[{"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","citation":{"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.","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.","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, “Fast and scalable channels in Kotlin Coroutines,” in Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Montreal, QC, Canada, 2023, pp. 107–118.","apa":"Koval, N., Alistarh, D.-A., & Elizarov, R. (2023). Fast and scalable channels in Kotlin Coroutines. In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 107–118). Montreal, QC, Canada: Association for Computing Machinery. https://doi.org/10.1145/3572848.3577481"},"external_id":{"arxiv":["2211.04986"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.04986"}],"day":"25","month":"02","publication_identifier":{"isbn":["9798400700156"]},"article_processing_charge":"No","scopus_import":"1","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","first_name":"Nikita","last_name":"Koval"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Elizarov, Roman","last_name":"Elizarov","first_name":"Roman"}],"title":"Fast and scalable channels in Kotlin Coroutines","publication_status":"published","status":"public","publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"}],"_id":"12735","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Asynchronous programming has gained significant popularity over the last decade: support for this programming pattern is available in many popular languages via libraries and native language implementations, typically in the form of coroutines or the async/await construct. Instead of programming via shared memory, this concept assumes implicit synchronization through message passing. The key data structure enabling such communication is the rendezvous channel. Roughly, a rendezvous channel is a blocking queue of size zero, so both send(e) and receive() operations wait for each other, performing a rendezvous when they meet. To optimize the message passing pattern, channels are usually equipped with a fixed-size buffer, so sends do not suspend and put elements into the buffer until its capacity is exceeded. This primitive is known as a buffered channel.\r\n\r\nThis paper presents a fast and scalable algorithm for both rendezvous and buffered channels. Similarly to modern queues, our solution is based on an infinite array with two positional counters for send(e) and receive() operations, leveraging the unconditional Fetch-And-Add instruction to update them. Yet, the algorithm requires non-trivial modifications of this classic pattern, in order to support the full channel semantics, such as buffering and cancellation of waiting requests. We compare the performance of our solution to that of the Kotlin implementation, as well as against other academic proposals, showing up to 9.8× speedup. To showcase its expressiveness and performance, we also integrated the proposed algorithm into the standard Kotlin Coroutines library, replacing the previous channel implementations.","lang":"eng"}],"type":"conference"},{"language":[{"iso":"eng"}],"conference":{"end_date":"2023-03-01","location":"Montreal, QB, Canada","start_date":"2023-02-25","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"date_published":"2023-02-25T00:00:00Z","doi":"10.1145/3572848.3577512","quality_controlled":"1","page":"438-440","publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3572848.3577512"}],"citation":{"ieee":"V. Aksenov, T. A. Brown, A. Fedorov, and I. Kokorin, Unexpected scaling in path copying trees. Association for Computing Machinery, 2023, pp. 438–440.","apa":"Aksenov, V., Brown, T. A., Fedorov, A., & Kokorin, I. (2023). Unexpected scaling in path copying trees. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 438–440). Montreal, QB, Canada: Association for Computing Machinery. https://doi.org/10.1145/3572848.3577512","ista":"Aksenov V, Brown TA, Fedorov A, Kokorin I. 2023. Unexpected scaling in path copying trees, Association for Computing Machinery,p.","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","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.","short":"V. Aksenov, T.A. Brown, A. Fedorov, I. Kokorin, Unexpected Scaling in Path Copying Trees, Association for Computing Machinery, 2023.","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."},"month":"02","day":"25","article_processing_charge":"No","publication_identifier":{"isbn":["9798400700156"]},"date_updated":"2023-03-20T07:57:27Z","date_created":"2023-03-19T23:00:58Z","oa_version":"Published Version","author":[{"first_name":"Vitaly","last_name":"Aksenov","full_name":"Aksenov, Vitaly"},{"full_name":"Brown, Trevor A","first_name":"Trevor A","last_name":"Brown","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander","last_name":"Fedorov","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","full_name":"Fedorov, Alexander"},{"first_name":"Ilya","last_name":"Kokorin","full_name":"Kokorin, Ilya"}],"publication_status":"published","status":"public","title":"Unexpected scaling in path copying trees","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"publisher":"Association for Computing Machinery","_id":"12736","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.","year":"2023","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"},{"citation":{"apa":"Henzinger, M. H., Neumann, S., Räcke, H., & Schmid, S. (2023). Dynamic maintenance of monotone dynamic programs and applications. In 40th International Symposium on Theoretical Aspects of Computer Science (Vol. 254). Hamburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2023.36","ieee":"M. H. Henzinger, S. Neumann, H. Räcke, and S. Schmid, “Dynamic maintenance of monotone dynamic programs and applications,” in 40th International Symposium on Theoretical Aspects of Computer Science, Hamburg, Germany, 2023, vol. 254.","ista":"Henzinger MH, Neumann S, Räcke H, Schmid S. 2023. Dynamic maintenance of monotone dynamic programs and applications. 40th International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 254, 36.","ama":"Henzinger MH, Neumann S, Räcke H, Schmid S. Dynamic maintenance of monotone dynamic programs and applications. In: 40th International Symposium on Theoretical Aspects of Computer Science. Vol 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.STACS.2023.36","chicago":"Henzinger, Monika H, Stefan Neumann, Harald Räcke, and Stefan Schmid. “Dynamic Maintenance of Monotone Dynamic Programs and Applications.” In 40th International Symposium on Theoretical Aspects of Computer Science, Vol. 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.STACS.2023.36.","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."},"publication":"40th International Symposium on Theoretical Aspects of Computer Science","date_published":"2023-03-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12760","intvolume":" 254","status":"public","ddc":["000"],"title":"Dynamic maintenance of monotone dynamic programs and applications","oa_version":"Published Version","file":[{"checksum":"22141ab8bc55188e2dfff665e5daecbd","success":1,"date_created":"2023-03-27T06:37:22Z","date_updated":"2023-03-27T06:37:22Z","relation":"main_file","file_id":"12769","content_type":"application/pdf","file_size":872706,"creator":"dernst","access_level":"open_access","file_name":"2023_LIPICS_HenzingerM.pdf"}],"type":"conference","alternative_title":["LIPIcs"],"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"}],"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"]},"quality_controlled":"1","doi":"10.4230/LIPIcs.STACS.2023.36","conference":{"start_date":"2023-03-07","location":"Hamburg, Germany","end_date":"2023-03-09","name":"STACS: Symposium on Theoretical Aspects of Computer Science"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772662"]},"month":"03","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","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"MoHe"}],"publication_status":"published","author":[{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H"},{"first_name":"Stefan","last_name":"Neumann","full_name":"Neumann, Stefan"},{"last_name":"Räcke","first_name":"Harald","full_name":"Räcke, Harald"},{"first_name":"Stefan","last_name":"Schmid","full_name":"Schmid, Stefan"}],"volume":254,"date_updated":"2023-03-27T06:46:27Z","date_created":"2023-03-26T22:01:07Z","article_number":"36","file_date_updated":"2023-03-27T06:37:22Z","license":"https://creativecommons.org/licenses/by/4.0/"},{"file_date_updated":"2023-03-08T15:08:46Z","ec_funded":1,"author":[{"orcid":"0000-0002-8937-410X","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","last_name":"Burnett","first_name":"Laura","full_name":"Burnett, Laura"}],"date_updated":"2023-04-05T10:59:04Z","date_created":"2023-03-08T15:19:45Z","year":"2023","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"month":"03","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:12716","supervisor":[{"last_name":"Jösch","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"project":[{"name":"Circuits of Visual Attention","call_identifier":"H2020","grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"The process of detecting and evaluating sensory information to guide behaviour is termed perceptual decision-making (PDM), and is critical for the ability of an organism to interact with its external world. Individuals with autism, a neurodevelopmental condition primarily characterised by social and communication difficulties, frequently exhibit altered sensory processing and PDM difficulties are widely reported. Recent technological advancements have pushed forward our understanding of the genetic changes accompanying this condition, however our understanding of how these mutations affect the function of specific neuronal circuits and bring about the corresponding behavioural changes remains limited. Here, we use an innate PDM task, the looming avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality across three molecularly distinct genetic mouse models of autism (Cul3, Setd5 and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli, their responses are consistently delayed, requiring longer to initiate an appropriate response than their wild-type siblings. Mutant animals show abnormal adaptation in both their stimulus- evoked escape responses and exploratory dynamics following repeated stimulus presentations. Similarly delayed behavioural responses are observed in wild-type animals when faced with more ambiguous threats, suggesting the mutant phenotype could arise from a dysfunction in the flexible control of this PDM process.\r\nOur knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed dissection of the neuronal mechanisms underlying the behavioural impairment. In vivo extracellular recording revealed that visual responses were unaffected within a key brain region for the rapid processing of visual threats, the superior colliculus (SC), indicating that the behavioural delay was unlikely to originate from sensory impairments. Delayed behavioural responses were recapitulated in the Setd5 model following optogenetic stimulation of the excitatory output neurons of the SC, which are known to mediate escape initiation through the activation of cells in the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by the misregulation of voltage-gated potassium channels. Overall, our results show that the ability to use visual information to drive efficient escape responses is impaired in three diverse genetic mouse models of autism and that, in one of the models studied, this behavioural delay likely originates from differences in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore, this work showcases the use of an innate behavioural paradigm to mechanistically dissect PDM processes in autism."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"file_name":"Burnett_Thesis_2023.docx","access_level":"closed","file_size":23029260,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"lburnett","relation":"source_file","file_id":"12717","date_created":"2023-03-08T15:08:46Z","date_updated":"2023-03-08T15:08:46Z","checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332"},{"creator":"lburnett","file_size":11959869,"content_type":"application/pdf","access_level":"open_access","file_name":"Burnett_Thesis_2023_pdfA.pdf","success":1,"checksum":"cebc77705288bf4382db9b3541483cd0","date_updated":"2023-03-08T15:08:46Z","date_created":"2023-03-08T15:08:46Z","file_id":"12718","relation":"main_file"}],"oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12716","title":"To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism","status":"public","ddc":["599","573"],"day":"10","has_accepted_license":"1","article_processing_charge":"No","date_published":"2023-03-10T00:00:00Z","citation":{"chicago":"Burnett, Laura. “To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12716.","short":"L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism, Institute of Science and Technology Austria, 2023.","mla":"Burnett, Laura. To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12716.","apa":"Burnett, L. (2023). To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12716","ieee":"L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism,” Institute of Science and Technology Austria, 2023.","ista":"Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria.","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"},"page":"178"},{"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","date_published":"2023-04-20T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"20","intvolume":" 13994","title":"Bubaak: Runtime monitoring of program verifiers","status":"public","ddc":["000"],"_id":"12854","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"12864","relation":"main_file","success":1,"checksum":"120d2c2a38384058ad0630fdf8288312","date_created":"2023-04-25T06:58:36Z","date_updated":"2023-04-25T06:58:36Z","access_level":"open_access","file_name":"2023_LNCS_Chalupa.pdf","creator":"dernst","content_type":"application/pdf","file_size":16096413}],"oa_version":"Published Version","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"The main idea behind BUBAAK is to run multiple program analyses in parallel and use runtime monitoring and enforcement to observe and control their progress in real time. The analyses send information about (un)explored states of the program and discovered invariants to a monitor. The monitor processes the received data and can force an analysis to stop the search of certain program parts (which have already been analyzed by other analyses), or to make it utilize a program invariant found by another analysis.\r\nAt SV-COMP 2023, the implementation of data exchange between the monitor and the analyses was not yet completed, which is why BUBAAK only ran several analyses in parallel, without any coordination. Still, BUBAAK won the meta-category FalsificationOverall and placed very well in several other (sub)-categories of the competition.","lang":"eng"}],"project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-30820-8_32","conference":{"end_date":"2023-04-27","start_date":"2023-04-22","location":"Paris, France","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"publication_identifier":{"issn":["0302-9743"],"eisbn":["9783031308208"],"eissn":["1611-3349"],"isbn":["9783031308192"]},"month":"04","department":[{"_id":"ToHe"}],"publisher":"Springer Nature","publication_status":"published","acknowledgement":"This work was supported by the ERC-2020-AdG 10102009 grant.","year":"2023","volume":13994,"date_updated":"2023-04-25T07:02:43Z","date_created":"2023-04-20T08:22:53Z","author":[{"full_name":"Chalupa, Marek","last_name":"Chalupa","first_name":"Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"file_date_updated":"2023-04-25T06:58:36Z"},{"article_number":"2303.14555","type":"preprint","abstract":[{"lang":"eng","text":"We present a formula for the signed area of a spherical polygon via prequantization. In contrast to the traditional formula based on the Gauss-Bonnet theorem that requires measuring angles, the new formula mimics Green's theorem and is applicable to a wider range of degenerate spherical curves and polygons."}],"status":"public","publication_status":"submitted","title":"Area formula for spherical polygons via prequantization","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"_id":"12846","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","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).","date_created":"2023-04-18T19:16:06Z","date_updated":"2023-04-25T06:51:21Z","oa_version":"Preprint","author":[{"full_name":"Chern, Albert","last_name":"Chern","first_name":"Albert"},{"full_name":"Ishida, Sadashige","last_name":"Ishida","first_name":"Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425"}],"day":"25","month":"03","article_processing_charge":"No","project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"publication":"arXiv","citation":{"ama":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv. doi:10.48550/arXiv.2303.14555","apa":"Chern, A., & Ishida, S. (n.d.). Area formula for spherical polygons via prequantization. arXiv. https://doi.org/10.48550/arXiv.2303.14555","ieee":"A. Chern and S. Ishida, “Area formula for spherical polygons via prequantization,” arXiv. .","ista":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv, 2303.14555.","short":"A. Chern, S. Ishida, ArXiv (n.d.).","mla":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, 2303.14555, doi:10.48550/arXiv.2303.14555.","chicago":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2303.14555."},"main_file_link":[{"url":"https://arxiv.org/abs/2303.14555","open_access":"1"}],"external_id":{"arxiv":["2303.14555"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.48550/arXiv.2303.14555","date_published":"2023-03-25T00:00:00Z"},{"abstract":[{"lang":"eng","text":"As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both.\r\n\r\nWe present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\nWe implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Published Version","file":[{"success":1,"checksum":"17a7c8e08be609cf2408d37ea55e322c","date_created":"2023-04-25T07:16:36Z","date_updated":"2023-04-25T07:16:36Z","file_id":"12865","relation":"main_file","creator":"dernst","file_size":580828,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_LNCS_ChalupaM.pdf"}],"title":"Vamos: Middleware for best-effort third-party monitoring","ddc":["000"],"status":"public","intvolume":" 13991","_id":"12856","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"20","article_processing_charge":"No","has_accepted_license":"1","date_published":"2023-04-20T00:00:00Z","page":"260-281","publication":"Fundamental Approaches to Software Engineering","citation":{"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.","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.","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.","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","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.","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"},"file_date_updated":"2023-04-25T07:16:36Z","ec_funded":1,"date_updated":"2023-04-25T07:19:07Z","date_created":"2023-04-20T08:29:42Z","volume":13991,"author":[{"first_name":"Marek","last_name":"Chalupa","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","full_name":"Chalupa, Marek"},{"id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","orcid":"0000-0003-1548-0177","first_name":"Fabian","last_name":"Mühlböck","full_name":"Mühlböck, Fabian"},{"full_name":"Muroya Lei, Stefanie","first_name":"Stefanie","last_name":"Muroya Lei","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff"},{"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"}]},"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","month":"04","publication_identifier":{"isbn":["9783031308253"],"eissn":["1611-3349"],"eisbn":["9783031308260"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"conference":{"name":"FASE: Fundamental Approaches to Software Engineering","end_date":"2023-04-27","location":"Paris, France","start_date":"2023-04-22"},"doi":"10.1007/978-3-031-30826-0_15","quality_controlled":"1","project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"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},{"article_processing_charge":"No","has_accepted_license":"1","day":"27","keyword":["runtime monitoring","best effort","third party"],"date_published":"2023-01-27T00:00:00Z","page":"38","citation":{"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.","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.","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","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.","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.","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."},"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"}],"alternative_title":["IST Austria Technical Report"],"type":"technical_report","file":[{"relation":"main_file","file_id":"12408","date_updated":"2023-01-27T03:18:34Z","date_created":"2023-01-27T03:18:34Z","checksum":"55426e463fdeafe9777fc3ff635154c7","success":1,"file_name":"main.pdf","access_level":"open_access","file_size":662409,"content_type":"application/pdf","creator":"fmuehlbo"}],"oa_version":"Published Version","status":"public","ddc":["005"],"title":"VAMOS: Middleware for Best-Effort Third-Party Monitoring","_id":"12407","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2664-1690"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:12407","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","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"},"ec_funded":1,"file_date_updated":"2023-01-27T03:18:34Z","date_updated":"2023-04-25T07:19:06Z","date_created":"2023-01-27T03:18:08Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"12856"}]},"author":[{"full_name":"Chalupa, Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","last_name":"Chalupa","first_name":"Marek"},{"id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","orcid":"0000-0003-1548-0177","first_name":"Fabian","last_name":"Mühlböck","full_name":"Mühlböck, Fabian"},{"last_name":"Muroya Lei","first_name":"Stefanie","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","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"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"ToHe"}],"publication_status":"published","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. \r\nThe authors would like to thank the anonymous FASE reviewers for their valuable feedback and suggestions.","year":"2023"},{"scopus_import":"1","article_processing_charge":"No","day":"13","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","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","ieee":"L. Zhao et al., “Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat,” Genome Biology, vol. 24. Springer Nature, 2023.","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","date_published":"2023-01-13T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Background: Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive.\r\n\r\nResults: Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal–distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome.\r\n\r\nConclusions: Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12668","intvolume":" 24","status":"public","title":"Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat","oa_version":"Published Version","publication_identifier":{"issn":["1474-760X"]},"month":"01","external_id":{"pmid":["36639687"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1186/s13059-022-02844-2","open_access":"1"}],"quality_controlled":"1","doi":"10.1186/s13059-022-02844-2","language":[{"iso":"eng"}],"article_number":"7","extern":"1","pmid":1,"year":"2023","department":[{"_id":"XiFe"}],"publisher":"Springer Nature","publication_status":"published","author":[{"last_name":"Zhao","first_name":"Long","full_name":"Zhao, Long"},{"full_name":"Yang, Yiman","last_name":"Yang","first_name":"Yiman"},{"first_name":"Jinchao","last_name":"Chen","full_name":"Chen, Jinchao"},{"first_name":"Xuelei","last_name":"Lin","full_name":"Lin, Xuelei"},{"first_name":"Hao","last_name":"Zhang","full_name":"Zhang, Hao"},{"full_name":"Wang, Hao","first_name":"Hao","last_name":"Wang"},{"first_name":"Hongzhe","last_name":"Wang","full_name":"Wang, Hongzhe"},{"full_name":"Bie, Xiaomin","first_name":"Xiaomin","last_name":"Bie"},{"last_name":"Jiang","first_name":"Jiafu","full_name":"Jiang, Jiafu"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","last_name":"Feng","full_name":"Feng, Xiaoqi"},{"last_name":"Fu","first_name":"Xiangdong","full_name":"Fu, Xiangdong"},{"full_name":"Zhang, Xiansheng","last_name":"Zhang","first_name":"Xiansheng"},{"full_name":"Du, Zhuo","last_name":"Du","first_name":"Zhuo"},{"full_name":"Xiao, Jun","first_name":"Jun","last_name":"Xiao"}],"volume":24,"date_created":"2023-02-23T09:13:49Z","date_updated":"2023-05-08T10:52:49Z"},{"publication_identifier":{"eissn":["1521-3765"],"issn":["0947-6539"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1002/chem.202202967","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/chem.202202967"}],"extern":"1","article_number":"e202202967","volume":29,"date_updated":"2023-05-15T08:39:24Z","date_created":"2023-05-08T08:25:34Z","author":[{"full_name":"Traxler, Michael","first_name":"Michael","last_name":"Traxler"},{"last_name":"Reischauer","first_name":"Susanne","full_name":"Reischauer, Susanne"},{"full_name":"Vogl, Sarah","last_name":"Vogl","first_name":"Sarah"},{"full_name":"Roeser, Jérôme","first_name":"Jérôme","last_name":"Roeser"},{"full_name":"Rabeah, Jabor","first_name":"Jabor","last_name":"Rabeah"},{"full_name":"Penschke, Christopher","first_name":"Christopher","last_name":"Penschke"},{"last_name":"Saalfrank","first_name":"Peter","full_name":"Saalfrank, Peter"},{"full_name":"Pieber, Bartholomäus","first_name":"Bartholomäus","last_name":"Pieber","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","orcid":"0000-0001-8689-388X"},{"full_name":"Thomas, Arne","last_name":"Thomas","first_name":"Arne"}],"publisher":"Wiley","publication_status":"published","year":"2023","article_processing_charge":"No","day":"18","keyword":["General Chemistry","Catalysis","Organic Chemistry"],"scopus_import":"1","date_published":"2023-01-18T00:00:00Z","article_type":"original","citation":{"apa":"Traxler, M., Reischauer, S., Vogl, S., Roeser, J., Rabeah, J., Penschke, C., … Thomas, A. (2023). Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts. Chemistry – A European Journal. Wiley. https://doi.org/10.1002/chem.202202967","ieee":"M. Traxler et al., “Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts,” Chemistry – A European Journal, vol. 29, no. 4. Wiley, 2023.","ista":"Traxler M, Reischauer S, Vogl S, Roeser J, Rabeah J, Penschke C, Saalfrank P, Pieber B, Thomas A. 2023. Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts. Chemistry – A European Journal. 29(4), e202202967.","ama":"Traxler M, Reischauer S, Vogl S, et al. Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts. Chemistry – A European Journal. 2023;29(4). doi:10.1002/chem.202202967","chicago":"Traxler, Michael, Susanne Reischauer, Sarah Vogl, Jérôme Roeser, Jabor Rabeah, Christopher Penschke, Peter Saalfrank, Bartholomäus Pieber, and Arne Thomas. “Programmable Photocatalytic Activity of Multicomponent Covalent Organic Frameworks Used as Metallaphotocatalysts.” Chemistry – A European Journal. Wiley, 2023. https://doi.org/10.1002/chem.202202967.","short":"M. Traxler, S. Reischauer, S. Vogl, J. Roeser, J. Rabeah, C. Penschke, P. Saalfrank, B. Pieber, A. Thomas, Chemistry – A European Journal 29 (2023).","mla":"Traxler, Michael, et al. “Programmable Photocatalytic Activity of Multicomponent Covalent Organic Frameworks Used as Metallaphotocatalysts.” Chemistry – A European Journal, vol. 29, no. 4, e202202967, Wiley, 2023, doi:10.1002/chem.202202967."},"publication":"Chemistry – A European Journal","issue":"4","abstract":[{"lang":"eng","text":"The multicomponent approach allows to incorporate several functionalities into a single covalent organic framework (COF) and consequently allows the construction of bifunctional materials for cooperative catalysis. The well-defined structure of such multicomponent COFs is furthermore ideally suited for structure-activity relationship studies. We report a series of multicomponent COFs that contain acridine- and 2,2’-bipyridine linkers connected through 1,3,5-benzenetrialdehyde derivatives. The acridine motif is responsible for broad light absorption, while the bipyridine unit enables complexation of nickel catalysts. These features enable the usage of the framework materials as catalysts for light-mediated carbon−heteroatom cross-couplings. Variation of the node units shows that the catalytic activity correlates to the keto-enamine tautomer isomerism. This allows switching between high charge-carrier mobility and persistent, localized charge-separated species depending on the nodes, a tool to tailor the materials for specific reactions. Moreover, nickel-loaded COFs are recyclable and catalyze cross-couplings even using red light irradiation."}],"type":"journal_article","oa_version":"Published Version","intvolume":" 29","title":"Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12920"},{"publication_identifier":{"eissn":["1867-3899"],"issn":["1867-3880"]},"month":"04","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1002/cctc.202201583","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1002/cctc.202201583","article_number":"e202201583","extern":"1","publisher":"Wiley","publication_status":"published","year":"2023","volume":15,"date_updated":"2023-05-15T08:35:48Z","date_created":"2023-05-08T08:25:55Z","author":[{"first_name":"Amiera","last_name":"Madani","full_name":"Madani, Amiera"},{"full_name":"Pieber, Bartholomäus","first_name":"Bartholomäus","last_name":"Pieber","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","orcid":"0000-0001-8689-388X"}],"keyword":["Inorganic Chemistry","Organic Chemistry","Physical and Theoretical Chemistry","Catalysis"],"scopus_import":"1","article_processing_charge":"No","day":"06","article_type":"original","citation":{"chicago":"Madani, Amiera, and Bartholomäus Pieber. “In Situ Reaction Monitoring in Photocatalytic Organic Synthesis.” ChemCatChem. Wiley, 2023. https://doi.org/10.1002/cctc.202201583.","mla":"Madani, Amiera, and Bartholomäus Pieber. “In Situ Reaction Monitoring in Photocatalytic Organic Synthesis.” ChemCatChem, vol. 15, no. 7, e202201583, Wiley, 2023, doi:10.1002/cctc.202201583.","short":"A. Madani, B. Pieber, ChemCatChem 15 (2023).","ista":"Madani A, Pieber B. 2023. In situ reaction monitoring in photocatalytic organic synthesis. ChemCatChem. 15(7), e202201583.","ieee":"A. Madani and B. Pieber, “In situ reaction monitoring in photocatalytic organic synthesis,” ChemCatChem, vol. 15, no. 7. Wiley, 2023.","apa":"Madani, A., & Pieber, B. (2023). In situ reaction monitoring in photocatalytic organic synthesis. ChemCatChem. Wiley. https://doi.org/10.1002/cctc.202201583","ama":"Madani A, Pieber B. In situ reaction monitoring in photocatalytic organic synthesis. ChemCatChem. 2023;15(7). doi:10.1002/cctc.202201583"},"publication":"ChemCatChem","date_published":"2023-04-06T00:00:00Z","type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"Visible-light photocatalysis provides numerous useful methodologies for synthetic organic chemistry. However, the mechanisms of these reactions are often not fully understood. Common mechanistic experiments mainly aim to characterize excited state properties of photocatalysts and their interaction with other species. Recently, in situ reaction monitoring using dedicated techniques was shown to be well-suited for the identification of intermediates and to obtain kinetic insights, thereby providing more holistic pictures of the reactions of interest. This minireview surveys these technologies and discusses selected examples where reaction monitoring was used to elucidate the mechanism of photocatalytic reactions."}],"intvolume":" 15","status":"public","title":"In situ reaction monitoring in photocatalytic organic synthesis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12921","oa_version":"Published Version"},{"abstract":[{"text":"In this paper we introduce a pruning of the medial axis called the (λ,α)-medial axis (axλα). We prove that the (λ,α)-medial axis of a set K is stable in a Gromov-Hausdorff sense under weak assumptions. More formally we prove that if K and K′ are close in the Hausdorff (dH) sense then the (λ,α)-medial axes of K and K′ are close as metric spaces, that is the Gromov-Hausdorff distance (dGH) between the two is 1/4-Hölder in the sense that dGH (axλα(K),axλα(K′)) ≲ dH(K,K′)1/4. The Hausdorff distance between the two medial axes is also bounded, by dH (axλα(K),λα(K′)) ≲ dH(K,K′)1/2. These quantified stability results provide guarantees for practical computations of medial axes from approximations. Moreover, they provide key ingredients for studying the computability of the medial axis in the context of computable analysis.","lang":"eng"}],"type":"conference","oa_version":"Preprint","status":"public","title":"Hausdorff and Gromov-Hausdorff stable subsets of the medial axis","_id":"13048","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"02","article_processing_charge":"No","date_published":"2023-06-02T00:00:00Z","page":"1768-1776","publication":"Proceedings of the 55th Annual ACM Symposium on Theory of Computing","citation":{"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.","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.","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.","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","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.","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","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."},"ec_funded":1,"date_created":"2023-05-22T08:02:02Z","date_updated":"2023-05-22T08:15:19Z","author":[{"full_name":"Lieutier, André","last_name":"Lieutier","first_name":"André"},{"last_name":"Wintraecken","first_name":"Mathijs","orcid":"0000-0002-7472-2220","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","full_name":"Wintraecken, Mathijs"}],"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Association for Computing Machinery","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.","month":"06","publication_identifier":{"isbn":["9781450399135"]},"language":[{"iso":"eng"}],"conference":{"name":"STOC: Symposium on Theory of Computing","end_date":"2023-06-23","location":"Orlando, FL, United States","start_date":"2023-06-20"},"doi":"10.1145/3564246.3585113","quality_controlled":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"M03073","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","name":"Learning and triangulating manifolds via collapses"}],"main_file_link":[{"url":"https://arxiv.org/abs/2303.04014","open_access":"1"}],"external_id":{"arxiv":["2303.04014"]},"oa":1},{"month":"05","article_processing_charge":"No","conference":{"name":"ICLR: International Conference on Learning Representations","end_date":"2023-05-05","location":"Kigali, Rwanda ","start_date":"2023-05-01"},"date_published":"2023-05-01T00:00:00Z","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"publication":"11th International Conference on Learning Representations ","oa":1,"main_file_link":[{"open_access":"1","url":"https://openreview.net/pdf?id=_eTZBs-yedr"}],"external_id":{"arxiv":["2207.14200"]},"citation":{"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 .","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 .","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 .","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.","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 .","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."},"quality_controlled":"1","project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"}],"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"}],"ec_funded":1,"type":"conference","author":[{"full_name":"Peste, Elena-Alexandra","first_name":"Elena-Alexandra","last_name":"Peste","id":"32D78294-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vladu","first_name":"Adrian","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"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"13074"}]},"date_updated":"2023-06-01T12:54:45Z","date_created":"2023-05-23T11:36:18Z","oa_version":"Preprint","_id":"13053","year":"2023","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)-","status":"public","title":"CrAM: A Compression-Aware Minimizer","publication_status":"accepted","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}]},{"author":[{"id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7","last_name":"Hoffmann","first_name":"Charlotte","full_name":"Hoffmann, Charlotte"},{"full_name":"Hubáček, Pavel","first_name":"Pavel","last_name":"Hubáček"},{"full_name":"Kamath, Chethan","last_name":"Kamath","first_name":"Chethan"},{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak"}],"date_updated":"2023-06-19T08:03:37Z","date_created":"2023-06-18T22:00:47Z","volume":13940,"year":"2023","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.","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer Nature","conference":{"name":"PKC: Public-Key Cryptography","end_date":"2023-05-10","start_date":"2023-05-07","location":"Atlanta, GA, United States"},"doi":"10.1007/978-3-031-31368-4_19","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2023/238"}],"quality_controlled":"1","month":"05","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031313677"],"issn":["0302-9743"]},"oa_version":"Submitted Version","_id":"13143","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Certifying giant nonprimes","intvolume":" 13940","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."}],"type":"conference","alternative_title":["LNCS"],"date_published":"2023-05-02T00:00:00Z","publication":"Public-Key Cryptography - PKC 2023","citation":{"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","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.","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.","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","mla":"Hoffmann, Charlotte, et al. “Certifying Giant Nonprimes.” Public-Key Cryptography - PKC 2023, vol. 13940, Springer Nature, 2023, pp. 530–53, doi:10.1007/978-3-031-31368-4_19.","short":"C. Hoffmann, P. Hubáček, C. Kamath, K.Z. Pietrzak, in:, Public-Key Cryptography - PKC 2023, Springer Nature, 2023, pp. 530–553.","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."},"page":"530-553","day":"02","article_processing_charge":"No","scopus_import":"1"},{"type":"conference","alternative_title":["LNCS"],"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"}],"_id":"13142","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A learner-verifier framework for neural network controllers and certificates of stochastic systems","status":"public","ddc":["000"],"intvolume":" 13993","file":[{"relation":"main_file","file_id":"13150","date_created":"2023-06-19T08:29:30Z","date_updated":"2023-06-19T08:29:30Z","checksum":"3d8a8bb24d211bc83360dfc2fd744307","success":1,"file_name":"2023_LNCS_Chatterjee.pdf","access_level":"open_access","content_type":"application/pdf","file_size":528455,"creator":"dernst"}],"oa_version":"Published Version","scopus_import":"1","day":"22","has_accepted_license":"1","article_processing_charge":"No","publication":"Tools and Algorithms for the Construction and Analysis of Systems ","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"},"page":"3-25","date_published":"2023-04-22T00:00:00Z","file_date_updated":"2023-06-19T08:29:30Z","ec_funded":1,"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.","year":"2023","publication_status":"published","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Springer Nature","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner"},{"first_name":"Dorde","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde"}],"date_updated":"2023-06-19T08:30:54Z","date_created":"2023-06-18T22:00:47Z","volume":13993,"month":"04","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031308222"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"conference":{"location":"Paris, France","start_date":"2023-04-22","end_date":"2023-04-27","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"doi":"10.1007/978-3-031-30823-9_1","language":[{"iso":"eng"}]},{"file_date_updated":"2023-06-19T08:43:21Z","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2023","volume":13994,"date_updated":"2023-06-19T08:49:46Z","date_created":"2023-06-18T22:00:47Z","author":[{"first_name":"Ashwani","last_name":"Anand","full_name":"Anand, Ashwani"},{"orcid":"0000-0001-9864-7475","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","last_name":"Mallik","first_name":"Kaushik","full_name":"Mallik, Kaushik"},{"last_name":"Nayak","first_name":"Satya Prakash","full_name":"Nayak, Satya Prakash"},{"full_name":"Schmuck, Anne Kathrin","first_name":"Anne Kathrin","last_name":"Schmuck"}],"publication_identifier":{"isbn":["9783031308192"],"eissn":["1611-3349"],"issn":["0302-9743"]},"month":"04","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-30820-8_15","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2023-04-22","location":"Paris, France","end_date":"2023-04-27"},"alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"We automatically compute a new class of environment assumptions in two-player turn-based finite graph games which characterize an “adequate cooperation” needed from the environment to allow the system player to win. Given an ω-regular winning condition Φ for the system player, we compute an ω-regular assumption Ψ for the environment player, such that (i) every environment strategy compliant with Ψ allows the system to fulfill Φ (sufficiency), (ii) Ψ\r\n can be fulfilled by the environment for every strategy of the system (implementability), and (iii) Ψ does not prevent any cooperative strategy choice (permissiveness).\r\nFor parity games, which are canonical representations of ω-regular games, we present a polynomial-time algorithm for the symbolic computation of adequately permissive assumptions and show that our algorithm runs faster and produces better assumptions than existing approaches—both theoretically and empirically. To the best of our knowledge, for ω\r\n-regular games, we provide the first algorithm to compute sufficient and implementable environment assumptions that are also permissive."}],"intvolume":" 13994","status":"public","ddc":["000"],"title":"Computing adequately permissive assumptions for synthesis","_id":"13141","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_LNCS_Anand.pdf","creator":"dernst","content_type":"application/pdf","file_size":521425,"file_id":"13151","relation":"main_file","success":1,"checksum":"60dcafc1b4f6f070be43bad3fe877974","date_created":"2023-06-19T08:43:21Z","date_updated":"2023-06-19T08:43:21Z"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"20","page":"211-228","citation":{"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.","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"},"publication":"TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems","date_published":"2023-04-20T00:00:00Z"},{"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"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":14507243,"creator":"vpokusae","access_level":"closed","file_name":"Thesis_Pokusaeva.docx","checksum":"5f589a9af025f7eeebfd0c186209913e","date_updated":"2023-04-20T09:26:51Z","date_created":"2023-04-20T09:14:38Z","relation":"source_file","file_id":"12857"},{"file_id":"12858","relation":"main_file","success":1,"checksum":"bbeed76db45a996b4c91a9abe12ce0ec","date_created":"2023-04-20T09:14:44Z","date_updated":"2023-04-20T09:14:44Z","access_level":"open_access","file_name":"Thesis_Pokusaeva.pdf","creator":"vpokusae","file_size":10090711,"content_type":"application/pdf"}],"oa_version":"Published Version","status":"public","ddc":["570","571"],"title":"Neural control of optic flow-based navigation in Drosophila melanogaster","_id":"12826","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"18","has_accepted_license":"1","article_processing_charge":"No","date_published":"2023-04-18T00:00:00Z","page":"106","citation":{"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.","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.","apa":"Pokusaeva, V. (2023). Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12826","ieee":"V. Pokusaeva, “Neural control of optic flow-based navigation in Drosophila melanogaster,” Institute of Science and Technology Austria, 2023.","ista":"Pokusaeva V. 2023. Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria.","ama":"Pokusaeva V. Neural control of optic flow-based navigation in Drosophila melanogaster. 2023. doi:10.15479/at:ista:12826"},"file_date_updated":"2023-04-20T09:26:51Z","ec_funded":1,"date_updated":"2023-06-23T09:47:36Z","date_created":"2023-04-14T14:56:04Z","author":[{"full_name":"Pokusaeva, Victoria","last_name":"Pokusaeva","first_name":"Victoria","orcid":"0000-0001-7660-444X","id":"3184041C-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"MaJö"},{"_id":"GradSch"}],"year":"2023","month":"04","publication_identifier":{"issn":["2663 - 337X"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Jösch, Maximilian A","last_name":"Jösch","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12826","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"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"}},{"ec_funded":1,"file_date_updated":"2023-01-20T10:02:48Z","volume":85,"date_created":"2022-09-11T22:01:57Z","date_updated":"2023-06-27T12:53:43Z","author":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F","last_name":"Osang","full_name":"Osang, Georg F"}],"department":[{"_id":"HeEd"}],"publisher":"Springer Nature","publication_status":"published","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.","year":"2023","publication_identifier":{"eissn":["1432-0541"],"issn":["0178-4617"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1007/s00453-022-01027-6","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","call_identifier":"H2020","name":"Alpha Shape Theory Extended"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35"}],"isi":1,"quality_controlled":"1","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,"abstract":[{"lang":"eng","text":"We present a simple algorithm for computing higher-order Delaunay mosaics that works in Euclidean spaces of any finite dimensions. The algorithm selects the vertices of the order-k mosaic from incrementally constructed lower-order mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box to construct the order-k mosaic from its vertices. Beyond this black-box, the algorithm uses only combinatorial operations, thus facilitating easy implementation. We extend this algorithm to compute higher-order α-shapes and provide open-source implementations. We present experimental results for properties of higher-order Delaunay mosaics of random point sets."}],"type":"journal_article","oa_version":"Published Version","file":[{"success":1,"checksum":"71685ca5121f4c837f40c3f8eb50c915","date_created":"2023-01-20T10:02:48Z","date_updated":"2023-01-20T10:02:48Z","file_id":"12322","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":911017,"access_level":"open_access","file_name":"2023_Algorithmica_Edelsbrunner.pdf"}],"intvolume":" 85","title":"A simple algorithm for higher-order Delaunay mosaics and alpha shapes","status":"public","ddc":["510"],"_id":"12086","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","date_published":"2023-01-01T00:00:00Z","page":"277-295","article_type":"original","citation":{"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.","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"},"publication":"Algorithmica"},{"issue":"1","abstract":[{"lang":"eng","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."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"12325","relation":"main_file","date_created":"2023-01-20T10:45:06Z","date_updated":"2023-01-20T10:45:06Z","success":1,"checksum":"1f34f3e2cb521033de6154f274ea3a4e","file_name":"2023_JourEvolutionEquations_DelloSchiavo.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":422612}],"_id":"12104","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 23","title":"Ergodic decompositions of Dirichlet forms under order isomorphisms","ddc":["510"],"status":"public","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2023-01-01T00:00:00Z","citation":{"ista":"Dello Schiavo L, Wirth M. 2023. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 23(1), 9.","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.","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.","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.","short":"L. Dello Schiavo, M. Wirth, Journal of Evolution Equations 23 (2023)."},"publication":"Journal of Evolution Equations","article_type":"original","ec_funded":1,"file_date_updated":"2023-01-20T10:45:06Z","article_number":"9","author":[{"full_name":"Dello Schiavo, Lorenzo","orcid":"0000-0002-9881-6870","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","last_name":"Dello Schiavo","first_name":"Lorenzo"},{"id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","orcid":"0000-0002-0519-4241","first_name":"Melchior","last_name":"Wirth","full_name":"Wirth, Melchior"}],"volume":23,"date_updated":"2023-06-28T11:54:35Z","date_created":"2023-01-08T23:00:53Z","year":"2023","acknowledgement":"Research supported by the Austrian Science Fund (FWF) grant F65 at the Institute of Science and Technology Austria and by the European Research Council (ERC) (Grant agreement No. 716117 awarded to Prof. Dr. Jan Maas). L.D.S. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 208). M.W. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 156).","publisher":"Springer Nature","department":[{"_id":"JaMa"}],"publication_status":"published","publication_identifier":{"issn":["1424-3199"],"eissn":["1424-3202"]},"month":"01","doi":"10.1007/s00028-022-00859-7","language":[{"iso":"eng"}],"external_id":{"isi":["000906214600004"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"},{"_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","grant_number":"E208","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"}],"quality_controlled":"1","isi":1},{"file_date_updated":"2023-06-19T10:28:09Z","ec_funded":1,"acknowledgement":"We thank the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093.","year":"2023","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"publisher":"Springer Nature","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","last_name":"Mazzocchi","first_name":"Nicolas Adrien","full_name":"Mazzocchi, Nicolas Adrien"},{"full_name":"Sarac, Naci E","first_name":"Naci E","last_name":"Sarac","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425"}],"date_updated":"2023-07-14T11:20:27Z","date_created":"2023-01-31T07:23:56Z","volume":13992,"month":"04","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031308284"],"eissn":["1611-3349"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2301.11175"]},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"conference":{"name":"FOSSACS: Foundations of Software Science and Computation Structures","end_date":"2023-04-27","start_date":"2023-04-22","location":"Paris, France"},"doi":"10.1007/978-3-031-30829-1_17","language":[{"iso":"eng"}],"type":"conference","alternative_title":["LNCS"],"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."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12467","ddc":["000"],"status":"public","title":"Quantitative safety and liveness","intvolume":" 13992","oa_version":"Published Version","file":[{"file_id":"12468","relation":"main_file","date_updated":"2023-01-31T07:22:21Z","date_created":"2023-01-31T07:22:21Z","success":1,"checksum":"981025aed580b6b27c426cb8856cf63e","file_name":"qsl.pdf","access_level":"open_access","creator":"esarac","file_size":449027,"content_type":"application/pdf"},{"creator":"dernst","file_size":1048171,"content_type":"application/pdf","file_name":"2023_LNCS_HenzingerT.pdf","access_level":"open_access","date_updated":"2023-06-19T10:28:09Z","date_created":"2023-06-19T10:28:09Z","success":1,"checksum":"f16e2af1e0eb243158ab0f0fe74e7d5a","file_id":"13153","relation":"main_file"}],"scopus_import":"1","day":"21","article_processing_charge":"No","has_accepted_license":"1","publication":"26th International Conference Foundations of Software Science and Computation Structures","citation":{"mla":"Henzinger, Thomas A., et al. “Quantitative Safety and Liveness.” 26th International Conference Foundations of Software Science and Computation Structures, vol. 13992, Springer Nature, 2023, pp. 349–70, doi:10.1007/978-3-031-30829-1_17.","short":"T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 26th International Conference Foundations of Software Science and Computation Structures, Springer Nature, 2023, pp. 349–370.","chicago":"Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Quantitative Safety and Liveness.” In 26th International Conference Foundations of Software Science and Computation Structures, 13992:349–70. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30829-1_17.","ama":"Henzinger TA, Mazzocchi NA, Sarac NE. Quantitative safety and liveness. In: 26th International Conference Foundations of Software Science and Computation Structures. Vol 13992. Springer Nature; 2023:349-370. doi:10.1007/978-3-031-30829-1_17","ista":"Henzinger TA, Mazzocchi NA, Sarac NE. 2023. Quantitative safety and liveness. 26th International Conference Foundations of Software Science and Computation Structures. FOSSACS: Foundations of Software Science and Computation Structures, LNCS, vol. 13992, 349–370.","ieee":"T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Quantitative safety and liveness,” in 26th International Conference Foundations of Software Science and Computation Structures, Paris, France, 2023, vol. 13992, pp. 349–370.","apa":"Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2023). Quantitative safety and liveness. In 26th International Conference Foundations of Software Science and Computation Structures (Vol. 13992, pp. 349–370). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30829-1_17"},"page":"349-370","date_published":"2023-04-21T00:00:00Z"},{"oa_version":"Published Version","file":[{"creator":"alisjak","file_size":1266773,"content_type":"application/pdf","file_name":"2023_ACMProgram.Lang._Koval.pdf","access_level":"open_access","date_created":"2023-07-03T13:09:39Z","date_updated":"2023-07-03T13:09:39Z","success":1,"checksum":"5dba6e73f0ed79adbdae14d165bc2f68","file_id":"13187","relation":"main_file"}],"intvolume":" 7","title":"CQS: A formally-verified framework for fair and abortable synchronization","ddc":["000"],"status":"public","_id":"13179","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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","date_published":"2023-06-06T00:00:00Z","article_type":"original","citation":{"ama":"Koval N, Khalanskiy D, Alistarh D-A. CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. 2023;7. doi:10.1145/3591230","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.","ieee":"N. Koval, D. Khalanskiy, and D.-A. Alistarh, “CQS: A formally-verified framework for fair and abortable synchronization,” Proceedings of the ACM on Programming Languages, vol. 7. Association for Computing Machinery , 2023.","apa":"Koval, N., Khalanskiy, D., & Alistarh, D.-A. (2023). CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. Association for Computing Machinery . https://doi.org/10.1145/3591230","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.","short":"N. Koval, D. Khalanskiy, D.-A. Alistarh, Proceedings of the ACM on Programming Languages 7 (2023).","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."},"publication":"Proceedings of the ACM on Programming Languages","article_processing_charge":"No","has_accepted_license":"1","day":"06","scopus_import":"1","volume":7,"date_updated":"2023-07-17T08:43:19Z","date_created":"2023-07-02T22:00:43Z","author":[{"full_name":"Koval, Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","first_name":"Nikita","last_name":"Koval"},{"full_name":"Khalanskiy, Dmitry","first_name":"Dmitry","last_name":"Khalanskiy"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"}],"department":[{"_id":"DaAl"}],"publisher":"Association for Computing Machinery ","publication_status":"published","year":"2023","file_date_updated":"2023-07-03T13:09:39Z","article_number":"116","language":[{"iso":"eng"}],"doi":"10.1145/3591230","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":{"eissn":["2475-1421"]},"month":"06"},{"scopus_import":"1","day":"26","article_processing_charge":"No","publication":"Involve","citation":{"apa":"Browning, T. D., Lyczak, J., & Sarapin, R. (2023). Local solubility for a family of quadrics over a split quadric surface. Involve. Mathematical Sciences Publishers. https://doi.org/10.2140/involve.2023.16.331","ieee":"T. D. Browning, J. Lyczak, and R. Sarapin, “Local solubility for a family of quadrics over a split quadric surface,” Involve, vol. 16, no. 2. Mathematical Sciences Publishers, pp. 331–342, 2023.","ista":"Browning TD, Lyczak J, Sarapin R. 2023. Local solubility for a family of quadrics over a split quadric surface. Involve. 16(2), 331–342.","ama":"Browning TD, Lyczak J, Sarapin R. Local solubility for a family of quadrics over a split quadric surface. Involve. 2023;16(2):331-342. doi:10.2140/involve.2023.16.331","chicago":"Browning, Timothy D, Julian Lyczak, and Roman Sarapin. “Local Solubility for a Family of Quadrics over a Split Quadric Surface.” Involve. Mathematical Sciences Publishers, 2023. https://doi.org/10.2140/involve.2023.16.331.","short":"T.D. Browning, J. Lyczak, R. Sarapin, Involve 16 (2023) 331–342.","mla":"Browning, Timothy D., et al. “Local Solubility for a Family of Quadrics over a Split Quadric Surface.” Involve, vol. 16, no. 2, Mathematical Sciences Publishers, 2023, pp. 331–42, doi:10.2140/involve.2023.16.331."},"article_type":"original","page":"331-342","date_published":"2023-05-26T00:00:00Z","type":"journal_article","abstract":[{"text":"We study the density of everywhere locally soluble diagonal quadric surfaces, parameterised by rational points that lie on a split quadric surface","lang":"eng"}],"issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13180","title":"Local solubility for a family of quadrics over a split quadric surface","status":"public","intvolume":" 16","oa_version":"Preprint","month":"05","publication_identifier":{"issn":["1944-4176"],"eissn":["1944-4184"]},"external_id":{"arxiv":["2203.06881"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2203.06881","open_access":"1"}],"quality_controlled":"1","doi":"10.2140/involve.2023.16.331","language":[{"iso":"eng"}],"year":"2023","publication_status":"published","publisher":"Mathematical Sciences Publishers","department":[{"_id":"TiBr"}],"author":[{"full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning"},{"full_name":"Lyczak, Julian","id":"3572849A-F248-11E8-B48F-1D18A9856A87","first_name":"Julian","last_name":"Lyczak"},{"last_name":"Sarapin","first_name":"Roman","full_name":"Sarapin, Roman"}],"date_updated":"2023-07-17T08:39:19Z","date_created":"2023-07-02T22:00:43Z","volume":16},{"conference":{"end_date":"2023-06-15","start_date":"2023-06-12","location":"Maribor, Slovenia","name":"ASHPC: Austrian-Slovenian HPC Meeting"},"date_published":"2023-07-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"citation":{"mla":"Elefante, Stefano, et al. “Cryo-EM Software Packages: A Sys-Admins Point of View.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, pp. 42–42.","short":"S. Elefante, S. Stadlbauer, M.F. Alexander, A. Schlögl, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, n.d., pp. 42–42.","chicago":"Elefante, Stefano, Stephan Stadlbauer, Michael F Alexander, and Alois Schlögl. “Cryo-EM Software Packages: A Sys-Admins Point of View.” In ASHPC23 - Austrian-Slovenian HPC Meeting 2023, 42–42. EuroCC, n.d.","ama":"Elefante S, Stadlbauer S, Alexander MF, Schlögl A. Cryo-EM software packages: A sys-admins point of view. In: ASHPC23 - Austrian-Slovenian HPC Meeting 2023. EuroCC; :42-42.","ista":"Elefante S, Stadlbauer S, Alexander MF, Schlögl A. Cryo-EM software packages: A sys-admins point of view. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 42–42.","ieee":"S. Elefante, S. Stadlbauer, M. F. Alexander, and A. Schlögl, “Cryo-EM software packages: A sys-admins point of view,” in ASHPC23 - Austrian-Slovenian HPC Meeting 2023, Maribor, Slovenia, pp. 42–42.","apa":"Elefante, S., Stadlbauer, S., Alexander, M. F., & Schlögl, A. (n.d.). Cryo-EM software packages: A sys-admins point of view. In ASHPC23 - Austrian-Slovenian HPC Meeting 2023 (pp. 42–42). Maribor, Slovenia: EuroCC."},"quality_controlled":"1","page":"42-42","month":"07","day":"01","has_accepted_license":"1","article_processing_charge":"No","author":[{"id":"490F40CE-F248-11E8-B48F-1D18A9856A87","last_name":"Elefante","first_name":"Stefano","full_name":"Elefante, Stefano"},{"id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","first_name":"Stephan","last_name":"Stadlbauer","full_name":"Stadlbauer, Stephan"},{"id":"3A02A8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael F","last_name":"Alexander","full_name":"Alexander, Michael F"},{"first_name":"Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois"}],"date_created":"2023-06-23T11:03:18Z","date_updated":"2023-07-18T09:32:16Z","oa_version":"Submitted Version","file":[{"file_name":"2023_ASHPC_Elefante.pdf","access_level":"open_access","file_size":380354,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"13250","date_updated":"2023-07-18T09:28:30Z","date_created":"2023-07-18T09:28:30Z","checksum":"0ab6173cd5c5634ed773cd37ff012681","success":1}],"year":"2023","_id":"13162","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Cryo-EM software packages: A sys-admins point of view","status":"public","publication_status":"accepted","ddc":["000"],"publisher":"EuroCC","department":[{"_id":"ScienComp"}],"file_date_updated":"2023-07-18T09:28:30Z","type":"conference_abstract"},{"date_created":"2023-06-23T11:01:23Z","date_updated":"2023-07-18T09:30:54Z","author":[{"full_name":"Schlögl, Alois","first_name":"Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100"},{"last_name":"Elefante","first_name":"Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","full_name":"Elefante, Stefano"},{"full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","first_name":"Victor-Valentin"}],"publication_status":"inpress","department":[{"_id":"ScienComp"},{"_id":"EM-Fac"}],"publisher":"EuroCC","acknowledgement":"Thanks to Jesse Hansen for his suggestions on improving the abstract.","year":"2023","file_date_updated":"2023-07-18T09:18:55Z","language":[{"iso":"eng"}],"conference":{"end_date":"2023-06-15","location":"Maribor, Slovenia","start_date":"2023-06-13","name":"ASHPC: Austrian-Slovenian HPC Meeting"},"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"07","oa_version":"Submitted Version","file":[{"file_id":"13249","relation":"main_file","date_updated":"2023-07-18T09:18:55Z","date_created":"2023-07-18T09:18:55Z","success":1,"checksum":"ec8e4295d54171032cdd1b01423eb4a6","file_name":"2023_ASHPC_Schloegl.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":316959}],"status":"public","ddc":["000"],"title":"Running Windows-applications on a Linux HPC cluster using WINE","_id":"13161","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference_abstract","date_published":"2023-07-01T00:00:00Z","page":"59-59","publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","citation":{"chicago":"Schlögl, Alois, Stefano Elefante, and Victor-Valentin Hodirnau. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” In ASHPC23 - Austrian-Slovenian HPC Meeting 2023, 59–59. EuroCC, n.d.","short":"A. Schlögl, S. Elefante, V.-V. Hodirnau, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, n.d., pp. 59–59.","mla":"Schlögl, Alois, et al. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, pp. 59–59.","ieee":"A. Schlögl, S. Elefante, and V.-V. Hodirnau, “Running Windows-applications on a Linux HPC cluster using WINE,” in ASHPC23 - Austrian-Slovenian HPC Meeting 2023, Maribor, Slovenia, pp. 59–59.","apa":"Schlögl, A., Elefante, S., & Hodirnau, V.-V. (n.d.). Running Windows-applications on a Linux HPC cluster using WINE. In ASHPC23 - Austrian-Slovenian HPC Meeting 2023 (pp. 59–59). Maribor, Slovenia: EuroCC.","ista":"Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 59–59.","ama":"Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. In: ASHPC23 - Austrian-Slovenian HPC Meeting 2023. EuroCC; :59-59."},"day":"01","article_processing_charge":"No","has_accepted_license":"1"},{"year":"2023","acknowledgement":"We thank Bingqing Cheng and Hong-Zhou Ye for valuable discussions; Y.W.’s work at IST Austria was supported through ISTernship summer internship program funded by OeADGmbH; D.L. and Z.A. acknowledge support by IST Austria (ISTA); M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).\r\nA.A.Z. and O.M.B. acknowledge support by KAUST.","publication_status":"published","department":[{"_id":"MiLe"},{"_id":"ZhAl"}],"publisher":"American Chemical Society","author":[{"orcid":"0000-0001-8913-9719","id":"0c5ff007-2600-11ee-b896-98bd8d663294","last_name":"Wei","first_name":"Yujing","full_name":"Wei, Yujing"},{"orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem","full_name":"Volosniev, Artem"},{"full_name":"Lorenc, Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","last_name":"Lorenc","first_name":"Dusan"},{"full_name":"Zhumekenov, Ayan A.","first_name":"Ayan A.","last_name":"Zhumekenov"},{"full_name":"Bakr, Osman M.","first_name":"Osman M.","last_name":"Bakr"},{"first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Alpichshev","first_name":"Zhanybek","full_name":"Alpichshev, Zhanybek"}],"date_created":"2023-07-18T11:13:17Z","date_updated":"2023-07-19T06:59:19Z","volume":14,"file_date_updated":"2023-07-19T06:55:39Z","ec_funded":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001022811500001"],"arxiv":["2304.14198"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770"}],"doi":"10.1021/acs.jpclett.3c01158","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"eissn":["1948-7185"]},"_id":"13251","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"title":"Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites","status":"public","intvolume":" 14","file":[{"success":1,"checksum":"c0c040063f06a51b9c463adc504f1a23","date_created":"2023-07-19T06:55:39Z","date_updated":"2023-07-19T06:55:39Z","file_id":"13253","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":2121252,"access_level":"open_access","file_name":"2023_JourPhysChemistry_Wei.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"A rotating organic cation and a dynamically disordered soft inorganic cage are the hallmark features of organic-inorganic lead-halide perovskites. Understanding the interplay between these two subsystems is a challenging problem, but it is this coupling that is widely conjectured to be responsible for the unique behavior of photocarriers in these materials. In this work, we use the fact that the polarizability of the organic cation strongly depends on the ambient electrostatic environment to put the molecule forward as a sensitive probe of the local crystal fields inside the lattice cell. We measure the average polarizability of the C/N–H bond stretching mode by means of infrared spectroscopy, which allows us to deduce the character of the motion of the cation molecule, find the magnitude of the local crystal field, and place an estimate on the strength of the hydrogen bond between the hydrogen and halide atoms. Our results pave the way for understanding electric fields in lead-halide perovskites using infrared bond spectroscopy."}],"issue":"27","publication":"The Journal of Physical Chemistry Letters","citation":{"chicago":"Wei, Yujing, Artem Volosniev, Dusan Lorenc, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” The Journal of Physical Chemistry Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpclett.3c01158.","mla":"Wei, Yujing, et al. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” The Journal of Physical Chemistry Letters, vol. 14, no. 27, American Chemical Society, 2023, pp. 6309–14, doi:10.1021/acs.jpclett.3c01158.","short":"Y. Wei, A. Volosniev, D. Lorenc, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, The Journal of Physical Chemistry Letters 14 (2023) 6309–6314.","ista":"Wei Y, Volosniev A, Lorenc D, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. 14(27), 6309–6314.","apa":"Wei, Y., Volosniev, A., Lorenc, D., Zhumekenov, A. A., Bakr, O. M., Lemeshko, M., & Alpichshev, Z. (2023). Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.3c01158","ieee":"Y. Wei et al., “Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites,” The Journal of Physical Chemistry Letters, vol. 14, no. 27. American Chemical Society, pp. 6309–6314, 2023.","ama":"Wei Y, Volosniev A, Lorenc D, et al. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. 2023;14(27):6309-6314. doi:10.1021/acs.jpclett.3c01158"},"article_type":"original","page":"6309-6314","date_published":"2023-07-05T00:00:00Z","keyword":["General Materials Science","Physical and Theoretical Chemistry"],"day":"05","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)"},{"day":"05","has_accepted_license":"1","article_processing_charge":"Yes","publication":"50th International Colloquium on Automata, Languages, and Programming","citation":{"chicago":"Henzinger, Thomas A, Pavol Kebis, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Regular Methods for Operator Precedence Languages.” In 50th International Colloquium on Automata, Languages, and Programming, 261:129:1--129:20. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.129.","mla":"Henzinger, Thomas A., et al. “Regular Methods for Operator Precedence Languages.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20, doi:10.4230/LIPIcs.ICALP.2023.129.","short":"T.A. Henzinger, P. Kebis, N.A. Mazzocchi, N.E. Sarac, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20.","ista":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. 2023. Regular methods for operator precedence languages. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 129:1--129:20.","ieee":"T. A. Henzinger, P. Kebis, N. A. Mazzocchi, and N. E. Sarac, “Regular methods for operator precedence languages,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261, p. 129:1--129:20.","apa":"Henzinger, T. A., Kebis, P., Mazzocchi, N. A., & Sarac, N. E. (2023). Regular methods for operator precedence languages. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261, p. 129:1--129:20). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.129","ama":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. Regular methods for operator precedence languages. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023:129:1--129:20. doi:10.4230/LIPIcs.ICALP.2023.129"},"page":"129:1--129:20","date_published":"2023-07-05T00:00:00Z","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"The operator precedence languages (OPLs) represent the largest known subclass of the context-free languages which enjoys all desirable closure and decidability properties. This includes the decidability of language inclusion, which is the ultimate verification problem. Operator precedence grammars, automata, and logics have been investigated and used, for example, to verify programs with arithmetic expressions and exceptions (both of which are deterministic pushdown but lie outside the scope of the visibly pushdown languages). In this paper, we complete the picture and give, for the first time, an algebraic characterization of the class of OPLs in the form of a syntactic congruence that has finitely many equivalence classes exactly for the operator precedence languages. This is a generalization of the celebrated Myhill-Nerode theorem for the regular languages to OPLs. As one of the consequences, we show that universality and language inclusion for nondeterministic operator precedence automata can be solved by an antichain algorithm. Antichain algorithms avoid determinization and complementation through an explicit subset construction, by leveraging a quasi-order on words, which allows the pruning of the search space for counterexample words without sacrificing completeness. Antichain algorithms can be implemented symbolically, and these implementations are today the best-performing algorithms in practice for the inclusion of finite automata. We give a generic construction of the quasi-order needed for antichain algorithms from a finite syntactic congruence. This yields the first antichain algorithm for OPLs, an algorithm that solves the ExpTime-hard language inclusion problem for OPLs in exponential time."}],"_id":"13292","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Regular methods for operator precedence languages","ddc":["000"],"status":"public","intvolume":" 261","oa_version":"Published Version","file":[{"file_name":"icalp23.pdf","access_level":"open_access","creator":"esarac","file_size":859379,"content_type":"application/pdf","file_id":"13293","relation":"main_file","date_updated":"2023-07-24T15:11:05Z","date_created":"2023-07-24T15:11:05Z","success":1,"checksum":"5d4c8932ef3450615a53b9bb15d92eb2"}],"month":"07","publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959772785"]},"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":["2305.03447"]},"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","start_date":"2023-07-10","location":"Paderborn, Germany","end_date":"2023-07-14"},"doi":"10.4230/LIPIcs.ICALP.2023.129","language":[{"iso":"eng"}],"file_date_updated":"2023-07-24T15:11:05Z","ec_funded":1,"year":"2023","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093.\r\nWe thank Pierre Ganty for early discussions and the anonymous reviewers for their helpful comments.\r\n","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"author":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Pavol","last_name":"Kebis","full_name":"Kebis, Pavol"},{"full_name":"Mazzocchi, Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85","first_name":"Nicolas Adrien","last_name":"Mazzocchi"},{"last_name":"Sarac","first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","full_name":"Sarac, Naci E"}],"date_created":"2023-07-24T15:11:41Z","date_updated":"2023-07-31T08:38:38Z","volume":261},{"date_published":"2023-04-14T00:00:00Z","publication":"SciPost Physics Core","citation":{"ama":"Tucci G, De Nicola S, Wald S, Gambassi A. Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. 2023;6(2). doi:10.21468/scipostphyscore.6.2.029","ista":"Tucci G, De Nicola S, Wald S, Gambassi A. 2023. Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. 6(2), 029.","apa":"Tucci, G., De Nicola, S., Wald, S., & Gambassi, A. (2023). Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. SciPost Foundation. https://doi.org/10.21468/scipostphyscore.6.2.029","ieee":"G. Tucci, S. De Nicola, S. Wald, and A. Gambassi, “Stochastic representation of the quantum quartic oscillator,” SciPost Physics Core, vol. 6, no. 2. SciPost Foundation, 2023.","mla":"Tucci, Gennaro, et al. “Stochastic Representation of the Quantum Quartic Oscillator.” SciPost Physics Core, vol. 6, no. 2, 029, SciPost Foundation, 2023, doi:10.21468/scipostphyscore.6.2.029.","short":"G. Tucci, S. De Nicola, S. Wald, A. Gambassi, SciPost Physics Core 6 (2023).","chicago":"Tucci, Gennaro, Stefano De Nicola, Sascha Wald, and Andrea Gambassi. “Stochastic Representation of the Quantum Quartic Oscillator.” SciPost Physics Core. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscore.6.2.029."},"article_type":"original","day":"14","has_accepted_license":"1","article_processing_charge":"No","keyword":["Statistical and Nonlinear Physics","Atomic and Molecular Physics","and Optics","Nuclear and High Energy Physics","Condensed Matter Physics"],"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"13329","checksum":"b472bc82108747eda5d52adf9e2ac7f3","success":1,"date_updated":"2023-07-31T09:02:27Z","date_created":"2023-07-31T09:02:27Z","access_level":"open_access","file_name":"2023_SciPostPhysCore_Tucci.pdf","content_type":"application/pdf","file_size":523236,"creator":"dernst"}],"_id":"13277","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["530"],"title":"Stochastic representation of the quantum quartic oscillator","intvolume":" 6","abstract":[{"lang":"eng","text":"Recent experimental advances have inspired the development of theoretical tools to describe the non-equilibrium dynamics of quantum systems. Among them an exact representation of quantum spin systems in terms of classical stochastic processes has been proposed. Here we provide first steps towards the extension of this stochastic approach to bosonic systems by considering the one-dimensional quantum quartic oscillator. We show how to exactly parameterize the time evolution of this prototypical model via the dynamics of a set of classical variables. We interpret these variables as stochastic processes, which allows us to propose a novel way to numerically simulate the time evolution of the system. We benchmark our findings by considering analytically solvable limits and providing alternative derivations of known results."}],"issue":"2","type":"journal_article","doi":"10.21468/scipostphyscore.6.2.029","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":["2211.01923"]},"quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"month":"04","publication_identifier":{"issn":["2666-9366"]},"author":[{"full_name":"Tucci, Gennaro","last_name":"Tucci","first_name":"Gennaro"},{"orcid":"0000-0002-4842-6671","id":"42832B76-F248-11E8-B48F-1D18A9856A87","last_name":"De Nicola","first_name":"Stefano","full_name":"De Nicola, Stefano"},{"last_name":"Wald","first_name":"Sascha","full_name":"Wald, Sascha"},{"full_name":"Gambassi, Andrea","first_name":"Andrea","last_name":"Gambassi"}],"date_updated":"2023-07-31T09:03:28Z","date_created":"2023-07-24T10:47:46Z","volume":6,"acknowledgement":"S. De Nicola acknowledges funding from the Institute of Science and Technology Austria (ISTA), and from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. S. De Nicola also acknowledges funding from the EPSRC Center for Doctoral Training in Cross-Disciplinary Approaches to NonEquilibrium Systems (CANES) under Grant EP/L015854/1. ","year":"2023","publication_status":"published","publisher":"SciPost Foundation","department":[{"_id":"MaSe"}],"file_date_updated":"2023-07-31T09:02:27Z","ec_funded":1,"article_number":"029"},{"author":[{"last_name":"Rammelmüller","first_name":"Lukas","full_name":"Rammelmüller, Lukas"},{"full_name":"Huber, David","first_name":"David","last_name":"Huber"},{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"13275"}]},"date_created":"2023-07-24T10:47:15Z","date_updated":"2023-07-31T09:16:02Z","acknowledgement":"We acknowledge fruitful discussions with Hans-Werner Hammer and thank Gerhard Zürn and\r\nPietro Massignan for sending us their data. We thank Fabian Brauneis for beta-testing the\r\nprovided code-package, and comments on the manuscript.\r\nL.R. is supported by FP7/ERC Consolidator Grant QSIMCORR, No.\r\n771891, and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under\r\nGermany’s Excellence Strategy –EXC–2111–390814868. A.G.V. acknowledges support\r\nby European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411.","year":"2023","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"SciPost Foundation","file_date_updated":"2023-07-31T09:09:23Z","ec_funded":1,"article_number":"12","doi":"10.21468/scipostphyscodeb.12","language":[{"iso":"eng"}],"external_id":{"arxiv":["2202.04603"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"month":"04","publication_identifier":{"issn":["2949-804X"]},"file":[{"file_name":"2023_SciPostPhysCodebase_Rammelmueller.pdf","access_level":"open_access","file_size":551418,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"13330","date_updated":"2023-07-31T09:09:23Z","date_created":"2023-07-31T09:09:23Z","checksum":"f583a70fe915d2208c803f5afb426daa","success":1}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13276","ddc":["530"],"title":"A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D","status":"public","abstract":[{"text":"We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost.","lang":"eng"}],"type":"journal_article","date_published":"2023-04-19T00:00:00Z","publication":"SciPost Physics Codebases","citation":{"chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “A Modular Implementation of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.” SciPost Physics Codebases. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscodeb.12.","mla":"Rammelmüller, Lukas, et al. “A Modular Implementation of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.” SciPost Physics Codebases, 12, SciPost Foundation, 2023, doi:10.21468/scipostphyscodeb.12.","short":"L. Rammelmüller, D. Huber, A. Volosniev, SciPost Physics Codebases (2023).","ista":"Rammelmüller L, Huber D, Volosniev A. 2023. A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases., 12.","apa":"Rammelmüller, L., Huber, D., & Volosniev, A. (2023). A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases. SciPost Foundation. https://doi.org/10.21468/scipostphyscodeb.12","ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D,” SciPost Physics Codebases. SciPost Foundation, 2023.","ama":"Rammelmüller L, Huber D, Volosniev A. A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases. 2023. doi:10.21468/scipostphyscodeb.12"},"article_type":"original","day":"19","has_accepted_license":"1","article_processing_charge":"No"},{"article_processing_charge":"No","day":"19","month":"04","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"citation":{"ama":"Rammelmüller L, Huber D, Volosniev A. Codebase release 1.0 for FermiFCI. 2023. doi:10.21468/scipostphyscodeb.12-r1.0","ista":"Rammelmüller L, Huber D, Volosniev A. 2023. Codebase release 1.0 for FermiFCI, SciPost Foundation, 10.21468/scipostphyscodeb.12-r1.0.","apa":"Rammelmüller, L., Huber, D., & Volosniev, A. (2023). Codebase release 1.0 for FermiFCI. SciPost Foundation. https://doi.org/10.21468/scipostphyscodeb.12-r1.0","ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “Codebase release 1.0 for FermiFCI.” SciPost Foundation, 2023.","mla":"Rammelmüller, Lukas, et al. Codebase Release 1.0 for FermiFCI. SciPost Foundation, 2023, doi:10.21468/scipostphyscodeb.12-r1.0.","short":"L. Rammelmüller, D. Huber, A. Volosniev, (2023).","chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “Codebase Release 1.0 for FermiFCI.” SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscodeb.12-r1.0."},"main_file_link":[{"url":"https://doi.org/10.21468/SciPostPhysCodeb.12-r1.0","open_access":"1"}],"oa":1,"date_published":"2023-04-19T00:00:00Z","doi":"10.21468/scipostphyscodeb.12-r1.0","type":"research_data_reference","ec_funded":1,"abstract":[{"lang":"eng","text":"We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost."}],"department":[{"_id":"MiLe"}],"publisher":"SciPost Foundation","ddc":["530"],"status":"public","title":"Codebase release 1.0 for FermiFCI","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13275","year":"2023","oa_version":"Published Version","date_updated":"2023-07-31T09:16:02Z","date_created":"2023-07-24T10:46:23Z","related_material":{"record":[{"id":"13276","status":"public","relation":"used_in_publication"}]},"author":[{"last_name":"Rammelmüller","first_name":"Lukas","full_name":"Rammelmüller, Lukas"},{"first_name":"David","last_name":"Huber","full_name":"Huber, David"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev","full_name":"Volosniev, Artem"}]},{"scopus_import":"1","day":"17","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","publication":"Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures","citation":{"ista":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. 2023. Provably-efficient and internally-deterministic parallel Union-Find. Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 261–271.","ieee":"A. Fedorov, D. Hashemi, G. Nadiradze, and D.-A. Alistarh, “Provably-efficient and internally-deterministic parallel Union-Find,” in Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Orlando, FL, United States, 2023, pp. 261–271.","apa":"Fedorov, A., Hashemi, D., Nadiradze, G., & Alistarh, D.-A. (2023). Provably-efficient and internally-deterministic parallel Union-Find. In Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures (pp. 261–271). Orlando, FL, United States: Association for Computing Machinery. https://doi.org/10.1145/3558481.3591082","ama":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. Provably-efficient and internally-deterministic parallel Union-Find. In: Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. Association for Computing Machinery; 2023:261-271. doi:10.1145/3558481.3591082","chicago":"Fedorov, Alexander, Diba Hashemi, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” In Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, 261–71. Association for Computing Machinery, 2023. https://doi.org/10.1145/3558481.3591082.","mla":"Fedorov, Alexander, et al. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–71, doi:10.1145/3558481.3591082.","short":"A. Fedorov, D. Hashemi, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–271."},"page":"261-271","date_published":"2023-06-17T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"Determining the degree of inherent parallelism in classical sequential algorithms and leveraging it for fast parallel execution is a key topic in parallel computing, and detailed analyses are known for a wide range of classical algorithms. In this paper, we perform the first such analysis for the fundamental Union-Find problem, in which we are given a graph as a sequence of edges, and must maintain its connectivity structure under edge additions. We prove that classic sequential algorithms for this problem are well-parallelizable under reasonable assumptions, addressing a conjecture by [Blelloch, 2017]. More precisely, we show via a new potential argument that, under uniform random edge ordering, parallel union-find operations are unlikely to interfere: T concurrent threads processing the graph in parallel will encounter memory contention O(T2 · log |V| · log |E|) times in expectation, where |E| and |V| are the number of edges and nodes in the graph, respectively. We leverage this result to design a new parallel Union-Find algorithm that is both internally deterministic, i.e., its results are guaranteed to match those of a sequential execution, but also work-efficient and scalable, as long as the number of threads T is O(|E|1 over 3 - ε), for an arbitrarily small constant ε > 0, which holds for most large real-world graphs. We present lower bounds which show that our analysis is close to optimal, and experimental results suggesting that the performance cost of internal determinism is limited."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13262","ddc":["000"],"status":"public","title":"Provably-efficient and internally-deterministic parallel Union-Find","file":[{"checksum":"72e312aabf0c5248c99b5cd3a88e4c88","success":1,"date_updated":"2023-07-31T10:53:08Z","date_created":"2023-07-31T10:53:08Z","relation":"main_file","file_id":"13334","file_size":2087937,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_SPAA_Fedorov.pdf"}],"oa_version":"Published Version","month":"06","publication_identifier":{"isbn":["9781450395458"]},"external_id":{"arxiv":["2304.09331"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","conference":{"start_date":"2023-06-17","location":"Orlando, FL, United States","end_date":"2023-06-19","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"doi":"10.1145/3558481.3591082","language":[{"iso":"eng"}],"file_date_updated":"2023-07-31T10:53:08Z","year":"2023","publication_status":"published","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"publisher":"Association for Computing Machinery","author":[{"id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","first_name":"Alexander","last_name":"Fedorov","full_name":"Fedorov, Alexander"},{"full_name":"Hashemi, Diba","id":"ed9595ea-2f8f-11ee-ba95-d2b546540783","first_name":"Diba","last_name":"Hashemi"},{"id":"3279A00C-F248-11E8-B48F-1D18A9856A87","last_name":"Nadiradze","first_name":"Giorgi","full_name":"Nadiradze, Giorgi"},{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"date_updated":"2023-07-31T10:54:32Z","date_created":"2023-07-23T22:01:12Z"},{"publication_identifier":{"eissn":["1752-4571"]},"month":"02","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000815663700001"]},"language":[{"iso":"eng"}],"doi":"10.1111/eva.13428","file_date_updated":"2023-02-27T07:10:17Z","publisher":"Wiley","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"publication_status":"published","year":"2023","acknowledgement":"We greatly thank all the corresponding authors of the studies that were included in our synthesis for the sharing of additional data: Thomas Broquet, Dmitry Filatov, Quentin Rougemont, Paolo Momigliano, Pierre-Alexandre Gagnaire, Carlos Prada, Ahmed Souissi, Michael Møller Hansen, Sylvie Lapègue, Joseph Di Battista, Michael Hellberg and Carlos Prada. RKB and ADJ were supported by the European Research Council. MR was supported by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243; to MR) and Formas (grant number 2019-00882; to KJ and MR), and by additional grants from the European Research Council (to RKB) and Vetenskapsrådet (to KJ) through the Centre for Marine Evolutionary Biology (https://www.gu.se/en/cemeb-marine-evolutionary-biology).","volume":16,"date_updated":"2023-08-01T12:25:44Z","date_created":"2022-07-03T22:01:33Z","author":[{"full_name":"De Jode, Aurélien","last_name":"De Jode","first_name":"Aurélien"},{"last_name":"Le Moan","first_name":"Alan","full_name":"Le Moan, Alan"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean"},{"full_name":"Westram, Anja M","first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","page":"542-559","article_type":"original","citation":{"chicago":"De Jode, Aurélien, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski, Anja M Westram, Roger K. Butlin, Marina Rafajlović, and Christelle Fraisse. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications. Wiley, 2023. https://doi.org/10.1111/eva.13428.","short":"A. De Jode, A. Le Moan, K. Johannesson, R. Faria, S. Stankowski, A.M. Westram, R.K. Butlin, M. Rafajlović, C. Fraisse, Evolutionary Applications 16 (2023) 542–559.","mla":"De Jode, Aurélien, et al. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications, vol. 16, no. 2, Wiley, 2023, pp. 542–59, doi:10.1111/eva.13428.","ieee":"A. De Jode et al., “Ten years of demographic modelling of divergence and speciation in the sea,” Evolutionary Applications, vol. 16, no. 2. Wiley, pp. 542–559, 2023.","apa":"De Jode, A., Le Moan, A., Johannesson, K., Faria, R., Stankowski, S., Westram, A. M., … Fraisse, C. (2023). Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. Wiley. https://doi.org/10.1111/eva.13428","ista":"De Jode A, Le Moan A, Johannesson K, Faria R, Stankowski S, Westram AM, Butlin RK, Rafajlović M, Fraisse C. 2023. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 16(2), 542–559.","ama":"De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 2023;16(2):542-559. doi:10.1111/eva.13428"},"publication":"Evolutionary Applications","date_published":"2023-02-01T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results."}],"intvolume":" 16","status":"public","title":"Ten years of demographic modelling of divergence and speciation in the sea","ddc":["576"],"_id":"11479","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"content_type":"application/pdf","file_size":2269822,"creator":"dernst","file_name":"2023_EvolutionaryApplications_DeJode.pdf","access_level":"open_access","date_updated":"2023-02-27T07:10:17Z","date_created":"2023-02-27T07:10:17Z","checksum":"d4d6fa9ddf36643af994a6a757919afb","success":1,"relation":"main_file","file_id":"12685"}],"oa_version":"Published Version"},{"month":"01","publication_identifier":{"eissn":["2045-2322"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41598-022-19827-9","isi":1,"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":{"isi":["001003345000051"]},"file_date_updated":"2023-01-23T07:53:23Z","article_number":"468","date_created":"2023-01-22T23:00:55Z","date_updated":"2023-08-01T12:31:40Z","volume":13,"author":[{"full_name":"Gómez, Arturo","first_name":"Arturo","last_name":"Gómez"},{"full_name":"Oliveira, Goncalo","id":"58abbde8-f455-11eb-a497-98c8fd71b905","first_name":"Goncalo","last_name":"Oliveira"}],"publication_status":"published","department":[{"_id":"TaHa"}],"publisher":"Springer Nature","year":"2023","acknowledgement":"Gonçalo Oliveira is supported by the NOMIS Foundation, Fundação Serrapilheira 1812-27395, by CNPq grants 428959/2018-0 and 307475/2018-2, and by FAPERJ through the grant Jovem Cientista do Nosso Estado E-26/202.793/2019.","day":"10","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2023-01-10T00:00:00Z","article_type":"original","publication":"Scientific Reports","citation":{"chicago":"Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling on Networks.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-022-19827-9.","short":"A. Gómez, G. Oliveira, Scientific Reports 13 (2023).","mla":"Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling on Networks.” Scientific Reports, vol. 13, 468, Springer Nature, 2023, doi:10.1038/s41598-022-19827-9.","ieee":"A. Gómez and G. Oliveira, “New approaches to epidemic modeling on networks,” Scientific Reports, vol. 13. Springer Nature, 2023.","apa":"Gómez, A., & Oliveira, G. (2023). New approaches to epidemic modeling on networks. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-19827-9","ista":"Gómez A, Oliveira G. 2023. New approaches to epidemic modeling on networks. Scientific Reports. 13, 468.","ama":"Gómez A, Oliveira G. New approaches to epidemic modeling on networks. Scientific Reports. 2023;13. doi:10.1038/s41598-022-19827-9"},"abstract":[{"lang":"eng","text":"In this article, we develop two independent and new approaches to model epidemic spread in a network. Contrary to the most studied models, those developed here allow for contacts with different probabilities of transmitting the disease (transmissibilities). We then examine each of these models using some mean field type approximations. The first model looks at the late-stage effects of an epidemic outbreak and allows for the computation of the probability that a given vertex was infected. This computation is based on a mean field approximation and only depends on the number of contacts and their transmissibilities. This approach shares many similarities with percolation models in networks. The second model we develop is a dynamic model which we analyze using a mean field approximation which highly reduces the dimensionality of the system. In particular, the original system which individually analyses each vertex of the network is reduced to one with as many equations as different transmissibilities. Perhaps the greatest contribution of this article is the observation that, in both these models, the existence and size of an epidemic outbreak are linked to the properties of a matrix which we call the R-matrix. This is a generalization of the basic reproduction number which more precisely characterizes the main routes of infection."}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12336","checksum":"a8b83739f4a951e83e0b2a778f03b327","success":1,"date_created":"2023-01-23T07:53:23Z","date_updated":"2023-01-23T07:53:23Z","access_level":"open_access","file_name":"2023_ScientificReports_Gomez.pdf","content_type":"application/pdf","file_size":2167792,"creator":"dernst"}],"title":"New approaches to epidemic modeling on networks","status":"public","ddc":["510"],"intvolume":" 13","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12329"},{"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1901.08503","open_access":"1"}],"external_id":{"arxiv":["1901.08503"],"isi":["000773116000001"]},"language":[{"iso":"eng"}],"doi":"10.1093/imrn/rnac048","month":"04","publication_identifier":{"issn":["1073-7928"],"eissn":["1687-0247"]},"publication_status":"published","publisher":"Oxford Academic","department":[{"_id":"TiBr"}],"acknowledgement":"This work was supported by the German Academic Exchange Service. Parts of this article were prepared at the Institut de Mathémathiques de Jussieu—Paris Rive Gauche. I wish to thank Antoine Chambert-Loir for his remarks and the institute for its hospitality, as well as the anonymous referee for several useful remarks and suggestions for improvements.","year":"2023","date_created":"2021-01-22T09:31:09Z","date_updated":"2023-08-01T12:23:55Z","volume":2023,"author":[{"full_name":"Wilsch, Florian Alexander","last_name":"Wilsch","first_name":"Florian Alexander","orcid":"0000-0001-7302-8256","id":"560601DA-8D36-11E9-A136-7AC1E5697425"}],"article_type":"original","page":"6780-6808","publication":"International Mathematics Research Notices","citation":{"ista":"Wilsch FA. 2023. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023(8), 6780–6808.","apa":"Wilsch, F. A. (2023). Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. Oxford Academic. https://doi.org/10.1093/imrn/rnac048","ieee":"F. A. Wilsch, “Integral points of bounded height on a log Fano threefold,” International Mathematics Research Notices, vol. 2023, no. 8. Oxford Academic, pp. 6780–6808, 2023.","ama":"Wilsch FA. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023;2023(8):6780-6808. doi:10.1093/imrn/rnac048","chicago":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices. Oxford Academic, 2023. https://doi.org/10.1093/imrn/rnac048.","mla":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices, vol. 2023, no. 8, Oxford Academic, 2023, pp. 6780–808, doi:10.1093/imrn/rnac048.","short":"F.A. Wilsch, International Mathematics Research Notices 2023 (2023) 6780–6808."},"date_published":"2023-04-01T00:00:00Z","day":"01","article_processing_charge":"No","title":"Integral points of bounded height on a log Fano threefold","status":"public","intvolume":" 2023","_id":"9034","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We determine an asymptotic formula for the number of integral points of bounded height on a blow-up of P3 outside certain planes using universal torsors."}],"issue":"8"},{"intvolume":" 14","ddc":["570"],"title":"Antiviral immune response reveals host-specific virus infections in natural ant populations","status":"public","_id":"12469","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_FrontMicrobiology_Viljakainen.pdf","file_size":4866332,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"12843","checksum":"cd52292963acce1111634d9fac08c699","success":1,"date_updated":"2023-04-17T07:49:09Z","date_created":"2023-04-17T07:49:09Z"}],"type":"journal_article","abstract":[{"text":"Hosts can carry many viruses in their bodies, but not all of them cause disease. We studied ants as a social host to determine both their overall viral repertoire and the subset of actively infecting viruses across natural populations of three subfamilies: the Argentine ant (Linepithema humile, Dolichoderinae), the invasive garden ant (Lasius neglectus, Formicinae) and the red ant (Myrmica rubra, Myrmicinae). We used a dual sequencing strategy to reconstruct complete virus genomes by RNA-seq and to simultaneously determine the small interfering RNAs (siRNAs) by small RNA sequencing (sRNA-seq), which constitute the host antiviral RNAi immune response. This approach led to the discovery of 41 novel viruses in ants and revealed a host ant-specific RNAi response (21 vs. 22 nt siRNAs) in the different ant species. The efficiency of the RNAi response (sRNA/RNA read count ratio) depended on the virus and the respective ant species, but not its population. Overall, we found the highest virus abundance and diversity per population in Li. humile, followed by La. neglectus and M. rubra. Argentine ants also shared a high proportion of viruses between populations, whilst overlap was nearly absent in M. rubra. Only one of the 59 viruses was found to infect two of the ant species as hosts, revealing high host-specificity in active infections. In contrast, six viruses actively infected one ant species, but were found as contaminants only in the others. Disentangling spillover of disease-causing infection from non-infecting contamination across species is providing relevant information for disease ecology and ecosystem management.","lang":"eng"}],"article_type":"original","citation":{"short":"L. Viljakainen, M. Fürst, A.V. Grasse, J. Jurvansuu, J. Oh, L. Tolonen, T. Eder, T. Rattei, S. Cremer, Frontiers in Microbiology 14 (2023).","mla":"Viljakainen, Lumi, et al. “Antiviral Immune Response Reveals Host-Specific Virus Infections in Natural Ant Populations.” Frontiers in Microbiology, vol. 14, 1119002, Frontiers, 2023, doi:10.3389/fmicb.2023.1119002.","chicago":"Viljakainen, Lumi, Matthias Fürst, Anna V Grasse, Jaana Jurvansuu, Jinook Oh, Lassi Tolonen, Thomas Eder, Thomas Rattei, and Sylvia Cremer. “Antiviral Immune Response Reveals Host-Specific Virus Infections in Natural Ant Populations.” Frontiers in Microbiology. Frontiers, 2023. https://doi.org/10.3389/fmicb.2023.1119002.","ama":"Viljakainen L, Fürst M, Grasse AV, et al. Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. 2023;14. doi:10.3389/fmicb.2023.1119002","apa":"Viljakainen, L., Fürst, M., Grasse, A. V., Jurvansuu, J., Oh, J., Tolonen, L., … Cremer, S. (2023). Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2023.1119002","ieee":"L. Viljakainen et al., “Antiviral immune response reveals host-specific virus infections in natural ant populations,” Frontiers in Microbiology, vol. 14. Frontiers, 2023.","ista":"Viljakainen L, Fürst M, Grasse AV, Jurvansuu J, Oh J, Tolonen L, Eder T, Rattei T, Cremer S. 2023. Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. 14, 1119002."},"publication":"Frontiers in Microbiology","date_published":"2023-03-16T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"16","department":[{"_id":"SyCr"}],"publisher":"Frontiers","publication_status":"published","pmid":1,"year":"2023","acknowledgement":"We thank D.J. Obbard for sharing the details of the dual RNA-seq/sRNA-seq approach, S.\r\nMetzler and R. Ferrigato for the photographs (Figure 1), M. Konrad, B. Casillas-Perez, C.D.\r\nPull and X. Espadaler for help with ant collection, and the Social Immunity Team at IST\r\nAustria, in particular J. Robb, A. Franschitz, E. Naderlinger, E. Dawson and B. Casillas-Perez\r\nfor support and comments on the manuscript. The study was funded by the Austrian Science\r\nFund (FWF; M02076-B25 to MAF) and the Academy of Finland (343022 to LV). ","volume":14,"date_created":"2023-01-31T08:13:40Z","date_updated":"2023-08-01T12:39:58Z","author":[{"full_name":"Viljakainen, Lumi","last_name":"Viljakainen","first_name":"Lumi"},{"last_name":"Fürst","first_name":"Matthias","orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87","full_name":"Fürst, Matthias"},{"full_name":"Grasse, Anna V","last_name":"Grasse","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jurvansuu","first_name":"Jaana","full_name":"Jurvansuu, Jaana"},{"orcid":"0000-0001-7425-2372","id":"403169A4-080F-11EA-9993-BF3F3DDC885E","last_name":"Oh","first_name":"Jinook","full_name":"Oh, Jinook"},{"full_name":"Tolonen, Lassi","first_name":"Lassi","last_name":"Tolonen"},{"first_name":"Thomas","last_name":"Eder","full_name":"Eder, Thomas"},{"full_name":"Rattei, Thomas","last_name":"Rattei","first_name":"Thomas"},{"full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"article_number":"1119002","file_date_updated":"2023-04-17T07:49:09Z","project":[{"grant_number":"M02076","_id":"25DF61D8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Viral pathogens and social immunity in ants"}],"quality_controlled":"1","isi":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":["000961542100001"],"pmid":["PPR559293 "]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3389/fmicb.2023.1119002","publication_identifier":{"eissn":["1664-302X"]},"month":"03"},{"month":"01","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"external_id":{"isi":["000862193600001"]},"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","isi":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Learning and triangulating manifolds via collapses","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","grant_number":"M03073"}],"doi":"10.1007/s00454-022-00431-7","language":[{"iso":"eng"}],"file_date_updated":"2023-02-02T11:01:10Z","ec_funded":1,"acknowledgement":"This work has been funded by the European Research Council under the European Union’s ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). Arijit Ghosh is supported by Ramanujan Fellowship (No. SB/S2/RJN-064/2015). Part of this work was done when Arijit Ghosh was a Researcher at Max-Planck-Institute for Informatics, Germany, supported by the IndoGerman Max Planck Center for Computer Science (IMPECS). Mathijs Wintraecken also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411 and the Austrian Science Fund (FWF): M-3073. A part of the results described in this paper were presented at SoCG 2018 and in [3]. \r\nOpen access funding provided by the Austrian Science Fund (FWF).","year":"2023","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","author":[{"full_name":"Boissonnat, Jean-Daniel","first_name":"Jean-Daniel","last_name":"Boissonnat"},{"first_name":"Ramsay","last_name":"Dyer","full_name":"Dyer, Ramsay"},{"full_name":"Ghosh, Arijit","last_name":"Ghosh","first_name":"Arijit"},{"id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220","first_name":"Mathijs","last_name":"Wintraecken","full_name":"Wintraecken, Mathijs"}],"date_created":"2023-01-16T10:04:06Z","date_updated":"2023-08-01T12:47:32Z","volume":69,"scopus_import":"1","keyword":["Computational Theory and Mathematics","Discrete Mathematics and Combinatorics","Geometry and Topology","Theoretical Computer Science"],"day":"01","article_processing_charge":"No","has_accepted_license":"1","publication":"Discrete & Computational Geometry","citation":{"ista":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. 2023. Local criteria for triangulating general manifolds. Discrete & Computational Geometry. 69, 156–191.","ieee":"J.-D. Boissonnat, R. Dyer, A. Ghosh, and M. Wintraecken, “Local criteria for triangulating general manifolds,” Discrete & Computational Geometry, vol. 69. Springer Nature, pp. 156–191, 2023.","apa":"Boissonnat, J.-D., Dyer, R., Ghosh, A., & Wintraecken, M. (2023). Local criteria for triangulating general manifolds. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00431-7","ama":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. Local criteria for triangulating general manifolds. Discrete & Computational Geometry. 2023;69:156-191. doi:10.1007/s00454-022-00431-7","chicago":"Boissonnat, Jean-Daniel, Ramsay Dyer, Arijit Ghosh, and Mathijs Wintraecken. “Local Criteria for Triangulating General Manifolds.” Discrete & Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00431-7.","mla":"Boissonnat, Jean-Daniel, et al. “Local Criteria for Triangulating General Manifolds.” Discrete & Computational Geometry, vol. 69, Springer Nature, 2023, pp. 156–91, doi:10.1007/s00454-022-00431-7.","short":"J.-D. Boissonnat, R. Dyer, A. Ghosh, M. Wintraecken, Discrete & Computational Geometry 69 (2023) 156–191."},"article_type":"original","page":"156-191","date_published":"2023-01-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We present criteria for establishing a triangulation of a manifold. Given a manifold M, a simplicial complex A, and a map H from the underlying space of A to M, our criteria are presented in local coordinate charts for M, and ensure that H is a homeomorphism. These criteria do not require a differentiable structure, or even an explicit metric on M. No Delaunay property of A is assumed. The result provides a triangulation guarantee for algorithms that construct a simplicial complex by working in local coordinate patches. Because the criteria are easily verified in such a setting, they are expected to be of general use."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12287","ddc":["510"],"title":"Local criteria for triangulating general manifolds","status":"public","intvolume":" 69","file":[{"success":1,"checksum":"46352e0ee71e460848f88685ca852681","date_updated":"2023-02-02T11:01:10Z","date_created":"2023-02-02T11:01:10Z","file_id":"12488","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":582850,"access_level":"open_access","file_name":"2023_DiscreteCompGeometry_Boissonnat.pdf"}],"oa_version":"Published Version"},{"file_date_updated":"2023-03-16T07:58:16Z","year":"2023","acknowledgement":"We apologize for not being able to mention and cite additional excellent work that would have fit the scope of this review, due to space restraints. We thank Jesse Hansen for comments on the manuscript. We acknowledge support from the Austrian Science Fund (FWF): P33367 and the Institute of Science and Technology Austria.","department":[{"_id":"FlSc"}],"publisher":"Portland Press","publication_status":"published","author":[{"first_name":"Florian","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian"},{"id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","last_name":"Javoor","first_name":"Manjunath","full_name":"Javoor, Manjunath"},{"full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"}],"volume":51,"date_updated":"2023-08-01T12:55:32Z","date_created":"2023-01-27T10:08:19Z","publication_identifier":{"eissn":["1470-8752"],"issn":["0300-5127"]},"month":"02","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000926043100001"]},"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"isi":1,"quality_controlled":"1","doi":"10.1042/bst20220221","language":[{"iso":"eng"}],"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"The actin cytoskeleton plays a key role in cell migration and cellular morphodynamics in most eukaryotes. The ability of the actin cytoskeleton to assemble and disassemble in a spatiotemporally controlled manner allows it to form higher-order structures, which can generate forces required for a cell to explore and navigate through its environment. It is regulated not only via a complex synergistic and competitive interplay between actin-binding proteins (ABP), but also by filament biochemistry and filament geometry. The lack of structural insights into how geometry and ABPs regulate the actin cytoskeleton limits our understanding of the molecular mechanisms that define actin cytoskeleton remodeling and, in turn, impact emerging cell migration characteristics. With the advent of cryo-electron microscopy (cryo-EM) and advanced computational methods, it is now possible to define these molecular mechanisms involving actin and its interactors at both atomic and ultra-structural levels in vitro and in cellulo. In this review, we will provide an overview of the available cryo-EM methods, applicable to further our understanding of the actin cytoskeleton, specifically in the context of cell migration. We will discuss how these methods have been employed to elucidate ABP- and geometry-defined regulatory mechanisms in initiating, maintaining, and disassembling cellular actin networks in migratory protrusions."}],"_id":"12421","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 51","ddc":["570"],"title":"Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM","status":"public","file":[{"access_level":"open_access","file_name":"2023_BioChemicalSocietyTransactions_Faessler.pdf","content_type":"application/pdf","file_size":10045006,"creator":"dernst","relation":"main_file","file_id":"12728","checksum":"4e7069845e3dad22bb44fb71ec624c60","success":1,"date_created":"2023-03-16T07:58:16Z","date_updated":"2023-03-16T07:58:16Z"}],"oa_version":"Published Version","scopus_import":"1","keyword":["Biochemistry"],"has_accepted_license":"1","article_processing_charge":"No","day":"01","citation":{"apa":"Fäßler, F., Javoor, M., & Schur, F. K. (2023). Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. Portland Press. https://doi.org/10.1042/bst20220221","ieee":"F. Fäßler, M. Javoor, and F. K. Schur, “Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM,” Biochemical Society Transactions, vol. 51, no. 1. Portland Press, pp. 87–99, 2023.","ista":"Fäßler F, Javoor M, Schur FK. 2023. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. 51(1), 87–99.","ama":"Fäßler F, Javoor M, Schur FK. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. 2023;51(1):87-99. doi:10.1042/bst20220221","chicago":"Fäßler, Florian, Manjunath Javoor, and Florian KM Schur. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” Biochemical Society Transactions. Portland Press, 2023. https://doi.org/10.1042/bst20220221.","short":"F. Fäßler, M. Javoor, F.K. Schur, Biochemical Society Transactions 51 (2023) 87–99.","mla":"Fäßler, Florian, et al. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” Biochemical Society Transactions, vol. 51, no. 1, Portland Press, 2023, pp. 87–99, doi:10.1042/bst20220221."},"publication":"Biochemical Society Transactions","page":"87-99","article_type":"original","date_published":"2023-02-01T00:00:00Z"},{"citation":{"ama":"Marensi E, Yalniz G, Hof B, Budanur NB. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. 2023;954. doi:10.1017/jfm.2022.1001","apa":"Marensi, E., Yalniz, G., Hof, B., & Budanur, N. B. (2023). Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2022.1001","ieee":"E. Marensi, G. Yalniz, B. Hof, and N. B. Budanur, “Symmetry-reduced dynamic mode decomposition of near-wall turbulence,” Journal of Fluid Mechanics, vol. 954. Cambridge University Press, 2023.","ista":"Marensi E, Yalniz G, Hof B, Budanur NB. 2023. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. 954, A10.","short":"E. Marensi, G. Yalniz, B. Hof, N.B. Budanur, Journal of Fluid Mechanics 954 (2023).","mla":"Marensi, Elena, et al. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” Journal of Fluid Mechanics, vol. 954, A10, Cambridge University Press, 2023, doi:10.1017/jfm.2022.1001.","chicago":"Marensi, Elena, Gökhan Yalniz, Björn Hof, and Nazmi B Budanur. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” Journal of Fluid Mechanics. Cambridge University Press, 2023. https://doi.org/10.1017/jfm.2022.1001."},"publication":"Journal of Fluid Mechanics","article_type":"original","date_published":"2023-01-10T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"10","_id":"12105","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 954","ddc":["530"],"title":"Symmetry-reduced dynamic mode decomposition of near-wall turbulence","status":"public","oa_version":"Published Version","file":[{"success":1,"checksum":"9224f987caefe5dd85a70814d3cce65c","date_created":"2023-02-02T12:34:54Z","date_updated":"2023-02-02T12:34:54Z","file_id":"12489","relation":"main_file","creator":"dernst","file_size":1931647,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_JourFluidMechanics_Marensi.pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Data-driven dimensionality reduction methods such as proper orthogonal decomposition and dynamic mode decomposition have proven to be useful for exploring complex phenomena within fluid dynamics and beyond. A well-known challenge for these techniques is posed by the continuous symmetries, e.g. translations and rotations, of the system under consideration, as drifts in the data dominate the modal expansions without providing an insight into the dynamics of the problem. In the present study, we address this issue for fluid flows in rectangular channels by formulating a continuous symmetry reduction method that eliminates the translations in the streamwise and spanwise directions simultaneously. We demonstrate our method by computing the symmetry-reduced dynamic mode decomposition (SRDMD) of sliding windows of data obtained from the transitional plane-Couette and turbulent plane-Poiseuille flow simulations. In the former setting, SRDMD captures the dynamics in the vicinity of the invariant solutions with translation symmetries, i.e. travelling waves and relative periodic orbits, whereas in the latter, our calculations reveal episodes of turbulent time evolution that can be approximated by a low-dimensional linear expansion."}],"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":["2101.07516"],"isi":["000903336600001"]},"project":[{"name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","grant_number":"662960"}],"isi":1,"quality_controlled":"1","doi":"10.1017/jfm.2022.1001","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1469-7645"],"issn":["0022-1120"]},"month":"01","year":"2023","acknowledgement":"E.M. acknowledges funding from the ISTplus fellowship programme. G.Y. and B.H. acknowledge\r\na grant from the Simons Foundation (662960, BH).","department":[{"_id":"BjHo"}],"publisher":"Cambridge University Press","publication_status":"published","author":[{"first_name":"Elena","last_name":"Marensi","id":"0BE7553A-1004-11EA-B805-18983DDC885E","full_name":"Marensi, Elena"},{"full_name":"Yalniz, Gökhan","last_name":"Yalniz","first_name":"Gökhan","orcid":"0000-0002-8490-9312","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"},{"full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010","first_name":"Nazmi B","last_name":"Budanur"}],"volume":954,"date_created":"2023-01-08T23:00:53Z","date_updated":"2023-08-01T12:53:23Z","article_number":"A10","file_date_updated":"2023-02-02T12:34:54Z"},{"scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Evolution: International journal of organic evolution","citation":{"ieee":"D. I. Bolnick et al., “A multivariate view of the speciation continuum,” Evolution: International journal of organic evolution, vol. 77, no. 1. Oxford University Press, pp. 318–328, 2023.","apa":"Bolnick, D. I., Hund, A. K., Nosil, P., Peng, F., Ravinet, M., Stankowski, S., … Yukilevich, R. (2023). A multivariate view of the speciation continuum. Evolution: International Journal of Organic Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpac004","ista":"Bolnick DI, Hund AK, Nosil P, Peng F, Ravinet M, Stankowski S, Subramanian S, Wolf JBW, Yukilevich R. 2023. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 77(1), 318–328.","ama":"Bolnick DI, Hund AK, Nosil P, et al. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 2023;77(1):318-328. doi:10.1093/evolut/qpac004","chicago":"Bolnick, Daniel I., Amanda K. Hund, Patrik Nosil, Foen Peng, Mark Ravinet, Sean Stankowski, Swapna Subramanian, Jochen B.W. Wolf, and Roman Yukilevich. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution. Oxford University Press, 2023. https://doi.org/10.1093/evolut/qpac004.","short":"D.I. Bolnick, A.K. Hund, P. Nosil, F. Peng, M. Ravinet, S. Stankowski, S. Subramanian, J.B.W. Wolf, R. Yukilevich, Evolution: International Journal of Organic Evolution 77 (2023) 318–328.","mla":"Bolnick, Daniel I., et al. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution, vol. 77, no. 1, Oxford University Press, 2023, pp. 318–28, doi:10.1093/evolut/qpac004."},"article_type":"original","page":"318-328","date_published":"2023-01-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model."}],"issue":"1","_id":"12514","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"A multivariate view of the speciation continuum","intvolume":" 77","oa_version":"Published Version","month":"01","publication_identifier":{"eissn":["1558-5646"]},"external_id":{"pmid":["36622661"],"isi":["001021686300024"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1093/evolut/qpac004","open_access":"1"}],"quality_controlled":"1","isi":1,"doi":"10.1093/evolut/qpac004","language":[{"iso":"eng"}],"acknowledgement":"The authors of this article were supported by LMU Munich (J.B.W.W.), a James S. McDonnell Foundation postdoctoral fellowship (A.K.H.). P.N. received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant agreement No. 770826 EE-Dynamics).\r\nWe thank participants in the 2019 Gordon Conference on Speciation for the extensive conversation on this topic. Thanks to Dan Funk for providing permission to use data from Funk et al. 2006, and for comments on the manuscript.","year":"2023","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","author":[{"full_name":"Bolnick, Daniel I.","last_name":"Bolnick","first_name":"Daniel I."},{"last_name":"Hund","first_name":"Amanda K.","full_name":"Hund, Amanda K."},{"full_name":"Nosil, Patrik","last_name":"Nosil","first_name":"Patrik"},{"first_name":"Foen","last_name":"Peng","full_name":"Peng, Foen"},{"full_name":"Ravinet, Mark","first_name":"Mark","last_name":"Ravinet"},{"last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"full_name":"Subramanian, Swapna","first_name":"Swapna","last_name":"Subramanian"},{"full_name":"Wolf, Jochen B.W.","first_name":"Jochen B.W.","last_name":"Wolf"},{"first_name":"Roman","last_name":"Yukilevich","full_name":"Yukilevich, Roman"}],"date_created":"2023-02-05T23:00:59Z","date_updated":"2023-08-01T12:58:30Z","volume":77},{"file":[{"creator":"fkarimip","content_type":"application/pdf","file_size":1183339,"access_level":"open_access","file_name":"Visual Analysis_Mobility_COVID19 - SocDM2022.pdf","success":1,"checksum":"c253bee25e6dfe484f96662daa119cb6","date_updated":"2023-02-14T07:58:26Z","date_created":"2023-02-14T07:58:26Z","file_id":"12549","relation":"main_file"}],"oa_version":"Submitted Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12548","title":"Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic","ddc":["600"],"status":"public","abstract":[{"text":"The limited exchange between human communities is a key factor in preventing the spread of COVID-19. This paper introduces a digital framework that combines an integration of real mobility data at the country scale with a series of modeling techniques and visual capabilities that highlight mobility patterns before and during the pandemic. The findings not only significantly exhibit mobility trends and different degrees of similarities at regional and local levels but also provide potential insight into the emergence of a pandemic on human behavior patterns and their likely socio-economic impacts.","lang":"eng"}],"type":"conference","date_published":"2023-02-08T00:00:00Z","publication":"2022 IEEE International Conference on Data Mining Workshops","citation":{"mla":"Forghani, Mohammad, et al. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” 2022 IEEE International Conference on Data Mining Workshops, 00093, Institute of Electrical and Electronics Engineers, 2023, doi:10.1109/icdmw58026.2022.00093.","short":"M. Forghani, C. Claramunt, F. Karimipour, G. Heiler, in:, 2022 IEEE International Conference on Data Mining Workshops, Institute of Electrical and Electronics Engineers, 2023.","chicago":"Forghani, Mohammad, Christophe Claramunt, Farid Karimipour, and Georg Heiler. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” In 2022 IEEE International Conference on Data Mining Workshops. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/icdmw58026.2022.00093.","ama":"Forghani M, Claramunt C, Karimipour F, Heiler G. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In: 2022 IEEE International Conference on Data Mining Workshops. Institute of Electrical and Electronics Engineers; 2023. doi:10.1109/icdmw58026.2022.00093","ista":"Forghani M, Claramunt C, Karimipour F, Heiler G. 2023. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. 2022 IEEE International Conference on Data Mining Workshops. ICDMW: Conference on Data Mining Workshops, 00093.","apa":"Forghani, M., Claramunt, C., Karimipour, F., & Heiler, G. (2023). Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In 2022 IEEE International Conference on Data Mining Workshops. Orlando, FL, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/icdmw58026.2022.00093","ieee":"M. Forghani, C. Claramunt, F. Karimipour, and G. Heiler, “Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic,” in 2022 IEEE International Conference on Data Mining Workshops, Orlando, FL, United States, 2023."},"day":"08","article_processing_charge":"No","has_accepted_license":"1","author":[{"full_name":"Forghani, Mohammad","last_name":"Forghani","first_name":"Mohammad"},{"full_name":"Claramunt, Christophe","first_name":"Christophe","last_name":"Claramunt"},{"full_name":"Karimipour, Farid","first_name":"Farid","last_name":"Karimipour","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","orcid":"0000-0001-6746-4174"},{"full_name":"Heiler, Georg","last_name":"Heiler","first_name":"Georg"}],"date_created":"2023-02-14T07:56:21Z","date_updated":"2023-08-01T13:15:48Z","year":"2023","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Institute of Electrical and Electronics Engineers","file_date_updated":"2023-02-14T07:58:26Z","article_number":"00093","conference":{"end_date":"2022-12-01","start_date":"2022-11-28","location":"Orlando, FL, United States","name":"ICDMW: Conference on Data Mining Workshops"},"doi":"10.1109/icdmw58026.2022.00093","language":[{"iso":"eng"}],"external_id":{"isi":["000971492200145"]},"oa":1,"isi":1,"quality_controlled":"1","month":"02","publication_identifier":{"eissn":["2375-9259"],"eisbn":["9798350346091"]}},{"intvolume":" 52","status":"public","title":"Topology and adjunction in promise constraint satisfaction","_id":"12563","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","issue":"1","abstract":[{"text":"he approximate graph coloring problem, whose complexity is unresolved in most cases, concerns finding a c-coloring of a graph that is promised to be k-colorable, where c≥k. This problem naturally generalizes to promise graph homomorphism problems and further to promise constraint satisfaction problems. The complexity of these problems has recently been studied through an algebraic approach. In this paper, we introduce two new techniques to analyze the complexity of promise CSPs: one is based on topology and the other on adjunction. We apply these techniques, together with the previously introduced algebraic approach, to obtain new unconditional NP-hardness results for a significant class of approximate graph coloring and promise graph homomorphism problems.","lang":"eng"}],"page":"38-79","article_type":"original","citation":{"chicago":"Krokhin, Andrei, Jakub Opršal, Marcin Wrochna, and Stanislav Živný. “Topology and Adjunction in Promise Constraint Satisfaction.” SIAM Journal on Computing. Society for Industrial & Applied Mathematics, 2023. https://doi.org/10.1137/20m1378223.","short":"A. Krokhin, J. Opršal, M. Wrochna, S. Živný, SIAM Journal on Computing 52 (2023) 38–79.","mla":"Krokhin, Andrei, et al. “Topology and Adjunction in Promise Constraint Satisfaction.” SIAM Journal on Computing, vol. 52, no. 1, Society for Industrial & Applied Mathematics, 2023, pp. 38–79, doi:10.1137/20m1378223.","apa":"Krokhin, A., Opršal, J., Wrochna, M., & Živný, S. (2023). Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/20m1378223","ieee":"A. Krokhin, J. Opršal, M. Wrochna, and S. Živný, “Topology and adjunction in promise constraint satisfaction,” SIAM Journal on Computing, vol. 52, no. 1. Society for Industrial & Applied Mathematics, pp. 38–79, 2023.","ista":"Krokhin A, Opršal J, Wrochna M, Živný S. 2023. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 52(1), 38–79.","ama":"Krokhin A, Opršal J, Wrochna M, Živný S. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 2023;52(1):38-79. doi:10.1137/20m1378223"},"publication":"SIAM Journal on Computing","date_published":"2023-01-01T00:00:00Z","keyword":["General Mathematics","General Computer Science"],"scopus_import":"1","article_processing_charge":"No","day":"01","publisher":"Society for Industrial & Applied Mathematics","department":[{"_id":"UlWa"}],"publication_status":"published","year":"2023","acknowledgement":"Andrei Krokhin and Jakub Opršal were supported by the UK EPSRC grant EP/R034516/1. Jakub Opršal has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No 101034413. Stanislav Živný was supported by a Royal Society University Research Fellowship. 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 714532). The paper re\u001eects only the authors’ views and not the views of the ERC or the European Commission. ","volume":52,"date_updated":"2023-08-01T13:11:30Z","date_created":"2023-02-16T07:03:52Z","author":[{"first_name":"Andrei","last_name":"Krokhin","full_name":"Krokhin, Andrei"},{"full_name":"Opršal, Jakub","first_name":"Jakub","last_name":"Opršal","id":"ec596741-c539-11ec-b829-c79322a91242","orcid":"0000-0003-1245-3456"},{"full_name":"Wrochna, Marcin","first_name":"Marcin","last_name":"Wrochna"},{"last_name":"Živný","first_name":"Stanislav","full_name":"Živný, Stanislav"}],"ec_funded":1,"project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2003.11351"}],"external_id":{"isi":["000955000000001"],"arxiv":["2003.11351"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1137/20m1378223","publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"month":"01"},{"date_published":"2023-01-24T00:00:00Z","citation":{"chicago":"Rojas Vega, Mauricio Nicolas, Pablo De Castro, and Rodrigo Soto. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.014608.","mla":"Rojas Vega, Mauricio Nicolas, et al. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” Physical Review E, vol. 107, no. 1, 014608, American Physical Society, 2023, doi:10.1103/PhysRevE.107.014608.","short":"M.N. Rojas Vega, P. De Castro, R. Soto, Physical Review E 107 (2023).","ista":"Rojas Vega MN, De Castro P, Soto R. 2023. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 107(1), 014608.","apa":"Rojas Vega, M. N., De Castro, P., & Soto, R. (2023). Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.014608","ieee":"M. N. Rojas Vega, P. De Castro, and R. Soto, “Wetting dynamics by mixtures of fast and slow self-propelled particles,” Physical Review E, vol. 107, no. 1. American Physical Society, 2023.","ama":"Rojas Vega MN, De Castro P, Soto R. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 2023;107(1). doi:10.1103/PhysRevE.107.014608"},"publication":"Physical Review E","article_type":"original","article_processing_charge":"No","day":"24","scopus_import":"1","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12545","intvolume":" 107","status":"public","title":"Wetting dynamics by mixtures of fast and slow self-propelled particles","issue":"1","abstract":[{"text":"We study active surface wetting using a minimal model of bacteria that takes into account the intrinsic motility diversity of living matter. A mixture of “fast” and “slow” self-propelled Brownian particles is considered in the presence of a wall. The evolution of the wetting layer thickness shows an overshoot before stationarity and its composition evolves in two stages, equilibrating after a slow elimination of excess particles. Nonmonotonic evolutions are shown to arise from delayed avalanches towards the dilute phase combined with the emergence of a transient particle front.","lang":"eng"}],"type":"journal_article","doi":"10.1103/PhysRevE.107.014608","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.01856"}],"external_id":{"arxiv":["2301.01856"],"isi":["000963909800006"]},"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"month":"01","author":[{"first_name":"Mauricio Nicolas","last_name":"Rojas Vega","id":"441e7207-f91f-11ec-b67c-9e6fe3d8fd6d","full_name":"Rojas Vega, Mauricio Nicolas"},{"full_name":"De Castro, Pablo","last_name":"De Castro","first_name":"Pablo"},{"full_name":"Soto, Rodrigo","first_name":"Rodrigo","last_name":"Soto"}],"volume":107,"date_updated":"2023-08-01T13:09:45Z","date_created":"2023-02-12T23:00:59Z","acknowledgement":"MR-V and RS are supported by Fondecyt Grant No. 1220536 and ANID – Millennium Science Initiative Program – NCN19 170D, Chile. PdC is supported by grant #2021/10139-2, Sao Paulo Research Foundation (FAPESP), Brazil.","year":"2023","publisher":"American Physical Society","department":[{"_id":"GradSch"}],"publication_status":"published","article_number":"014608"},{"date_published":"2023-01-01T00:00:00Z","citation":{"ista":"Balestrieri F. 2023. Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. 151(3), 907–914.","apa":"Balestrieri, F. (2023). Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/15239","ieee":"F. Balestrieri, “Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups,” Proceedings of the American Mathematical Society, vol. 151, no. 3. American Mathematical Society, pp. 907–914, 2023.","ama":"Balestrieri F. Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. 2023;151(3):907-914. doi:10.1090/proc/15239","chicago":"Balestrieri, Francesca. “Some Remarks on Strong Approximation and Applications to Homogeneous Spaces of Linear Algebraic Groups.” Proceedings of the American Mathematical Society. American Mathematical Society, 2023. https://doi.org/10.1090/proc/15239.","mla":"Balestrieri, Francesca. “Some Remarks on Strong Approximation and Applications to Homogeneous Spaces of Linear Algebraic Groups.” Proceedings of the American Mathematical Society, vol. 151, no. 3, American Mathematical Society, 2023, pp. 907–14, doi:10.1090/proc/15239.","short":"F. Balestrieri, Proceedings of the American Mathematical Society 151 (2023) 907–914."},"publication":"Proceedings of the American Mathematical Society","page":"907-914","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12427","intvolume":" 151","title":"Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups","status":"public","issue":"3","abstract":[{"lang":"eng","text":"Let k be a number field and X a smooth, geometrically integral quasi-projective variety over k. For any linear algebraic group G over k and any G-torsor g : Z → X, we observe that if the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for all twists of Z by elements in H^1(k, G), then the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for X. As an application, we show that any homogeneous space of the form G/H with G a connected linear algebraic group over k satisfies strong approximation off the infinite places with étale-Brauer obstruction, under some compactness assumptions when k is totally real. We also prove more refined strong approximation results for homogeneous spaces of the form G/H with G semisimple simply connected and H finite, using the theory of torsors and descent."}],"type":"journal_article","doi":"10.1090/proc/15239","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://hal.science/hal-03013498/","open_access":"1"}],"external_id":{"isi":["000898440000001"]},"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1088-6826"],"issn":["0002-9939"]},"month":"01","author":[{"full_name":"Balestrieri, Francesca","id":"3ACCD756-F248-11E8-B48F-1D18A9856A87","first_name":"Francesca","last_name":"Balestrieri"}],"volume":151,"date_updated":"2023-08-01T13:03:32Z","date_created":"2023-01-29T23:00:58Z","year":"2023","department":[{"_id":"TiBr"}],"publisher":"American Mathematical Society","publication_status":"published"},{"publication_identifier":{"eissn":["1422-0067"]},"month":"01","doi":"10.3390/ijms24032128","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":{"isi":["000930324700001"]},"isi":1,"quality_controlled":"1","file_date_updated":"2023-02-20T07:09:27Z","article_number":"2128","author":[{"last_name":"Mrestani","first_name":"Achmed","full_name":"Mrestani, Achmed"},{"id":"39302e62-fcfc-11ec-8196-8b01447dbd3d","first_name":"Katharina","last_name":"Lichter","full_name":"Lichter, Katharina"},{"first_name":"Anna Leena","last_name":"Sirén","full_name":"Sirén, Anna Leena"},{"last_name":"Heckmann","first_name":"Manfred","full_name":"Heckmann, Manfred"},{"full_name":"Paul, Mila M.","last_name":"Paul","first_name":"Mila M."},{"full_name":"Pauli, Martin","first_name":"Martin","last_name":"Pauli"}],"volume":24,"date_created":"2023-02-19T23:00:56Z","date_updated":"2023-08-01T13:16:36Z","acknowledgement":"This work has been supported by funding of the German Research Foundation (Deutsche Forschungsgemeinschaft [DFG], CRC 166, Project B06 to M.H. and A.-L.S., FOR 3004 SYNABS P1 to M.H.) and by the Interdisciplinary Clinical Research Center (IZKF) Würzburg (Z-3/69 to M.M.P., N-229 to M.H. and A.-L.S.). A.M. is funded by the University of Leipzig Clinician Scientist Program.","year":"2023","publisher":"MDPI","department":[{"_id":"PeJo"}],"publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"21","scopus_import":"1","date_published":"2023-01-21T00:00:00Z","citation":{"ama":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 2023;24(3). doi:10.3390/ijms24032128","ista":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. 2023. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 24(3), 2128.","apa":"Mrestani, A., Lichter, K., Sirén, A. L., Heckmann, M., Paul, M. M., & Pauli, M. (2023). Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms24032128","ieee":"A. Mrestani, K. Lichter, A. L. Sirén, M. Heckmann, M. M. Paul, and M. Pauli, “Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation,” International Journal of Molecular Sciences, vol. 24, no. 3. MDPI, 2023.","mla":"Mrestani, Achmed, et al. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International Journal of Molecular Sciences, vol. 24, no. 3, 2128, MDPI, 2023, doi:10.3390/ijms24032128.","short":"A. Mrestani, K. Lichter, A.L. Sirén, M. Heckmann, M.M. Paul, M. Pauli, International Journal of Molecular Sciences 24 (2023).","chicago":"Mrestani, Achmed, Katharina Lichter, Anna Leena Sirén, Manfred Heckmann, Mila M. Paul, and Martin Pauli. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International Journal of Molecular Sciences. MDPI, 2023. https://doi.org/10.3390/ijms24032128."},"publication":"International Journal of Molecular Sciences","article_type":"original","issue":"3","abstract":[{"lang":"eng","text":"Single-molecule localization microscopy (SMLM) greatly advances structural studies of diverse biological tissues. For example, presynaptic active zone (AZ) nanotopology is resolved in increasing detail. Immunofluorescence imaging of AZ proteins usually relies on epitope preservation using aldehyde-based immunocompetent fixation. Cryofixation techniques, such as high-pressure freezing (HPF) and freeze substitution (FS), are widely used for ultrastructural studies of presynaptic architecture in electron microscopy (EM). HPF/FS demonstrated nearer-to-native preservation of AZ ultrastructure, e.g., by facilitating single filamentous structures. Here, we present a protocol combining the advantages of HPF/FS and direct stochastic optical reconstruction microscopy (dSTORM) to quantify nanotopology of the AZ scaffold protein Bruchpilot (Brp) at neuromuscular junctions (NMJs) of Drosophila melanogaster. Using this standardized model, we tested for preservation of Brp clusters in different FS protocols compared to classical aldehyde fixation. In HPF/FS samples, presynaptic boutons were structurally well preserved with ~22% smaller Brp clusters that allowed quantification of subcluster topology. In summary, we established a standardized near-to-native preparation and immunohistochemistry protocol for SMLM analyses of AZ protein clusters in a defined model synapse. Our protocol could be adapted to study protein arrangements at single-molecule resolution in other intact tissue preparations."}],"type":"journal_article","file":[{"date_updated":"2023-02-20T07:09:27Z","date_created":"2023-02-20T07:09:27Z","checksum":"69a35dcd3e0249f902ab881b06ee2e58","success":1,"relation":"main_file","file_id":"12569","content_type":"application/pdf","file_size":2823025,"creator":"dernst","file_name":"2023_IJMS_Mrestani.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12567","intvolume":" 24","ddc":["570"],"status":"public","title":"Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation"},{"publication_identifier":{"issn":["0304-3975"]},"month":"02","language":[{"iso":"eng"}],"doi":"10.1016/j.tcs.2023.113733","project":[{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"},{"name":"Coordination in constrained and natural distributed systems","call_identifier":"H2020","grant_number":"840605","_id":"26A5D39A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000934262700001"]},"ec_funded":1,"file_date_updated":"2023-02-20T07:30:20Z","article_number":"113733","volume":948,"date_updated":"2023-08-01T13:17:20Z","date_created":"2023-02-19T23:00:55Z","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Ellen, Faith","first_name":"Faith","last_name":"Ellen"},{"last_name":"Rybicki","first_name":"Joel","orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","full_name":"Rybicki, Joel"}],"department":[{"_id":"DaAl"}],"publisher":"Elsevier","publication_status":"published","year":"2023","acknowledgement":"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. 805223 ScaleML) and under the Marie Skłodowska-Curie grant agreement No. 840605 and from the Natural Sciences and Engineering Research Council of Canada grant RGPIN-2020-04178. Part of this work was done while Faith Ellen was visiting IST Austria.","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"28","scopus_import":"1","date_published":"2023-02-28T00:00:00Z","article_type":"original","citation":{"short":"D.-A. Alistarh, F. Ellen, J. Rybicki, Theoretical Computer Science 948 (2023).","mla":"Alistarh, Dan-Adrian, et al. “Wait-Free Approximate Agreement on Graphs.” Theoretical Computer Science, vol. 948, no. 2, 113733, Elsevier, 2023, doi:10.1016/j.tcs.2023.113733.","chicago":"Alistarh, Dan-Adrian, Faith Ellen, and Joel Rybicki. “Wait-Free Approximate Agreement on Graphs.” Theoretical Computer Science. Elsevier, 2023. https://doi.org/10.1016/j.tcs.2023.113733.","ama":"Alistarh D-A, Ellen F, Rybicki J. Wait-free approximate agreement on graphs. Theoretical Computer Science. 2023;948(2). doi:10.1016/j.tcs.2023.113733","apa":"Alistarh, D.-A., Ellen, F., & Rybicki, J. (2023). Wait-free approximate agreement on graphs. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2023.113733","ieee":"D.-A. Alistarh, F. Ellen, and J. Rybicki, “Wait-free approximate agreement on graphs,” Theoretical Computer Science, vol. 948, no. 2. Elsevier, 2023.","ista":"Alistarh D-A, Ellen F, Rybicki J. 2023. Wait-free approximate agreement on graphs. Theoretical Computer Science. 948(2), 113733."},"publication":"Theoretical Computer Science","issue":"2","abstract":[{"lang":"eng","text":"Approximate agreement is one of the few variants of consensus that can be solved in a wait-free manner in asynchronous systems where processes communicate by reading and writing to shared memory. In this work, we consider a natural generalisation of approximate agreement on arbitrary undirected connected graphs. Each process is given a node of the graph as input and, if non-faulty, must output a node such that\r\n– all the outputs are within distance 1 of one another, and\r\n– each output value lies on a shortest path between two input values.\r\nFrom prior work, it is known that there is no wait-free algorithm among processes for this problem on any cycle of length , by reduction from 2-set agreement (Castañeda et al., 2018).\r\n\r\nIn this work, we investigate the solvability of this task on general graphs. We give a new, direct proof of the impossibility of approximate agreement on cycles of length , via a generalisation of Sperner's Lemma to convex polygons. We also extend the reduction from 2-set agreement to a larger class of graphs, showing that approximate agreement on these graphs is unsolvable. On the positive side, we present a wait-free algorithm for a different class of graphs, which properly contains the class of chordal graphs."}],"type":"journal_article","file":[{"creator":"dernst","content_type":"application/pdf","file_size":602333,"access_level":"open_access","file_name":"2023_TheoreticalCompScience_Alistarh.pdf","success":1,"checksum":"b27c5290f2f1500c403494364ee39c9f","date_updated":"2023-02-20T07:30:20Z","date_created":"2023-02-20T07:30:20Z","file_id":"12570","relation":"main_file"}],"oa_version":"Published Version","intvolume":" 948","ddc":["000"],"title":"Wait-free approximate agreement on graphs","status":"public","_id":"12566","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000915418100026"]},"quality_controlled":"1","isi":1,"doi":"10.1146/annurev-fluid-032822-025933","language":[{"iso":"eng"}],"month":"01","publication_identifier":{"issn":["0066-4189"],"eissn":["1545-4479"]},"year":"2023","acknowledgement":"Part of the material presented here is based upon work supported by the National Science Foundation CBET (Chemical, Bioengineering, Environmental and Transport Systems) award 1805636 (to Y.D.), the Binational Science Foundation award 2016145 (to Y.D. and Victor Steinberg), a FRIA (Fund for Research Training in Industry and Agriculture) grant of the Belgian F.R.S.-FNRS (National Fund for Scientific Research) (to V.E.T.), the Marie Curie FP7 Career Integration grant PCIG10-GA-2011-304073 (to V.E.T.), and the Fonds spéciaux pour la recherche grant C-13/19 of the University of Liege (to V.E.T.). Computational resources have been provided by the Consortium des Équipements de Calcul Intensif (CECI) funded by the Belgian F.R.S.-FNRS, the Vermont Advanced Computing Center (VACC), the Partnership for Advanced Computing in Europe (PRACE), and the Tier-1 supercomputer of the Fédération Wallonie-Bruxelles funded by the Walloon Region (grant agreement 117545).","publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"Annual Reviews","author":[{"full_name":"Dubief, Yves","first_name":"Yves","last_name":"Dubief"},{"last_name":"Terrapon","first_name":"Vincent E.","full_name":"Terrapon, Vincent E."},{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"date_updated":"2023-08-01T13:19:47Z","date_created":"2023-02-26T23:01:01Z","volume":55,"file_date_updated":"2023-02-27T09:23:02Z","publication":"Annual Review of Fluid Mechanics","citation":{"mla":"Dubief, Yves, et al. “Elasto-Inertial Turbulence.” Annual Review of Fluid Mechanics, vol. 55, no. 1, Annual Reviews, 2023, pp. 675–705, doi:10.1146/annurev-fluid-032822-025933.","short":"Y. Dubief, V.E. Terrapon, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 675–705.","chicago":"Dubief, Yves, Vincent E. Terrapon, and Björn Hof. “Elasto-Inertial Turbulence.” Annual Review of Fluid Mechanics. Annual Reviews, 2023. https://doi.org/10.1146/annurev-fluid-032822-025933.","ama":"Dubief Y, Terrapon VE, Hof B. Elasto-inertial turbulence. Annual Review of Fluid Mechanics. 2023;55(1):675-705. doi:10.1146/annurev-fluid-032822-025933","ista":"Dubief Y, Terrapon VE, Hof B. 2023. Elasto-inertial turbulence. Annual Review of Fluid Mechanics. 55(1), 675–705.","ieee":"Y. Dubief, V. E. Terrapon, and B. Hof, “Elasto-inertial turbulence,” Annual Review of Fluid Mechanics, vol. 55, no. 1. Annual Reviews, pp. 675–705, 2023.","apa":"Dubief, Y., Terrapon, V. E., & Hof, B. (2023). Elasto-inertial turbulence. Annual Review of Fluid Mechanics. Annual Reviews. https://doi.org/10.1146/annurev-fluid-032822-025933"},"article_type":"original","page":"675-705","date_published":"2023-01-19T00:00:00Z","scopus_import":"1","day":"19","has_accepted_license":"1","article_processing_charge":"No","_id":"12681","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["530"],"status":"public","title":"Elasto-inertial turbulence","intvolume":" 55","oa_version":"Published Version","file":[{"success":1,"checksum":"2666aa3af2a25252d35eb8681d3edff7","date_created":"2023-02-27T09:23:02Z","date_updated":"2023-02-27T09:23:02Z","file_id":"12690","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":4036706,"access_level":"open_access","file_name":"2023_AnnReviewFluidMech_Dubief.pdf"}],"type":"journal_article","abstract":[{"text":"The dissolution of minute concentration of polymers in wall-bounded flows is well-known for its unparalleled ability to reduce turbulent friction drag. Another phenomenon, elasto-inertial turbulence (EIT), has been far less studied even though elastic instabilities have already been observed in dilute polymer solutions before the discovery of polymer drag reduction. EIT is a chaotic state driven by polymer dynamics that is observed across many orders of magnitude in Reynolds number. It involves energy transfer from small elastic scales to large flow scales. The investigation of the mechanisms of EIT offers the possibility to better understand other complex phenomena such as elastic turbulence and maximum drag reduction. In this review, we survey recent research efforts that are advancing the understanding of the dynamics of EIT. We highlight the fundamental differences between EIT and Newtonian/inertial turbulence from the perspective of experiments, numerical simulations, instabilities, and coherent structures. Finally, we discuss the possible links between EIT and elastic turbulence and polymer drag reduction, as well as the remaining challenges in unraveling the self-sustaining mechanism of EIT.","lang":"eng"}],"issue":"1"},{"page":"575-602","article_type":"original","citation":{"ama":"Avila M, Barkley D, Hof B. Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. 2023;55:575-602. doi:10.1146/annurev-fluid-120720-025957","apa":"Avila, M., Barkley, D., & Hof, B. (2023). Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. Annual Reviews. https://doi.org/10.1146/annurev-fluid-120720-025957","ieee":"M. Avila, D. Barkley, and B. Hof, “Transition to turbulence in pipe flow,” Annual Review of Fluid Mechanics, vol. 55. Annual Reviews, pp. 575–602, 2023.","ista":"Avila M, Barkley D, Hof B. 2023. Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. 55, 575–602.","short":"M. Avila, D. Barkley, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 575–602.","mla":"Avila, Marc, et al. “Transition to Turbulence in Pipe Flow.” Annual Review of Fluid Mechanics, vol. 55, Annual Reviews, 2023, pp. 575–602, doi:10.1146/annurev-fluid-120720-025957.","chicago":"Avila, Marc, Dwight Barkley, and Björn Hof. “Transition to Turbulence in Pipe Flow.” Annual Review of Fluid Mechanics. Annual Reviews, 2023. https://doi.org/10.1146/annurev-fluid-120720-025957."},"publication":"Annual Review of Fluid Mechanics","date_published":"2023-01-19T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"19","intvolume":" 55","title":"Transition to turbulence in pipe flow","ddc":["530"],"status":"public","_id":"12682","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_updated":"2023-02-27T09:35:52Z","date_created":"2023-02-27T09:35:52Z","checksum":"f99ef30f76cabc9e5e1946b380c16db4","success":1,"relation":"main_file","file_id":"12691","content_type":"application/pdf","file_size":4769537,"creator":"dernst","file_name":"2023_AnnReviewFluidMech_Avila.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Since the seminal studies by Osborne Reynolds in the nineteenth century, pipe flow has served as a primary prototype for investigating the transition to turbulence in wall-bounded flows. Despite the apparent simplicity of this flow, various facets of this problem have occupied researchers for more than a century. Here we review insights from three distinct perspectives: (a) stability and susceptibility of laminar flow, (b) phase transition and spatiotemporal dynamics, and (c) dynamical systems analysis of the Navier—Stokes equations. We show how these perspectives have led to a profound understanding of the onset of turbulence in pipe flow. Outstanding open points, applications to flows of complex fluids, and similarities with other wall-bounded flows are discussed.","lang":"eng"}],"project":[{"grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000915418100023"]},"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":"10.1146/annurev-fluid-120720-025957","publication_identifier":{"issn":["0066-4189"]},"month":"01","department":[{"_id":"BjHo"}],"publisher":"Annual Reviews","publication_status":"published","year":"2023","acknowledgement":"The authors are very grateful to Laurette Tuckerman for her helpful comments. This work was supported by grants from the Simons Foundation (grant numbers 662985, D.B., and 662960, B.H.) and the Priority Programme “SPP 1881: Turbulent Superstructures” of the Deutsche Forschungsgemeinschaft (grant number AV120/3-2 to M.A.).","volume":55,"date_updated":"2023-08-01T13:20:30Z","date_created":"2023-02-26T23:01:01Z","author":[{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"},{"full_name":"Barkley, Dwight","first_name":"Dwight","last_name":"Barkley"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"}],"file_date_updated":"2023-02-27T09:35:52Z"},{"ec_funded":1,"file_date_updated":"2023-03-07T09:19:41Z","year":"2023","acknowledgement":"All authors are grateful to the Lorentz Center for providing a venue for stimulating scientific discussions and to sponsor a workshop on the topic of “Self-organisation under confinement” along with the 4TU Federation, the J. M. Burgers Center for Fluid Dynamics and the MESA+ Institute for Nanotechnology at the University of Twente. The authors are also grateful to Paolo Malgaretti, Federico Toschi, Twan Wilting and Jaap den Toonder for valuable feedback. N. A. acknowledges financial support from the Portuguese Foundation for Science and Technology (FCT) under Contracts no. PTDC/FIS-MAC/28146/2017 (LISBOA-01-0145-FEDER-028146), UIDB/00618/2020, and UIDP/00618/2020. L. M. C. J. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through a START-UP, Physics Projectruimte, and Vidi grant. I. C. was supported in part by a grant from by the Army Research Office (ARO W911NF-18-1-0032) and the Cornell Center for Materials Research (DMR-1719875). O. D. acknowledges funding by the Agence Nationale pour la Recherche under Grant No ANR-18-CE33-0006 MSR. M. D. acknowledges financial support from the European Research Council (Grant No. ERC-2019-ADV-H2020 884902 SoftML). W. M. D. acknowledges funding from a BBSRC New Investigator Grant (BB/R018383/1). S. G. was supported by DARPA Young Faculty Award # D19AP00046, and NSF IIS grant # 1955210. H. G. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through Veni Grant No. 680-47-451. R. G. acknowledges support from the Max Planck School Matter to Life and the MaxSynBio Consortium, which are jointly funded by the Federal Ministry of Education and Research (BMBF) of Germany, and the Max Planck Society. L. I. acknowledges funding from the Horizon Europe ERC Consolidator Grant ACTIVE_ ADAPTIVE (Grant No. 101001514). G. H. K. gratefully acknowledges the NWO Talent Programme which is financed by the Dutch Research Council (project number VI.C.182.004). H. L. and N. V. acknowledge funding from the Deutsche Forschungsgemeinschaft (DFG) under grant numbers VO 1824/8-1 and LO 418/22-1. R. M. acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG) under grant number ME 1535/13-1 and ME 1535/16-1. M. P. acknowledges funding from the Ramón y Cajal Program, grant no. RYC-2018-02534, and the Leverhulme Trust, grant no. RPG-2018-345. A. Š. acknowledges financial support from the European Research Council (Grant No. ERC-2018-STG-H2020 802960 NEPA). A. S. acknowledges funding from an ATTRACT Investigator Grant (No. A17/MS/11572821/MBRACE) from the Luxembourg National Research Fund. C. S. acknowledges funding from the French Agence Nationale pour la Recherche (ANR), grant ANR-14-CE090006 and ANR-12-BSV5001401, by the Fondation pour la Recherche Médicale (FRM), grant DEQ20120323737, and from the PIC3I of Institut Curie, France. I. T. acknowledges funding from grant IED2019-00058I/AEI/10.13039/501100011033. M. P. and I. T. also acknowledge funding from grant PID2019-104232B-I00/AEI/10.13039/501100011033 and from the H2020 MSCA ITN PHYMOT (Grant agreement No 95591). I. Z. acknowledges funding from Project PID2020-114839GB-I00 MINECO/AEI/FEDER, UE. A. M. acknowledges funding from the European Research Council, Starting Grant No. 678573 NanoPacks. G. V. acknowledges sponsorship for this work by the US Office of Naval Research Global (Award No. N62909-18-1-2170).","publisher":"Royal Society of Chemistry","department":[{"_id":"AnSa"}],"publication_status":"published","author":[{"last_name":"Araújo","first_name":"Nuno A.M.","full_name":"Araújo, Nuno A.M."},{"first_name":"Liesbeth M.C.","last_name":"Janssen","full_name":"Janssen, Liesbeth M.C."},{"last_name":"Barois","first_name":"Thomas","full_name":"Barois, Thomas"},{"full_name":"Boffetta, Guido","last_name":"Boffetta","first_name":"Guido"},{"full_name":"Cohen, Itai","last_name":"Cohen","first_name":"Itai"},{"full_name":"Corbetta, Alessandro","last_name":"Corbetta","first_name":"Alessandro"},{"last_name":"Dauchot","first_name":"Olivier","full_name":"Dauchot, Olivier"},{"full_name":"Dijkstra, Marjolein","first_name":"Marjolein","last_name":"Dijkstra"},{"last_name":"Durham","first_name":"William M.","full_name":"Durham, William M."},{"last_name":"Dussutour","first_name":"Audrey","full_name":"Dussutour, Audrey"},{"full_name":"Garnier, Simon","first_name":"Simon","last_name":"Garnier"},{"full_name":"Gelderblom, Hanneke","first_name":"Hanneke","last_name":"Gelderblom"},{"last_name":"Golestanian","first_name":"Ramin","full_name":"Golestanian, Ramin"},{"full_name":"Isa, Lucio","last_name":"Isa","first_name":"Lucio"},{"first_name":"Gijsje H.","last_name":"Koenderink","full_name":"Koenderink, Gijsje H."},{"full_name":"Löwen, Hartmut","first_name":"Hartmut","last_name":"Löwen"},{"first_name":"Ralf","last_name":"Metzler","full_name":"Metzler, Ralf"},{"last_name":"Polin","first_name":"Marco","full_name":"Polin, Marco"},{"full_name":"Royall, C. Patrick","last_name":"Royall","first_name":"C. Patrick"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela"},{"full_name":"Sengupta, Anupam","last_name":"Sengupta","first_name":"Anupam"},{"full_name":"Sykes, Cécile","last_name":"Sykes","first_name":"Cécile"},{"full_name":"Trianni, Vito","first_name":"Vito","last_name":"Trianni"},{"full_name":"Tuval, Idan","first_name":"Idan","last_name":"Tuval"},{"full_name":"Vogel, Nicolas","first_name":"Nicolas","last_name":"Vogel"},{"last_name":"Yeomans","first_name":"Julia M.","full_name":"Yeomans, Julia M."},{"last_name":"Zuriguel","first_name":"Iker","full_name":"Zuriguel, Iker"},{"full_name":"Marin, Alvaro","first_name":"Alvaro","last_name":"Marin"},{"full_name":"Volpe, Giorgio","last_name":"Volpe","first_name":"Giorgio"}],"volume":19,"date_updated":"2023-08-01T13:28:39Z","date_created":"2023-03-05T23:01:06Z","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"month":"02","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":["2204.10059"],"isi":["000940388100001"]},"project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"quality_controlled":"1","isi":1,"doi":"10.1039/d2sm01562e","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has highlighted how self-organisation can be both mediated and controlled by confinement. Confinement is an action over a system that limits its units’ translational and rotational degrees of freedom, thus also influencing the system's phase space probability density; it can function as either a catalyst or inhibitor of self-organisation. Confinement can then become a means to actively steer the emergence or suppression of collective phenomena in space and time. Here, to provide a common framework and perspective for future research, we examine the role of confinement in the self-organisation of soft-matter systems and identify overarching scientific challenges that need to be addressed to harness its full scientific and technological potential in soft matter and related fields. By drawing analogies with other disciplines, this framework will accelerate a common deeper understanding of self-organisation and trigger the development of innovative strategies to steer it using confinement, with impact on, e.g., the design of smarter materials, tissue engineering for biomedicine and in guiding active matter."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12708","intvolume":" 19","title":"Steering self-organisation through confinement","ddc":["540"],"status":"public","file":[{"creator":"cchlebak","file_size":3581939,"content_type":"application/pdf","file_name":"2023_SoftMatter_Araujo.pdf","access_level":"open_access","date_updated":"2023-03-07T09:19:41Z","date_created":"2023-03-07T09:19:41Z","success":1,"checksum":"af95aa18b9b01e32fb8f13477c0e2687","file_id":"12711","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"06","citation":{"ama":"Araújo NAM, Janssen LMC, Barois T, et al. Steering self-organisation through confinement. Soft Matter. 2023;19:1695-1704. doi:10.1039/d2sm01562e","ieee":"N. A. M. Araújo et al., “Steering self-organisation through confinement,” Soft Matter, vol. 19. Royal Society of Chemistry, pp. 1695–1704, 2023.","apa":"Araújo, N. A. M., Janssen, L. M. C., Barois, T., Boffetta, G., Cohen, I., Corbetta, A., … Volpe, G. (2023). Steering self-organisation through confinement. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d2sm01562e","ista":"Araújo NAM, Janssen LMC, Barois T, Boffetta G, Cohen I, Corbetta A, Dauchot O, Dijkstra M, Durham WM, Dussutour A, Garnier S, Gelderblom H, Golestanian R, Isa L, Koenderink GH, Löwen H, Metzler R, Polin M, Royall CP, Šarić A, Sengupta A, Sykes C, Trianni V, Tuval I, Vogel N, Yeomans JM, Zuriguel I, Marin A, Volpe G. 2023. Steering self-organisation through confinement. Soft Matter. 19, 1695–1704.","short":"N.A.M. Araújo, L.M.C. Janssen, T. Barois, G. Boffetta, I. Cohen, A. Corbetta, O. Dauchot, M. Dijkstra, W.M. Durham, A. Dussutour, S. Garnier, H. Gelderblom, R. Golestanian, L. Isa, G.H. Koenderink, H. Löwen, R. Metzler, M. Polin, C.P. Royall, A. Šarić, A. Sengupta, C. Sykes, V. Trianni, I. Tuval, N. Vogel, J.M. Yeomans, I. Zuriguel, A. Marin, G. Volpe, Soft Matter 19 (2023) 1695–1704.","mla":"Araújo, Nuno A. M., et al. “Steering Self-Organisation through Confinement.” Soft Matter, vol. 19, Royal Society of Chemistry, 2023, pp. 1695–704, doi:10.1039/d2sm01562e.","chicago":"Araújo, Nuno A.M., Liesbeth M.C. Janssen, Thomas Barois, Guido Boffetta, Itai Cohen, Alessandro Corbetta, Olivier Dauchot, et al. “Steering Self-Organisation through Confinement.” Soft Matter. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d2sm01562e."},"publication":"Soft Matter","page":"1695-1704","article_type":"original","date_published":"2023-02-06T00:00:00Z"},{"publication_identifier":{"eissn":["2041-1723"]},"month":"02","project":[{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}],"quality_controlled":"1","isi":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":["36843123"],"isi":["000939678300002"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-36841-1","article_number":"1104","file_date_updated":"2023-03-07T10:58:00Z","publisher":"Springer Nature","department":[{"_id":"BiCh"}],"publication_status":"published","pmid":1,"year":"2023","acknowledgement":"BC thanks Daan Frenkel for stimulating discussions. We thank Aleks Reinhardt, Daan Frenkel, Marius Millot, Federica Coppari, Rhys Bunting, and Chris J. Pickard for critically reading the manuscript and providing useful suggestions. BC acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital grant EP/P020259/1. SH acknowledges support from LDRD 19-ERD-031 and computing support from the Lawrence Livermore National Laboratory (LLNL) Institutional Computing Grand Challenge program. Lawrence Livermore National Laboratory is operated by Lawrence Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear Security Administration under Contract DE-AC52-07NA27344. MB acknowledges support by the European Horizon 2020 program within the Marie Skłodowska-Curie actions (xICE grant number 894725), funding from the NOMIS foundation and computational resources at the North-German Supercomputing Alliance (HLRN) facilities.","volume":14,"date_updated":"2023-08-01T13:36:11Z","date_created":"2023-03-05T23:01:04Z","author":[{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","first_name":"Bingqing"},{"full_name":"Hamel, Sebastien","last_name":"Hamel","first_name":"Sebastien"},{"id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","orcid":"0000-0002-1838-2129","first_name":"Mandy","last_name":"Bethkenhagen","full_name":"Bethkenhagen, Mandy"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"27","article_type":"original","citation":{"ieee":"B. Cheng, S. Hamel, and M. Bethkenhagen, “Thermodynamics of diamond formation from hydrocarbon mixtures in planets,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Cheng, B., Hamel, S., & Bethkenhagen, M. (2023). Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-36841-1","ista":"Cheng B, Hamel S, Bethkenhagen M. 2023. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. 14, 1104.","ama":"Cheng B, Hamel S, Bethkenhagen M. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. 2023;14. doi:10.1038/s41467-023-36841-1","chicago":"Cheng, Bingqing, Sebastien Hamel, and Mandy Bethkenhagen. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-36841-1.","short":"B. Cheng, S. Hamel, M. Bethkenhagen, Nature Communications 14 (2023).","mla":"Cheng, Bingqing, et al. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” Nature Communications, vol. 14, 1104, Springer Nature, 2023, doi:10.1038/s41467-023-36841-1."},"publication":"Nature Communications","date_published":"2023-02-27T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Hydrocarbon mixtures are extremely abundant in the Universe, and diamond formation from them can play a crucial role in shaping the interior structure and evolution of planets. With first-principles accuracy, we first estimate the melting line of diamond, and then reveal the nature of chemical bonding in hydrocarbons at extreme conditions. We finally establish the pressure-temperature phase boundary where it is thermodynamically possible for diamond to form from hydrocarbon mixtures with different atomic fractions of carbon. Notably, here we show a depletion zone at pressures above 200 GPa and temperatures below 3000 K-3500 K where diamond formation is thermodynamically favorable regardless of the carbon atomic fraction, due to a phase separation mechanism. The cooler condition of the interior of Neptune compared to Uranus means that the former is much more likely to contain the depletion zone. Our findings can help explain the dichotomy of the two ice giants manifested by the low luminosity of Uranus, and lead to a better understanding of (exo-)planetary formation and evolution."}],"intvolume":" 14","status":"public","ddc":["540"],"title":"Thermodynamics of diamond formation from hydrocarbon mixtures in planets","_id":"12702","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":1946443,"creator":"cchlebak","access_level":"open_access","file_name":"2023_NatComm_Cheng.pdf","checksum":"5ff61ad21511950c15abb73b18613883","success":1,"date_created":"2023-03-07T10:58:00Z","date_updated":"2023-03-07T10:58:00Z","relation":"main_file","file_id":"12713"}]},{"publication_identifier":{"eissn":["1756-994X"]},"month":"02","isi":1,"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":{"isi":["000940286600001"]},"language":[{"iso":"eng"}],"doi":"10.1186/s13073-023-01161-y","article_number":"12","file_date_updated":"2023-03-14T10:29:47Z","publisher":"Springer Nature","department":[{"_id":"MaRo"}],"publication_status":"published","acknowledgement":"We are grateful to all the families who took part, the general practitioners, and the Scottish School of Primary Care for their help in recruiting them and the whole GS team that includes interviewers, computer and laboratory technicians, clerical workers, research scientists, volunteers, managers, receptionists, healthcare assistants, and nurses.","year":"2023","volume":15,"date_updated":"2023-08-01T13:38:12Z","date_created":"2023-03-12T23:01:02Z","author":[{"last_name":"Bernabeu","first_name":"Elena","full_name":"Bernabeu, Elena"},{"last_name":"Mccartney","first_name":"Daniel L.","full_name":"Mccartney, Daniel L."},{"full_name":"Gadd, Danni A.","first_name":"Danni A.","last_name":"Gadd"},{"last_name":"Hillary","first_name":"Robert F.","full_name":"Hillary, Robert F."},{"full_name":"Lu, Ake T.","last_name":"Lu","first_name":"Ake T."},{"last_name":"Murphy","first_name":"Lee","full_name":"Murphy, Lee"},{"last_name":"Wrobel","first_name":"Nicola","full_name":"Wrobel, Nicola"},{"full_name":"Campbell, Archie","last_name":"Campbell","first_name":"Archie"},{"last_name":"Harris","first_name":"Sarah E.","full_name":"Harris, Sarah E."},{"full_name":"Liewald, David","first_name":"David","last_name":"Liewald"},{"last_name":"Hayward","first_name":"Caroline","full_name":"Hayward, Caroline"},{"last_name":"Sudlow","first_name":"Cathie","full_name":"Sudlow, Cathie"},{"full_name":"Cox, Simon R.","first_name":"Simon R.","last_name":"Cox"},{"first_name":"Kathryn L.","last_name":"Evans","full_name":"Evans, Kathryn L."},{"full_name":"Horvath, Steve","last_name":"Horvath","first_name":"Steve"},{"last_name":"Mcintosh","first_name":"Andrew M.","full_name":"Mcintosh, Andrew M."},{"full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","last_name":"Robinson"},{"last_name":"Vallejos","first_name":"Catalina A.","full_name":"Vallejos, Catalina A."},{"full_name":"Marioni, Riccardo E.","last_name":"Marioni","first_name":"Riccardo E."}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"28","article_type":"original","citation":{"mla":"Bernabeu, Elena, et al. “Refining Epigenetic Prediction of Chronological and Biological Age.” Genome Medicine, vol. 15, 12, Springer Nature, 2023, doi:10.1186/s13073-023-01161-y.","short":"E. Bernabeu, D.L. Mccartney, D.A. Gadd, R.F. Hillary, A.T. Lu, L. Murphy, N. Wrobel, A. Campbell, S.E. Harris, D. Liewald, C. Hayward, C. Sudlow, S.R. Cox, K.L. Evans, S. Horvath, A.M. Mcintosh, M.R. Robinson, C.A. Vallejos, R.E. Marioni, Genome Medicine 15 (2023).","chicago":"Bernabeu, Elena, Daniel L. Mccartney, Danni A. Gadd, Robert F. Hillary, Ake T. Lu, Lee Murphy, Nicola Wrobel, et al. “Refining Epigenetic Prediction of Chronological and Biological Age.” Genome Medicine. Springer Nature, 2023. https://doi.org/10.1186/s13073-023-01161-y.","ama":"Bernabeu E, Mccartney DL, Gadd DA, et al. Refining epigenetic prediction of chronological and biological age. Genome Medicine. 2023;15. doi:10.1186/s13073-023-01161-y","ista":"Bernabeu E, Mccartney DL, Gadd DA, Hillary RF, Lu AT, Murphy L, Wrobel N, Campbell A, Harris SE, Liewald D, Hayward C, Sudlow C, Cox SR, Evans KL, Horvath S, Mcintosh AM, Robinson MR, Vallejos CA, Marioni RE. 2023. Refining epigenetic prediction of chronological and biological age. Genome Medicine. 15, 12.","ieee":"E. Bernabeu et al., “Refining epigenetic prediction of chronological and biological age,” Genome Medicine, vol. 15. Springer Nature, 2023.","apa":"Bernabeu, E., Mccartney, D. L., Gadd, D. A., Hillary, R. F., Lu, A. T., Murphy, L., … Marioni, R. E. (2023). Refining epigenetic prediction of chronological and biological age. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-023-01161-y"},"publication":"Genome Medicine","date_published":"2023-02-28T00:00:00Z","type":"journal_article","abstract":[{"text":"Background\r\nEpigenetic clocks can track both chronological age (cAge) and biological age (bAge). The latter is typically defined by physiological biomarkers and risk of adverse health outcomes, including all-cause mortality. As cohort sample sizes increase, estimates of cAge and bAge become more precise. Here, we aim to develop accurate epigenetic predictors of cAge and bAge, whilst improving our understanding of their epigenomic architecture.\r\n\r\nMethods\r\nFirst, we perform large-scale (N = 18,413) epigenome-wide association studies (EWAS) of chronological age and all-cause mortality. Next, to create a cAge predictor, we use methylation data from 24,674 participants from the Generation Scotland study, the Lothian Birth Cohorts (LBC) of 1921 and 1936, and 8 other cohorts with publicly available data. In addition, we train a predictor of time to all-cause mortality as a proxy for bAge using the Generation Scotland cohort (1214 observed deaths). For this purpose, we use epigenetic surrogates (EpiScores) for 109 plasma proteins and the 8 component parts of GrimAge, one of the current best epigenetic predictors of survival. We test this bAge predictor in four external cohorts (LBC1921, LBC1936, the Framingham Heart Study and the Women’s Health Initiative study).\r\n\r\nResults\r\nThrough the inclusion of linear and non-linear age-CpG associations from the EWAS, feature pre-selection in advance of elastic net regression, and a leave-one-cohort-out (LOCO) cross-validation framework, we obtain cAge prediction with a median absolute error equal to 2.3 years. Our bAge predictor was found to slightly outperform GrimAge in terms of the strength of its association to survival (HRGrimAge = 1.47 [1.40, 1.54] with p = 1.08 × 10−52, and HRbAge = 1.52 [1.44, 1.59] with p = 2.20 × 10−60). Finally, we introduce MethylBrowsR, an online tool to visualise epigenome-wide CpG-age associations.\r\n\r\nConclusions\r\nThe integration of multiple large datasets, EpiScores, non-linear DNAm effects, and new approaches to feature selection has facilitated improvements to the blood-based epigenetic prediction of biological and chronological age.","lang":"eng"}],"intvolume":" 15","status":"public","title":"Refining epigenetic prediction of chronological and biological age","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12719","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12722","date_updated":"2023-03-14T10:29:47Z","date_created":"2023-03-14T10:29:47Z","checksum":"833b837910c4db42fb5f0f34125f77a7","success":1,"file_name":"2023_GenomeMed_Bernabeu.pdf","access_level":"open_access","file_size":4275987,"content_type":"application/pdf","creator":"cchlebak"}]},{"abstract":[{"lang":"eng","text":"Adversarial training (i.e., training on adversarially perturbed input data) is a well-studied method for making neural networks robust to potential adversarial attacks during inference. However, the improved robustness does not come for free but rather is accompanied by a decrease in overall model accuracy and performance. Recent work has shown that, in practical robot learning applications, the effects of adversarial training do not pose a fair trade-off but inflict a net loss when measured in holistic robot performance. This work revisits the robustness-accuracy trade-off in robot learning by systematically analyzing if recent advances in robust training methods and theory in conjunction with adversarial robot learning, are capable of making adversarial training suitable for real-world robot applications. We evaluate three different robot learning tasks ranging from autonomous driving in a high-fidelity environment amenable to sim-to-real deployment to mobile robot navigation and gesture recognition. Our results demonstrate that, while these techniques make incremental improvements on the trade-off on a relative scale, the negative impact on the nominal accuracy caused by adversarial training still outweighs the improved robustness by an order of magnitude. We conclude that although progress is happening, further advances in robust learning methods are necessary before they can benefit robot learning tasks in practice."}],"issue":"3","type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12714","checksum":"5a75dcd326ea66685de2b1aaec259e85","success":1,"date_updated":"2023-03-07T12:22:23Z","date_created":"2023-03-07T12:22:23Z","access_level":"open_access","file_name":"2023_IEEERobAutLetters_Lechner.pdf","file_size":944052,"content_type":"application/pdf","creator":"cchlebak"}],"status":"public","ddc":["000"],"title":"Revisiting the adversarial robustness-accuracy tradeoff in robot learning","intvolume":" 8","_id":"12704","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2023-03-01T00:00:00Z","article_type":"original","page":"1595-1602","publication":"IEEE Robotics and Automation Letters","citation":{"ama":"Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. 2023;8(3):1595-1602. doi:10.1109/LRA.2023.3240930","apa":"Lechner, M., Amini, A., Rus, D., & Henzinger, T. A. (2023). Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LRA.2023.3240930","ieee":"M. Lechner, A. Amini, D. Rus, and T. A. Henzinger, “Revisiting the adversarial robustness-accuracy tradeoff in robot learning,” IEEE Robotics and Automation Letters, vol. 8, no. 3. Institute of Electrical and Electronics Engineers, pp. 1595–1602, 2023.","ista":"Lechner M, Amini A, Rus D, Henzinger TA. 2023. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. 8(3), 1595–1602.","short":"M. Lechner, A. Amini, D. Rus, T.A. Henzinger, IEEE Robotics and Automation Letters 8 (2023) 1595–1602.","mla":"Lechner, Mathias, et al. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” IEEE Robotics and Automation Letters, vol. 8, no. 3, Institute of Electrical and Electronics Engineers, 2023, pp. 1595–602, doi:10.1109/LRA.2023.3240930.","chicago":"Lechner, Mathias, Alexander Amini, Daniela Rus, and Thomas A Henzinger. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” IEEE Robotics and Automation Letters. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/LRA.2023.3240930."},"file_date_updated":"2023-03-07T12:22:23Z","date_updated":"2023-08-01T13:36:50Z","date_created":"2023-03-05T23:01:04Z","volume":8,"author":[{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner","full_name":"Lechner, Mathias"},{"last_name":"Amini","first_name":"Alexander","full_name":"Amini, Alexander"},{"last_name":"Rus","first_name":"Daniela","full_name":"Rus, Daniela"},{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"related_material":{"record":[{"id":"11366","status":"public","relation":"earlier_version"}]},"publication_status":"published","publisher":"Institute of Electrical and Electronics Engineers","department":[{"_id":"ToHe"}],"acknowledgement":"We thank Christoph Lampert for inspiring this work. The\r\nviews and conclusions contained in this document are those of\r\nthe authors and should not be interpreted as representing the\r\nofficial policies, either expressed or implied, of the United States\r\nAir Force or the U.S. Government. The U.S. Government is\r\nauthorized to reproduce and distribute reprints for Government\r\npurposes notwithstanding any copyright notation herein.","year":"2023","month":"03","publication_identifier":{"eissn":["2377-3766"]},"language":[{"iso":"eng"}],"doi":"10.1109/LRA.2023.3240930","quality_controlled":"1","isi":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":["000936534100012"],"arxiv":["2204.07373"]},"oa":1}]