name":"Naidu","full_name":"Naidu, Rohan P."},{"last_name":"Brammer","first_name":"Gabriel","full_name":"Brammer, Gabriel"},{"full_name":"Chisholm, John","first_name":"John","last_name":"Chisholm"},{"last_name":"Eilers","first_name":"Anna-Christina","full_name":"Eilers, Anna-Christina"},{"full_name":"Goulding, Andy","last_name":"Goulding","first_name":"Andy"},{"first_name":"Jenny","last_name":"Greene","full_name":"Greene, Jenny"},{"last_name":"Kashino","first_name":"Daichi","full_name":"Kashino, Daichi"},{"last_name":"Labbe","first_name":"Ivo","full_name":"Labbe, Ivo"},{"first_name":"Simon J.","last_name":"Lilly","full_name":"Lilly, Simon J."},{"first_name":"Ruari","last_name":"Mackenzie","full_name":"Mackenzie, Ruari"},{"full_name":"Oesch, Pascal A.","first_name":"Pascal A.","last_name":"Oesch"},{"full_name":"Weibel, Andrea","last_name":"Weibel","first_name":"Andrea"},{"last_name":"Wuyts","first_name":"Stijn","full_name":"Wuyts, Stijn"},{"last_name":"Xiao","first_name":"Mengyuan","full_name":"Xiao, Mengyuan"},{"first_name":"Rongmon","last_name":"Bordoloi","full_name":"Bordoloi, Rongmon"},{"first_name":"Rychard","last_name":"Bouwens","full_name":"Bouwens, Rychard"},{"full_name":"van Dokkum, Pieter","last_name":"van Dokkum","first_name":"Pieter"},{"full_name":"Illingworth, Garth","last_name":"Illingworth","first_name":"Garth"},{"last_name":"Kramarenko","first_name":"Ivan","full_name":"Kramarenko, Ivan"},{"first_name":"Michael V.","last_name":"Maseda","full_name":"Maseda, Michael V."},{"first_name":"Charlotte","last_name":"Mason","full_name":"Mason, Charlotte"},{"first_name":"Romain A.","last_name":"Meyer","full_name":"Meyer, Romain A."},{"first_name":"Erica J.","last_name":"Nelson","full_name":"Nelson, Erica J."},{"last_name":"Reddy","first_name":"Naveen A.","full_name":"Reddy, Naveen A."},{"full_name":"Shivaei, Irene","last_name":"Shivaei","first_name":"Irene"},{"full_name":"Simcoe, Robert A.","first_name":"Robert A.","last_name":"Simcoe"},{"full_name":"Yue, Minghao","last_name":"Yue","first_name":"Minghao"}],"volume":963,"date_created":"2024-03-25T08:54:47Z","date_updated":"2024-03-25T09:37:27Z","year":"2024","acknowledgement":"We thank the anonymous referee for constructive comments that helped improve the manuscript. This work is based on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are associated with program Nos. 1243 and 1895. The specific observations analyzed can be accessed via doi:10.17909/4xx0-zj76. Funded by the European Union (ERC, AGENTS, 101076224). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. R.P.N. acknowledges funding from JWST programs GO-1933 and GO-2279. Support for this work for R.P.N. was provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. Support for this work for G.I. was provided by NASA through grant JWST-GO-01895 awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract No. MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation under grant No. 140.\r\nFacility: JWST - James Webb Space Telescope, HST - Hubble Space Telescope satellite\r\nSoftware: Python, matplotlib (Hunter 2007), numpy (Harris et al. 2020), scipy (Virtanen et al. 2020), Astropy (Astropy Collaboration et al. 2013, 2018), Imfit (Erwin 2015).","department":[{"_id":"JoMa"}],"publisher":"American Astronomical Society","publication_status":"published","file_date_updated":"2024-03-25T09:31:58Z","article_number":"129"},{"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes","article_type":"original","publication":"Science Advances","citation":{"apa":"Palkina, K. A., Karataeva, T. A., Perfilov, M. M., Fakhranurova, L. I., Markina, N. M., Gonzalez Somermeyer, L., … Sarkisyan, K. S. (2024). A hybrid pathway for self-sustained luminescence. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adk1992","ieee":"K. A. Palkina et al., “A hybrid pathway for self-sustained luminescence,” Science Advances, vol. 10, no. 10. American Association for the Advancement of Science, 2024.","ista":"Palkina KA, Karataeva TA, Perfilov MM, Fakhranurova LI, Markina NM, Gonzalez Somermeyer L, Garcia-Perez E, Vazquez-Vilar M, Rodriguez-Rodriguez M, Vazquez-Vilriales V, Shakhova ES, Mitiouchkina T, Belozerova OA, Kovalchuk SI, Alekberova A, Malyshevskaia AK, Bugaeva EN, Guglya EB, Balakireva A, Sytov N, Bezlikhotnova A, Boldyreva DI, Babenko VV, Kondrashov F, Choob VV, Orzaez D, Yampolsky IV, Mishin AS, Sarkisyan KS. 2024. A hybrid pathway for self-sustained luminescence. Science Advances. 10(10), adk1992.","ama":"Palkina KA, Karataeva TA, Perfilov MM, et al. A hybrid pathway for self-sustained luminescence. Science Advances. 2024;10(10). doi:10.1126/sciadv.adk1992","chicago":"Palkina, Kseniia A., Tatiana A. Karataeva, Maxim M. Perfilov, Liliia I. Fakhranurova, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, Elena Garcia-Perez, et al. “A Hybrid Pathway for Self-Sustained Luminescence.” Science Advances. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adk1992.","short":"K.A. Palkina, T.A. Karataeva, M.M. Perfilov, L.I. Fakhranurova, N.M. Markina, L. Gonzalez Somermeyer, E. Garcia-Perez, M. Vazquez-Vilar, M. Rodriguez-Rodriguez, V. Vazquez-Vilriales, E.S. Shakhova, T. Mitiouchkina, O.A. Belozerova, S.I. Kovalchuk, A. Alekberova, A.K. Malyshevskaia, E.N. Bugaeva, E.B. Guglya, A. Balakireva, N. Sytov, A. Bezlikhotnova, D.I. Boldyreva, V.V. Babenko, F. Kondrashov, V.V. Choob, D. Orzaez, I.V. Yampolsky, A.S. Mishin, K.S. Sarkisyan, Science Advances 10 (2024).","mla":"Palkina, Kseniia A., et al. “A Hybrid Pathway for Self-Sustained Luminescence.” Science Advances, vol. 10, no. 10, adk1992, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adk1992."},"date_published":"2024-03-01T00:00:00Z","type":"journal_article","abstract":[{"text":"The fungal bioluminescence pathway can be reconstituted in other organisms allowing luminescence imaging without exogenously supplied substrate. The pathway starts from hispidin biosynthesis—a step catalyzed by a large fungal polyketide synthase that requires a posttranslational modification for activity. Here, we report identification of alternative compact hispidin synthases encoded by a phylogenetically diverse group of plants. A hybrid bioluminescence pathway that combines plant and fungal genes is more compact, not dependent on availability of machinery for posttranslational modifications, and confers autonomous bioluminescence in yeast, mammalian, and plant hosts. The compact size of plant hispidin synthases enables additional modes of delivery of autoluminescence, such as delivery with viral vectors.","lang":"eng"}],"issue":"10","title":"A hybrid pathway for self-sustained luminescence","ddc":["580"],"status":"public","intvolume":" 10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15179","oa_version":"Published Version","file":[{"success":1,"checksum":"a19c43b260ea0bbaf895a29712e3153c","date_created":"2024-03-25T09:42:10Z","date_updated":"2024-03-25T09:42:10Z","file_id":"15185","relation":"main_file","creator":"dernst","file_size":1499302,"content_type":"application/pdf","access_level":"open_access","file_name":"2024_ScienceAdv_Palkina.pdf"}],"month":"03","publication_identifier":{"issn":["2375-2548"]},"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":"10.1126/sciadv.adk1992","article_number":"adk1992","file_date_updated":"2024-03-25T09:42:10Z","publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"FyKo"}],"acknowledgement":"We thank Milaboratory (milaboratory.com) for the access to computing and storage infrastructure. We thank J. Petrasek for providing the BY-2 cell culture line. We thank Konstantin Lukyanov laboratory and Sergey Deyev laboratory for assistance with experiments.\r\nThis study was partially funded by Light Bio and Planta. The Synthetic biology Group is funded by the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0). Cloning and luminescent assays performed in BY-2 were partially supported by RSF, project number 22-14-00400, https://rscf.ru/project/22-14-00400/. Plant transformations were funded by RFBR and MOST, project number 21-54-52004. Plant imaging experiments were funded by RSF, project number 22-74-00124, https://rscf.ru/project/22-74-00124/. Viral delivery experiments were funded by the grant PID2019-108203RB-I00 Plan Nacional I + D from the Ministerio de Ciencia e Innovación (Spain) through the Agencia Estatal de Investigación (cofinanced by the European Regional Development Fund).","year":"2024","date_updated":"2024-03-25T09:44:53Z","date_created":"2024-03-25T08:54:33Z","volume":10,"author":[{"full_name":"Palkina, Kseniia A.","last_name":"Palkina","first_name":"Kseniia A."},{"full_name":"Karataeva, Tatiana A.","first_name":"Tatiana A.","last_name":"Karataeva"},{"first_name":"Maxim M.","last_name":"Perfilov","full_name":"Perfilov, Maxim M."},{"full_name":"Fakhranurova, Liliia I.","last_name":"Fakhranurova","first_name":"Liliia I."},{"last_name":"Markina","first_name":"Nadezhda M.","full_name":"Markina, Nadezhda M."},{"full_name":"Gonzalez Somermeyer, Louisa","orcid":"0000-0001-9139-5383","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","last_name":"Gonzalez Somermeyer","first_name":"Louisa"},{"full_name":"Garcia-Perez, Elena","last_name":"Garcia-Perez","first_name":"Elena"},{"first_name":"Marta","last_name":"Vazquez-Vilar","full_name":"Vazquez-Vilar, Marta"},{"last_name":"Rodriguez-Rodriguez","first_name":"Marta","full_name":"Rodriguez-Rodriguez, Marta"},{"last_name":"Vazquez-Vilriales","first_name":"Victor","full_name":"Vazquez-Vilriales, Victor"},{"full_name":"Shakhova, Ekaterina S.","first_name":"Ekaterina S.","last_name":"Shakhova"},{"full_name":"Mitiouchkina, Tatiana","last_name":"Mitiouchkina","first_name":"Tatiana"},{"last_name":"Belozerova","first_name":"Olga A.","full_name":"Belozerova, Olga A."},{"full_name":"Kovalchuk, Sergey I.","first_name":"Sergey I.","last_name":"Kovalchuk"},{"full_name":"Alekberova, Anna","first_name":"Anna","last_name":"Alekberova"},{"first_name":"Alena K.","last_name":"Malyshevskaia","full_name":"Malyshevskaia, Alena K."},{"full_name":"Bugaeva, Evgenia N.","first_name":"Evgenia N.","last_name":"Bugaeva"},{"first_name":"Elena B.","last_name":"Guglya","full_name":"Guglya, Elena B."},{"full_name":"Balakireva, Anastasia","first_name":"Anastasia","last_name":"Balakireva"},{"full_name":"Sytov, Nikita","first_name":"Nikita","last_name":"Sytov"},{"first_name":"Anastasia","last_name":"Bezlikhotnova","full_name":"Bezlikhotnova, Anastasia"},{"last_name":"Boldyreva","first_name":"Daria I.","full_name":"Boldyreva, Daria I."},{"first_name":"Vladislav V.","last_name":"Babenko","full_name":"Babenko, Vladislav V."},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor"},{"full_name":"Choob, Vladimir V.","last_name":"Choob","first_name":"Vladimir V."},{"first_name":"Diego","last_name":"Orzaez","full_name":"Orzaez, Diego"},{"first_name":"Ilia V.","last_name":"Yampolsky","full_name":"Yampolsky, Ilia V."},{"first_name":"Alexander S.","last_name":"Mishin","full_name":"Mishin, Alexander S."},{"full_name":"Sarkisyan, Karen S.","first_name":"Karen S.","last_name":"Sarkisyan"}]},{"oa":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"},"project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"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","doi":"10.1029/2023gl106523","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0094-8276"],"eissn":["1944-8007"]},"month":"03","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","department":[{"_id":"CaMu"}],"publisher":"American Geophysical Union","publication_status":"published","author":[{"full_name":"Hwong, Yi-Ling","first_name":"Yi-Ling","last_name":"Hwong","id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22","orcid":"0000-0001-9281-3479"},{"full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","first_name":"Caroline J"}],"volume":51,"date_updated":"2024-03-25T11:32:06Z","date_created":"2024-03-25T10:27:30Z","article_number":" e2023GL106523","ec_funded":1,"file_date_updated":"2024-03-25T11:28:25Z","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.","short":"Y.-L. Hwong, C.J. Muller, Geophysical Research Letters 51 (2024).","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.","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.","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","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.","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","article_type":"original","date_published":"2024-03-19T00:00:00Z","keyword":["General Earth and Planetary Sciences","Geophysics"],"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"19","_id":"15186","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 51","title":"The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation","ddc":["550"],"status":"public","file":[{"relation":"main_file","file_id":"15187","checksum":"eacb011091a503b9e7b748fef639ba4c","success":1,"date_created":"2024-03-25T11:28:25Z","date_updated":"2024-03-25T11:28:25Z","access_level":"open_access","file_name":"2024_GeophysResLetters_Hwong.pdf","file_size":1280108,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","issue":"6","abstract":[{"lang":"eng","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."}]},{"file":[{"file_id":"15183","relation":"main_file","success":1,"checksum":"4e0e58d1f58386fb016284c84db2a300","date_created":"2024-03-25T09:24:55Z","date_updated":"2024-03-25T09:24:55Z","access_level":"open_access","file_name":"2024_PhysicalReviewResearch_Becker.pdf","creator":"dernst","content_type":"application/pdf","file_size":2207067}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15181","status":"public","title":"Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions","ddc":["530"],"intvolume":" 6","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"}],"issue":"1","type":"journal_article","date_published":"2024-03-01T00:00:00Z","publication":"Physical Review Research","citation":{"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","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)."},"article_type":"original","day":"01","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","author":[{"full_name":"Becker, A.","first_name":"A.","last_name":"Becker"},{"id":"d7b23d3a-9e21-11ec-b482-f76739596b95","first_name":"Georgios","last_name":"Koutentakis","full_name":"Koutentakis, Georgios"},{"last_name":"Schmelcher","first_name":"P.","full_name":"Schmelcher, P."}],"date_updated":"2024-03-25T09:27:37Z","date_created":"2024-03-25T08:57:07Z","volume":6,"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","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","file_date_updated":"2024-03-25T09:24:55Z","ec_funded":1,"article_number":"013257","doi":"10.1103/physrevresearch.6.013257","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2310.17995"]},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"month":"03","publication_identifier":{"issn":["2643-1564"]}},{"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","day":"13","article_type":"original","citation":{"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","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.","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.","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","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.","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).","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."},"publication":"Advanced Energy Materials","date_published":"2024-03-13T00:00:00Z","type":"journal_article","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."}],"status":"public","title":"A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se","_id":"15182","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","publication_identifier":{"eissn":["1614-6840"],"issn":["1614-6832"]},"month":"03","project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/aenm.202400408"}],"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"doi":"10.1002/aenm.202400408","article_number":"2400408","department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"publisher":"Wiley","publication_status":"epub_ahead","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.","date_created":"2024-03-25T08:57:40Z","date_updated":"2024-03-25T09:21:05Z","author":[{"full_name":"Kleinhanns, Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias","last_name":"Kleinhanns"},{"id":"38b830db-ea88-11ee-bf9b-929beaf79054","last_name":"Milillo","first_name":"Francesco","full_name":"Milillo, Francesco"},{"last_name":"Calcabrini","first_name":"Mariano","orcid":"0000-0003-4566-5877","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","full_name":"Calcabrini, Mariano"},{"first_name":"Christine","last_name":"Fiedler","id":"bd3fceba-dc74-11ea-a0a7-c17f71817366","full_name":"Fiedler, Christine"},{"full_name":"Horta, Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","first_name":"Sharona","last_name":"Horta"},{"full_name":"Balazs, Daniel","last_name":"Balazs","first_name":"Daniel","orcid":"0000-0001-7597-043X","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E"},{"first_name":"Marissa J.","last_name":"Strumolo","full_name":"Strumolo, Marissa J."},{"last_name":"Hasler","first_name":"Roger","full_name":"Hasler, Roger"},{"last_name":"Llorca","first_name":"Jordi","full_name":"Llorca, Jordi"},{"full_name":"Tkadletz, Michael","first_name":"Michael","last_name":"Tkadletz"},{"full_name":"Brutchey, Richard L.","first_name":"Richard L.","last_name":"Brutchey"},{"last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"}]},{"title":"A pre-monsoon signal of false alarms of Indian monsoon droughts","status":"public","ddc":["550"],"intvolume":" 51","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15165","file":[{"creator":"dernst","file_size":2887134,"content_type":"application/pdf","access_level":"open_access","file_name":"2024_GeophysResLetters_Goswami.pdf","success":1,"checksum":"243bd966aca968ec7d9e474af8639f8d","date_created":"2024-03-25T08:36:00Z","date_updated":"2024-03-25T08:36:00Z","file_id":"15178","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","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."}],"issue":"5","article_type":"original","publication":"Geophysical Research Letters","citation":{"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.","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).","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","ama":"GOSWAMI BB. A pre-monsoon signal of false alarms of Indian monsoon droughts. Geophysical Research Letters. 2024;51(5). doi:10.1029/2023GL106569"},"date_published":"2024-03-16T00:00:00Z","scopus_import":"1","day":"16","has_accepted_license":"1","article_processing_charge":"Yes","publication_status":"published","publisher":"Wiley","department":[{"_id":"CaMu"}],"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","date_created":"2024-03-24T23:00:58Z","date_updated":"2024-03-25T10:00:57Z","volume":51,"author":[{"full_name":"Goswami, Bidyut B","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","orcid":"0000-0001-8602-3083","first_name":"Bidyut B","last_name":"Goswami"}],"article_number":"e2023GL106569","file_date_updated":"2024-03-25T08:36:00Z","ec_funded":1,"quality_controlled":"1","project":[{"grant_number":"805041","_id":"629205d8-2b32-11ec-9570-e1356ff73576","name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate","call_identifier":"H2020"}],"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","month":"03","publication_identifier":{"eissn":["1944-8007"],"issn":["0094-8276"]}},{"year":"2024","acknowledgement":"The authors thank the Werner-Siemens-Stiftung and the Institute of Science and Technology Austria for financial support.","publisher":"American Association for the Advancement of Science","department":[{"_id":"MaIb"}],"publication_status":"published","author":[{"id":"6ebe278d-ba0b-11ee-8184-f34cdc671de4","first_name":"Navita","last_name":"Navita","full_name":"Navita, Navita"},{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria"}],"volume":383,"date_created":"2024-03-24T23:00:58Z","date_updated":"2024-03-25T10:31:20Z","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","doi":"10.1126/science.ado4077","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15166","intvolume":" 383","title":"Electron highways are cooler","status":"public","oa_version":"None","type":"journal_article","issue":"6688","abstract":[{"text":"Reducing defects boosts room-temperature performance of a thermoelectric device","lang":"eng"}],"citation":{"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","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."},"publication":"Science","page":"1184","article_type":"letter_note","date_published":"2024-03-14T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"14"},{"department":[{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"publisher":"Rockefeller University Press","publication_status":"published","pmid":1,"acknowledgement":"Open Access funding provided by IST Austria. We thank Armel Nicolas and his team at the ISTA proteomics facility, Alois Schloegl, Stefano Elefante, and colleagues at the ISTA Scientific Computing facility, Tommaso Constanzo and Ludek Lovicar at the Electron Microsocpy Facility (EMF), and Thomas Menner at the Miba Machine shop for their support. We also thank Wanda Kukulski (University of Bern) as well as Darío Porley, Andreas Thader, and other members of the Schur group for helpful discussions. Matt Swulius and Jessica Heebner provided great support in using Dragonfly. We thank Dorotea Fracciolla (Art & Science) for support in figure illustration.\r\n\r\nThis research was supported by the Scientific Service Units of ISTA through resources provided by Scientific Computing, the Lab Support Facility, and the Electron Microscopy Facility. We acknowledge funding support from the following sources: Austrian Science Fund (FWF) grant P33367 (to F.K.M. Schur), the Federation of European Biochemical Societies (to F.K.M. Schur), Niederösterreich (NÖ) Fonds (to B. Zens), FWF grant E435 (to J.M. Hansen), European Research Council under the European Union’s Horizon 2020 research (grant agreement No. 724373) (to M. Sixt), and Jenny and Antti Wihuri Foundation (to J. Alanko). This publication has been made possible in part by CZI grant DAF2021-234754 and grant DOI https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (to F.K.M. Schur).","year":"2024","volume":223,"date_updated":"2024-03-25T13:03:57Z","date_created":"2024-03-21T06:45:51Z","author":[{"id":"45FD126C-F248-11E8-B48F-1D18A9856A87","last_name":"Zens","first_name":"Bettina","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","last_name":"Hansen","first_name":"Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild"},{"full_name":"Datler, Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3616-8580","first_name":"Julia","last_name":"Datler"},{"full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zheden, Vanessa","last_name":"Zheden","first_name":"Vanessa","orcid":"0000-0002-9438-4783","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Alanko, Jonna H","orcid":"0000-0002-7698-3061","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alanko","first_name":"Jonna H"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"article_number":"e202309125","ec_funded":1,"file_date_updated":"2024-03-25T12:52:04Z","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"},{"name":"In Situ Actin Structures via Hybrid Cryo-electron Microscopy","_id":"7bd318a1-9f16-11ee-852c-cc9217763180","grant_number":"E435"},{"name":"Cellular navigation along spatial gradients","call_identifier":"H2020","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"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"},{"name":"CryoMinflux-guided in-situ visual proteomics and structure determination","_id":"62909c6f-2b32-11ec-9570-e1476aab5308","grant_number":"CZI01"}],"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":{"pmid":["38506714"]},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"M-Shop"}],"doi":"10.1083/jcb.202309125","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"month":"03","intvolume":" 223","status":"public","ddc":["570"],"title":"Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15146","oa_version":"Published Version","file":[{"file_id":"15188","relation":"main_file","date_created":"2024-03-25T12:52:04Z","date_updated":"2024-03-25T12:52:04Z","success":1,"checksum":"90d1984a93660735e506c2a304bc3f73","file_name":"2024_JCB_Zens.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":11907016}],"type":"journal_article","issue":"6","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."}],"article_type":"original","citation":{"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","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.","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.","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."},"publication":"Journal of Cell Biology","date_published":"2024-03-20T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"20"},{"month":"01","publication_identifier":{"issn":["0022-1236"],"eissn":["1096--0783"]},"doi":"10.1016/j.jfa.2024.110320","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["2301.04894"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jfa.2024.110320"}],"quality_controlled":"1","project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"name":"Mathematical Challenges in BCS Theory of Superconductivity","grant_number":"I06427","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b"}],"ec_funded":1,"article_number":"110320","author":[{"full_name":"Lauritsen, Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","last_name":"Lauritsen","first_name":"Asbjørn Bækgaard"},{"last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"date_created":"2024-02-04T23:00:53Z","date_updated":"2024-03-28T10:54:02Z","volume":286,"acknowledgement":"A.B.L. would like to thank Johannes Agerskov and Jan Philip Solovej for valuable discussions. We thank Alessandro Giuliani for helpful discussions and for pointing out the reference [18]. Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is acknowledged. Financial support by the Austrian Science Fund (FWF) through project number I 6427-N (as part of the SFB/TRR 352) is gratefully acknowledged.","year":"2024","publication_status":"epub_ahead","publisher":"Elsevier","department":[{"_id":"RoSe"}],"day":"24","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2024-01-24T00:00:00Z","publication":"Journal of Functional Analysis","citation":{"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.","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","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.","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","chicago":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal of Functional Analysis. Elsevier, 2024. https://doi.org/10.1016/j.jfa.2024.110320.","mla":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal of Functional Analysis, vol. 286, no. 7, 110320, Elsevier, 2024, doi:10.1016/j.jfa.2024.110320.","short":"A.B. Lauritsen, R. Seiringer, Journal of Functional Analysis 286 (2024)."},"article_type":"original","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","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"14931","title":"Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion","status":"public","intvolume":" 286"},{"date_updated":"2023-02-03T10:58:56Z","date_created":"2023-01-29T23:00:58Z","volume":2608,"author":[{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"last_name":"Scheele","first_name":"Colinda L.G.J.","full_name":"Scheele, Colinda L.G.J."}],"publication_status":"published","editor":[{"last_name":"Margadant","first_name":"Coert","full_name":"Margadant, Coert"}],"department":[{"_id":"EdHa"}],"publisher":"Springer Nature","year":"2023","pmid":1,"file_date_updated":"2023-02-03T10:56:39Z","language":[{"iso":"eng"}],"doi":"10.1007/978-1-0716-2887-4_12","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,"external_id":{"pmid":["36653709"]},"month":"01","publication_identifier":{"eisbn":["9781071628874"],"eissn":["1940-6029"],"isbn":["9781071628867"]},"file":[{"access_level":"open_access","file_name":"2023_MIMB_Hannezo.pdf","creator":"dernst","content_type":"application/pdf","file_size":826598,"file_id":"12500","relation":"main_file","success":1,"checksum":"aec1b8d3ba938ddf9d8fcb777f3c38ee","date_created":"2023-02-03T10:56:39Z","date_updated":"2023-02-03T10:56:39Z"}],"oa_version":"Published Version","ddc":["570"],"title":"A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland","status":"public","intvolume":" 2608","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12428","abstract":[{"lang":"eng","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."}],"alternative_title":["Methods in Molecular Biology"],"type":"book_chapter","date_published":"2023-01-19T00:00:00Z","page":"183-205","publication":"Cell Migration in Three Dimensions","citation":{"chicago":"Hannezo, Edouard B, and Colinda L.G.J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” In Cell Migration in Three Dimensions, edited by Coert Margadant, 2608:183–205. MIMB. Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-2887-4_12.","mla":"Hannezo, Edouard B., and Colinda L. G. J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” Cell Migration in Three Dimensions, edited by Coert Margadant, vol. 2608, Springer Nature, 2023, pp. 183–205, doi:10.1007/978-1-0716-2887-4_12.","short":"E.B. Hannezo, C.L.G.J. Scheele, in:, C. Margadant (Ed.), Cell Migration in Three Dimensions, Springer Nature, 2023, pp. 183–205.","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.","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.","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"},"day":"19","has_accepted_license":"1","article_processing_charge":"No","series_title":"MIMB","scopus_import":"1"},{"month":"01","publication_identifier":{"issn":["2643-1564"]},"language":[{"iso":"eng"}],"doi":"10.1103/physrevresearch.5.013029","quality_controlled":"1","project":[{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2023-02-13T10:38:10Z","ec_funded":1,"article_number":"013029","date_updated":"2023-02-20T07:02:00Z","date_created":"2023-02-10T09:02:26Z","volume":5,"author":[{"full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","first_name":"Areg"},{"id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","orcid":"0000-0001-6110-2359","first_name":"Alberto","last_name":"Cappellaro","full_name":"Cappellaro, Alberto"},{"full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"},{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev"}],"publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","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).","day":"20","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2023-01-20T00:00:00Z","article_type":"original","publication":"Physical Review Research","citation":{"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.","apa":"Ghazaryan, A., Cappellaro, A., Lemeshko, M., & Volosniev, A. (2023). Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.5.013029","ieee":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Dissipative dynamics of an impurity with spin-orbit coupling,” Physical Review Research, vol. 5, no. 1. American Physical Society, 2023.","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"},"abstract":[{"lang":"eng","text":"Brownian motion of a mobile impurity in a bath is affected by spin-orbit coupling (SOC). Here, we discuss a Caldeira-Leggett-type model that can be used to propose and interpret quantum simulators of this problem in cold Bose gases. First, we derive a master equation that describes the model and explore it in a one-dimensional (1D) setting. To validate the standard assumptions needed for our derivation, we analyze available experimental data without SOC; as a byproduct, this analysis suggests that the quench dynamics of the impurity is beyond the 1D Bose-polaron approach at temperatures currently accessible in a cold-atom laboratory—motion of the impurity is mainly driven by dissipation. For systems with SOC, we demonstrate that 1D spin-orbit coupling can be gauged out even in the presence of dissipation—the information about SOC is incorporated in the initial conditions. Observables sensitive to this information (such as spin densities) can be used to study formation of steady spin polarization domains during quench dynamics."}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2023_PhysicalReviewResearch_Ghazaryan.pdf","access_level":"open_access","content_type":"application/pdf","file_size":865150,"creator":"dernst","relation":"main_file","file_id":"12546","date_created":"2023-02-13T10:38:10Z","date_updated":"2023-02-13T10:38:10Z","checksum":"6068b62874c0099628a108bb9c5c6bd2","success":1}],"title":"Dissipative dynamics of an impurity with spin-orbit coupling","status":"public","ddc":["530"],"intvolume":" 5","_id":"12534","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1137/1.9781611977554.ch173"}],"quality_controlled":"1","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"conference":{"end_date":"2023-01-25","start_date":"2023-01-22","location":"Florence, Italy","name":"SODA: Symposium on Discrete Algorithms"},"doi":"10.1137/1.9781611977554.ch173","language":[{"iso":"eng"}],"month":"02","publication_identifier":{"isbn":["9781611977554"]},"year":"2023","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant.","publication_status":"published","publisher":"Society for Industrial and Applied Mathematics","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Meggendorfer, Tobias","orcid":"0000-0002-1712-2165","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","last_name":"Meggendorfer","first_name":"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"},{"last_name":"Svoboda","first_name":"Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","full_name":"Svoboda, Jakub"}],"date_created":"2023-02-24T12:20:47Z","date_updated":"2023-02-27T09:01:16Z","ec_funded":1,"publication":"Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms","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.","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.","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.","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.","apa":"Chatterjee, K., Meggendorfer, T., Saona Urmeneta, R. J., & Svoboda, J. (2023). Faster algorithm for turn-based stochastic games with bounded treewidth. In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 4590–4605). Florence, Italy: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977554.ch173","ieee":"K. Chatterjee, T. Meggendorfer, R. J. Saona Urmeneta, and J. Svoboda, “Faster algorithm for turn-based stochastic games with bounded treewidth,” in Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Florence, Italy, 2023, pp. 4590–4605.","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"},"page":"4590-4605","date_published":"2023-02-01T00:00:00Z","day":"01","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12676","title":"Faster algorithm for turn-based stochastic games with bounded treewidth","status":"public","oa_version":"Published Version","type":"conference","abstract":[{"lang":"eng","text":"Turn-based stochastic games (aka simple stochastic games) are two-player zero-sum games played on directed graphs with probabilistic transitions. The goal of player-max is to maximize the probability to reach a target state against the adversarial player-min. These games lie in NP ∩ coNP and are among the rare combinatorial problems that belong to this complexity class for which the existence of polynomial-time algorithm is a major open question. While randomized sub-exponential time algorithm exists, all known deterministic algorithms require exponential time in the worst-case. An important open question has been whether faster algorithms can be obtained parametrized by the treewidth of the game graph. Even deterministic sub-exponential time algorithm for constant treewidth turn-based stochastic games has remain elusive. In this work our main result is a deterministic algorithm to solve turn-based stochastic games that, given a game with n states, treewidth at most t, and the bit-complexity of the probabilistic transition function log D, has running time O ((tn2 log D)t log n). In particular, our algorithm is quasi-polynomial time for games with constant or poly-logarithmic treewidth."}]},{"date_published":"2023-03-01T00:00:00Z","publication":"DNA Manipulation and Analysis","citation":{"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.","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.","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","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","chicago":"Arroyo-Urea, Sandra, Jake Watson, and Javier García-Nafría. “Molecular Cloning Using In Vivo DNA Assembly.” In DNA Manipulation and Analysis, edited by Garry Scarlett, 2633:33–44. MIMB. New York, NY, United States: Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-3004-4_3.","mla":"Arroyo-Urea, Sandra, et al. “Molecular Cloning Using In Vivo DNA Assembly.” DNA Manipulation and Analysis, edited by Garry Scarlett, vol. 2633, Springer Nature, 2023, pp. 33–44, doi:10.1007/978-1-0716-3004-4_3.","short":"S. Arroyo-Urea, J. Watson, J. García-Nafría, in:, G. Scarlett (Ed.), DNA Manipulation and Analysis, Springer Nature, New York, NY, United States, 2023, pp. 33–44."},"page":"33-44","day":"01","article_processing_charge":"No","scopus_import":"1","series_title":"MIMB","oa_version":"None","_id":"12720","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Molecular Cloning Using In Vivo DNA Assembly","intvolume":" 2633","abstract":[{"lang":"eng","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."}],"type":"book_chapter","alternative_title":["Methods in Molecular Biology"],"doi":"10.1007/978-1-0716-3004-4_3","language":[{"iso":"eng"}],"external_id":{"pmid":["36853454"]},"quality_controlled":"1","month":"03","publication_identifier":{"eissn":["1940-6029"],"isbn":["978-1-0716-3003-7"],"eisbn":["978-1-0716-3004-4"],"issn":["1064-3745"]},"author":[{"first_name":"Sandra","last_name":"Arroyo-Urea","full_name":"Arroyo-Urea, Sandra"},{"last_name":"Watson","first_name":"Jake","orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E","full_name":"Watson, Jake"},{"last_name":"García-Nafría","first_name":"Javier","full_name":"García-Nafría, Javier"}],"date_updated":"2023-03-16T08:34:24Z","date_created":"2023-03-12T23:01:02Z","volume":2633,"year":"2023","pmid":1,"publication_status":"published","editor":[{"full_name":"Scarlett, Garry","last_name":"Scarlett","first_name":"Garry"}],"department":[{"_id":"PeJo"}],"publisher":"Springer Nature","place":"New York, NY, United States"},{"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."}],"type":"conference","date_updated":"2023-03-20T07:29:28Z","date_created":"2023-03-19T23:00:58Z","oa_version":"Preprint","author":[{"full_name":"Koval, Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","last_name":"Koval","first_name":"Nikita"},{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Elizarov","first_name":"Roman","full_name":"Elizarov, Roman"}],"status":"public","publication_status":"published","title":"Fast and scalable channels in Kotlin Coroutines","publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"}],"_id":"12735","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","day":"25","month":"02","article_processing_charge":"No","publication_identifier":{"isbn":["9798400700156"]},"scopus_import":"1","language":[{"iso":"eng"}],"conference":{"end_date":"2023-03-01","location":"Montreal, QC, Canada","start_date":"2023-02-25","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"date_published":"2023-02-25T00:00:00Z","doi":"10.1145/3572848.3577481","quality_controlled":"1","page":"107-118","publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.04986","open_access":"1"}],"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","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.","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","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.","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.","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.","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},{"author":[{"full_name":"Aksenov, Vitaly","first_name":"Vitaly","last_name":"Aksenov"},{"full_name":"Brown, Trevor A","last_name":"Brown","first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fedorov, Alexander","last_name":"Fedorov","first_name":"Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6"},{"last_name":"Kokorin","first_name":"Ilya","full_name":"Kokorin, Ilya"}],"oa_version":"Published Version","date_updated":"2023-03-20T07:57:27Z","date_created":"2023-03-19T23:00:58Z","_id":"12736","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"publisher":"Association for Computing Machinery","title":"Unexpected scaling in path copying trees","publication_status":"published","status":"public","abstract":[{"lang":"eng","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."}],"type":"conference_poster","date_published":"2023-02-25T00:00:00Z","doi":"10.1145/3572848.3577512","conference":{"end_date":"2023-03-01","start_date":"2023-02-25","location":"Montreal, QB, Canada","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"language":[{"iso":"eng"}],"citation":{"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","ista":"Aksenov V, Brown TA, Fedorov A, Kokorin I. 2023. Unexpected scaling in path copying trees, Association for Computing Machinery,p.","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","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.","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.","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."},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1145/3572848.3577512","open_access":"1"}],"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","page":"438-440","quality_controlled":"1","publication_identifier":{"isbn":["9798400700156"]},"article_processing_charge":"No","month":"02","day":"25"},{"file_date_updated":"2023-03-27T06:37:22Z","article_number":"36","volume":254,"date_updated":"2023-03-27T06:46:27Z","date_created":"2023-03-26T22:01:07Z","author":[{"first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"full_name":"Neumann, Stefan","last_name":"Neumann","first_name":"Stefan"},{"full_name":"Räcke, Harald","first_name":"Harald","last_name":"Räcke"},{"last_name":"Schmid","first_name":"Stefan","full_name":"Schmid, Stefan"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"MoHe"}],"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","publication_identifier":{"isbn":["9783959772662"],"issn":["1868-8969"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.STACS.2023.36","conference":{"name":"STACS: Symposium on Theoretical Aspects of Computer Science","location":"Hamburg, Germany","start_date":"2023-03-07","end_date":"2023-03-09"},"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":["2301.01744"]},"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"}],"alternative_title":["LIPIcs"],"type":"conference","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":872706,"creator":"dernst","file_name":"2023_LIPICS_HenzingerM.pdf","access_level":"open_access","date_created":"2023-03-27T06:37:22Z","date_updated":"2023-03-27T06:37:22Z","checksum":"22141ab8bc55188e2dfff665e5daecbd","success":1,"relation":"main_file","file_id":"12769"}],"intvolume":" 254","status":"public","ddc":["000"],"title":"Dynamic maintenance of monotone dynamic programs and applications","_id":"12760","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2023-03-01T00:00:00Z","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","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.","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","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"},{"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","ista":"Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria.","apa":"Burnett, L. (2023). To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12716","ieee":"L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism,” Institute of Science and Technology Austria, 2023.","mla":"Burnett, Laura. To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12716.","short":"L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism, Institute of Science and Technology Austria, 2023.","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","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"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.","lang":"eng"}],"status":"public","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"],"_id":"12716","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","file":[{"file_name":"Burnett_Thesis_2023.docx","access_level":"closed","creator":"lburnett","file_size":23029260,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","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_pdfA.pdf","access_level":"open_access","creator":"lburnett","content_type":"application/pdf","file_size":11959869,"file_id":"12718","relation":"main_file","date_updated":"2023-03-08T15:08:46Z","date_created":"2023-03-08T15:08:46Z","success":1,"checksum":"cebc77705288bf4382db9b3541483cd0"}],"month":"03","publication_identifier":{"issn":["2663-337X"]},"project":[{"call_identifier":"H2020","name":"Circuits of Visual Attention","grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"}],"oa":1,"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","last_name":"Jösch"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12716","file_date_updated":"2023-03-08T15:08:46Z","ec_funded":1,"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"publisher":"Institute of Science and Technology Austria","year":"2023","date_updated":"2023-04-05T10:59:04Z","date_created":"2023-03-08T15:19:45Z","author":[{"full_name":"Burnett, Laura","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8937-410X","first_name":"Laura","last_name":"Burnett"}]},{"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":16096413,"creator":"dernst","file_name":"2023_LNCS_Chalupa.pdf","access_level":"open_access","date_updated":"2023-04-25T06:58:36Z","date_created":"2023-04-25T06:58:36Z","checksum":"120d2c2a38384058ad0630fdf8288312","success":1,"relation":"main_file","file_id":"12864"}],"intvolume":" 13994","title":"Bubaak: Runtime monitoring of program verifiers","status":"public","ddc":["000"],"_id":"12854","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The main idea behind BUBAAK is to run multiple program analyses in parallel and use runtime monitoring and enforcement to observe and control their progress in real time. The analyses send information about (un)explored states of the program and discovered invariants to a monitor. The monitor processes the received data and can force an analysis to stop the search of certain program parts (which have already been analyzed by other analyses), or to make it utilize a program invariant found by another analysis.\r\nAt SV-COMP 2023, the implementation of data exchange between the monitor and the analyses was not yet completed, which is why BUBAAK only ran several analyses in parallel, without any coordination. Still, BUBAAK won the meta-category FalsificationOverall and placed very well in several other (sub)-categories of the competition."}],"alternative_title":["LNCS"],"type":"conference","date_published":"2023-04-20T00:00:00Z","page":"535-540","citation":{"ieee":"M. Chalupa and T. A. Henzinger, “Bubaak: Runtime monitoring of program verifiers,” in Tools and Algorithms for the Construction and Analysis of Systems, Paris, France, 2023, vol. 13994, pp. 535–540.","apa":"Chalupa, M., & Henzinger, T. A. (2023). Bubaak: Runtime monitoring of program verifiers. In Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13994, pp. 535–540). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30820-8_32","ista":"Chalupa M, Henzinger TA. 2023. Bubaak: Runtime monitoring of program verifiers. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994, 535–540.","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.","short":"M. Chalupa, T.A. Henzinger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 535–540.","mla":"Chalupa, Marek, and Thomas A. Henzinger. “Bubaak: Runtime Monitoring of Program Verifiers.” Tools and Algorithms for the Construction and Analysis of Systems, vol. 13994, Springer Nature, 2023, pp. 535–40, doi:10.1007/978-3-031-30820-8_32."},"publication":"Tools and Algorithms for the Construction and Analysis of Systems","has_accepted_license":"1","article_processing_charge":"No","day":"20","volume":13994,"date_updated":"2023-04-25T07:02:43Z","date_created":"2023-04-20T08:22:53Z","author":[{"id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","last_name":"Chalupa","first_name":"Marek","full_name":"Chalupa, Marek"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Springer Nature","department":[{"_id":"ToHe"}],"publication_status":"published","acknowledgement":"This work was supported by the ERC-2020-AdG 10102009 grant.","year":"2023","ec_funded":1,"file_date_updated":"2023-04-25T06:58:36Z","language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-30820-8_32","conference":{"start_date":"2023-04-22","location":"Paris, France","end_date":"2023-04-27","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"issn":["0302-9743"],"eisbn":["9783031308208"],"eissn":["1611-3349"],"isbn":["9783031308192"]},"month":"04"},{"article_processing_charge":"No","day":"25","month":"03","citation":{"short":"A. Chern, S. Ishida, ArXiv (n.d.).","mla":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, 2303.14555, doi:10.48550/arXiv.2303.14555.","chicago":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2303.14555.","ama":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv. doi:10.48550/arXiv.2303.14555","ieee":"A. Chern and S. Ishida, “Area formula for spherical polygons via prequantization,” arXiv. .","apa":"Chern, A., & Ishida, S. (n.d.). Area formula for spherical polygons via prequantization. arXiv. https://doi.org/10.48550/arXiv.2303.14555","ista":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv, 2303.14555."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2303.14555"}],"external_id":{"arxiv":["2303.14555"]},"publication":"arXiv","project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083"}],"date_published":"2023-03-25T00:00:00Z","doi":"10.48550/arXiv.2303.14555","language":[{"iso":"eng"}],"type":"preprint","article_number":"2303.14555","abstract":[{"text":"We present a formula for the signed area of a spherical polygon via prequantization. In contrast to the traditional formula based on the Gauss-Bonnet theorem that requires measuring angles, the new formula mimics Green's theorem and is applicable to a wider range of degenerate spherical curves and polygons.","lang":"eng"}],"year":"2023","_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).","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"status":"public","publication_status":"submitted","title":"Area formula for spherical polygons via prequantization","author":[{"first_name":"Albert","last_name":"Chern","full_name":"Chern, Albert"},{"last_name":"Ishida","first_name":"Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","full_name":"Ishida, Sadashige"}],"oa_version":"Preprint","date_created":"2023-04-18T19:16:06Z","date_updated":"2023-04-25T06:51:21Z"},{"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. The authors would like to thank the anonymous FASE reviewers for their valuable feedback and suggestions.","year":"2023","date_updated":"2023-04-25T07:19:07Z","date_created":"2023-04-20T08:29:42Z","volume":13991,"author":[{"full_name":"Chalupa, Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","first_name":"Marek","last_name":"Chalupa"},{"id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","orcid":"0000-0003-1548-0177","first_name":"Fabian","last_name":"Mühlböck","full_name":"Mühlböck, Fabian"},{"id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","first_name":"Stefanie","last_name":"Muroya Lei","full_name":"Muroya Lei, Stefanie"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"related_material":{"record":[{"id":"12407","relation":"earlier_version","status":"public"}]},"file_date_updated":"2023-04-25T07:16:36Z","ec_funded":1,"quality_controlled":"1","project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"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"}],"conference":{"end_date":"2023-04-27","location":"Paris, France","start_date":"2023-04-22","name":"FASE: Fundamental Approaches to Software Engineering"},"doi":"10.1007/978-3-031-30826-0_15","month":"04","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031308253"],"issn":["0302-9743"],"eisbn":["9783031308260"]},"status":"public","title":"Vamos: Middleware for best-effort third-party monitoring","ddc":["000"],"intvolume":" 13991","_id":"12856","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"12865","relation":"main_file","date_created":"2023-04-25T07:16:36Z","date_updated":"2023-04-25T07:16:36Z","success":1,"checksum":"17a7c8e08be609cf2408d37ea55e322c","file_name":"2023_LNCS_ChalupaM.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":580828}],"alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both.\r\n\r\nWe present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\nWe implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch.","lang":"eng"}],"page":"260-281","publication":"Fundamental Approaches to Software Engineering","citation":{"ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. Vamos: Middleware for best-effort third-party monitoring. In: Fundamental Approaches to Software Engineering. Vol 13991. Springer Nature; 2023:260-281. doi:10.1007/978-3-031-30826-0_15","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023). Vamos: Middleware for best-effort third-party monitoring. In Fundamental Approaches to Software Engineering (Vol. 13991, pp. 260–281). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30826-0_15","ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, “Vamos: Middleware for best-effort third-party monitoring,” in Fundamental Approaches to Software Engineering, Paris, France, 2023, vol. 13991, pp. 260–281.","ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. Vamos: Middleware for best-effort third-party monitoring. Fundamental Approaches to Software Engineering. FASE: Fundamental Approaches to Software Engineering, LNCS, vol. 13991, 260–281.","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, in:, Fundamental Approaches to Software Engineering, Springer Nature, 2023, pp. 260–281.","mla":"Chalupa, Marek, et al. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” Fundamental Approaches to Software Engineering, vol. 13991, Springer Nature, 2023, pp. 260–81, doi:10.1007/978-3-031-30826-0_15.","chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” In Fundamental Approaches to Software Engineering, 13991:260–81. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30826-0_15."},"date_published":"2023-04-20T00:00:00Z","day":"20","has_accepted_license":"1","article_processing_charge":"No"},{"alternative_title":["IST Austria Technical Report"],"type":"technical_report","abstract":[{"text":"As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both.\r\n\r\nWe present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\n\r\nWe implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch.","lang":"eng"}],"title":"VAMOS: Middleware for Best-Effort Third-Party Monitoring","status":"public","ddc":["005"],"_id":"12407","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"55426e463fdeafe9777fc3ff635154c7","success":1,"date_created":"2023-01-27T03:18:34Z","date_updated":"2023-01-27T03:18:34Z","relation":"main_file","file_id":"12408","content_type":"application/pdf","file_size":662409,"creator":"fmuehlbo","access_level":"open_access","file_name":"main.pdf"}],"oa_version":"Published Version","keyword":["runtime monitoring","best effort","third party"],"article_processing_charge":"No","has_accepted_license":"1","day":"27","page":"38","citation":{"chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12407.","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, VAMOS: Middleware for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria, 2023.","mla":"Chalupa, Marek, et al. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12407.","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023). VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12407","ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023.","ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. VAMOS: Middleware for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria, 38p.","ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria; 2023. doi:10.15479/AT:ISTA:12407"},"date_published":"2023-01-27T00:00:00Z","ec_funded":1,"file_date_updated":"2023-01-27T03:18:34Z","department":[{"_id":"ToHe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2023","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. \r\nThe authors would like to thank the anonymous FASE reviewers for their valuable feedback and suggestions.","date_created":"2023-01-27T03:18:08Z","date_updated":"2023-04-25T07:19:06Z","related_material":{"record":[{"id":"12856","status":"public","relation":"later_version"}]},"author":[{"id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","first_name":"Marek","last_name":"Chalupa","full_name":"Chalupa, Marek"},{"full_name":"Mühlböck, Fabian","first_name":"Fabian","last_name":"Mühlböck","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","orcid":"0000-0003-1548-0177"},{"id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","last_name":"Muroya Lei","first_name":"Stefanie","full_name":"Muroya Lei, Stefanie"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"}],"publication_identifier":{"eissn":["2664-1690"]},"month":"01","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:12407"},{"month":"02","day":"01","article_processing_charge":"No","publication_identifier":{"isbn":["9780128188736"]},"date_published":"2023-02-01T00:00:00Z","doi":"10.1016/b978-0-12-818872-9.00129-1","language":[{"iso":"eng"}],"publication":"Encyclopedia of Child and Adolescent Health","citation":{"short":"C. Currin, C. Beyer, in:, B. Halpern-Felsher (Ed.), Encyclopedia of Child and Adolescent Health, 1st ed., Elsevier, 2023, pp. 86–98.","mla":"Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development in Autism and Epilepsy.” Encyclopedia of Child and Adolescent Health, edited by Bonnie Halpern-Felsher, 1st ed., Elsevier, 2023, pp. 86–98, doi:10.1016/b978-0-12-818872-9.00129-1.","chicago":"Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development in Autism and Epilepsy.” In Encyclopedia of Child and Adolescent Health, edited by Bonnie Halpern-Felsher, 1st ed., 86–98. Elsevier, 2023. https://doi.org/10.1016/b978-0-12-818872-9.00129-1.","ama":"Currin C, Beyer C. Altered childhood brain development in autism and epilepsy. In: Halpern-Felsher B, ed. Encyclopedia of Child and Adolescent Health. 1st ed. Elsevier; 2023:86-98. doi:10.1016/b978-0-12-818872-9.00129-1","apa":"Currin, C., & Beyer, C. (2023). Altered childhood brain development in autism and epilepsy. In B. Halpern-Felsher (Ed.), Encyclopedia of Child and Adolescent Health (1st ed., pp. 86–98). Elsevier. https://doi.org/10.1016/b978-0-12-818872-9.00129-1","ieee":"C. Currin and C. Beyer, “Altered childhood brain development in autism and epilepsy,” in Encyclopedia of Child and Adolescent Health, 1st ed., B. Halpern-Felsher, Ed. Elsevier, 2023, pp. 86–98.","ista":"Currin C, Beyer C. 2023.Altered childhood brain development in autism and epilepsy. In: Encyclopedia of Child and Adolescent Health. Vol. 1: Biological Development and Physical Health, , 86–98."},"quality_controlled":"1","page":"86-98","abstract":[{"lang":"eng","text":"Autism spectrum disorder (ASD) and epilepsy are frequently comorbid neurodevelopmental disorders. Extensive research has demonstrated shared pathological pathways, etiologies, and phenotypes. Many risk factors for these disorders, like genetic mutations and environmental pressures, are linked to changes in childhood brain development, which is a critical period for their manifestation.\r\nDecades of research have yielded many signatures for ASD and epilepsy, some shared and others unique or opposing. The anatomical, physiological, and behavioral correlates of these disorders are discussed in this chapter in the context of understanding shared pathological pathways. We end with important takeaways on the presentation, prevention, intervention, and policy changes for ASD and epilepsy. This chapter aims to explore the complexity of these disorders, both in etiology and phenotypes, with the further goal of appreciating the expanse of unknowns still to explore about the brain."}],"type":"book_chapter","alternative_title":["Vol. 1: Biological Development and Physical Health"],"author":[{"first_name":"Christopher","last_name":"Currin","id":"e8321fc5-3091-11eb-8a53-83f309a11ac9","orcid":"0000-0002-4809-5059","full_name":"Currin, Christopher"},{"full_name":"Beyer, Chad","last_name":"Beyer","first_name":"Chad"}],"edition":"1","date_created":"2023-04-25T07:52:43Z","date_updated":"2023-04-25T09:25:40Z","oa_version":"None","_id":"12866","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","status":"public","title":"Altered childhood brain development in autism and epilepsy","publication_status":"published","department":[{"_id":"TiVo"}],"editor":[{"full_name":"Halpern-Felsher, Bonnie","first_name":"Bonnie","last_name":"Halpern-Felsher"}],"publisher":"Elsevier"},{"month":"04","publication_identifier":{"issn":["2663 - 337X"]},"doi":"10.15479/at:ista:12809","supervisor":[{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"project":[{"name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?","_id":"267DFB90-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2023-04-07T06:18:05Z","author":[{"id":"3A96634C-F248-11E8-B48F-1D18A9856A87","last_name":"Alcarva","first_name":"Catarina","full_name":"Alcarva, Catarina"}],"date_updated":"2023-04-26T12:16:56Z","date_created":"2023-04-06T07:54:09Z","year":"2023","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"RySh"}],"day":"06","article_processing_charge":"No","has_accepted_license":"1","date_published":"2023-04-06T00:00:00Z","citation":{"short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023.","mla":"Alcarva, Catarina. Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12809.","chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12809.","ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:10.15479/at:ista:12809","ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023.","apa":"Alcarva, C. (2023). Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12809","ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria."},"page":"115","abstract":[{"text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. ","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"access_level":"closed","file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf","embargo_to":"open_access","creator":"cchlebak","content_type":"application/pdf","file_size":9881969,"file_id":"12814","embargo":"2024-04-07","relation":"main_file","checksum":"35b5997d2b0acb461f9d33d073da0df5","date_updated":"2023-04-07T06:16:06Z","date_created":"2023-04-07T06:16:06Z"},{"content_type":"application/pdf","file_size":44201583,"creator":"cchlebak","file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf","access_level":"closed","date_created":"2023-04-07T06:17:11Z","date_updated":"2023-04-07T06:17:11Z","checksum":"81198f63c294890f6d58e8b29782efdc","relation":"source_file","file_id":"12815"},{"creator":"cchlebak","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":84731244,"file_name":"Thesis_CatarinaAlcarva_final.docx","access_level":"closed","date_updated":"2023-04-07T06:18:05Z","date_created":"2023-04-07T06:18:05Z","checksum":"0317bf7f457bb585f99d453ffa69eb53","file_id":"12816","relation":"source_file"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12809","title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","ddc":["570"],"status":"public"},{"date_published":"2023-01-13T00:00:00Z","citation":{"ama":"Zhao L, Yang Y, Chen J, et al. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. 2023;24. doi:10.1186/s13059-022-02844-2","ieee":"L. Zhao et al., “Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat,” Genome Biology, vol. 24. Springer Nature, 2023.","apa":"Zhao, L., Yang, Y., Chen, J., Lin, X., Zhang, H., Wang, H., … Xiao, J. (2023). Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-022-02844-2","ista":"Zhao L, Yang Y, Chen J, Lin X, Zhang H, Wang H, Wang H, Bie X, Jiang J, Feng X, Fu X, Zhang X, Du Z, Xiao J. 2023. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. 24, 7.","short":"L. Zhao, Y. Yang, J. Chen, X. Lin, H. Zhang, H. Wang, H. Wang, X. Bie, J. Jiang, X. Feng, X. Fu, X. Zhang, Z. Du, J. Xiao, Genome Biology 24 (2023).","mla":"Zhao, Long, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” Genome Biology, vol. 24, 7, Springer Nature, 2023, doi:10.1186/s13059-022-02844-2.","chicago":"Zhao, Long, Yiman Yang, Jinchao Chen, Xuelei Lin, Hao Zhang, Hao Wang, Hongzhe Wang, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” Genome Biology. Springer Nature, 2023. https://doi.org/10.1186/s13059-022-02844-2."},"publication":"Genome Biology","article_type":"original","article_processing_charge":"No","day":"13","scopus_import":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12668","intvolume":" 24","status":"public","title":"Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat","abstract":[{"text":"Background: Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive.\r\n\r\nResults: Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal–distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome.\r\n\r\nConclusions: Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis.","lang":"eng"}],"type":"journal_article","doi":"10.1186/s13059-022-02844-2","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["36639687"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s13059-022-02844-2"}],"quality_controlled":"1","publication_identifier":{"issn":["1474-760X"]},"month":"01","author":[{"last_name":"Zhao","first_name":"Long","full_name":"Zhao, Long"},{"full_name":"Yang, Yiman","first_name":"Yiman","last_name":"Yang"},{"full_name":"Chen, Jinchao","last_name":"Chen","first_name":"Jinchao"},{"full_name":"Lin, Xuelei","first_name":"Xuelei","last_name":"Lin"},{"full_name":"Zhang, Hao","first_name":"Hao","last_name":"Zhang"},{"full_name":"Wang, Hao","last_name":"Wang","first_name":"Hao"},{"full_name":"Wang, Hongzhe","last_name":"Wang","first_name":"Hongzhe"},{"full_name":"Bie, Xiaomin","last_name":"Bie","first_name":"Xiaomin"},{"full_name":"Jiang, Jiafu","last_name":"Jiang","first_name":"Jiafu"},{"full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","first_name":"Xiaoqi"},{"first_name":"Xiangdong","last_name":"Fu","full_name":"Fu, Xiangdong"},{"full_name":"Zhang, Xiansheng","last_name":"Zhang","first_name":"Xiansheng"},{"first_name":"Zhuo","last_name":"Du","full_name":"Du, Zhuo"},{"full_name":"Xiao, Jun","first_name":"Jun","last_name":"Xiao"}],"volume":24,"date_updated":"2023-05-08T10:52:49Z","date_created":"2023-02-23T09:13:49Z","pmid":1,"year":"2023","publisher":"Springer Nature","department":[{"_id":"XiFe"}],"publication_status":"published","extern":"1","article_number":"7"},{"title":"Hausdorff and Gromov-Hausdorff stable subsets of the medial axis","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13048","oa_version":"Preprint","type":"conference","abstract":[{"text":"In this paper we introduce a pruning of the medial axis called the (λ,α)-medial axis (axλα). We prove that the (λ,α)-medial axis of a set K is stable in a Gromov-Hausdorff sense under weak assumptions. More formally we prove that if K and K′ are close in the Hausdorff (dH) sense then the (λ,α)-medial axes of K and K′ are close as metric spaces, that is the Gromov-Hausdorff distance (dGH) between the two is 1/4-Hölder in the sense that dGH (axλα(K),axλα(K′)) ≲ dH(K,K′)1/4. The Hausdorff distance between the two medial axes is also bounded, by dH (axλα(K),λα(K′)) ≲ dH(K,K′)1/2. These quantified stability results provide guarantees for practical computations of medial axes from approximations. Moreover, they provide key ingredients for studying the computability of the medial axis in the context of computable analysis.","lang":"eng"}],"page":"1768-1776","publication":"Proceedings of the 55th Annual ACM Symposium on Theory of Computing","citation":{"ieee":"A. Lieutier and M. Wintraecken, “Hausdorff and Gromov-Hausdorff stable subsets of the medial axis,” in Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Orlando, FL, United States, 2023, pp. 1768–1776.","apa":"Lieutier, A., & Wintraecken, M. (2023). Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. In Proceedings of the 55th Annual ACM Symposium on Theory of Computing (pp. 1768–1776). Orlando, FL, United States: Association for Computing Machinery. https://doi.org/10.1145/3564246.3585113","ista":"Lieutier A, Wintraecken M. 2023. Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. Proceedings of the 55th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 1768–1776.","ama":"Lieutier A, Wintraecken M. Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. In: Proceedings of the 55th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2023:1768-1776. doi:10.1145/3564246.3585113","chicago":"Lieutier, André, and Mathijs Wintraecken. “Hausdorff and Gromov-Hausdorff Stable Subsets of the Medial Axis.” In Proceedings of the 55th Annual ACM Symposium on Theory of Computing, 1768–76. Association for Computing Machinery, 2023. https://doi.org/10.1145/3564246.3585113.","short":"A. Lieutier, M. Wintraecken, in:, Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2023, pp. 1768–1776.","mla":"Lieutier, André, and Mathijs Wintraecken. “Hausdorff and Gromov-Hausdorff Stable Subsets of the Medial Axis.” Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2023, pp. 1768–76, doi:10.1145/3564246.3585113."},"date_published":"2023-06-02T00:00:00Z","day":"02","article_processing_charge":"No","publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"HeEd"}],"year":"2023","acknowledgement":"We are greatly indebted to Erin Chambers for posing a number of questions that eventually led to this paper. We would also like to thank the other organizers of the workshop on ‘Algorithms\r\nfor the medial axis’. We are also indebted to Tatiana Ezubova for helping with the search for and translation of Russian literature. The second author thanks all members of the Edelsbrunner and Datashape groups for the atmosphere in which the research was conducted.\r\nThe research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement No. 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions). Supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411. The Austrian science fund (FWF) M-3073.","date_updated":"2023-05-22T08:15:19Z","date_created":"2023-05-22T08:02:02Z","author":[{"last_name":"Lieutier","first_name":"André","full_name":"Lieutier, André"},{"full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken","first_name":"Mathijs"}],"ec_funded":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"grant_number":"M03073","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","name":"Learning and triangulating manifolds via collapses"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2303.04014"}],"external_id":{"arxiv":["2303.04014"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"STOC: Symposium on Theory of Computing","start_date":"2023-06-20","location":"Orlando, FL, United States","end_date":"2023-06-23"},"doi":"10.1145/3564246.3585113","month":"06","publication_identifier":{"isbn":["9781450399135"]}},{"article_processing_charge":"No","month":"05","oa":1,"citation":{"chicago":"Peste, Elena-Alexandra, Adrian Vladu, Eldar Kurtic, Christoph Lampert, and Dan-Adrian Alistarh. “CrAM: A Compression-Aware Minimizer.” In 11th International Conference on Learning Representations , n.d.","short":"E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, D.-A. Alistarh, in:, 11th International Conference on Learning Representations , n.d.","mla":"Peste, Elena-Alexandra, et al. “CrAM: A Compression-Aware Minimizer.” 11th International Conference on Learning Representations .","ieee":"E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, and D.-A. Alistarh, “CrAM: A Compression-Aware Minimizer,” in 11th International Conference on Learning Representations , Kigali, Rwanda .","apa":"Peste, E.-A., Vladu, A., Kurtic, E., Lampert, C., & Alistarh, D.-A. (n.d.). CrAM: A Compression-Aware Minimizer. In 11th International Conference on Learning Representations . Kigali, Rwanda .","ista":"Peste E-A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. 11th International Conference on Learning Representations . ICLR: International Conference on Learning Representations.","ama":"Peste E-A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. In: 11th International Conference on Learning Representations ."},"main_file_link":[{"url":"https://openreview.net/pdf?id=_eTZBs-yedr","open_access":"1"}],"external_id":{"arxiv":["2207.14200"]},"publication":"11th International Conference on Learning Representations ","project":[{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"}],"quality_controlled":"1","date_published":"2023-05-01T00:00:00Z","conference":{"name":"ICLR: International Conference on Learning Representations","location":"Kigali, Rwanda ","start_date":"2023-05-01","end_date":"2023-05-05"},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"type":"conference","ec_funded":1,"abstract":[{"text":"Deep neural networks (DNNs) often have to be compressed, via pruning and/or quantization, before they can be deployed in practical settings. In this work we propose a new compression-aware minimizer dubbed CrAM that modifies the optimization step in a principled way, in order to produce models whose local loss behavior is stable under compression operations such as pruning. Thus, dense models trained via CrAM should be compressible post-training, in a single step, without significant accuracy loss. Experimental results on standard benchmarks, such as residual networks for ImageNet classification and BERT models for language modelling, show that CrAM produces dense models that can be more accurate than the standard SGD/Adam-based baselines, but which are stable under weight pruning: specifically, we can prune models in one-shot to 70-80% sparsity with almost no accuracy loss, and to 90% with reasonable (∼1%) accuracy loss, which is competitive with gradual compression methods. Additionally, CrAM can produce sparse models which perform well for transfer learning, and it also works for semi-structured 2:4 pruning patterns supported by GPU hardware. The code for reproducing the results is available at this https URL .","lang":"eng"}],"year":"2023","_id":"13053","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"AP, EK, DA received funding from the European Research Council (ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). AV acknowledges the support of the French Agence Nationale de la Recherche (ANR), under grant ANR-21-CE48-0016 (project COMCOPT). We further acknowledge the support from the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp)-","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"title":"CrAM: A Compression-Aware Minimizer","publication_status":"accepted","status":"public","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"13074"}]},"author":[{"first_name":"Elena-Alexandra","last_name":"Peste","id":"32D78294-F248-11E8-B48F-1D18A9856A87","full_name":"Peste, Elena-Alexandra"},{"first_name":"Adrian","last_name":"Vladu","full_name":"Vladu, Adrian"},{"full_name":"Kurtic, Eldar","last_name":"Kurtic","first_name":"Eldar","id":"47beb3a5-07b5-11eb-9b87-b108ec578218"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"},{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"}],"oa_version":"Preprint","date_created":"2023-05-23T11:36:18Z","date_updated":"2023-06-01T12:54:45Z"},{"scopus_import":"1","article_processing_charge":"No","day":"02","page":"530-553","citation":{"apa":"Hoffmann, C., Hubáček, P., Kamath, C., & Pietrzak, K. Z. (2023). Certifying giant nonprimes. In Public-Key Cryptography - PKC 2023 (Vol. 13940, pp. 530–553). Atlanta, GA, United States: Springer Nature. https://doi.org/10.1007/978-3-031-31368-4_19","ieee":"C. Hoffmann, P. Hubáček, C. Kamath, and K. Z. Pietrzak, “Certifying giant nonprimes,” in Public-Key Cryptography - PKC 2023, Atlanta, GA, United States, 2023, vol. 13940, pp. 530–553.","ista":"Hoffmann C, Hubáček P, Kamath C, Pietrzak KZ. 2023. Certifying giant nonprimes. Public-Key Cryptography - PKC 2023. PKC: Public-Key Cryptography, LNCS, vol. 13940, 530–553.","ama":"Hoffmann C, Hubáček P, Kamath C, Pietrzak KZ. Certifying giant nonprimes. In: Public-Key Cryptography - PKC 2023. Vol 13940. Springer Nature; 2023:530-553. doi:10.1007/978-3-031-31368-4_19","chicago":"Hoffmann, Charlotte, Pavel Hubáček, Chethan Kamath, and Krzysztof Z Pietrzak. “Certifying Giant Nonprimes.” In Public-Key Cryptography - PKC 2023, 13940:530–53. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-31368-4_19.","short":"C. Hoffmann, P. Hubáček, C. Kamath, K.Z. Pietrzak, in:, Public-Key Cryptography - PKC 2023, Springer Nature, 2023, pp. 530–553.","mla":"Hoffmann, Charlotte, et al. “Certifying Giant Nonprimes.” Public-Key Cryptography - PKC 2023, vol. 13940, Springer Nature, 2023, pp. 530–53, doi:10.1007/978-3-031-31368-4_19."},"publication":"Public-Key Cryptography - PKC 2023","date_published":"2023-05-02T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"GIMPS and PrimeGrid are large-scale distributed projects dedicated to searching giant prime numbers, usually of special forms like Mersenne and Proth primes. The numbers in the current search-space are millions of digits large and the participating volunteers need to run resource-consuming primality tests. Once a candidate prime N has been found, the only way for another party to independently verify the primality of N used to be by repeating the expensive primality test. To avoid the need for second recomputation of each primality test, these projects have recently adopted certifying mechanisms that enable efficient verification of performed tests. However, the mechanisms presently in place only detect benign errors and there is no guarantee against adversarial behavior: a malicious volunteer can mislead the project to reject a giant prime as being non-prime.\r\nIn this paper, we propose a practical, cryptographically-sound mechanism for certifying the non-primality of Proth numbers. That is, a volunteer can – parallel to running the primality test for N – generate an efficiently verifiable proof at a little extra cost certifying that N is not prime. The interactive protocol has statistical soundness and can be made non-interactive using the Fiat-Shamir heuristic.\r\nOur approach is based on a cryptographic primitive called Proof of Exponentiation (PoE) which, for a group G, certifies that a tuple (x,y,T)∈G2×N satisfies x2T=y (Pietrzak, ITCS 2019 and Wesolowski, J. Cryptol. 2020). In particular, we show how to adapt Pietrzak’s PoE at a moderate additional cost to make it a cryptographically-sound certificate of non-primality."}],"intvolume":" 13940","status":"public","title":"Certifying giant nonprimes","_id":"13143","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","publication_identifier":{"isbn":["9783031313677"],"eissn":["1611-3349"],"issn":["0302-9743"]},"month":"05","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2023/238","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-31368-4_19","conference":{"location":"Atlanta, GA, United States","start_date":"2023-05-07","end_date":"2023-05-10","name":"PKC: Public-Key Cryptography"},"publisher":"Springer Nature","department":[{"_id":"KrPi"}],"publication_status":"published","acknowledgement":"We are grateful to Pavel Atnashev for clarifying via e-mail several aspects of the primality tests implementated in the PrimeGrid project. Pavel Hubáček is supported by the Czech Academy of Sciences (RVO 67985840), the Grant Agency of the Czech Republic under the grant agreement no. 19-27871X, and by the Charles University project UNCE/SCI/004. Chethan Kamath is supported by Azrieli International Postdoctoral Fellowship, ISF grants 484/18 and 1789/19, and ERC StG project SPP: Secrecy Preserving Proofs.","year":"2023","volume":13940,"date_created":"2023-06-18T22:00:47Z","date_updated":"2023-06-19T08:03:37Z","author":[{"full_name":"Hoffmann, Charlotte","id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7","last_name":"Hoffmann","first_name":"Charlotte"},{"full_name":"Hubáček, Pavel","first_name":"Pavel","last_name":"Hubáček"},{"full_name":"Kamath, Chethan","first_name":"Chethan","last_name":"Kamath"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"}]},{"intvolume":" 13993","ddc":["000"],"status":"public","title":"A learner-verifier framework for neural network controllers and certificates of stochastic systems","_id":"13142","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_name":"2023_LNCS_Chatterjee.pdf","access_level":"open_access","creator":"dernst","file_size":528455,"content_type":"application/pdf","file_id":"13150","relation":"main_file","date_created":"2023-06-19T08:29:30Z","date_updated":"2023-06-19T08:29:30Z","success":1,"checksum":"3d8a8bb24d211bc83360dfc2fd744307"}],"alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Reinforcement learning has received much attention for learning controllers of deterministic systems. We consider a learner-verifier framework for stochastic control systems and survey recent methods that formally guarantee a conjunction of reachability and safety properties. Given a property and a lower bound on the probability of the property being satisfied, our framework jointly learns a control policy and a formal certificate to ensure the satisfaction of the property with a desired probability threshold. Both the control policy and the formal certificate are continuous functions from states to reals, which are learned as parameterized neural networks. While in the deterministic case, the certificates are invariant and barrier functions for safety, or Lyapunov and ranking functions for liveness, in the stochastic case the certificates are supermartingales. For certificate verification, we use interval arithmetic abstract interpretation to bound the expected values of neural network functions.","lang":"eng"}],"page":"3-25","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Mathias Lechner, and Dorde Zikelic. “A Learner-Verifier Framework for Neural Network Controllers and Certificates of Stochastic Systems.” In Tools and Algorithms for the Construction and Analysis of Systems , 13993:3–25. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30823-9_1.","short":"K. Chatterjee, T.A. Henzinger, M. Lechner, D. Zikelic, in:, Tools and Algorithms for the Construction and Analysis of Systems , Springer Nature, 2023, pp. 3–25.","mla":"Chatterjee, Krishnendu, et al. “A Learner-Verifier Framework for Neural Network Controllers and Certificates of Stochastic Systems.” Tools and Algorithms for the Construction and Analysis of Systems , vol. 13993, Springer Nature, 2023, pp. 3–25, doi:10.1007/978-3-031-30823-9_1.","apa":"Chatterjee, K., Henzinger, T. A., Lechner, M., & Zikelic, D. (2023). A learner-verifier framework for neural network controllers and certificates of stochastic systems. In Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13993, pp. 3–25). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30823-9_1","ieee":"K. Chatterjee, T. A. Henzinger, M. Lechner, and D. Zikelic, “A learner-verifier framework for neural network controllers and certificates of stochastic systems,” in Tools and Algorithms for the Construction and Analysis of Systems , Paris, France, 2023, vol. 13993, pp. 3–25.","ista":"Chatterjee K, Henzinger TA, Lechner M, Zikelic D. 2023. A learner-verifier framework for neural network controllers and certificates of stochastic systems. Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13993, 3–25.","ama":"Chatterjee K, Henzinger TA, Lechner M, Zikelic D. A learner-verifier framework for neural network controllers and certificates of stochastic systems. In: Tools and Algorithms for the Construction and Analysis of Systems . Vol 13993. Springer Nature; 2023:3-25. doi:10.1007/978-3-031-30823-9_1"},"publication":"Tools and Algorithms for the Construction and Analysis of Systems ","date_published":"2023-04-22T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"22","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Springer Nature","publication_status":"published","year":"2023","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","volume":13993,"date_created":"2023-06-18T22:00:47Z","date_updated":"2023-06-19T08:30:54Z","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"},{"full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner"},{"full_name":"Zikelic, Dorde","first_name":"Dorde","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"file_date_updated":"2023-06-19T08:29:30Z","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-30823-9_1","conference":{"end_date":"2023-04-27","location":"Paris, France","start_date":"2023-04-22","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031308222"],"issn":["0302-9743"]},"month":"04"},{"year":"2023","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"publication_status":"published","author":[{"last_name":"Anand","first_name":"Ashwani","full_name":"Anand, Ashwani"},{"full_name":"Mallik, Kaushik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","orcid":"0000-0001-9864-7475","first_name":"Kaushik","last_name":"Mallik"},{"full_name":"Nayak, Satya Prakash","last_name":"Nayak","first_name":"Satya Prakash"},{"full_name":"Schmuck, Anne Kathrin","first_name":"Anne Kathrin","last_name":"Schmuck"}],"volume":13994,"date_updated":"2023-06-19T08:49:46Z","date_created":"2023-06-18T22:00:47Z","file_date_updated":"2023-06-19T08:43:21Z","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":"10.1007/978-3-031-30820-8_15","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","location":"Paris, France","start_date":"2023-04-22","end_date":"2023-04-27"},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031308192"],"issn":["0302-9743"]},"month":"04","_id":"13141","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 13994","ddc":["000"],"status":"public","title":"Computing adequately permissive assumptions for synthesis","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":521425,"creator":"dernst","file_name":"2023_LNCS_Anand.pdf","access_level":"open_access","date_created":"2023-06-19T08:43:21Z","date_updated":"2023-06-19T08:43:21Z","checksum":"60dcafc1b4f6f070be43bad3fe877974","success":1,"relation":"main_file","file_id":"13151"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"We automatically compute a new class of environment assumptions in two-player turn-based finite graph games which characterize an “adequate cooperation” needed from the environment to allow the system player to win. Given an ω-regular winning condition Φ for the system player, we compute an ω-regular assumption Ψ for the environment player, such that (i) every environment strategy compliant with Ψ allows the system to fulfill Φ (sufficiency), (ii) Ψ\r\n can be fulfilled by the environment for every strategy of the system (implementability), and (iii) Ψ does not prevent any cooperative strategy choice (permissiveness).\r\nFor parity games, which are canonical representations of ω-regular games, we present a polynomial-time algorithm for the symbolic computation of adequately permissive assumptions and show that our algorithm runs faster and produces better assumptions than existing approaches—both theoretically and empirically. To the best of our knowledge, for ω\r\n-regular games, we provide the first algorithm to compute sufficient and implementable environment assumptions that are also permissive.","lang":"eng"}],"citation":{"ista":"Anand A, Mallik K, Nayak SP, Schmuck AK. 2023. Computing adequately permissive assumptions for synthesis. TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994, 211–228.","ieee":"A. Anand, K. Mallik, S. P. Nayak, and A. K. Schmuck, “Computing adequately permissive assumptions for synthesis,” in TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Paris, France, 2023, vol. 13994, pp. 211–228.","apa":"Anand, A., Mallik, K., Nayak, S. P., & Schmuck, A. K. (2023). Computing adequately permissive assumptions for synthesis. In TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13994, pp. 211–228). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30820-8_15","ama":"Anand A, Mallik K, Nayak SP, Schmuck AK. Computing adequately permissive assumptions for synthesis. In: TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems. Vol 13994. Springer Nature; 2023:211-228. doi:10.1007/978-3-031-30820-8_15","chicago":"Anand, Ashwani, Kaushik Mallik, Satya Prakash Nayak, and Anne Kathrin Schmuck. “Computing Adequately Permissive Assumptions for Synthesis.” In TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, 13994:211–28. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30820-8_15.","mla":"Anand, Ashwani, et al. “Computing Adequately Permissive Assumptions for Synthesis.” TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, vol. 13994, Springer Nature, 2023, pp. 211–28, doi:10.1007/978-3-031-30820-8_15.","short":"A. Anand, K. Mallik, S.P. Nayak, A.K. Schmuck, in:, TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 211–228."},"publication":"TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems","page":"211-228","date_published":"2023-04-20T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"20"},{"oa_version":"Published Version","file":[{"date_created":"2023-04-20T09:14:38Z","date_updated":"2023-04-20T09:26:51Z","checksum":"5f589a9af025f7eeebfd0c186209913e","file_id":"12857","relation":"source_file","creator":"vpokusae","file_size":14507243,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Pokusaeva.docx","access_level":"closed"},{"relation":"main_file","file_id":"12858","date_created":"2023-04-20T09:14:44Z","date_updated":"2023-04-20T09:14:44Z","checksum":"bbeed76db45a996b4c91a9abe12ce0ec","success":1,"file_name":"Thesis_Pokusaeva.pdf","access_level":"open_access","content_type":"application/pdf","file_size":10090711,"creator":"vpokusae"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12826","status":"public","ddc":["570","571"],"title":"Neural control of optic flow-based navigation in Drosophila melanogaster","abstract":[{"text":"During navigation, animals can infer the structure of the environment by computing the optic flow cues elicited by their own movements, and subsequently use this information to instruct proper locomotor actions. These computations require a panoramic assessment of the visual environment in order to disambiguate similar sensory experiences that may require distinct behavioral responses. The estimation of the global motion patterns is therefore essential for successful navigation. Yet, our understanding of the algorithms and implementations that enable coherent panoramic visual perception remains scarce. Here I pursue this problem by dissecting the functional aspects of interneuronal communication in the lobula plate tangential cell network in Drosophila melanogaster. The results presented in the thesis demonstrate that the basis for effective interpretation of the optic flow in this circuit are stereotyped synaptic connections that mediate the formation of distinct subnetworks, each extracting a particular pattern of global motion. \r\nFirstly, I show that gap junctions are essential for a correct interpretation of binocular motion cues by horizontal motion-sensitive cells. HS cells form electrical synapses with contralateral H2 neurons that are involved in detecting yaw rotation and translation. I developed an FlpStop-mediated mutant of a gap junction protein ShakB that disrupts these electrical synapses. While the loss of electrical synapses does not affect the tuning of the direction selectivity in HS neurons, it severely alters their sensitivity to horizontal motion in the contralateral side. These physiological changes result in an inappropriate integration of binocular motion cues in walking animals. While wild-type flies form a binocular perception of visual motion by non-linear integration of monocular optic flow cues, the mutant flies sum the monocular inputs linearly. These results indicate that rather than averaging signals in neighboring neurons, gap-junctions operate in conjunction with chemical synapses to mediate complex non-linear optic flow computations.\r\nSecondly, I show that stochastic manipulation of neuronal activity in the lobula plate tangential cell network is a powerful approach to study the neuronal implementation of optic flow-based navigation in flies. Tangential neurons form multiple subnetworks, each mediating course-stabilizing response to a particular global pattern of visual motion. Application of genetic mosaic techniques can provide sparse optogenetic activation of HS cells in numerous combinations. These distinct combinations of activated neurons drive an array of distinct behavioral responses, providing important insights into how visuomotor transformation is performed in the lobula plate tangential cell network. This approach can be complemented by stochastic silencing of tangential neurons, enabling direct assessment of the functional role of individual tangential neurons in the processing of specific visual motion patterns.\r\n\tTaken together, the findings presented in this thesis suggest that establishing specific activity patterns of tangential cells via stereotyped synaptic connectivity is a key to efficient optic flow-based navigation in Drosophila melanogaster.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2023-04-18T00:00:00Z","citation":{"short":"V. Pokusaeva, Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster, Institute of Science and Technology Austria, 2023.","mla":"Pokusaeva, Victoria. Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12826.","chicago":"Pokusaeva, Victoria. “Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12826.","ama":"Pokusaeva V. Neural control of optic flow-based navigation in Drosophila melanogaster. 2023. doi:10.15479/at:ista:12826","ieee":"V. Pokusaeva, “Neural control of optic flow-based navigation in Drosophila melanogaster,” Institute of Science and Technology Austria, 2023.","apa":"Pokusaeva, V. (2023). Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12826","ista":"Pokusaeva V. 2023. Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria."},"page":"106","day":"18","has_accepted_license":"1","article_processing_charge":"No","author":[{"last_name":"Pokusaeva","first_name":"Victoria","orcid":"0000-0001-7660-444X","id":"3184041C-F248-11E8-B48F-1D18A9856A87","full_name":"Pokusaeva, Victoria"}],"date_updated":"2023-06-23T09:47:36Z","date_created":"2023-04-14T14:56:04Z","year":"2023","publication_status":"published","department":[{"_id":"MaJö"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-04-20T09:26:51Z","ec_funded":1,"doi":"10.15479/at:ista:12826","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","first_name":"Maximilian A","full_name":"Jösch, Maximilian A"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"month":"04","publication_identifier":{"issn":["2663 - 337X"]}},{"date_updated":"2023-06-27T12:53:43Z","date_created":"2022-09-11T22:01:57Z","volume":85,"author":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"full_name":"Osang, Georg F","last_name":"Osang","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","year":"2023","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.","file_date_updated":"2023-01-20T10:02:48Z","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00453-022-01027-6","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes"}],"external_id":{"isi":["000846967100001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"01","publication_identifier":{"eissn":["1432-0541"],"issn":["0178-4617"]},"oa_version":"Published Version","file":[{"creator":"dernst","file_size":911017,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_Algorithmica_Edelsbrunner.pdf","success":1,"checksum":"71685ca5121f4c837f40c3f8eb50c915","date_created":"2023-01-20T10:02:48Z","date_updated":"2023-01-20T10:02:48Z","file_id":"12322","relation":"main_file"}],"status":"public","title":"A simple algorithm for higher-order Delaunay mosaics and alpha shapes","ddc":["510"],"intvolume":" 85","_id":"12086","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We present a simple algorithm for computing higher-order Delaunay mosaics that works in Euclidean spaces of any finite dimensions. The algorithm selects the vertices of the order-k mosaic from incrementally constructed lower-order mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box to construct the order-k mosaic from its vertices. Beyond this black-box, the algorithm uses only combinatorial operations, thus facilitating easy implementation. We extend this algorithm to compute higher-order α-shapes and provide open-source implementations. We present experimental results for properties of higher-order Delaunay mosaics of random point sets.","lang":"eng"}],"type":"journal_article","date_published":"2023-01-01T00:00:00Z","article_type":"original","page":"277-295","publication":"Algorithmica","citation":{"apa":"Edelsbrunner, H., & Osang, G. F. (2023). A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. Springer Nature. https://doi.org/10.1007/s00453-022-01027-6","ieee":"H. Edelsbrunner and G. F. Osang, “A simple algorithm for higher-order Delaunay mosaics and alpha shapes,” Algorithmica, vol. 85. Springer Nature, pp. 277–295, 2023.","ista":"Edelsbrunner H, Osang GF. 2023. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 85, 277–295.","ama":"Edelsbrunner H, Osang GF. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 2023;85:277-295. doi:10.1007/s00453-022-01027-6","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica. Springer Nature, 2023. https://doi.org/10.1007/s00453-022-01027-6.","short":"H. Edelsbrunner, G.F. Osang, Algorithmica 85 (2023) 277–295.","mla":"Edelsbrunner, Herbert, and Georg F. Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica, vol. 85, Springer Nature, 2023, pp. 277–95, doi:10.1007/s00453-022-01027-6."},"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1"},{"project":[{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"},{"grant_number":"E208","_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","name":"Configuration Spaces over Non-Smooth Spaces"},{"name":"Gradient flow techniques for quantum Markov semigroups","_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833","grant_number":"ESP156_N"}],"isi":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"},"external_id":{"isi":["000906214600004"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00028-022-00859-7","publication_identifier":{"issn":["1424-3199"],"eissn":["1424-3202"]},"month":"01","publisher":"Springer Nature","department":[{"_id":"JaMa"}],"publication_status":"published","acknowledgement":"Research supported by the Austrian Science Fund (FWF) grant F65 at the Institute of Science and Technology Austria and by the European Research Council (ERC) (Grant agreement No. 716117 awarded to Prof. Dr. Jan Maas). L.D.S. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 208). M.W. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 156).","year":"2023","volume":23,"date_updated":"2023-06-28T11:54:35Z","date_created":"2023-01-08T23:00:53Z","author":[{"id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","orcid":"0000-0002-9881-6870","first_name":"Lorenzo","last_name":"Dello Schiavo","full_name":"Dello Schiavo, Lorenzo"},{"full_name":"Wirth, Melchior","orcid":"0000-0002-0519-4241","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","last_name":"Wirth","first_name":"Melchior"}],"article_number":"9","ec_funded":1,"file_date_updated":"2023-01-20T10:45:06Z","article_type":"original","citation":{"apa":"Dello Schiavo, L., & Wirth, M. (2023). Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. Springer Nature. https://doi.org/10.1007/s00028-022-00859-7","ieee":"L. Dello Schiavo and M. Wirth, “Ergodic decompositions of Dirichlet forms under order isomorphisms,” Journal of Evolution Equations, vol. 23, no. 1. Springer Nature, 2023.","ista":"Dello Schiavo L, Wirth M. 2023. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 23(1), 9.","ama":"Dello Schiavo L, Wirth M. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 2023;23(1). doi:10.1007/s00028-022-00859-7","chicago":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” Journal of Evolution Equations. Springer Nature, 2023. https://doi.org/10.1007/s00028-022-00859-7.","short":"L. Dello Schiavo, M. Wirth, Journal of Evolution Equations 23 (2023).","mla":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” Journal of Evolution Equations, vol. 23, no. 1, 9, Springer Nature, 2023, doi:10.1007/s00028-022-00859-7."},"publication":"Journal of Evolution Equations","date_published":"2023-01-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","intvolume":" 23","ddc":["510"],"title":"Ergodic decompositions of Dirichlet forms under order isomorphisms","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12104","file":[{"date_updated":"2023-01-20T10:45:06Z","date_created":"2023-01-20T10:45:06Z","success":1,"checksum":"1f34f3e2cb521033de6154f274ea3a4e","file_id":"12325","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":422612,"file_name":"2023_JourEvolutionEquations_DelloSchiavo.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"text":"We study ergodic decompositions of Dirichlet spaces under intertwining via unitary order isomorphisms. We show that the ergodic decomposition of a quasi-regular Dirichlet space is unique up to a unique isomorphism of the indexing space. Furthermore, every unitary order isomorphism intertwining two quasi-regular Dirichlet spaces is decomposable over their ergodic decompositions up to conjugation via an isomorphism of the corresponding indexing spaces.","lang":"eng"}]},{"abstract":[{"text":"The Indian summer monsoon rainfall (ISMR) has been declining since the 1950s. However, since 2002 it is reported to have revived. For these observed changes in the ISMR, several explanations have been reported. Among these explanations, however, the role of the eastern equatorial Indian Ocean (EEIO) is missing despite being one of the warmest regions in the Indian Ocean, and monotonously warming. A recent study reported that EEIO warming impacts the rainfall over northern India. Here we report that warming in the EEIO weakens the low-level Indian summer monsoon circulation and reduces ISMR. A warm EEIO drives easterly winds in the Indo–Pacific sector as a Gill response. The warm EEIO also enhances nocturnal convection offshore the western coast of Sumatra. The latent heating associated with the increased convection augments the Gill response and the resultant circulation opposes the monsoon low-level circulation and weakens the seasonal rainfall.","lang":"eng"}],"type":"journal_article","oa_version":"None","status":"public","title":"Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend","intvolume":" 60","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11434","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2023-01-01T00:00:00Z","article_type":"original","page":"427-442","publication":"Climate Dynamics","citation":{"mla":"GOSWAMI, BIDYUT B. “Role of the Eastern Equatorial Indian Ocean Warming in the Indian Summer Monsoon Rainfall Trend.” Climate Dynamics, vol. 60, Springer Nature, 2023, pp. 427–42, doi:10.1007/s00382-022-06337-7.","short":"B.B. GOSWAMI, Climate Dynamics 60 (2023) 427–442.","chicago":"GOSWAMI, BIDYUT B. “Role of the Eastern Equatorial Indian Ocean Warming in the Indian Summer Monsoon Rainfall Trend.” Climate Dynamics. Springer Nature, 2023. https://doi.org/10.1007/s00382-022-06337-7.","ama":"GOSWAMI BB. Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. 2023;60:427-442. doi:10.1007/s00382-022-06337-7","ista":"GOSWAMI BB. 2023. Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. 60, 427–442.","apa":"GOSWAMI, B. B. (2023). Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. Springer Nature. https://doi.org/10.1007/s00382-022-06337-7","ieee":"B. B. GOSWAMI, “Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend,” Climate Dynamics, vol. 60. Springer Nature, pp. 427–442, 2023."},"date_created":"2022-06-05T22:01:50Z","date_updated":"2023-06-28T11:49:58Z","volume":60,"author":[{"first_name":"Bidyut B","last_name":"Goswami","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","full_name":"Goswami, Bidyut B"}],"related_material":{"link":[{"relation":"erratum","url":" https://doi.org/10.1007/s00382-022-06401-2"}]},"publication_status":"published","department":[{"_id":"CaMu"}],"publisher":"Springer Nature","acknowledgement":"This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (NRF-2018R1A5A1024958). Model simulation and data transfer were supported by the National Supercomputing Center with supercomputing resources including technical support (KSC-2019-CHA-0005), the National Center for Meteorological Supercomputer of Korea Meteorological Administration, and by the Korea Research Environment Open NETwork (KREONET), respectively. The authors declare no conflicts of interest.","year":"2023","month":"01","publication_identifier":{"issn":["0930-7575"],"eissn":["1432-0894"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00382-022-06337-7","quality_controlled":"1","isi":1,"external_id":{"isi":["000803119400002"]}},{"ec_funded":1,"file_date_updated":"2023-06-19T10:28:09Z","volume":13992,"date_created":"2023-01-31T07:23:56Z","date_updated":"2023-07-14T11:20:27Z","author":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"b26baa86-3308-11ec-87b0-8990f34baa85","first_name":"Nicolas Adrien","last_name":"Mazzocchi","full_name":"Mazzocchi, Nicolas Adrien"},{"full_name":"Sarac, Naci E","first_name":"Naci E","last_name":"Sarac","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425"}],"publisher":"Springer Nature","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"publication_status":"published","year":"2023","acknowledgement":"We thank the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093.","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031308284"],"eissn":["1611-3349"]},"month":"04","language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-30829-1_17","conference":{"name":"FOSSACS: Foundations of Software Science and Computation Structures","end_date":"2023-04-27","location":"Paris, France","start_date":"2023-04-22"},"project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","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"},"external_id":{"arxiv":["2301.11175"]},"abstract":[{"lang":"eng","text":"Safety and liveness are elementary concepts of computation, and the foundation of many verification paradigms. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In quantitative specification and verification, properties assign not truth values, but quantitative values to infinite traces (e.g., a cost, or the distance to a boolean property). We introduce quantitative safety and liveness, and we prove that our definitions induce conservative quantitative generalizations of both (1)~the safety-progress hierarchy of boolean properties and (2)~the safety-liveness decomposition of boolean properties. In particular, we show that every quantitative property can be written as the pointwise minimum of a quantitative safety property and a quantitative liveness property. Consequently, like boolean properties, also quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. Moreover, quantitative properties can be approximated naturally. We prove that every quantitative property that has both safe and co-safe approximations can be monitored arbitrarily precisely by a monitor that uses only a finite number of states."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12468","checksum":"981025aed580b6b27c426cb8856cf63e","success":1,"date_created":"2023-01-31T07:22:21Z","date_updated":"2023-01-31T07:22:21Z","access_level":"open_access","file_name":"qsl.pdf","file_size":449027,"content_type":"application/pdf","creator":"esarac"},{"file_name":"2023_LNCS_HenzingerT.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1048171,"creator":"dernst","relation":"main_file","file_id":"13153","date_created":"2023-06-19T10:28:09Z","date_updated":"2023-06-19T10:28:09Z","checksum":"f16e2af1e0eb243158ab0f0fe74e7d5a","success":1}],"intvolume":" 13992","title":"Quantitative safety and liveness","status":"public","ddc":["000"],"_id":"12467","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","has_accepted_license":"1","day":"21","scopus_import":"1","date_published":"2023-04-21T00:00:00Z","page":"349-370","citation":{"apa":"Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2023). Quantitative safety and liveness. In 26th International Conference Foundations of Software Science and Computation Structures (Vol. 13992, pp. 349–370). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30829-1_17","ieee":"T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Quantitative safety and liveness,” in 26th International Conference Foundations of Software Science and Computation Structures, Paris, France, 2023, vol. 13992, pp. 349–370.","ista":"Henzinger TA, Mazzocchi NA, Sarac NE. 2023. Quantitative safety and liveness. 26th International Conference Foundations of Software Science and Computation Structures. FOSSACS: Foundations of Software Science and Computation Structures, LNCS, vol. 13992, 349–370.","ama":"Henzinger TA, Mazzocchi NA, Sarac NE. Quantitative safety and liveness. In: 26th International Conference Foundations of Software Science and Computation Structures. Vol 13992. Springer Nature; 2023:349-370. doi:10.1007/978-3-031-30829-1_17","chicago":"Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Quantitative Safety and Liveness.” In 26th International Conference Foundations of Software Science and Computation Structures, 13992:349–70. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30829-1_17.","short":"T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 26th International Conference Foundations of Software Science and Computation Structures, Springer Nature, 2023, pp. 349–370.","mla":"Henzinger, Thomas A., et al. “Quantitative Safety and Liveness.” 26th International Conference Foundations of Software Science and Computation Structures, vol. 13992, Springer Nature, 2023, pp. 349–70, doi:10.1007/978-3-031-30829-1_17."},"publication":"26th International Conference Foundations of Software Science and Computation Structures"},{"date_published":"2023-06-06T00:00:00Z","publication":"Proceedings of the ACM on Programming Languages","citation":{"chicago":"Koval, Nikita, Dmitry Khalanskiy, and Dan-Adrian Alistarh. “CQS: A Formally-Verified Framework for Fair and Abortable Synchronization.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery , 2023. https://doi.org/10.1145/3591230.","short":"N. Koval, D. Khalanskiy, D.-A. Alistarh, Proceedings of the ACM on Programming Languages 7 (2023).","mla":"Koval, Nikita, et al. “CQS: A Formally-Verified Framework for Fair and Abortable Synchronization.” Proceedings of the ACM on Programming Languages, vol. 7, 116, Association for Computing Machinery , 2023, doi:10.1145/3591230.","apa":"Koval, N., Khalanskiy, D., & Alistarh, D.-A. (2023). CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. Association for Computing Machinery . https://doi.org/10.1145/3591230","ieee":"N. Koval, D. Khalanskiy, and D.-A. Alistarh, “CQS: A formally-verified framework for fair and abortable synchronization,” Proceedings of the ACM on Programming Languages, vol. 7. Association for Computing Machinery , 2023.","ista":"Koval N, Khalanskiy D, Alistarh D-A. 2023. CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. 7, 116.","ama":"Koval N, Khalanskiy D, Alistarh D-A. CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. 2023;7. doi:10.1145/3591230"},"article_type":"original","day":"06","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"creator":"alisjak","file_size":1266773,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_ACMProgram.Lang._Koval.pdf","success":1,"checksum":"5dba6e73f0ed79adbdae14d165bc2f68","date_created":"2023-07-03T13:09:39Z","date_updated":"2023-07-03T13:09:39Z","file_id":"13187","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13179","title":"CQS: A formally-verified framework for fair and abortable synchronization","ddc":["000"],"status":"public","intvolume":" 7","abstract":[{"lang":"eng","text":"Writing concurrent code that is both correct and efficient is notoriously difficult. Thus, programmers often prefer to use synchronization abstractions, which render code simpler and easier to reason about. Despite a wealth of work on this topic, there is still a gap between the rich semantics provided by synchronization abstractions in modern programming languages—specifically, fair FIFO ordering of synchronization requests and support for abortable operations—and frameworks for implementing it correctly and efficiently. Supporting such semantics is critical given the rising popularity of constructs for asynchronous programming, such as coroutines, which abort frequently and are cheaper to suspend and resume compared to native threads.\r\n\r\nThis paper introduces a new framework called CancellableQueueSynchronizer (CQS), which enables simple yet efficient implementations of a wide range of fair and abortable synchronization primitives: mutexes, semaphores, barriers, count-down latches, and blocking pools. Our main contribution is algorithmic, as implementing both fairness and abortability efficiently at this level of generality is non-trivial. Importantly, all our algorithms, including the CQS framework and the primitives built on top of it, come with formal proofs in the Iris framework for Coq for many of their properties. These proofs are modular, so it is easy to show correctness for new primitives implemented on top of CQS. From a practical perspective, implementation of CQS for native threads on the JVM improves throughput by up to two orders of magnitude over Java’s AbstractQueuedSynchronizer, the only practical abstraction offering similar semantics. Further, we successfully integrated CQS as a core component of the popular Kotlin Coroutines library, validating the framework’s practical impact and expressiveness in a real-world environment. In sum, CancellableQueueSynchronizer is the first framework to combine expressiveness with formal guarantees and solid practical performance. Our approach should be extensible to other languages and families of synchronization primitives."}],"type":"journal_article","doi":"10.1145/3591230","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","month":"06","publication_identifier":{"eissn":["2475-1421"]},"author":[{"full_name":"Koval, Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","last_name":"Koval","first_name":"Nikita"},{"first_name":"Dmitry","last_name":"Khalanskiy","full_name":"Khalanskiy, Dmitry"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"}],"date_updated":"2023-07-17T08:43:19Z","date_created":"2023-07-02T22:00:43Z","volume":7,"year":"2023","publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"Association for Computing Machinery ","file_date_updated":"2023-07-03T13:09:39Z","article_number":"116"}]