[{"citation":{"chicago":"Phuong, Mary. “Underspecification in Deep Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9418.","mla":"Phuong, Mary. Underspecification in Deep Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9418.","short":"M. Phuong, Underspecification in Deep Learning, Institute of Science and Technology Austria, 2021.","ista":"Phuong M. 2021. Underspecification in deep learning. Institute of Science and Technology Austria.","ieee":"M. Phuong, “Underspecification in deep learning,” Institute of Science and Technology Austria, 2021.","apa":"Phuong, M. (2021). Underspecification in deep learning. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9418","ama":"Phuong M. Underspecification in deep learning. 2021. doi:10.15479/AT:ISTA:9418"},"page":"125","date_published":"2021-05-30T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"30","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9418","title":"Underspecification in deep learning","status":"public","ddc":["000"],"oa_version":"Published Version","file":[{"file_size":2673905,"content_type":"application/pdf","creator":"bphuong","file_name":"mph-thesis-v519-pdfimages.pdf","access_level":"open_access","date_created":"2021-05-24T11:22:29Z","date_updated":"2021-05-24T11:22:29Z","checksum":"4f0abe64114cfed264f9d36e8d1197e3","success":1,"relation":"main_file","file_id":"9419"},{"creator":"bphuong","file_size":92995100,"content_type":"application/zip","access_level":"closed","file_name":"thesis.zip","checksum":"f5699e876bc770a9b0df8345a77720a2","date_created":"2021-05-24T11:56:02Z","date_updated":"2021-05-24T11:56:02Z","file_id":"9420","relation":"source_file"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Deep learning is best known for its empirical success across a wide range of applications\r\nspanning computer vision, natural language processing and speech. Of equal significance,\r\nthough perhaps less known, are its ramifications for learning theory: deep networks have\r\nbeen observed to perform surprisingly well in the high-capacity regime, aka the overfitting\r\nor underspecified regime. Classically, this regime on the far right of the bias-variance curve\r\nis associated with poor generalisation; however, recent experiments with deep networks\r\nchallenge this view.\r\n\r\nThis thesis is devoted to investigating various aspects of underspecification in deep learning.\r\nFirst, we argue that deep learning models are underspecified on two levels: a) any given\r\ntraining dataset can be fit by many different functions, and b) any given function can be\r\nexpressed by many different parameter configurations. We refer to the second kind of\r\nunderspecification as parameterisation redundancy and we precisely characterise its extent.\r\nSecond, we characterise the implicit criteria (the inductive bias) that guide learning in the\r\nunderspecified regime. Specifically, we consider a nonlinear but tractable classification\r\nsetting, and show that given the choice, neural networks learn classifiers with a large margin.\r\nThird, we consider learning scenarios where the inductive bias is not by itself sufficient to\r\ndeal with underspecification. We then study different ways of ‘tightening the specification’: i)\r\nIn the setting of representation learning with variational autoencoders, we propose a hand-\r\ncrafted regulariser based on mutual information. ii) In the setting of binary classification, we\r\nconsider soft-label (real-valued) supervision. We derive a generalisation bound for linear\r\nnetworks supervised in this way and verify that soft labels facilitate fast learning. Finally, we\r\nexplore an application of soft-label supervision to the training of multi-exit models."}],"oa":1,"doi":"10.15479/AT:ISTA:9418","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"},{"_id":"E-Lib"}],"supervisor":[{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"05","year":"2021","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"publication_status":"published","related_material":{"record":[{"id":"7435","status":"deleted","relation":"part_of_dissertation"},{"id":"7481","status":"public","relation":"part_of_dissertation"},{"id":"9416","relation":"part_of_dissertation","status":"public"},{"id":"7479","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Bui Thi Mai, Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","last_name":"Bui Thi Mai","first_name":"Phuong"}],"date_created":"2021-05-24T13:06:23Z","date_updated":"2023-09-08T11:11:12Z","file_date_updated":"2021-05-24T11:56:02Z"},{"publication":"arXiv","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2111.12171"}],"citation":{"chicago":"Koval, Illya. “Local Strong Birkhoff Conjecture and Local Spectral Rigidity of Almost Every Ellipse.” ArXiv, n.d. https://doi.org/10.48550/ARXIV.2111.12171.","short":"I. Koval, ArXiv (n.d.).","mla":"Koval, Illya. “Local Strong Birkhoff Conjecture and Local Spectral Rigidity of Almost Every Ellipse.” ArXiv, 2111.12171, doi:10.48550/ARXIV.2111.12171.","ieee":"I. Koval, “Local strong Birkhoff conjecture and local spectral rigidity of almost every ellipse,” arXiv. .","apa":"Koval, I. (n.d.). Local strong Birkhoff conjecture and local spectral rigidity of almost every ellipse. arXiv. https://doi.org/10.48550/ARXIV.2111.12171","ista":"Koval I. Local strong Birkhoff conjecture and local spectral rigidity of almost every ellipse. arXiv, 2111.12171.","ama":"Koval I. Local strong Birkhoff conjecture and local spectral rigidity of almost every ellipse. arXiv. doi:10.48550/ARXIV.2111.12171"},"external_id":{"arxiv":["2111.12171"]},"language":[{"iso":"eng"}],"doi":"10.48550/ARXIV.2111.12171","date_published":"2021-11-23T00:00:00Z","month":"11","day":"23","article_processing_charge":"No","publication_status":"submitted","title":"Local strong Birkhoff conjecture and local spectral rigidity of almost every ellipse","status":"public","department":[{"_id":"GradSch"}],"year":"2021","_id":"14278","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-15T06:44:00Z","date_created":"2023-09-06T08:35:43Z","oa_version":"Preprint","author":[{"full_name":"Koval, Illya","last_name":"Koval","first_name":"Illya","id":"2eed1f3b-896a-11ed-bdf8-93c7c4bf159e"}],"article_number":"2111.12171","type":"preprint","abstract":[{"text":"The Birkhoff conjecture says that the boundary of a strictly convex integrable billiard table is necessarily an ellipse. In this article, we consider a stronger notion of integrability, namely, integrability close to the boundary, and prove a local version of this conjecture: a small perturbation of almost every ellipse that preserves integrability near the boundary, is itself an ellipse. We apply this result to study local spectral rigidity of ellipses using the connection between the wave trace of the Laplacian and the dynamics near the boundary and establish rigidity for almost all of them.","lang":"eng"}]},{"day":"31","has_accepted_license":"1","article_processing_charge":"No","keyword":["concurrency","verification","model checking"],"date_published":"2021-10-31T00:00:00Z","page":"166","citation":{"ista":"Toman V. 2021. Improved verification techniques for concurrent systems. Institute of Science and Technology Austria.","ieee":"V. Toman, “Improved verification techniques for concurrent systems,” Institute of Science and Technology Austria, 2021.","apa":"Toman, V. (2021). Improved verification techniques for concurrent systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10199","ama":"Toman V. Improved verification techniques for concurrent systems. 2021. doi:10.15479/at:ista:10199","chicago":"Toman, Viktor. “Improved Verification Techniques for Concurrent Systems.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10199.","mla":"Toman, Viktor. Improved Verification Techniques for Concurrent Systems. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10199.","short":"V. Toman, Improved Verification Techniques for Concurrent Systems, Institute of Science and Technology Austria, 2021."},"abstract":[{"text":"The design and verification of concurrent systems remains an open challenge due to the non-determinism that arises from the inter-process communication. In particular, concurrent programs are notoriously difficult both to be written correctly and to be analyzed formally, as complex thread interaction has to be accounted for. The difficulties are further exacerbated when concurrent programs get executed on modern-day hardware, which contains various buffering and caching mechanisms for efficiency reasons. This causes further subtle non-determinism, which can often produce very unintuitive behavior of the concurrent programs. Model checking is at the forefront of tackling the verification problem, where the task is to decide, given as input a concurrent system and a desired property, whether the system satisfies the property. The inherent state-space explosion problem in model checking of concurrent systems causes naïve explicit methods not to scale, thus more inventive methods are required. One such method is stateless model checking (SMC), which explores in memory-efficient manner the program executions rather than the states of the program. State-of-the-art SMC is typically coupled with partial order reduction (POR) techniques, which argue that certain executions provably produce identical system behavior, thus limiting the amount of executions one needs to explore in order to cover all possible behaviors. Another method to tackle the state-space explosion is symbolic model checking, where the considered techniques operate on a succinct implicit representation of the input system rather than explicitly accessing the system. In this thesis we present new techniques for verification of concurrent systems. We present several novel POR methods for SMC of concurrent programs under various models of semantics, some of which account for write-buffering mechanisms. Additionally, we present novel algorithms for symbolic model checking of finite-state concurrent systems, where the desired property of the systems is to ensure a formally defined notion of fairness.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"creator":"vtoman","content_type":"application/pdf","file_size":2915234,"access_level":"open_access","file_name":"toman_th_final.pdf","checksum":"4f412a1ee60952221b499a4b1268df35","date_updated":"2021-11-08T14:12:22Z","date_created":"2021-11-08T14:12:22Z","file_id":"10225","relation":"main_file"},{"access_level":"closed","file_name":"toman_thesis.zip","creator":"vtoman","content_type":"application/zip","file_size":8616056,"file_id":"10226","relation":"source_file","checksum":"9584943f99127be2dd2963f6784c37d4","date_updated":"2021-11-09T09:00:50Z","date_created":"2021-11-08T14:12:46Z"}],"ddc":["000"],"title":"Improved verification techniques for concurrent systems","status":"public","_id":"10199","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"10","publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"SSU"}],"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:10199","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"oa":1,"file_date_updated":"2021-11-09T09:00:50Z","ec_funded":1,"date_created":"2021-10-29T20:09:01Z","date_updated":"2023-09-19T09:59:54Z","author":[{"id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9036-063X","first_name":"Viktor","last_name":"Toman","full_name":"Toman, Viktor"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10190"},{"relation":"part_of_dissertation","status":"public","id":"10191"},{"status":"public","relation":"part_of_dissertation","id":"9987"},{"id":"141","relation":"part_of_dissertation","status":"public"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"year":"2021"},{"type":"journal_article","abstract":[{"text":"We develop a Bayesian model (BayesRR-RC) that provides robust SNP-heritability estimation, an alternative to marker discovery, and accurate genomic prediction, taking 22 seconds per iteration to estimate 8.4 million SNP-effects and 78 SNP-heritability parameters in the UK Biobank. We find that only ≤10% of the genetic variation captured for height, body mass index, cardiovascular disease, and type 2 diabetes is attributable to proximal regulatory regions within 10kb upstream of genes, while 12-25% is attributed to coding regions, 32–44% to introns, and 22-28% to distal 10-500kb upstream regions. Up to 24% of all cis and coding regions of each chromosome are associated with each trait, with over 3,100 independent exonic and intronic regions and over 5,400 independent regulatory regions having ≥95% probability of contributing ≥0.001% to the genetic variance of these four traits. Our open-source software (GMRM) provides a scalable alternative to current approaches for biobank data.","lang":"eng"}],"issue":"1","title":"Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits","status":"public","ddc":["610"],"intvolume":" 12","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8429","file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":6519771,"access_level":"open_access","file_name":"2021_NatComm_Paxtot.pdf","success":1,"checksum":"384681be17aff902c149a48f52d13d4f","date_created":"2021-12-06T07:47:11Z","date_updated":"2021-12-06T07:47:11Z","file_id":"10419","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","day":"30","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"Nature Communications","citation":{"apa":"Patxot, M., Trejo Banos, D., Kousathanas, A., Orliac, E. J., Ojavee, S. E., Moser, G., … Robinson, M. R. (2021). Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-27258-9","ieee":"M. Patxot et al., “Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","ista":"Patxot M, Trejo Banos D, Kousathanas A, Orliac EJ, Ojavee SE, Moser G, Sidorenko J, Kutalik Z, Magi R, Visscher PM, Ronnegard L, Robinson MR. 2021. Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits. Nature Communications. 12(1), 6972.","ama":"Patxot M, Trejo Banos D, Kousathanas A, et al. Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-27258-9","chicago":"Patxot, Marion, Daniel Trejo Banos, Athanasios Kousathanas, Etienne J Orliac, Sven E Ojavee, Gerhard Moser, Julia Sidorenko, et al. “Probabilistic Inference of the Genetic Architecture Underlying Functional Enrichment of Complex Traits.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-27258-9.","short":"M. Patxot, D. Trejo Banos, A. Kousathanas, E.J. Orliac, S.E. Ojavee, G. Moser, J. Sidorenko, Z. Kutalik, R. Magi, P.M. Visscher, L. Ronnegard, M.R. Robinson, Nature Communications 12 (2021).","mla":"Patxot, Marion, et al. “Probabilistic Inference of the Genetic Architecture Underlying Functional Enrichment of Complex Traits.” Nature Communications, vol. 12, no. 1, 6972, Springer Nature, 2021, doi:10.1038/s41467-021-27258-9."},"date_published":"2021-11-30T00:00:00Z","article_number":"6972","file_date_updated":"2021-12-06T07:47:11Z","publication_status":"published","department":[{"_id":"MaRo"}],"publisher":"Springer Nature","year":"2021","acknowledgement":"This project was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by core funding from the Institute of Science and Technology Austria. We would like to thank the participants of the cohort studies, and the Ecole Polytechnique Federal Lausanne (EPFL) SCITAS for their excellent compute resources, their generosity with their time and the kindness of their support. P.M.V. acknowledges funding from the Australian National Health and Medical Research Council (1113400) and the Australian Research Council (FL180100072). L.R. acknowledges funding from the Kjell & Märta Beijer Foundation (Stockholm, Sweden). We also would like to acknowledge Simone Rubinacci, Oliver Delanau, Alexander Terenin, Eleonora Porcu, and Mike Goddard for their useful comments and suggestions.","date_updated":"2023-09-26T10:36:14Z","date_created":"2020-09-17T10:52:38Z","volume":12,"author":[{"last_name":"Patxot","first_name":"Marion","full_name":"Patxot, Marion"},{"full_name":"Trejo Banos, Daniel","first_name":"Daniel","last_name":"Trejo Banos"},{"full_name":"Kousathanas, Athanasios","first_name":"Athanasios","last_name":"Kousathanas"},{"full_name":"Orliac, Etienne J","last_name":"Orliac","first_name":"Etienne J"},{"full_name":"Ojavee, Sven E","first_name":"Sven E","last_name":"Ojavee"},{"full_name":"Moser, Gerhard","last_name":"Moser","first_name":"Gerhard"},{"last_name":"Sidorenko","first_name":"Julia","full_name":"Sidorenko, Julia"},{"last_name":"Kutalik","first_name":"Zoltan","full_name":"Kutalik, Zoltan"},{"full_name":"Magi, Reedik","first_name":"Reedik","last_name":"Magi"},{"first_name":"Peter M","last_name":"Visscher","full_name":"Visscher, Peter M"},{"first_name":"Lars","last_name":"Ronnegard","full_name":"Ronnegard, Lars"},{"full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"13063"}]},"month":"11","publication_identifier":{"eissn":["2041-1723"]},"quality_controlled":"1","isi":1,"external_id":{"isi":["000724450600023"]},"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":"10.1038/s41467-021-27258-9"},{"type":"conference","abstract":[{"lang":"eng","text":"Consider a distributed task where the communication network is fixed but the local inputs given to the nodes of the distributed system may change over time. In this work, we explore the following question: if some of the local inputs change, can an existing solution be updated efficiently, in a dynamic and distributed manner?\r\nTo address this question, we define the batch dynamic CONGEST model in which we are given a bandwidth-limited communication network and a dynamic edge labelling defines the problem input. The task is to maintain a solution to a graph problem on the labelled graph under batch changes. We investigate, when a batch of alpha edge label changes arrive, - how much time as a function of alpha we need to update an existing solution, and - how much information the nodes have to keep in local memory between batches in order to update the solution quickly.\r\nOur work lays the foundations for the theory of input-dynamic distributed network algorithms. We give a general picture of the complexity landscape in this model, design both universal algorithms and algorithms for concrete problems, and present a general framework for lower bounds. The diverse time complexity of our model spans from constant time, through time polynomial in alpha, and to alpha time, which we show to be enough for any task."}],"status":"public","title":"Input-dynamic distributed algorithms for communication networks","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10854","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"01","page":"71-72","citation":{"short":"K.-T. Foerster, J. Korhonen, A. Paz, J. Rybicki, S. Schmid, in:, Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems, Association for Computing Machinery, 2021, pp. 71–72.","mla":"Foerster, Klaus-Tycho, et al. “Input-Dynamic Distributed Algorithms for Communication Networks.” Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems, Association for Computing Machinery, 2021, pp. 71–72, doi:10.1145/3410220.3453923.","chicago":"Foerster, Klaus-Tycho, Janne Korhonen, Ami Paz, Joel Rybicki, and Stefan Schmid. “Input-Dynamic Distributed Algorithms for Communication Networks.” In Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems, 71–72. Association for Computing Machinery, 2021. https://doi.org/10.1145/3410220.3453923.","ama":"Foerster K-T, Korhonen J, Paz A, Rybicki J, Schmid S. Input-dynamic distributed algorithms for communication networks. In: Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems. Association for Computing Machinery; 2021:71-72. doi:10.1145/3410220.3453923","apa":"Foerster, K.-T., Korhonen, J., Paz, A., Rybicki, J., & Schmid, S. (2021). Input-dynamic distributed algorithms for communication networks. In Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems (pp. 71–72). Virtual, Online: Association for Computing Machinery. https://doi.org/10.1145/3410220.3453923","ieee":"K.-T. Foerster, J. Korhonen, A. Paz, J. Rybicki, and S. Schmid, “Input-dynamic distributed algorithms for communication networks,” in Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems, Virtual, Online, 2021, pp. 71–72.","ista":"Foerster K-T, Korhonen J, Paz A, Rybicki J, Schmid S. 2021. Input-dynamic distributed algorithms for communication networks. Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems. SIGMETRICS: International Conference on Measurement and Modeling of Computer Systems, 71–72."},"publication":"Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems","date_published":"2021-05-01T00:00:00Z","ec_funded":1,"department":[{"_id":"DaAl"}],"publisher":"Association for Computing Machinery","publication_status":"published","acknowledgement":"We thank Jukka Suomela for discussions. We also thank our shepherd Mohammad Hajiesmaili and the reviewers for their time and suggestions on how to improve the paper. 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), from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska–Curie grant agreement No. 840605, from the Vienna Science and Technology Fund (WWTF) project WHATIF, ICT19-045, 2020-2024, and from the Austrian Science Fund (FWF) and netIDEE SCIENCE project P 33775-N.","year":"2021","date_updated":"2023-09-26T10:40:55Z","date_created":"2022-03-18T08:48:41Z","related_material":{"record":[{"id":"10855","relation":"extended_version","status":"public"}]},"author":[{"last_name":"Foerster","first_name":"Klaus-Tycho","full_name":"Foerster, Klaus-Tycho"},{"id":"C5402D42-15BC-11E9-A202-CA2BE6697425","first_name":"Janne","last_name":"Korhonen","full_name":"Korhonen, Janne"},{"last_name":"Paz","first_name":"Ami","full_name":"Paz, Ami"},{"full_name":"Rybicki, Joel","last_name":"Rybicki","first_name":"Joel","orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schmid","first_name":"Stefan","full_name":"Schmid, Stefan"}],"publication_identifier":{"isbn":["9781450380720"]},"month":"05","project":[{"call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"},{"grant_number":"840605","_id":"26A5D39A-B435-11E9-9278-68D0E5697425","name":"Coordination in constrained and natural distributed systems","call_identifier":"H2020"}],"quality_controlled":"1","oa":1,"external_id":{"arxiv":["2005.07637"]},"main_file_link":[{"url":"https://arxiv.org/abs/2005.07637","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1145/3410220.3453923","conference":{"name":"SIGMETRICS: International Conference on Measurement and Modeling of Computer Systems","end_date":"2021-06-18","start_date":"2021-06-14","location":"Virtual, Online"}},{"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2005.07637"}],"external_id":{"arxiv":["2005.07637"]},"project":[{"_id":"26A5D39A-B435-11E9-9278-68D0E5697425","grant_number":"840605","call_identifier":"H2020","name":"Coordination in constrained and natural distributed systems"},{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"}],"quality_controlled":"1","doi":"10.1145/3447384","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2476-1249"]},"month":"03","acknowledgement":"We thank Jukka Suomela for discussions. We also thank our shepherd Mohammad Hajiesmaili\r\nand the reviewers for their time and suggestions on how to improve the paper. This project\r\nhas received funding from the European Research Council (ERC) under the European Union’s\r\nHorizon 2020 research and innovation programme (grant agreement No 805223 ScaleML), from the European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSk lodowska–Curie grant agreement No. 840605, from the Vienna Science and Technology Fund (WWTF) project WHATIF, ICT19-045, 2020-2024, and from the Austrian Science Fund (FWF) and netIDEE SCIENCE project P 33775-N.","year":"2021","department":[{"_id":"DaAl"}],"publisher":"Association for Computing Machinery","publication_status":"published","related_material":{"record":[{"status":"public","relation":"shorter_version","id":"10854"}]},"author":[{"full_name":"Foerster, Klaus-Tycho","first_name":"Klaus-Tycho","last_name":"Foerster"},{"full_name":"Korhonen, Janne","first_name":"Janne","last_name":"Korhonen","id":"C5402D42-15BC-11E9-A202-CA2BE6697425"},{"last_name":"Paz","first_name":"Ami","full_name":"Paz, Ami"},{"last_name":"Rybicki","first_name":"Joel","orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","full_name":"Rybicki, Joel"},{"full_name":"Schmid, Stefan","first_name":"Stefan","last_name":"Schmid"}],"volume":5,"date_created":"2022-03-18T09:10:27Z","date_updated":"2023-09-26T10:40:55Z","ec_funded":1,"citation":{"short":"K.-T. Foerster, J. Korhonen, A. Paz, J. Rybicki, S. Schmid, Proceedings of the ACM on Measurement and Analysis of Computing Systems 5 (2021) 1–33.","mla":"Foerster, Klaus-Tycho, et al. “Input-Dynamic Distributed Algorithms for Communication Networks.” Proceedings of the ACM on Measurement and Analysis of Computing Systems, vol. 5, no. 1, Association for Computing Machinery, 2021, pp. 1–33, doi:10.1145/3447384.","chicago":"Foerster, Klaus-Tycho, Janne Korhonen, Ami Paz, Joel Rybicki, and Stefan Schmid. “Input-Dynamic Distributed Algorithms for Communication Networks.” Proceedings of the ACM on Measurement and Analysis of Computing Systems. Association for Computing Machinery, 2021. https://doi.org/10.1145/3447384.","ama":"Foerster K-T, Korhonen J, Paz A, Rybicki J, Schmid S. Input-dynamic distributed algorithms for communication networks. Proceedings of the ACM on Measurement and Analysis of Computing Systems. 2021;5(1):1-33. doi:10.1145/3447384","apa":"Foerster, K.-T., Korhonen, J., Paz, A., Rybicki, J., & Schmid, S. (2021). Input-dynamic distributed algorithms for communication networks. Proceedings of the ACM on Measurement and Analysis of Computing Systems. Association for Computing Machinery. https://doi.org/10.1145/3447384","ieee":"K.-T. Foerster, J. Korhonen, A. Paz, J. Rybicki, and S. Schmid, “Input-dynamic distributed algorithms for communication networks,” Proceedings of the ACM on Measurement and Analysis of Computing Systems, vol. 5, no. 1. Association for Computing Machinery, pp. 1–33, 2021.","ista":"Foerster K-T, Korhonen J, Paz A, Rybicki J, Schmid S. 2021. Input-dynamic distributed algorithms for communication networks. Proceedings of the ACM on Measurement and Analysis of Computing Systems. 5(1), 1–33."},"publication":"Proceedings of the ACM on Measurement and Analysis of Computing Systems","page":"1-33","article_type":"original","date_published":"2021-03-01T00:00:00Z","scopus_import":"1","keyword":["Computer Networks and Communications","Hardware and Architecture","Safety","Risk","Reliability and Quality","Computer Science (miscellaneous)"],"article_processing_charge":"No","day":"01","_id":"10855","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 5","title":"Input-dynamic distributed algorithms for communication networks","status":"public","oa_version":"Preprint","type":"journal_article","issue":"1","abstract":[{"text":"Consider a distributed task where the communication network is fixed but the local inputs given to the nodes of the distributed system may change over time. In this work, we explore the following question: if some of the local inputs change, can an existing solution be updated efficiently, in a dynamic and distributed manner? To address this question, we define the batch dynamic \\congest model in which we are given a bandwidth-limited communication network and a dynamic edge labelling defines the problem input. The task is to maintain a solution to a graph problem on the labeled graph under batch changes. We investigate, when a batch of α edge label changes arrive, \\beginitemize \\item how much time as a function of α we need to update an existing solution, and \\item how much information the nodes have to keep in local memory between batches in order to update the solution quickly. \\enditemize Our work lays the foundations for the theory of input-dynamic distributed network algorithms. We give a general picture of the complexity landscape in this model, design both universal algorithms and algorithms for concrete problems, and present a general framework for lower bounds. In particular, we derive non-trivial upper bounds for two selected, contrasting problems: maintaining a minimum spanning tree and detecting cliques.","lang":"eng"}]},{"month":"03","publication_identifier":{"issn":["0004-3702"]},"main_file_link":[{"url":"https://arxiv.org/abs/1804.07031","open_access":"1"}],"external_id":{"isi":["000657537500003"],"arxiv":["1804.07031"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1016/j.artint.2021.103499","language":[{"iso":"eng"}],"article_number":"103499","year":"2021","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Elsevier","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Dvořák","first_name":"Wolfgang","full_name":"Dvořák, Wolfgang"},{"full_name":"Henzinger, Monika H","first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530"},{"last_name":"Svozil","first_name":"Alexander","full_name":"Svozil, Alexander"}],"related_material":{"record":[{"id":"35","relation":"earlier_version","status":"public"}]},"date_created":"2021-03-28T22:01:40Z","date_updated":"2023-09-26T10:41:42Z","volume":297,"scopus_import":"1","day":"16","article_processing_charge":"No","publication":"Artificial Intelligence","citation":{"ista":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. 2021. Algorithms and conditional lower bounds for planning problems. Artificial Intelligence. 297(8), 103499.","apa":"Chatterjee, K., Dvořák, W., Henzinger, M. H., & Svozil, A. (2021). Algorithms and conditional lower bounds for planning problems. Artificial Intelligence. Elsevier. https://doi.org/10.1016/j.artint.2021.103499","ieee":"K. Chatterjee, W. Dvořák, M. H. Henzinger, and A. Svozil, “Algorithms and conditional lower bounds for planning problems,” Artificial Intelligence, vol. 297, no. 8. Elsevier, 2021.","ama":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. Algorithms and conditional lower bounds for planning problems. Artificial Intelligence. 2021;297(8). doi:10.1016/j.artint.2021.103499","chicago":"Chatterjee, Krishnendu, Wolfgang Dvořák, Monika H Henzinger, and Alexander Svozil. “Algorithms and Conditional Lower Bounds for Planning Problems.” Artificial Intelligence. Elsevier, 2021. https://doi.org/10.1016/j.artint.2021.103499.","mla":"Chatterjee, Krishnendu, et al. “Algorithms and Conditional Lower Bounds for Planning Problems.” Artificial Intelligence, vol. 297, no. 8, 103499, Elsevier, 2021, doi:10.1016/j.artint.2021.103499.","short":"K. Chatterjee, W. Dvořák, M.H. Henzinger, A. Svozil, Artificial Intelligence 297 (2021)."},"article_type":"original","date_published":"2021-03-16T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We consider planning problems for graphs, Markov Decision Processes (MDPs), and games on graphs in an explicit state space. While graphs represent the most basic planning model, MDPs represent interaction with nature and games on graphs represent interaction with an adversarial environment. We consider two planning problems with k different target sets: (a) the coverage problem asks whether there is a plan for each individual target set; and (b) the sequential target reachability problem asks whether the targets can be reached in a given sequence. For the coverage problem, we present a linear-time algorithm for graphs, and quadratic conditional lower bound for MDPs and games on graphs. For the sequential target problem, we present a linear-time algorithm for graphs, a sub-quadratic algorithm for MDPs, and a quadratic conditional lower bound for games on graphs. Our results with conditional lower bounds, based on the boolean matrix multiplication (BMM) conjecture and strong exponential time hypothesis (SETH), establish (i) model-separation results showing that for the coverage problem MDPs and games on graphs are harder than graphs, and for the sequential reachability problem games on graphs are harder than MDPs and graphs; and (ii) problem-separation results showing that for MDPs the coverage problem is harder than the sequential target problem."}],"issue":"8","_id":"9293","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Algorithms and conditional lower bounds for planning problems","intvolume":" 297","oa_version":"Preprint"},{"_id":"13063","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","status":"public","ddc":["570"],"title":"Probabilistic inference of the genetic architecture of functional enrichment of complex traits","department":[{"_id":"MaRo"}],"publisher":"Dryad","author":[{"full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813"}],"related_material":{"record":[{"id":"8429","relation":"used_in_publication","status":"public"}],"link":[{"relation":"software","url":"https://github.com/medical-genomics-group/gmrm"}]},"date_updated":"2023-09-26T10:36:15Z","date_created":"2023-05-23T16:20:16Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"text":"We develop a Bayesian model (BayesRR-RC) that provides robust SNP-heritability estimation, an alternative to marker discovery, and accurate genomic prediction, taking 22 seconds per iteration to estimate 8.4 million SNP-effects and 78 SNP-heritability parameters in the UK Biobank. We find that only $\\leq$ 10\\% of the genetic variation captured for height, body mass index, cardiovascular disease, and type 2 diabetes is attributable to proximal regulatory regions within 10kb upstream of genes, while 12-25% is attributed to coding regions, 32-44% to introns, and 22-28% to distal 10-500kb upstream regions. Up to 24% of all cis and coding regions of each chromosome are associated with each trait, with over 3,100 independent exonic and intronic regions and over 5,400 independent regulatory regions having >95% probability of contributing >0.001% to the genetic variance of these four traits. Our open-source software (GMRM) provides a scalable alternative to current approaches for biobank data.","lang":"eng"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"ista":"Robinson MR. 2021. Probabilistic inference of the genetic architecture of functional enrichment of complex traits, Dryad, 10.5061/dryad.sqv9s4n51.","ieee":"M. R. Robinson, “Probabilistic inference of the genetic architecture of functional enrichment of complex traits.” Dryad, 2021.","apa":"Robinson, M. R. (2021). Probabilistic inference of the genetic architecture of functional enrichment of complex traits. Dryad. https://doi.org/10.5061/dryad.sqv9s4n51","ama":"Robinson MR. Probabilistic inference of the genetic architecture of functional enrichment of complex traits. 2021. doi:10.5061/dryad.sqv9s4n51","chicago":"Robinson, Matthew Richard. “Probabilistic Inference of the Genetic Architecture of Functional Enrichment of Complex Traits.” Dryad, 2021. https://doi.org/10.5061/dryad.sqv9s4n51.","mla":"Robinson, Matthew Richard. Probabilistic Inference of the Genetic Architecture of Functional Enrichment of Complex Traits. Dryad, 2021, doi:10.5061/dryad.sqv9s4n51.","short":"M.R. Robinson, (2021)."},"oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.sqv9s4n51","open_access":"1"}],"doi":"10.5061/dryad.sqv9s4n51","date_published":"2021-11-04T00:00:00Z","day":"04","month":"11","article_processing_charge":"No"},{"issue":"8","abstract":[{"lang":"eng","text":"The high processing cost, poor mechanical properties and moderate performance of Bi2Te3–based alloys used in thermoelectric devices limit the cost-effectiveness of this energy conversion technology. Towards solving these current challenges, in the present work, we detail a low temperature solution-based approach to produce Bi2Te3-Cu2-xTe nanocomposites with improved thermoelectric performance. Our approach consists in combining proper ratios of colloidal nanoparticles and to consolidate the resulting mixture into nanocomposites using a hot press. The transport properties of the nanocomposites are characterized and compared with those of pure Bi2Te3 nanomaterials obtained following the same procedure. In contrast with most previous works, the presence of Cu2-xTe nanodomains does not result in a significant reduction of the lattice thermal conductivity of the reference Bi2Te3 nanomaterial, which is already very low. However, the introduction of Cu2-xTe yields a nearly threefold increase of the power factor associated to a simultaneous increase of the Seebeck coefficient and electrical conductivity at temperatures above 400 K. Taking into account the band alignment of the two materials, we rationalize this increase by considering that Cu2-xTe nanostructures, with a relatively low electron affinity, are able to inject electrons into Bi2Te3, enhancing in this way its electrical conductivity. The simultaneous increase of the Seebeck coefficient is related to the energy filtering of charge carriers at energy barriers within Bi2Te3 domains associated with the accumulation of electrons in regions nearby a Cu2-xTe/Bi2Te3 heterojunction. Overall, with the incorporation of a proper amount of Cu2-xTe nanoparticles, we demonstrate a 250% improvement of the thermoelectric figure of merit of Bi2Te3."}],"type":"journal_article","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9304","intvolume":" 418","title":"Influence of copper telluride nanodomains on the transport properties of n-type bismuth telluride","status":"public","article_processing_charge":"No","day":"15","scopus_import":"1","date_published":"2021-08-15T00:00:00Z","citation":{"short":"Y. Zhang, C. Xing, Y. Liu, M. Li, K. Xiao, P. Guardia, S. Lee, X. Han, A. Moghaddam, J.J. Roa, J. Arbiol, M. Ibáñez, K. Pan, M. Prato, Y. Xie, A. Cabot, Chemical Engineering Journal 418 (2021).","mla":"Zhang, Yu, et al. “Influence of Copper Telluride Nanodomains on the Transport Properties of N-Type Bismuth Telluride.” Chemical Engineering Journal, vol. 418, no. 8, 129374, Elsevier, 2021, doi:10.1016/j.cej.2021.129374.","chicago":"Zhang, Yu, Congcong Xing, Yu Liu, Mengyao Li, Ke Xiao, Pablo Guardia, Seungho Lee, et al. “Influence of Copper Telluride Nanodomains on the Transport Properties of N-Type Bismuth Telluride.” Chemical Engineering Journal. Elsevier, 2021. https://doi.org/10.1016/j.cej.2021.129374.","ama":"Zhang Y, Xing C, Liu Y, et al. Influence of copper telluride nanodomains on the transport properties of n-type bismuth telluride. Chemical Engineering Journal. 2021;418(8). doi:10.1016/j.cej.2021.129374","ieee":"Y. Zhang et al., “Influence of copper telluride nanodomains on the transport properties of n-type bismuth telluride,” Chemical Engineering Journal, vol. 418, no. 8. Elsevier, 2021.","apa":"Zhang, Y., Xing, C., Liu, Y., Li, M., Xiao, K., Guardia, P., … Cabot, A. (2021). Influence of copper telluride nanodomains on the transport properties of n-type bismuth telluride. Chemical Engineering Journal. Elsevier. https://doi.org/10.1016/j.cej.2021.129374","ista":"Zhang Y, Xing C, Liu Y, Li M, Xiao K, Guardia P, Lee S, Han X, Moghaddam A, Roa JJ, Arbiol J, Ibáñez M, Pan K, Prato M, Xie Y, Cabot A. 2021. Influence of copper telluride nanodomains on the transport properties of n-type bismuth telluride. Chemical Engineering Journal. 418(8), 129374."},"publication":"Chemical Engineering Journal","article_type":"original","ec_funded":1,"article_number":"129374","author":[{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"full_name":"Xing, Congcong","last_name":"Xing","first_name":"Congcong"},{"full_name":"Liu, Yu","first_name":"Yu","last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7313-6740"},{"full_name":"Li, Mengyao","last_name":"Li","first_name":"Mengyao"},{"full_name":"Xiao, Ke","last_name":"Xiao","first_name":"Ke"},{"first_name":"Pablo","last_name":"Guardia","full_name":"Guardia, Pablo"},{"full_name":"Lee, Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598","first_name":"Seungho","last_name":"Lee"},{"first_name":"Xu","last_name":"Han","full_name":"Han, Xu"},{"first_name":"Ahmad","last_name":"Moghaddam","full_name":"Moghaddam, Ahmad"},{"last_name":"Roa","first_name":"Joan J","full_name":"Roa, Joan J"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria","full_name":"Ibáñez, Maria"},{"last_name":"Pan","first_name":"Kai","full_name":"Pan, Kai"},{"first_name":"Mirko","last_name":"Prato","full_name":"Prato, Mirko"},{"first_name":"Ying","last_name":"Xie","full_name":"Xie, Ying"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"volume":418,"date_created":"2021-04-04T22:01:20Z","date_updated":"2023-09-27T07:36:29Z","year":"2021","acknowledgement":"This work was supported by the European Regional Development Funds and by the Generalitat de Catalunya through the project 2017SGR1246. Y.Z, C.X, M.L, K.X and X.H thank the China Scholarship Council for the scholarship support. MI acknowledges financial support from IST Austria. YL acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. ICN2\r\nacknowledges funding from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO project ENE2017-85087-C3. ICN2 is supported by the Severo Ochoa program from the Spanish MINECO (grant no. SEV-2017-0706) and is funded by the CERCA Program/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science PhD program.","publisher":"Elsevier","department":[{"_id":"MaIb"}],"publication_status":"published","publication_identifier":{"issn":["1385-8947"]},"month":"08","doi":"10.1016/j.cej.2021.129374","language":[{"iso":"eng"}],"external_id":{"isi":["000655672000005"]},"oa":1,"main_file_link":[{"url":"https://ddd.uab.cat/record/271949","open_access":"1"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1"},{"publisher":"Elsevier","department":[{"_id":"SiHi"}],"publication_status":"published","pmid":1,"year":"2021","acknowledgement":"This work was supported by the National Institutes of Health (R01 DA047258 and R01 NS102237 to C.E., F32 NS100392 to K.T.B.) and the Holland-Trice Brain Research Award (to C.E.). K.T.B. was supported by postdoctoral fellowships from the Foerster-Bernstein Family and The Hartwell Foundation. The Hippenmeyer lab was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovations program (725780 LinPro) to S.H. R.E. was supported by Ministerio de Ciencia y Tecnología (RTI2018-093493-B-I00). We thank the Duke Light Microscopy Core Facility, the Duke Transgenic Mouse Facility, Dr. U. Schulte for assistance with proteomic experiments, and Dr. D. Silver for critical review of the manuscript. Cartoon elements of figure panels were created using BioRender.com.","volume":109,"date_created":"2021-08-06T09:08:25Z","date_updated":"2023-09-27T07:46:09Z","author":[{"full_name":"Baldwin, Katherine T.","first_name":"Katherine T.","last_name":"Baldwin"},{"full_name":"Tan, Christabel X.","last_name":"Tan","first_name":"Christabel X."},{"first_name":"Samuel T.","last_name":"Strader","full_name":"Strader, Samuel T."},{"full_name":"Jiang, Changyu","first_name":"Changyu","last_name":"Jiang"},{"full_name":"Savage, Justin T.","last_name":"Savage","first_name":"Justin T."},{"full_name":"Elorza-Vidal, Xabier","first_name":"Xabier","last_name":"Elorza-Vidal"},{"full_name":"Contreras, Ximena","last_name":"Contreras","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas","last_name":"Rülicke","full_name":"Rülicke, Thomas"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"},{"full_name":"Estévez, Raúl","first_name":"Raúl","last_name":"Estévez"},{"last_name":"Ji","first_name":"Ru-Rong","full_name":"Ji, Ru-Rong"},{"last_name":"Eroglu","first_name":"Cagla","full_name":"Eroglu, Cagla"}],"ec_funded":1,"project":[{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780"}],"isi":1,"quality_controlled":"1","external_id":{"pmid":["34171291"],"isi":["000692851900010"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2021.05.025","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2021.05.025","publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"month":"08","intvolume":" 109","status":"public","title":"HepaCAM controls astrocyte self-organization and coupling","_id":"9793","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","issue":"15","abstract":[{"lang":"eng","text":"Astrocytes extensively infiltrate the neuropil to regulate critical aspects of synaptic development and function. This process is regulated by transcellular interactions between astrocytes and neurons via cell adhesion molecules. How astrocytes coordinate developmental processes among one another to parse out the synaptic neuropil and form non-overlapping territories is unknown. Here we identify a molecular mechanism regulating astrocyte-astrocyte interactions during development to coordinate astrocyte morphogenesis and gap junction coupling. We show that hepaCAM, a disease-linked, astrocyte-enriched cell adhesion molecule, regulates astrocyte competition for territory and morphological complexity in the developing mouse cortex. Furthermore, conditional deletion of Hepacam from developing astrocytes significantly impairs gap junction coupling between astrocytes and disrupts the balance between synaptic excitation and inhibition. Mutations in HEPACAM cause megalencephalic leukoencephalopathy with subcortical cysts in humans. Therefore, our findings suggest that disruption of astrocyte self-organization mechanisms could be an underlying cause of neural pathology."}],"page":"2427-2442.e10","article_type":"original","citation":{"ista":"Baldwin KT, Tan CX, Strader ST, Jiang C, Savage JT, Elorza-Vidal X, Contreras X, Rülicke T, Hippenmeyer S, Estévez R, Ji R-R, Eroglu C. 2021. HepaCAM controls astrocyte self-organization and coupling. Neuron. 109(15), 2427–2442.e10.","apa":"Baldwin, K. T., Tan, C. X., Strader, S. T., Jiang, C., Savage, J. T., Elorza-Vidal, X., … Eroglu, C. (2021). HepaCAM controls astrocyte self-organization and coupling. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2021.05.025","ieee":"K. T. Baldwin et al., “HepaCAM controls astrocyte self-organization and coupling,” Neuron, vol. 109, no. 15. Elsevier, p. 2427–2442.e10, 2021.","ama":"Baldwin KT, Tan CX, Strader ST, et al. HepaCAM controls astrocyte self-organization and coupling. Neuron. 2021;109(15):2427-2442.e10. doi:10.1016/j.neuron.2021.05.025","chicago":"Baldwin, Katherine T., Christabel X. Tan, Samuel T. Strader, Changyu Jiang, Justin T. Savage, Xabier Elorza-Vidal, Ximena Contreras, et al. “HepaCAM Controls Astrocyte Self-Organization and Coupling.” Neuron. Elsevier, 2021. https://doi.org/10.1016/j.neuron.2021.05.025.","mla":"Baldwin, Katherine T., et al. “HepaCAM Controls Astrocyte Self-Organization and Coupling.” Neuron, vol. 109, no. 15, Elsevier, 2021, p. 2427–2442.e10, doi:10.1016/j.neuron.2021.05.025.","short":"K.T. Baldwin, C.X. Tan, S.T. Strader, C. Jiang, J.T. Savage, X. Elorza-Vidal, X. Contreras, T. Rülicke, S. Hippenmeyer, R. Estévez, R.-R. Ji, C. Eroglu, Neuron 109 (2021) 2427–2442.e10."},"publication":"Neuron","date_published":"2021-08-04T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"04"},{"month":"07","publication_identifier":{"issn":["2211-2855"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://ddd.uab.cat/record/271947"}],"external_id":{"isi":["000663442200004"]},"isi":1,"quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"doi":"10.1016/j.nanoen.2021.105991","language":[{"iso":"eng"}],"article_number":"105991","ec_funded":1,"year":"2021","acknowledgement":"This work was supported by the European Regional Development Fund and by the Spanish Ministerio de Economía y Competitividad through the project SEHTOP (ENE2016-77798-C4-3-R). MI acknowledges financial support from IST Austria. YL acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. YZ, CX, XW, KX and TZ thank the China Scholarship Council for the scholarship support. ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO project ENE2017-85087-C3. ICN2 is supported by the Severo Ochoa program from the Spanish MINECO (grant no. SEV-2017-0706) and is funded by the CERCA program/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science Ph.D. program. M.C.S. has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754510 (PROBIST) and the Severo Ochoa programme. P.G. acknowledges financial support from the Spanish government (MICIU) through the RTI2018-102006-J-I00 project and the Catalan Agency of Competitiveness (ACCIO) through the TecnioSpring+ Marie Sklodowska-Curie action TECSPR16-1-0082. YZ and CX contributed equally to this work.","publication_status":"published","department":[{"_id":"MaIb"}],"publisher":"Elsevier","author":[{"full_name":"Zhang, Yu","first_name":"Yu","last_name":"Zhang"},{"last_name":"Xing","first_name":"Congcong","full_name":"Xing, Congcong"},{"orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","first_name":"Yu","full_name":"Liu, Yu"},{"last_name":"Spadaro","first_name":"Maria Chiara","full_name":"Spadaro, Maria Chiara"},{"full_name":"Wang, Xiang","last_name":"Wang","first_name":"Xiang"},{"full_name":"Li, Mengyao","last_name":"Li","first_name":"Mengyao"},{"last_name":"Xiao","first_name":"Ke","full_name":"Xiao, Ke"},{"first_name":"Ting","last_name":"Zhang","full_name":"Zhang, Ting"},{"last_name":"Guardia","first_name":"Pablo","full_name":"Guardia, Pablo"},{"last_name":"Lim","first_name":"Khak Ho","full_name":"Lim, Khak Ho"},{"full_name":"Moghaddam, Ahmad Ostovari","first_name":"Ahmad Ostovari","last_name":"Moghaddam"},{"last_name":"Llorca","first_name":"Jordi","full_name":"Llorca, Jordi"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"date_updated":"2023-09-27T07:41:00Z","date_created":"2021-04-04T22:01:21Z","volume":85,"scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Nano Energy","citation":{"ama":"Zhang Y, Xing C, Liu Y, et al. Doping-mediated stabilization of copper vacancies to promote thermoelectric properties of Cu2-xS. Nano Energy. 2021;85(7). doi:10.1016/j.nanoen.2021.105991","ieee":"Y. Zhang et al., “Doping-mediated stabilization of copper vacancies to promote thermoelectric properties of Cu2-xS,” Nano Energy, vol. 85, no. 7. Elsevier, 2021.","apa":"Zhang, Y., Xing, C., Liu, Y., Spadaro, M. C., Wang, X., Li, M., … Cabot, A. (2021). Doping-mediated stabilization of copper vacancies to promote thermoelectric properties of Cu2-xS. Nano Energy. Elsevier. https://doi.org/10.1016/j.nanoen.2021.105991","ista":"Zhang Y, Xing C, Liu Y, Spadaro MC, Wang X, Li M, Xiao K, Zhang T, Guardia P, Lim KH, Moghaddam AO, Llorca J, Arbiol J, Ibáñez M, Cabot A. 2021. Doping-mediated stabilization of copper vacancies to promote thermoelectric properties of Cu2-xS. Nano Energy. 85(7), 105991.","short":"Y. Zhang, C. Xing, Y. Liu, M.C. Spadaro, X. Wang, M. Li, K. Xiao, T. Zhang, P. Guardia, K.H. Lim, A.O. Moghaddam, J. Llorca, J. Arbiol, M. Ibáñez, A. Cabot, Nano Energy 85 (2021).","mla":"Zhang, Yu, et al. “Doping-Mediated Stabilization of Copper Vacancies to Promote Thermoelectric Properties of Cu2-XS.” Nano Energy, vol. 85, no. 7, 105991, Elsevier, 2021, doi:10.1016/j.nanoen.2021.105991.","chicago":"Zhang, Yu, Congcong Xing, Yu Liu, Maria Chiara Spadaro, Xiang Wang, Mengyao Li, Ke Xiao, et al. “Doping-Mediated Stabilization of Copper Vacancies to Promote Thermoelectric Properties of Cu2-XS.” Nano Energy. Elsevier, 2021. https://doi.org/10.1016/j.nanoen.2021.105991."},"article_type":"original","date_published":"2021-07-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Copper chalcogenides are outstanding thermoelectric materials for applications in the medium-high temperature range. Among different chalcogenides, while Cu2−xSe is characterized by higher thermoelectric figures of merit, Cu2−xS provides advantages in terms of low cost and element abundance. In the present work, we investigate the effect of different dopants to enhance the Cu2−xS performance and also its thermal stability. Among the tested options, Pb-doped Cu2−xS shows the highest improvement in stability against sulfur volatilization. Additionally, Pb incorporation allows tuning charge carrier concentration, which enables a significant improvement of the power factor. We demonstrate here that the introduction of an optimal additive amount of just 0.3% results in a threefold increase of the power factor in the middle-temperature range (500–800 K) and a record dimensionless thermoelectric figure of merit above 2 at 880 K."}],"issue":"7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9305","title":"Doping-mediated stabilization of copper vacancies to promote thermoelectric properties of Cu2-xS","status":"public","intvolume":" 85","oa_version":"Submitted Version"},{"article_number":"a039941","author":[{"full_name":"Cavallari, Nicola","last_name":"Cavallari","first_name":"Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Artner, Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","first_name":"Christina","last_name":"Artner"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"}],"volume":13,"date_created":"2021-03-01T10:08:32Z","date_updated":"2023-09-27T06:44:06Z","pmid":1,"year":"2021","acknowledgement":"We apologize to all the authors whose scientific work could not be cited and discussed because of space restrictions. We thank Dr. Inge Verstraeten (ISTAustria) and Dr. Juan Carlos Montesinos-Lopez (ETH Zürich) for helpful suggestions. This work was supported by the DOC Fellowship Programme of the Austrian Academy of Sciences (25008) to C.A.","department":[{"_id":"EvBe"}],"publisher":"Cold Spring Harbor Laboratory Press","publication_status":"published","publication_identifier":{"issn":["1943-0264"]},"month":"07","doi":"10.1101/cshperspect.a039941","language":[{"iso":"eng"}],"external_id":{"isi":["000692069100001"],"pmid":["33558367"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1101/cshperspect.a039941","open_access":"1"}],"project":[{"name":"Hormonal regulation of plant adaptive responses to environmental signals","_id":"2685A872-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","issue":"7","abstract":[{"lang":"eng","text":"Plant fitness is largely dependent on the root, the underground organ, which, besides its anchoring function, supplies the plant body with water and all nutrients necessary for growth and development. To exploit the soil effectively, roots must constantly integrate environmental signals and react through adjustment of growth and development. Important components of the root management strategy involve a rapid modulation of the root growth kinetics and growth direction, as well as an increase of the root system radius through formation of lateral roots (LRs). At the molecular level, such a fascinating growth and developmental flexibility of root organ requires regulatory networks that guarantee stability of the developmental program but also allows integration of various environmental inputs. The plant hormone auxin is one of the principal endogenous regulators of root system architecture by controlling primary root growth and formation of LR. In this review, we discuss recent progress in understanding molecular networks where auxin is one of the main players shaping the root system and acting as mediator between endogenous cues and environmental factors."}],"type":"journal_article","oa_version":"Published Version","_id":"9212","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 13","title":"Auxin-regulated lateral root organogenesis","status":"public","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2021-07-01T00:00:00Z","citation":{"ama":"Cavallari N, Artner C, Benková E. Auxin-regulated lateral root organogenesis. Cold Spring Harbor Perspectives in Biology. 2021;13(7). doi:10.1101/cshperspect.a039941","ista":"Cavallari N, Artner C, Benková E. 2021. Auxin-regulated lateral root organogenesis. Cold Spring Harbor Perspectives in Biology. 13(7), a039941.","ieee":"N. Cavallari, C. Artner, and E. Benková, “Auxin-regulated lateral root organogenesis,” Cold Spring Harbor Perspectives in Biology, vol. 13, no. 7. Cold Spring Harbor Laboratory Press, 2021.","apa":"Cavallari, N., Artner, C., & Benková, E. (2021). Auxin-regulated lateral root organogenesis. Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/cshperspect.a039941","mla":"Cavallari, Nicola, et al. “Auxin-Regulated Lateral Root Organogenesis.” Cold Spring Harbor Perspectives in Biology, vol. 13, no. 7, a039941, Cold Spring Harbor Laboratory Press, 2021, doi:10.1101/cshperspect.a039941.","short":"N. Cavallari, C. Artner, E. Benková, Cold Spring Harbor Perspectives in Biology 13 (2021).","chicago":"Cavallari, Nicola, Christina Artner, and Eva Benková. “Auxin-Regulated Lateral Root Organogenesis.” Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory Press, 2021. https://doi.org/10.1101/cshperspect.a039941."},"publication":"Cold Spring Harbor Perspectives in Biology","article_type":"original"},{"doi":"10.1016/j.bbi.2021.07.022","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.zora.uzh.ch/id/eprint/208855/1/ZORA208855.pdf"}],"external_id":{"isi":["000702878400007"],"pmid":["34343616"]},"oa":1,"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["0889-1591"]},"month":"10","author":[{"full_name":"Picard, Katherine","last_name":"Picard","first_name":"Katherine"},{"full_name":"Bisht, Kanchan","first_name":"Kanchan","last_name":"Bisht"},{"full_name":"Poggini, Silvia","last_name":"Poggini","first_name":"Silvia"},{"full_name":"Garofalo, Stefano","last_name":"Garofalo","first_name":"Stefano"},{"full_name":"Golia, Maria Teresa","first_name":"Maria Teresa","last_name":"Golia"},{"full_name":"Basilico, Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","orcid":"0000-0003-1843-3173","first_name":"Bernadette","last_name":"Basilico"},{"full_name":"Abdallah, Fatima","last_name":"Abdallah","first_name":"Fatima"},{"full_name":"Ciano Albanese, Naomi","first_name":"Naomi","last_name":"Ciano Albanese"},{"last_name":"Amrein","first_name":"Irmgard","full_name":"Amrein, Irmgard"},{"full_name":"Vernoux, Nathalie","first_name":"Nathalie","last_name":"Vernoux"},{"full_name":"Sharma, Kaushik","first_name":"Kaushik","last_name":"Sharma"},{"last_name":"Hui","first_name":"Chin Wai","full_name":"Hui, Chin Wai"},{"full_name":"C. Savage, Julie","last_name":"C. Savage","first_name":"Julie"},{"full_name":"Limatola, Cristina","first_name":"Cristina","last_name":"Limatola"},{"last_name":"Ragozzino","first_name":"Davide","full_name":"Ragozzino, Davide"},{"last_name":"Maggi","first_name":"Laura","full_name":"Maggi, Laura"},{"last_name":"Branchi","first_name":"Igor","full_name":"Branchi, Igor"},{"last_name":"Tremblay","first_name":"Marie Ève","full_name":"Tremblay, Marie Ève"}],"volume":97,"date_created":"2021-08-22T22:01:21Z","date_updated":"2023-10-03T09:49:18Z","pmid":1,"acknowledgement":"We acknowledge that Université Laval stands on the traditional and unceded land of the Huron-Wendat peoples; and that the University of Victoria exists on the territory of the Lekwungen peoples and that the Songhees, Esquimalt and WSÁNEÆ peoples have relationships to this land. We thank Emmanuel Planel for the access to the epifluorescence microscope and Julie-Christine Lévesque at the Bioimaging Platform of CRCHU de Québec-Université Laval for technical assistance. We also thank the Centre for Advanced Materials and Related Technology for the access to the confocal microscope with Airyscan. K.P. was supported by a doctoral scholarship from Fonds de Recherche du Québec – Santé (FRQS), an excellence award from Fondation du CHU de Québec, as well as from Centre Thématique de Recherche en Neurosciences and from Fondation Famille-Choquette. K.B. was supported by excellence scholarships from Université Laval and Fondation du CHU de Québec. S.G. is supported by FIRC-AIRC fellowship for Italy 22329/2018 and by Pilot ARISLA NKINALS 2019. C.W.H. and J.C.S. were supported by postdoctoral fellowships from FRQS. This study was funded by a Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery grant (RGPIN-2014-05308) awarded to M.E.T., by ERANET neuron 2017 MicroSynDep to M.E.T. and I.B., and by the Italian Ministry of Health, grant RF-2018-12367249 to I.B, by PRIN 2017, AIRC 2019 and Ministero della Salute RF2018 to C.L. M.E.T. is a Tier II Canada Research Chair in Neurobiology of Aging and Cognition.","year":"2021","department":[{"_id":"GaNo"}],"publisher":"Elsevier","publication_status":"published","date_published":"2021-10-01T00:00:00Z","citation":{"chicago":"Picard, Katherine, Kanchan Bisht, Silvia Poggini, Stefano Garofalo, Maria Teresa Golia, Bernadette Basilico, Fatima Abdallah, et al. “Microglial-Glucocorticoid Receptor Depletion Alters the Response of Hippocampal Microglia and Neurons in a Chronic Unpredictable Mild Stress Paradigm in Female Mice.” Brain, Behavior, and Immunity. Elsevier, 2021. https://doi.org/10.1016/j.bbi.2021.07.022.","short":"K. Picard, K. Bisht, S. Poggini, S. Garofalo, M.T. Golia, B. Basilico, F. Abdallah, N. Ciano Albanese, I. Amrein, N. Vernoux, K. Sharma, C.W. Hui, J. C. Savage, C. Limatola, D. Ragozzino, L. Maggi, I. Branchi, M.È. Tremblay, Brain, Behavior, and Immunity 97 (2021) 423–439.","mla":"Picard, Katherine, et al. “Microglial-Glucocorticoid Receptor Depletion Alters the Response of Hippocampal Microglia and Neurons in a Chronic Unpredictable Mild Stress Paradigm in Female Mice.” Brain, Behavior, and Immunity, vol. 97, Elsevier, 2021, pp. 423–39, doi:10.1016/j.bbi.2021.07.022.","apa":"Picard, K., Bisht, K., Poggini, S., Garofalo, S., Golia, M. T., Basilico, B., … Tremblay, M. È. (2021). Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice. Brain, Behavior, and Immunity. Elsevier. https://doi.org/10.1016/j.bbi.2021.07.022","ieee":"K. Picard et al., “Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice,” Brain, Behavior, and Immunity, vol. 97. Elsevier, pp. 423–439, 2021.","ista":"Picard K, Bisht K, Poggini S, Garofalo S, Golia MT, Basilico B, Abdallah F, Ciano Albanese N, Amrein I, Vernoux N, Sharma K, Hui CW, C. Savage J, Limatola C, Ragozzino D, Maggi L, Branchi I, Tremblay MÈ. 2021. Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice. Brain, Behavior, and Immunity. 97, 423–439.","ama":"Picard K, Bisht K, Poggini S, et al. Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice. Brain, Behavior, and Immunity. 2021;97:423-439. doi:10.1016/j.bbi.2021.07.022"},"publication":"Brain, Behavior, and Immunity","page":"423-439","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9953","intvolume":" 97","status":"public","title":"Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice","abstract":[{"lang":"eng","text":"Chronic psychological stress is one of the most important triggers and environmental risk factors for neuropsychiatric disorders. Chronic stress can influence all organs via the secretion of stress hormones, including glucocorticoids by the adrenal glands, which coordinate the stress response across the body. In the brain, glucocorticoid receptors (GR) are expressed by various cell types including microglia, which are its resident immune cells regulating stress-induced inflammatory processes. To study the roles of microglial GR under normal homeostatic conditions and following chronic stress, we generated a mouse model in which the GR gene is depleted in microglia specifically at adulthood to prevent developmental confounds. We first confirmed that microglia were depleted in GR in our model in males and females among the cingulate cortex and the hippocampus, both stress-sensitive brain regions. Then, cohorts of microglial-GR depleted and wild-type (WT) adult female mice were housed for 3 weeks in a standard or stressful condition, using a chronic unpredictable mild stress (CUMS) paradigm. CUMS induced stress-related behavior in both microglial-GR depleted and WT animals as demonstrated by a decrease of both saccharine preference and progressive ratio breakpoint. Nevertheless, the hippocampal microglial and neural mechanisms underlying the adaptation to stress occurred differently between the two genotypes. Upon CUMS exposure, microglial morphology was altered in the WT controls, without any apparent effect in microglial-GR depleted mice. Furthermore, in the standard environment condition, GR depleted-microglia showed increased expression of pro-inflammatory genes, and genes involved in microglial homeostatic functions (such as Trem2, Cx3cr1 and Mertk). On the contrary, in CUMS condition, GR depleted-microglia showed reduced expression levels of pro-inflammatory genes and increased neuroprotective as well as anti-inflammatory genes compared to WT-microglia. Moreover, in microglial-GR depleted mice, but not in WT mice, CUMS led to a significant reduction of CA1 long-term potentiation and paired-pulse ratio. Lastly, differences in adult hippocampal neurogenesis were observed between the genotypes during normal homeostatic conditions, with microglial-GR deficiency increasing the formation of newborn neurons in the dentate gyrus subgranular zone independently from stress exposure. Together, these findings indicate that, although the deletion of microglial GR did not prevent the animal’s ability to respond to stress, it contributed to modulating hippocampal functions in both standard and stressful conditions, notably by shaping the microglial response to chronic stress."}],"type":"journal_article"},{"ec_funded":1,"department":[{"_id":"MaIb"}],"publisher":"American Chemical Society ","publication_status":"published","pmid":1,"year":"2021","acknowledgement":"This work was supported by the European Regional Development Funds. M.L., Y.Z., X.H., and K.X. thank the China Scholarship Council for scholarship support. M. I. has been financially supported by IST Austria and the Werner Siemens Foundation. Y.L. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. J.L. is a Serra Húnter fellow and is grateful to ICREA Academia program and projects MICINN/FEDER RTI2018-093996-B-C31 and GC 2017 SGR 128. ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO project NANOGEN (PID2020-116093RB-C43). ICN2 was supported by the Severo Ochoa program from Spanish MINECO (grant no. SEV-2017-0706) and was funded by the CERCA Programme/Generalitat de Catalunya. X.H. thanks China Scholarship Council for scholarship support (201804910551). Part of the present work was performed in the framework of Universitat Autònoma de Barcelona Materials Science Ph.D. program.","volume":13,"date_updated":"2023-10-03T09:55:33Z","date_created":"2021-11-21T23:01:30Z","author":[{"first_name":"Mengyao","last_name":"Li","full_name":"Li, Mengyao"},{"full_name":"Liu, Yu","first_name":"Yu","last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7313-6740"},{"first_name":"Yu","last_name":"Zhang","full_name":"Zhang, Yu"},{"full_name":"Han, Xu","first_name":"Xu","last_name":"Han"},{"full_name":"Xiao, Ke","first_name":"Ke","last_name":"Xiao"},{"last_name":"Nabahat","first_name":"Mehran","full_name":"Nabahat, Mehran"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"first_name":"Jordi","last_name":"Llorca","full_name":"Llorca, Jordi"},{"full_name":"Ibáñez, Maria","last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"}],"publication_identifier":{"issn":["1944-8244"],"eissn":["1944-8252"]},"month":"10","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"pmid":["34665616"],"isi":["000715852100070"]},"main_file_link":[{"url":"https://upcommons.upc.edu/bitstream/2117/363528/1/Pb%20mengyao.pdf","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1021/acsami.1c15609","type":"journal_article","issue":"43","abstract":[{"lang":"eng","text":"Composite materials offer numerous advantages in a wide range of applications, including thermoelectrics. Here, semiconductor–metal composites are produced by just blending nanoparticles of a sulfide semiconductor obtained in aqueous solution and at room temperature with a metallic Cu powder. The obtained blend is annealed in a reducing atmosphere and afterward consolidated into dense polycrystalline pellets through spark plasma sintering (SPS). We observe that, during the annealing process, the presence of metallic copper activates a partial reduction of the PbS, resulting in the formation of PbS–Pb–CuxS composites. The presence of metallic lead during the SPS process habilitates the liquid-phase sintering of the composite. Besides, by comparing the transport properties of PbS, the PbS–Pb–CuxS composites, and PbS–CuxS composites obtained by blending PbS and CuxS nanoparticles, we demonstrate that the presence of metallic lead decisively contributes to a strong increase of the charge carrier concentration through spillover of charge carriers enabled by the low work function of lead. The increase in charge carrier concentration translates into much higher electrical conductivities and moderately lower Seebeck coefficients. These properties translate into power factors up to 2.1 mW m–1 K–2 at ambient temperature, well above those of PbS and PbS + CuxS. Additionally, the presence of multiple phases in the final composite results in a notable decrease in the lattice thermal conductivity. Overall, the introduction of metallic copper in the initial blend results in a significant improvement of the thermoelectric performance of PbS, reaching a dimensionless thermoelectric figure of merit ZT = 1.1 at 750 K, which represents about a 400% increase over bare PbS. Besides, an average ZTave = 0.72 in the temperature range 320–773 K is demonstrated."}],"intvolume":" 13","status":"public","title":"PbS–Pb–CuxS composites for thermoelectric application","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10327","oa_version":"Submitted Version","keyword":["CuxS","PbS","energy conversion","nanocomposite","nanoparticle","solution synthesis","thermoelectric"],"scopus_import":"1","article_processing_charge":"No","day":"19","page":"51373–51382","article_type":"original","citation":{"short":"M. Li, Y. Liu, Y. Zhang, X. Han, K. Xiao, M. Nabahat, J. Arbiol, J. Llorca, M. Ibáñez, A. Cabot, ACS Applied Materials and Interfaces 13 (2021) 51373–51382.","mla":"Li, Mengyao, et al. “PbS–Pb–CuxS Composites for Thermoelectric Application.” ACS Applied Materials and Interfaces, vol. 13, no. 43, American Chemical Society , 2021, pp. 51373–51382, doi:10.1021/acsami.1c15609.","chicago":"Li, Mengyao, Yu Liu, Yu Zhang, Xu Han, Ke Xiao, Mehran Nabahat, Jordi Arbiol, Jordi Llorca, Maria Ibáñez, and Andreu Cabot. “PbS–Pb–CuxS Composites for Thermoelectric Application.” ACS Applied Materials and Interfaces. American Chemical Society , 2021. https://doi.org/10.1021/acsami.1c15609.","ama":"Li M, Liu Y, Zhang Y, et al. PbS–Pb–CuxS composites for thermoelectric application. ACS Applied Materials and Interfaces. 2021;13(43):51373–51382. doi:10.1021/acsami.1c15609","apa":"Li, M., Liu, Y., Zhang, Y., Han, X., Xiao, K., Nabahat, M., … Cabot, A. (2021). PbS–Pb–CuxS composites for thermoelectric application. ACS Applied Materials and Interfaces. American Chemical Society . https://doi.org/10.1021/acsami.1c15609","ieee":"M. Li et al., “PbS–Pb–CuxS composites for thermoelectric application,” ACS Applied Materials and Interfaces, vol. 13, no. 43. American Chemical Society , pp. 51373–51382, 2021.","ista":"Li M, Liu Y, Zhang Y, Han X, Xiao K, Nabahat M, Arbiol J, Llorca J, Ibáñez M, Cabot A. 2021. PbS–Pb–CuxS composites for thermoelectric application. ACS Applied Materials and Interfaces. 13(43), 51373–51382."},"publication":"ACS Applied Materials and Interfaces","date_published":"2021-10-19T00:00:00Z"},{"publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]},"month":"03","quality_controlled":"1","isi":1,"external_id":{"pmid":["33645986"],"isi":["000634569100106"]},"oa":1,"main_file_link":[{"url":"https://upcommons.upc.edu/bitstream/handle/2117/363528/Pb%20mengyao.pdf?sequence=1&isAllowed=y","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1021/acsnano.0c09866","publisher":"American Chemical Society ","department":[{"_id":"MaIb"}],"publication_status":"published","pmid":1,"acknowledgement":"This work was supported by the European Regional Development Funds. M.Y.L., X.H., T.Z., and K.X. thank the China Scholarship Council for scholarship support. M.I. acknowledges financial support from IST Austria. J.L. acknowledges support from the National Natural Science Foundation of China (No. 22008091), the funding for scientific research startup of Jiangsu University (No. 19JDG044), and Jiangsu Provincial Program for High-Level Innovative and Entrepreneurial Talents Introduction. J.L. is a Serra Húnter fellow and is grateful to the ICREA Academia program and projects MICINN/FEDER RTI2018-093996-B-C31 and GC 2017 SGR 128. ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO ENE2017-85087-C3. ICN2 is supported by the Severo Ochoa program from Spanish MINECO (Grant No. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science PhD program. T.Z. has received funding from the CSC-UAB PhD scholarship program.","year":"2021","volume":15,"date_updated":"2023-10-03T09:59:55Z","date_created":"2021-03-10T20:12:45Z","author":[{"full_name":"Li, Mengyao","first_name":"Mengyao","last_name":"Li"},{"full_name":"Liu, Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7313-6740","first_name":"Yu","last_name":"Liu"},{"last_name":"Zhang","first_name":"Yu","full_name":"Zhang, Yu"},{"last_name":"Han","first_name":"Xu","full_name":"Han, Xu"},{"first_name":"Ting","last_name":"Zhang","full_name":"Zhang, Ting"},{"full_name":"Zuo, Yong","first_name":"Yong","last_name":"Zuo"},{"last_name":"Xie","first_name":"Chenyang","full_name":"Xie, Chenyang"},{"full_name":"Xiao, Ke","first_name":"Ke","last_name":"Xiao"},{"first_name":"Jordi","last_name":"Arbiol","full_name":"Arbiol, Jordi"},{"last_name":"Llorca","first_name":"Jordi","full_name":"Llorca, Jordi"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria"},{"last_name":"Liu","first_name":"Junfeng","full_name":"Liu, Junfeng"},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"}],"keyword":["General Engineering","General Physics and Astronomy","General Materials Science"],"scopus_import":"1","article_processing_charge":"No","day":"01","page":"4967–4978","article_type":"original","citation":{"ama":"Li M, Liu Y, Zhang Y, et al. Effect of the annealing atmosphere on crystal phase and thermoelectric properties of copper sulfide. ACS Nano. 2021;15(3):4967–4978. doi:10.1021/acsnano.0c09866","ista":"Li M, Liu Y, Zhang Y, Han X, Zhang T, Zuo Y, Xie C, Xiao K, Arbiol J, Llorca J, Ibáñez M, Liu J, Cabot A. 2021. Effect of the annealing atmosphere on crystal phase and thermoelectric properties of copper sulfide. ACS Nano. 15(3), 4967–4978.","apa":"Li, M., Liu, Y., Zhang, Y., Han, X., Zhang, T., Zuo, Y., … Cabot, A. (2021). Effect of the annealing atmosphere on crystal phase and thermoelectric properties of copper sulfide. ACS Nano. American Chemical Society . https://doi.org/10.1021/acsnano.0c09866","ieee":"M. Li et al., “Effect of the annealing atmosphere on crystal phase and thermoelectric properties of copper sulfide,” ACS Nano, vol. 15, no. 3. American Chemical Society , pp. 4967–4978, 2021.","mla":"Li, Mengyao, et al. “Effect of the Annealing Atmosphere on Crystal Phase and Thermoelectric Properties of Copper Sulfide.” ACS Nano, vol. 15, no. 3, American Chemical Society , 2021, pp. 4967–4978, doi:10.1021/acsnano.0c09866.","short":"M. Li, Y. Liu, Y. Zhang, X. Han, T. Zhang, Y. Zuo, C. Xie, K. Xiao, J. Arbiol, J. Llorca, M. Ibáñez, J. Liu, A. Cabot, ACS Nano 15 (2021) 4967–4978.","chicago":"Li, Mengyao, Yu Liu, Yu Zhang, Xu Han, Ting Zhang, Yong Zuo, Chenyang Xie, et al. “Effect of the Annealing Atmosphere on Crystal Phase and Thermoelectric Properties of Copper Sulfide.” ACS Nano. American Chemical Society , 2021. https://doi.org/10.1021/acsnano.0c09866."},"publication":"ACS Nano","date_published":"2021-03-01T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"text":"Cu2–xS has become one of the most promising thermoelectric materials for application in the middle-high temperature range. Its advantages include the abundance, low cost, and safety of its elements and a high performance at relatively elevated temperatures. However, stability issues limit its operation current and temperature, thus calling for the optimization of the material performance in the middle temperature range. Here, we present a synthetic protocol for large scale production of covellite CuS nanoparticles at ambient temperature and atmosphere, and using water as a solvent. The crystal phase and stoichiometry of the particles are afterward tuned through an annealing process at a moderate temperature under inert or reducing atmosphere. While annealing under argon results in Cu1.8S nanopowder with a rhombohedral crystal phase, annealing in an atmosphere containing hydrogen leads to tetragonal Cu1.96S. High temperature X-ray diffraction analysis shows the material annealed in argon to transform to the cubic phase at ca. 400 K, while the material annealed in the presence of hydrogen undergoes two phase transitions, first to hexagonal and then to the cubic structure. The annealing atmosphere, temperature, and time allow adjustment of the density of copper vacancies and thus tuning of the charge carrier concentration and material transport properties. In this direction, the material annealed under Ar is characterized by higher electrical conductivities but lower Seebeck coefficients than the material annealed in the presence of hydrogen. By optimizing the charge carrier concentration through the annealing time, Cu2–xS with record figures of merit in the middle temperature range, up to 1.41 at 710 K, is obtained. We finally demonstrate that this strategy, based on a low-cost and scalable solution synthesis process, is also suitable for the production of high performance Cu2–xS layers using high throughput and cost-effective printing technologies.","lang":"eng"}],"intvolume":" 15","status":"public","title":"Effect of the annealing atmosphere on crystal phase and thermoelectric properties of copper sulfide","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9235","oa_version":"Submitted Version"},{"publisher":"Royal Society of Chemistry ","department":[{"_id":"HeEd"}],"publication_status":"published","pmid":1,"year":"2021","acknowledgement":"MS acknowledges the support by Australian Research Council funding through the ARC Training Centre for M3D Innovation (IC180100008). MS thanks M. Hanifpour and N. Francois for their input and valuable discussions. 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 and from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.","volume":17,"date_created":"2021-10-31T23:01:30Z","date_updated":"2023-10-03T09:24:27Z","author":[{"last_name":"Osang","first_name":"Georg F","orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","full_name":"Osang, Georg F"},{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"full_name":"Saadatfar, Mohammad","first_name":"Mohammad","last_name":"Saadatfar"}],"ec_funded":1,"file_date_updated":"2023-10-03T09:21:42Z","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","call_identifier":"H2020","name":"Alpha Shape Theory Extended"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000700090000001"],"pmid":["34569592"]},"language":[{"iso":"eng"}],"doi":"10.1039/d1sm00774b","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"month":"10","intvolume":" 17","ddc":["540"],"title":"Topological signatures and stability of hexagonal close packing and Barlow stackings","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10204","file":[{"access_level":"open_access","file_name":"2021_SoftMatter_acceptedversion_Osang.pdf","content_type":"application/pdf","file_size":4678788,"creator":"dernst","relation":"main_file","file_id":"14385","checksum":"b4da0c420530295e61b153960f6cb350","success":1,"date_updated":"2023-10-03T09:21:42Z","date_created":"2023-10-03T09:21:42Z"}],"oa_version":"Submitted Version","type":"journal_article","issue":"40","abstract":[{"text":"Two common representations of close packings of identical spheres consisting of hexagonal layers, called Barlow stackings, appear abundantly in minerals and metals. These motifs, however, occupy an identical portion of space and bear identical first-order topological signatures as measured by persistent homology. Here we present a novel method based on k-fold covers that unambiguously distinguishes between these patterns. Moreover, our approach provides topological evidence that the FCC motif is the more stable of the two in the context of evolving experimental sphere packings during the transition from disordered to an ordered state. We conclude that our approach can be generalised to distinguish between various Barlow stackings manifested in minerals and metals.","lang":"eng"}],"page":"9107-9115","article_type":"original","citation":{"ista":"Osang GF, Edelsbrunner H, Saadatfar M. 2021. Topological signatures and stability of hexagonal close packing and Barlow stackings. Soft Matter. 17(40), 9107–9115.","ieee":"G. F. Osang, H. Edelsbrunner, and M. Saadatfar, “Topological signatures and stability of hexagonal close packing and Barlow stackings,” Soft Matter, vol. 17, no. 40. Royal Society of Chemistry , pp. 9107–9115, 2021.","apa":"Osang, G. F., Edelsbrunner, H., & Saadatfar, M. (2021). Topological signatures and stability of hexagonal close packing and Barlow stackings. Soft Matter. Royal Society of Chemistry . https://doi.org/10.1039/d1sm00774b","ama":"Osang GF, Edelsbrunner H, Saadatfar M. Topological signatures and stability of hexagonal close packing and Barlow stackings. Soft Matter. 2021;17(40):9107-9115. doi:10.1039/d1sm00774b","chicago":"Osang, Georg F, Herbert Edelsbrunner, and Mohammad Saadatfar. “Topological Signatures and Stability of Hexagonal Close Packing and Barlow Stackings.” Soft Matter. Royal Society of Chemistry , 2021. https://doi.org/10.1039/d1sm00774b.","mla":"Osang, Georg F., et al. “Topological Signatures and Stability of Hexagonal Close Packing and Barlow Stackings.” Soft Matter, vol. 17, no. 40, Royal Society of Chemistry , 2021, pp. 9107–15, doi:10.1039/d1sm00774b.","short":"G.F. Osang, H. Edelsbrunner, M. Saadatfar, Soft Matter 17 (2021) 9107–9115."},"publication":"Soft Matter","date_published":"2021-10-20T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"20"},{"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9464","status":"public","title":"Ge/Si quantum wires for quantum computing","abstract":[{"lang":"eng","text":"We firstly introduce the self-assembled growth of highly uniform Ge quantum wires with controllable position, distance and length on patterned Si (001) substrates. We then present the electrically tunable strong spin-orbit coupling, the first Ge hole spin qubit and ultrafast operation of hole spin qubit in the Ge/Si quantum wires."}],"type":"conference","date_published":"2021-04-08T00:00:00Z","publication":"2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021","citation":{"apa":"Gao, F., Zhang, J. Y., Wang, J. H., Ming, M., Wang, T., Zhang, J. J., … Guo, G. P. (2021). Ge/Si quantum wires for quantum computing. In 2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021. Virtual, Online: IEEE. https://doi.org/10.1109/EDTM50988.2021.9420817","ieee":"F. Gao et al., “Ge/Si quantum wires for quantum computing,” in 2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021, Virtual, Online, 2021.","ista":"Gao F, Zhang JY, Wang JH, Ming M, Wang T, Zhang JJ, Watzinger H, Kukucka J, Vukušić L, Katsaros G, Wang K, Xu G, Li HO, Guo GP. 2021. Ge/Si quantum wires for quantum computing. 2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021. EDTM: IEEE Electron Devices Technology and Manufacturing Conference, 9420817.","ama":"Gao F, Zhang JY, Wang JH, et al. Ge/Si quantum wires for quantum computing. In: 2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021. IEEE; 2021. doi:10.1109/EDTM50988.2021.9420817","chicago":"Gao, Fei, Jie Yin Zhang, Jian Huan Wang, Ming Ming, Tina Wang, Jian Jun Zhang, Hannes Watzinger, et al. “Ge/Si Quantum Wires for Quantum Computing.” In 2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021. IEEE, 2021. https://doi.org/10.1109/EDTM50988.2021.9420817.","short":"F. Gao, J.Y. Zhang, J.H. Wang, M. Ming, T. Wang, J.J. Zhang, H. Watzinger, J. Kukucka, L. Vukušić, G. Katsaros, K. Wang, G. Xu, H.O. Li, G.P. Guo, in:, 2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021, IEEE, 2021.","mla":"Gao, Fei, et al. “Ge/Si Quantum Wires for Quantum Computing.” 2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021, 9420817, IEEE, 2021, doi:10.1109/EDTM50988.2021.9420817."},"day":"08","article_processing_charge":"No","scopus_import":"1","author":[{"last_name":"Gao","first_name":"Fei","full_name":"Gao, Fei"},{"first_name":"Jie Yin","last_name":"Zhang","full_name":"Zhang, Jie Yin"},{"full_name":"Wang, Jian Huan","first_name":"Jian Huan","last_name":"Wang"},{"full_name":"Ming, Ming","last_name":"Ming","first_name":"Ming"},{"full_name":"Wang, Tina","last_name":"Wang","first_name":"Tina"},{"last_name":"Zhang","first_name":"Jian Jun","full_name":"Zhang, Jian Jun"},{"full_name":"Watzinger, Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes","last_name":"Watzinger"},{"full_name":"Kukucka, Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip","last_name":"Kukucka"},{"full_name":"Vukušić, Lada","first_name":"Lada","last_name":"Vukušić","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2424-8636"},{"orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios","full_name":"Katsaros, Georgios"},{"full_name":"Wang, Ke","last_name":"Wang","first_name":"Ke"},{"full_name":"Xu, Gang","first_name":"Gang","last_name":"Xu"},{"last_name":"Li","first_name":"Hai Ou","full_name":"Li, Hai Ou"},{"full_name":"Guo, Guo Ping","first_name":"Guo Ping","last_name":"Guo"}],"date_created":"2021-06-06T22:01:29Z","date_updated":"2023-10-03T12:51:59Z","acknowledgement":"This work was supported by the National Key R&D Program of China (Grant No. 2016YFA0301700) and the ERC Starting Grant no. 335497.","year":"2021","publication_status":"published","publisher":"IEEE","department":[{"_id":"GeKa"}],"ec_funded":1,"article_number":"9420817","conference":{"name":"EDTM: IEEE Electron Devices Technology and Manufacturing Conference","start_date":"2021-04-08","location":"Virtual, Online","end_date":"2021-04-11"},"doi":"10.1109/EDTM50988.2021.9420817","language":[{"iso":"eng"}],"external_id":{"isi":["000675595800006"]},"isi":1,"quality_controlled":"1","project":[{"name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","call_identifier":"FP7","grant_number":"335497","_id":"25517E86-B435-11E9-9278-68D0E5697425"}],"month":"04","publication_identifier":{"isbn":["9781728181769"]}},{"article_processing_charge":"No","has_accepted_license":"1","day":"02","scopus_import":"1","date_published":"2021-06-02T00:00:00Z","citation":{"chicago":"Corbet, René, Michael Kerber, Michael Lesnick, and Georg F Osang. “Computing the Multicover Bifiltration.” In Leibniz International Proceedings in Informatics, Vol. 189. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. https://doi.org/10.4230/LIPIcs.SoCG.2021.27.","short":"R. Corbet, M. Kerber, M. Lesnick, G.F. Osang, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","mla":"Corbet, René, et al. “Computing the Multicover Bifiltration.” Leibniz International Proceedings in Informatics, vol. 189, 27, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:10.4230/LIPIcs.SoCG.2021.27.","ieee":"R. Corbet, M. Kerber, M. Lesnick, and G. F. Osang, “Computing the multicover bifiltration,” in Leibniz International Proceedings in Informatics, Online, 2021, vol. 189.","apa":"Corbet, R., Kerber, M., Lesnick, M., & Osang, G. F. (2021). Computing the multicover bifiltration. In Leibniz International Proceedings in Informatics (Vol. 189). Online: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2021.27","ista":"Corbet R, Kerber M, Lesnick M, Osang GF. 2021. Computing the multicover bifiltration. Leibniz International Proceedings in Informatics. SoCG: International Symposium on Computational Geometry, LIPIcs, vol. 189, 27.","ama":"Corbet R, Kerber M, Lesnick M, Osang GF. Computing the multicover bifiltration. In: Leibniz International Proceedings in Informatics. Vol 189. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:10.4230/LIPIcs.SoCG.2021.27"},"publication":"Leibniz International Proceedings in Informatics","abstract":[{"text":"Given a finite set A ⊂ ℝ^d, let Cov_{r,k} denote the set of all points within distance r to at least k points of A. Allowing r and k to vary, we obtain a 2-parameter family of spaces that grow larger when r increases or k decreases, called the multicover bifiltration. Motivated by the problem of computing the homology of this bifiltration, we introduce two closely related combinatorial bifiltrations, one polyhedral and the other simplicial, which are both topologically equivalent to the multicover bifiltration and far smaller than a Čech-based model considered in prior work of Sheehy. Our polyhedral construction is a bifiltration of the rhomboid tiling of Edelsbrunner and Osang, and can be efficiently computed using a variant of an algorithm given by these authors as well. Using an implementation for dimension 2 and 3, we provide experimental results. Our simplicial construction is useful for understanding the polyhedral construction and proving its correctness. ","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference","file":[{"creator":"cziletti","file_size":"1367983","content_type":"application/pdf","access_level":"open_access","file_name":"2021_LIPIcs_Corbet.pdf","success":1,"checksum":"0de217501e7ba8b267d58deed0d51761","date_created":"2021-06-28T12:40:47Z","date_updated":"2021-06-28T12:40:47Z","file_id":"9610","relation":"main_file"}],"oa_version":"Published Version","intvolume":" 189","title":"Computing the multicover bifiltration","status":"public","ddc":["516"],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"9605","publication_identifier":{"isbn":["9783959771849"],"issn":["18688969"]},"month":"06","language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.SoCG.2021.27","conference":{"end_date":"2021-06-11","start_date":"2021-06-07","location":"Online","name":"SoCG: International Symposium on Computational Geometry"},"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2103.07823"]},"file_date_updated":"2021-06-28T12:40:47Z","article_number":"27","volume":189,"date_updated":"2023-10-04T12:03:39Z","date_created":"2021-06-27T22:01:49Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"12709"}],"link":[{"url":"https://arxiv.org/abs/2103.07823","relation":"extended_version"}]},"author":[{"first_name":"René","last_name":"Corbet","full_name":"Corbet, René"},{"last_name":"Kerber","first_name":"Michael","full_name":"Kerber, Michael"},{"full_name":"Lesnick, Michael","first_name":"Michael","last_name":"Lesnick"},{"full_name":"Osang, Georg F","last_name":"Osang","first_name":"Georg F","orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2021","acknowledgement":"The authors want to thank the reviewers for many helpful comments and suggestions."},{"file_date_updated":"2021-06-02T10:22:33Z","ec_funded":1,"place":"Dagstuhl, Germany","date_updated":"2023-10-10T07:34:34Z","date_created":"2021-06-02T10:10:55Z","volume":189,"author":[{"first_name":"Jean-Daniel","last_name":"Boissonnat","full_name":"Boissonnat, Jean-Daniel"},{"full_name":"Kachanovich, Siargey","first_name":"Siargey","last_name":"Kachanovich"},{"full_name":"Wintraecken, Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220","first_name":"Mathijs","last_name":"Wintraecken"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"12960"}]},"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"HeEd"}],"year":"2021","acknowledgement":"We thank Dominique Attali, Guilherme de Fonseca, Arijit Ghosh, Vincent Pilaud and Aurélien Alvarez for their comments and suggestions. We also acknowledge the reviewers.","month":"06","publication_identifier":{"isbn":["978-3-95977-184-9"],"issn":["1868-8969"]},"language":[{"iso":"eng"}],"conference":{"location":"Virtual","start_date":"2021-06-07","end_date":"2021-06-11","name":"SoCG: Symposium on Computational Geometry"},"doi":"10.4230/LIPIcs.SoCG.2021.17","quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"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":[{"text":"Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. submanifolds of ℝ^d defined as the zero set of some multivariate multivalued smooth function f: ℝ^d → ℝ^{d-n}, where n is the intrinsic dimension of the manifold. A natural way to approximate a smooth isomanifold M is to consider its Piecewise-Linear (PL) approximation M̂ based on a triangulation 𝒯 of the ambient space ℝ^d. In this paper, we describe a simple algorithm to trace isomanifolds from a given starting point. The algorithm works for arbitrary dimensions n and d, and any precision D. Our main result is that, when f (or M) has bounded complexity, the complexity of the algorithm is polynomial in d and δ = 1/D (and unavoidably exponential in n). Since it is known that for δ = Ω (d^{2.5}), M̂ is O(D²)-close and isotopic to M, our algorithm produces a faithful PL-approximation of isomanifolds of bounded complexity in time polynomial in d. Combining this algorithm with dimensionality reduction techniques, the dependency on d in the size of M̂ can be completely removed with high probability. We also show that the algorithm can handle isomanifolds with boundary and, more generally, isostratifolds. The algorithm for isomanifolds with boundary has been implemented and experimental results are reported, showing that it is practical and can handle cases that are far ahead of the state-of-the-art. ","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference","file":[{"access_level":"open_access","file_name":"LIPIcs-SoCG-2021-17.pdf","creator":"mwintrae","content_type":"application/pdf","file_size":1972902,"file_id":"9442","relation":"main_file","success":1,"checksum":"c322aa48d5d35a35877896cc565705b6","date_updated":"2021-06-02T10:22:33Z","date_created":"2021-06-02T10:22:33Z"}],"oa_version":"Published Version","ddc":["005","516","514"],"title":"Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations","status":"public","intvolume":" 189","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"9441","day":"02","has_accepted_license":"1","article_processing_charge":"No","series_title":"Leibniz International Proceedings in Informatics (LIPIcs)","date_published":"2021-06-02T00:00:00Z","page":"17:1-17:16","publication":"37th International Symposium on Computational Geometry (SoCG 2021)","citation":{"ama":"Boissonnat J-D, Kachanovich S, Wintraecken M. Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations. In: 37th International Symposium on Computational Geometry (SoCG 2021). Vol 189. Leibniz International Proceedings in Informatics (LIPIcs). Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021:17:1-17:16. doi:10.4230/LIPIcs.SoCG.2021.17","ista":"Boissonnat J-D, Kachanovich S, Wintraecken M. 2021. Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations. 37th International Symposium on Computational Geometry (SoCG 2021). SoCG: Symposium on Computational GeometryLeibniz International Proceedings in Informatics (LIPIcs), LIPIcs, vol. 189, 17:1-17:16.","ieee":"J.-D. Boissonnat, S. Kachanovich, and M. Wintraecken, “Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations,” in 37th International Symposium on Computational Geometry (SoCG 2021), Virtual, 2021, vol. 189, p. 17:1-17:16.","apa":"Boissonnat, J.-D., Kachanovich, S., & Wintraecken, M. (2021). Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations. In 37th International Symposium on Computational Geometry (SoCG 2021) (Vol. 189, p. 17:1-17:16). Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2021.17","mla":"Boissonnat, Jean-Daniel, et al. “Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter-Freudenthal-Kuhn Triangulations.” 37th International Symposium on Computational Geometry (SoCG 2021), vol. 189, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, p. 17:1-17:16, doi:10.4230/LIPIcs.SoCG.2021.17.","short":"J.-D. Boissonnat, S. Kachanovich, M. Wintraecken, in:, 37th International Symposium on Computational Geometry (SoCG 2021), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, Dagstuhl, Germany, 2021, p. 17:1-17:16.","chicago":"Boissonnat, Jean-Daniel, Siargey Kachanovich, and Mathijs Wintraecken. “Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter-Freudenthal-Kuhn Triangulations.” In 37th International Symposium on Computational Geometry (SoCG 2021), 189:17:1-17:16. Leibniz International Proceedings in Informatics (LIPIcs). Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. https://doi.org/10.4230/LIPIcs.SoCG.2021.17."}},{"abstract":[{"text":"We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean-payoff, the ratio, and the minimum initial credit for energy property. The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with bounded treewidth—a class that contains the control flow graphs of most programs. Let n denote the number of nodes of a graph, m the number of edges (for bounded treewidth 𝑚=𝑂(𝑛)) and W the largest absolute value of the weights. Our main theoretical results are as follows. First, for the minimum initial credit problem we show that (1) for general graphs the problem can be solved in 𝑂(𝑛2⋅𝑚) time and the associated decision problem in 𝑂(𝑛⋅𝑚) time, improving the previous known 𝑂(𝑛3⋅𝑚⋅log(𝑛⋅𝑊)) and 𝑂(𝑛2⋅𝑚) bounds, respectively; and (2) for bounded treewidth graphs we present an algorithm that requires 𝑂(𝑛⋅log𝑛) time. Second, for bounded treewidth graphs we present an algorithm that approximates the mean-payoff value within a factor of 1+𝜖 in time 𝑂(𝑛⋅log(𝑛/𝜖)) as compared to the classical exact algorithms on general graphs that require quadratic time. Third, for the ratio property we present an algorithm that for bounded treewidth graphs works in time 𝑂(𝑛⋅log(|𝑎⋅𝑏|))=𝑂(𝑛⋅log(𝑛⋅𝑊)), when the output is 𝑎𝑏, as compared to the previously best known algorithm on general graphs with running time 𝑂(𝑛2⋅log(𝑛⋅𝑊)). We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 57","status":"public","title":"Faster algorithms for quantitative verification in bounded treewidth graphs","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9393","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2021-09-01T00:00:00Z","page":"401-428","article_type":"original","citation":{"short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Formal Methods in System Design 57 (2021) 401–428.","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Quantitative Verification in Bounded Treewidth Graphs.” Formal Methods in System Design, vol. 57, Springer, 2021, pp. 401–28, doi:10.1007/s10703-021-00373-5.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Verification in Bounded Treewidth Graphs.” Formal Methods in System Design. Springer, 2021. https://doi.org/10.1007/s10703-021-00373-5.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for quantitative verification in bounded treewidth graphs. Formal Methods in System Design. 2021;57:401-428. doi:10.1007/s10703-021-00373-5","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for quantitative verification in bounded treewidth graphs,” Formal Methods in System Design, vol. 57. Springer, pp. 401–428, 2021.","apa":"Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2021). Faster algorithms for quantitative verification in bounded treewidth graphs. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-021-00373-5","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2021. Faster algorithms for quantitative verification in bounded treewidth graphs. Formal Methods in System Design. 57, 401–428."},"publication":"Formal Methods in System Design","ec_funded":1,"volume":57,"date_updated":"2023-10-10T11:13:20Z","date_created":"2021-05-16T22:01:47Z","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2021","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start Grant (279307: Graph Games), and Microsoft faculty fellows award.","publication_identifier":{"eissn":["1572-8102"],"issn":["0925-9856"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1007/s10703-021-00373-5","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1504.07384"],"isi":["000645490300001"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.07384"}]},{"article_processing_charge":"No","publication_identifier":{"isbn":["9783030678982"],"eissn":["1611-3349"],"issn":["0302-9743"]},"month":"01","day":"28","scopus_import":"1","doi":"10.1007/978-3-030-67899-9_28","date_published":"2021-01-28T00:00:00Z","conference":{"start_date":"2021-02-11","location":"Rupnagar, India","end_date":"2021-02-13","name":"CALDAM: Conference on Algorithms and Discrete Applied Mathematics"},"language":[{"iso":"eng"}],"citation":{"ama":"Bloch-Hansen A, Samei N, Solis-Oba R. Experimental evaluation of a local search approximation algorithm for the multiway cut problem. In: Conference on Algorithms and Discrete Applied Mathematics. Vol 12601. Springer Nature; 2021:346-358. doi:10.1007/978-3-030-67899-9_28","ieee":"A. Bloch-Hansen, N. Samei, and R. Solis-Oba, “Experimental evaluation of a local search approximation algorithm for the multiway cut problem,” in Conference on Algorithms and Discrete Applied Mathematics, Rupnagar, India, 2021, vol. 12601, pp. 346–358.","apa":"Bloch-Hansen, A., Samei, N., & Solis-Oba, R. (2021). Experimental evaluation of a local search approximation algorithm for the multiway cut problem. In Conference on Algorithms and Discrete Applied Mathematics (Vol. 12601, pp. 346–358). Rupnagar, India: Springer Nature. https://doi.org/10.1007/978-3-030-67899-9_28","ista":"Bloch-Hansen A, Samei N, Solis-Oba R. 2021. Experimental evaluation of a local search approximation algorithm for the multiway cut problem. Conference on Algorithms and Discrete Applied Mathematics. CALDAM: Conference on Algorithms and Discrete Applied Mathematics, LNCS, vol. 12601, 346–358.","short":"A. Bloch-Hansen, N. Samei, R. Solis-Oba, in:, Conference on Algorithms and Discrete Applied Mathematics, Springer Nature, 2021, pp. 346–358.","mla":"Bloch-Hansen, Andrew, et al. “Experimental Evaluation of a Local Search Approximation Algorithm for the Multiway Cut Problem.” Conference on Algorithms and Discrete Applied Mathematics, vol. 12601, Springer Nature, 2021, pp. 346–58, doi:10.1007/978-3-030-67899-9_28.","chicago":"Bloch-Hansen, Andrew, Nasim Samei, and Roberto Solis-Oba. “Experimental Evaluation of a Local Search Approximation Algorithm for the Multiway Cut Problem.” In Conference on Algorithms and Discrete Applied Mathematics, 12601:346–58. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-67899-9_28."},"publication":"Conference on Algorithms and Discrete Applied Mathematics","page":"346-358","quality_controlled":"1","abstract":[{"lang":"eng","text":"In the multiway cut problem we are given a weighted undirected graph G=(V,E) and a set T⊆V of k terminals. The goal is to find a minimum weight set of edges E′⊆E with the property that by removing E′ from G all the terminals become disconnected. In this paper we present a simple local search approximation algorithm for the multiway cut problem with approximation ratio 2−2k . We present an experimental evaluation of the performance of our local search algorithm and show that it greatly outperforms the isolation heuristic of Dalhaus et al. and it has similar performance as the much more complex algorithms of Calinescu et al., Sharma and Vondrak, and Buchbinder et al. which have the currently best known approximation ratios for this problem."}],"type":"conference","alternative_title":["LNCS"],"author":[{"last_name":"Bloch-Hansen","first_name":"Andrew","full_name":"Bloch-Hansen, Andrew"},{"full_name":"Samei, Nasim","last_name":"Samei","first_name":"Nasim","id":"C1531CAE-36E9-11EA-845F-33AA3DDC885E"},{"first_name":"Roberto","last_name":"Solis-Oba","full_name":"Solis-Oba, Roberto"}],"oa_version":"None","volume":12601,"date_updated":"2023-10-10T09:29:08Z","date_created":"2021-03-07T23:01:25Z","_id":"9227","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","department":[{"_id":"VlKo"}],"publisher":"Springer Nature","intvolume":" 12601","title":"Experimental evaluation of a local search approximation algorithm for the multiway cut problem","publication_status":"published","status":"public"},{"_id":"8817","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 93","status":"public","title":"An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems","oa_version":"None","type":"journal_article","issue":"2","abstract":[{"text":"The paper introduces an inertial extragradient subgradient method with self-adaptive step sizes for solving equilibrium problems in real Hilbert spaces. Weak convergence of the proposed method is obtained under the condition that the bifunction is pseudomonotone and Lipchitz continuous. Linear convergence is also given when the bifunction is strongly pseudomonotone and Lipchitz continuous. Numerical implementations and comparisons with other related inertial methods are given using test problems including a real-world application to Nash–Cournot oligopolistic electricity market equilibrium model.","lang":"eng"}],"citation":{"chicago":"Shehu, Yekini, Olaniyi S. Iyiola, Duong Viet Thong, and Nguyen Thi Cam Van. “An Inertial Subgradient Extragradient Algorithm Extended to Pseudomonotone Equilibrium Problems.” Mathematical Methods of Operations Research. Springer Nature, 2021. https://doi.org/10.1007/s00186-020-00730-w.","mla":"Shehu, Yekini, et al. “An Inertial Subgradient Extragradient Algorithm Extended to Pseudomonotone Equilibrium Problems.” Mathematical Methods of Operations Research, vol. 93, no. 2, Springer Nature, 2021, pp. 213–42, doi:10.1007/s00186-020-00730-w.","short":"Y. Shehu, O.S. Iyiola, D.V. Thong, N.T.C. Van, Mathematical Methods of Operations Research 93 (2021) 213–242.","ista":"Shehu Y, Iyiola OS, Thong DV, Van NTC. 2021. An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems. Mathematical Methods of Operations Research. 93(2), 213–242.","apa":"Shehu, Y., Iyiola, O. S., Thong, D. V., & Van, N. T. C. (2021). An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems. Mathematical Methods of Operations Research. Springer Nature. https://doi.org/10.1007/s00186-020-00730-w","ieee":"Y. Shehu, O. S. Iyiola, D. V. Thong, and N. T. C. Van, “An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems,” Mathematical Methods of Operations Research, vol. 93, no. 2. Springer Nature, pp. 213–242, 2021.","ama":"Shehu Y, Iyiola OS, Thong DV, Van NTC. An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems. Mathematical Methods of Operations Research. 2021;93(2):213-242. doi:10.1007/s00186-020-00730-w"},"publication":"Mathematical Methods of Operations Research","page":"213-242","article_type":"original","date_published":"2021-04-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","year":"2021","acknowledgement":"The authors are grateful to the two referees and the Associate Editor for their comments and suggestions which have improved the earlier version of the paper greatly. The project of Yekini Shehu has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7 - 2007-2013) (Grant agreement No. 616160).","department":[{"_id":"VlKo"}],"publisher":"Springer Nature","publication_status":"published","author":[{"id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9224-7139","first_name":"Yekini","last_name":"Shehu","full_name":"Shehu, Yekini"},{"full_name":"Iyiola, Olaniyi S.","first_name":"Olaniyi S.","last_name":"Iyiola"},{"full_name":"Thong, Duong Viet","last_name":"Thong","first_name":"Duong Viet"},{"full_name":"Van, Nguyen Thi Cam","last_name":"Van","first_name":"Nguyen Thi Cam"}],"volume":93,"date_created":"2020-11-29T23:01:18Z","date_updated":"2023-10-10T09:30:23Z","ec_funded":1,"external_id":{"isi":["000590497300001"]},"project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","doi":"10.1007/s00186-020-00730-w","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1432-5217"],"issn":["1432-2994"]},"month":"04"},{"publication_identifier":{"issn":["1422-6383"],"eissn":["1420-9012"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1007/s00025-021-01381-x","isi":1,"quality_controlled":"1","external_id":{"isi":["000632917700001"]},"article_number":"75","volume":76,"date_updated":"2023-10-10T09:47:33Z","date_created":"2021-04-11T22:01:14Z","author":[{"full_name":"Iyiola, Olaniyi S.","first_name":"Olaniyi S.","last_name":"Iyiola"},{"orcid":"0000-0001-9224-7139","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","last_name":"Shehu","first_name":"Yekini","full_name":"Shehu, Yekini"}],"publisher":"Springer Nature","department":[{"_id":"VlKo"}],"publication_status":"published","acknowledgement":"The research of this author is supported by the Postdoctoral Fellowship from Institute of Science and Technology (IST), Austria.","year":"2021","article_processing_charge":"No","day":"25","scopus_import":"1","date_published":"2021-03-25T00:00:00Z","article_type":"original","citation":{"ista":"Iyiola OS, Shehu Y. 2021. New convergence results for inertial Krasnoselskii–Mann iterations in Hilbert spaces with applications. Results in Mathematics. 76(2), 75.","ieee":"O. S. Iyiola and Y. Shehu, “New convergence results for inertial Krasnoselskii–Mann iterations in Hilbert spaces with applications,” Results in Mathematics, vol. 76, no. 2. Springer Nature, 2021.","apa":"Iyiola, O. S., & Shehu, Y. (2021). New convergence results for inertial Krasnoselskii–Mann iterations in Hilbert spaces with applications. Results in Mathematics. Springer Nature. https://doi.org/10.1007/s00025-021-01381-x","ama":"Iyiola OS, Shehu Y. New convergence results for inertial Krasnoselskii–Mann iterations in Hilbert spaces with applications. Results in Mathematics. 2021;76(2). doi:10.1007/s00025-021-01381-x","chicago":"Iyiola, Olaniyi S., and Yekini Shehu. “New Convergence Results for Inertial Krasnoselskii–Mann Iterations in Hilbert Spaces with Applications.” Results in Mathematics. Springer Nature, 2021. https://doi.org/10.1007/s00025-021-01381-x.","mla":"Iyiola, Olaniyi S., and Yekini Shehu. “New Convergence Results for Inertial Krasnoselskii–Mann Iterations in Hilbert Spaces with Applications.” Results in Mathematics, vol. 76, no. 2, 75, Springer Nature, 2021, doi:10.1007/s00025-021-01381-x.","short":"O.S. Iyiola, Y. Shehu, Results in Mathematics 76 (2021)."},"publication":"Results in Mathematics","issue":"2","abstract":[{"lang":"eng","text":"We consider inertial iteration methods for Fermat–Weber location problem and primal–dual three-operator splitting in real Hilbert spaces. To do these, we first obtain weak convergence analysis and nonasymptotic O(1/n) convergence rate of the inertial Krasnoselskii–Mann iteration for fixed point of nonexpansive operators in infinite dimensional real Hilbert spaces under some seemingly easy to implement conditions on the iterative parameters. One of our contributions is that the convergence analysis and rate of convergence results are obtained using conditions which appear not complicated and restrictive as assumed in other previous related results in the literature. We then show that Fermat–Weber location problem and primal–dual three-operator splitting are special cases of fixed point problem of nonexpansive mapping and consequently obtain the convergence analysis of inertial iteration methods for Fermat–Weber location problem and primal–dual three-operator splitting in real Hilbert spaces. Some numerical implementations are drawn from primal–dual three-operator splitting to support the theoretical analysis."}],"type":"journal_article","oa_version":"None","intvolume":" 76","title":"New convergence results for inertial Krasnoselskii–Mann iterations in Hilbert spaces with applications","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9315"},{"day":"14","article_processing_charge":"No","scopus_import":"1","date_published":"2021-04-14T00:00:00Z","article_type":"original","publication":"Optimization","citation":{"ama":"Ogbuisi FU, Shehu Y, Yao JC. Convergence analysis of new inertial method for the split common null point problem. Optimization. 2021. doi:10.1080/02331934.2021.1914035","apa":"Ogbuisi, F. U., Shehu, Y., & Yao, J. C. (2021). Convergence analysis of new inertial method for the split common null point problem. Optimization. Taylor and Francis. https://doi.org/10.1080/02331934.2021.1914035","ieee":"F. U. Ogbuisi, Y. Shehu, and J. C. Yao, “Convergence analysis of new inertial method for the split common null point problem,” Optimization. Taylor and Francis, 2021.","ista":"Ogbuisi FU, Shehu Y, Yao JC. 2021. Convergence analysis of new inertial method for the split common null point problem. Optimization.","short":"F.U. Ogbuisi, Y. Shehu, J.C. Yao, Optimization (2021).","mla":"Ogbuisi, Ferdinard U., et al. “Convergence Analysis of New Inertial Method for the Split Common Null Point Problem.” Optimization, Taylor and Francis, 2021, doi:10.1080/02331934.2021.1914035.","chicago":"Ogbuisi, Ferdinard U., Yekini Shehu, and Jen Chih Yao. “Convergence Analysis of New Inertial Method for the Split Common Null Point Problem.” Optimization. Taylor and Francis, 2021. https://doi.org/10.1080/02331934.2021.1914035."},"abstract":[{"text":"In this paper, we propose a new iterative method with alternated inertial step for solving split common null point problem in real Hilbert spaces. We obtain weak convergence of the proposed iterative algorithm. Furthermore, we introduce the notion of bounded linear regularity property for the split common null point problem and obtain the linear convergence property for the new algorithm under some mild assumptions. Finally, we provide some numerical examples to demonstrate the performance and efficiency of the proposed method.","lang":"eng"}],"type":"journal_article","oa_version":"None","title":"Convergence analysis of new inertial method for the split common null point problem","status":"public","_id":"9365","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","publication_identifier":{"issn":["0233-1934"],"eissn":["1029-4945"]},"language":[{"iso":"eng"}],"doi":"10.1080/02331934.2021.1914035","quality_controlled":"1","isi":1,"project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"external_id":{"isi":["000640109300001"]},"ec_funded":1,"date_created":"2021-05-02T22:01:29Z","date_updated":"2023-10-10T09:48:41Z","author":[{"full_name":"Ogbuisi, Ferdinard U.","last_name":"Ogbuisi","first_name":"Ferdinard U."},{"first_name":"Yekini","last_name":"Shehu","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9224-7139","full_name":"Shehu, Yekini"},{"full_name":"Yao, Jen Chih","last_name":"Yao","first_name":"Jen Chih"}],"publication_status":"published","department":[{"_id":"VlKo"}],"publisher":"Taylor and Francis","acknowledgement":"The second author has received funding from the European Research Council (ERC) under the European Union's Seventh Framework Program (FP7-2007-2013) (Grant agreement No. 616160).","year":"2021"},{"volume":17,"date_created":"2021-11-28T23:01:29Z","date_updated":"2023-10-16T06:31:54Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-cells-feel-curvature/","relation":"press_release","description":"News on IST Webpage"}]},"author":[{"first_name":"Marine","last_name":"Luciano","full_name":"Luciano, Marine"},{"full_name":"Xue, Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87","last_name":"Xue","first_name":"Shi-lei"},{"full_name":"De Vos, Winnok H.","last_name":"De Vos","first_name":"Winnok H."},{"first_name":"Lorena","last_name":"Redondo-Morata","full_name":"Redondo-Morata, Lorena"},{"full_name":"Surin, Mathieu","last_name":"Surin","first_name":"Mathieu"},{"full_name":"Lafont, Frank","first_name":"Frank","last_name":"Lafont"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gabriele","first_name":"Sylvain","full_name":"Gabriele, Sylvain"}],"publisher":"Springer Nature","department":[{"_id":"EdHa"}],"publication_status":"published","year":"2021","acknowledgement":"S.G. acknowledges funding from FEDER Prostem Research Project no. 1510614 (Wallonia DG06), F.R.S.-FNRS Epiforce Research Project no. T.0092.21 and Interreg MAT(T)ISSE project, which is financially supported by Interreg France-Wallonie-Vlaanderen (Fonds Européen de Développement Régional, FEDER-ERDF). This project was supported by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme grant agreement 851288 (to E.H.), and by the Austrian Science Fund (FWF) (P 31639; to E.H.). L.R.M. acknowledges funding from the Agence National de la Recherche (ANR), as part of the ‘Investments d’Avenir’ Programme (I-SITE ULNE/ANR-16-IDEX-0004 ULNE). This work benefited from ANR-10-EQPX-04-01 and FEDER 12001407 grants to F.L. W.D.V. is supported by the Research Foundation Flanders (FWO 1516619N, FWO GOO5819N, FWO I003420N, FWO IRI I000321N) and is member of the Research Excellence Consortium µNEURO at the University of Antwerp. M.L. is financially supported by FRIA (F.R.S.-FNRS). M.S. is a Senior Research Associate of the Fund for Scientific Research (F.R.S.-FNRS) and acknowledges EOS grant no. 30650939 (PRECISION). Sketches in Figs. 1a and 5e and Extended Data Fig. 9 were drawn by C. Levicek.","ec_funded":1,"file_date_updated":"2023-10-11T09:31:43Z","language":[{"iso":"eng"}],"doi":"10.1038/s41567-021-01374-1","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis"},{"_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639","call_identifier":"FWF","name":"Active mechano-chemical description of the cell cytoskeleton"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000720204300004"]},"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"month":"11","oa_version":"Submitted Version","file":[{"file_id":"14420","relation":"main_file","success":1,"checksum":"5d6d76750a71d7cb632bb15417c38ef7","date_created":"2023-10-11T09:31:43Z","date_updated":"2023-10-11T09:31:43Z","access_level":"open_access","file_name":"50145_4_merged_1630498627.pdf","creator":"channezo","file_size":40285498,"content_type":"application/pdf"}],"intvolume":" 17","title":"Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation","status":"public","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10365","issue":"12","abstract":[{"text":"The early development of many organisms involves the folding of cell monolayers, but this behaviour is difficult to reproduce in vitro; therefore, both mechanistic causes and effects of local curvature remain unclear. Here we study epithelial cell monolayers on corrugated hydrogels engineered into wavy patterns, examining how concave and convex curvatures affect cellular and nuclear shape. We find that substrate curvature affects monolayer thickness, which is larger in valleys than crests. We show that this feature generically arises in a vertex model, leading to the hypothesis that cells may sense curvature by modifying the thickness of the tissue. We find that local curvature also affects nuclear morphology and positioning, which we explain by extending the vertex model to take into account membrane–nucleus interactions, encoding thickness modulation in changes to nuclear deformation and position. We propose that curvature governs the spatial distribution of yes-associated proteins via nuclear shape and density changes. We show that curvature also induces significant variations in lamins, chromatin condensation and cell proliferation rate in folded epithelial tissues. Together, this work identifies active cell mechanics and nuclear mechanoadaptation as the key players of the mechanistic regulation of epithelia to substrate curvature.","lang":"eng"}],"type":"journal_article","date_published":"2021-11-18T00:00:00Z","page":"1382–1390","article_type":"original","citation":{"short":"M. Luciano, S. Xue, W.H. De Vos, L. Redondo-Morata, M. Surin, F. Lafont, E.B. Hannezo, S. Gabriele, Nature Physics 17 (2021) 1382–1390.","mla":"Luciano, Marine, et al. “Cell Monolayers Sense Curvature by Exploiting Active Mechanics and Nuclear Mechanoadaptation.” Nature Physics, vol. 17, no. 12, Springer Nature, 2021, pp. 1382–1390, doi:10.1038/s41567-021-01374-1.","chicago":"Luciano, Marine, Shi-lei Xue, Winnok H. De Vos, Lorena Redondo-Morata, Mathieu Surin, Frank Lafont, Edouard B Hannezo, and Sylvain Gabriele. “Cell Monolayers Sense Curvature by Exploiting Active Mechanics and Nuclear Mechanoadaptation.” Nature Physics. Springer Nature, 2021. https://doi.org/10.1038/s41567-021-01374-1.","ama":"Luciano M, Xue S, De Vos WH, et al. Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. Nature Physics. 2021;17(12):1382–1390. doi:10.1038/s41567-021-01374-1","apa":"Luciano, M., Xue, S., De Vos, W. H., Redondo-Morata, L., Surin, M., Lafont, F., … Gabriele, S. (2021). Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-021-01374-1","ieee":"M. Luciano et al., “Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation,” Nature Physics, vol. 17, no. 12. Springer Nature, pp. 1382–1390, 2021.","ista":"Luciano M, Xue S, De Vos WH, Redondo-Morata L, Surin M, Lafont F, Hannezo EB, Gabriele S. 2021. Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. Nature Physics. 17(12), 1382–1390."},"publication":"Nature Physics","article_processing_charge":"No","has_accepted_license":"1","day":"18","scopus_import":"1"},{"article_type":"review","page":"1-382","publication":"Autophagy","citation":{"chicago":"Klionsky, Daniel J., Amal Kamal Abdel-Aziz, Sara Abdelfatah, Mahmoud Abdellatif, Asghar Abdoli, Steffen Abel, Hagai Abeliovich, et al. “Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy (4th Edition).” Autophagy. Taylor & Francis, 2021. https://doi.org/10.1080/15548627.2020.1797280.","mla":"Klionsky, Daniel J., et al. “Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy (4th Edition).” Autophagy, vol. 17, no. 1, Taylor & Francis, 2021, pp. 1–382, doi:10.1080/15548627.2020.1797280.","short":"D.J. Klionsky, A.K. Abdel-Aziz, S. Abdelfatah, M. Abdellatif, A. Abdoli, S. Abel, H. Abeliovich, M.H. Abildgaard, Y.P. Abudu, A. Acevedo-Arozena, I.E. Adamopoulos, K. Adeli, T.E. Adolph, A. Adornetto, E. Aflaki, G. Agam, A. Agarwal, B.B. Aggarwal, M. Agnello, P. Agostinis, J.N. Agrewala, A. Agrotis, P.V. Aguilar, S.T. Ahmad, Z.M. Ahmed, U. Ahumada-Castro, S. Aits, S. Aizawa, Y. Akkoc, T. Akoumianaki, H.A. Akpinar, A.M. Al-Abd, L. Al-Akra, A. Al-Gharaibeh, M.A. Alaoui-Jamali, S. Alberti, E. Alcocer-Gómez, C. Alessandri, M. Ali, M.A. Alim Al-Bari, S. Aliwaini, J. Alizadeh, E. Almacellas, A. Almasan, A. Alonso, G.D. Alonso, N. Altan-Bonnet, D.C. Altieri, É.M.C. Álvarez, S. Alves, C. Alves Da Costa, M.M. Alzaharna, M. Amadio, C. Amantini, C. Amaral, S. Ambrosio, A.O. Amer, V. Ammanathan, Z. An, S.U. Andersen, S.A. Andrabi, M. Andrade-Silva, A.M. Andres, S. Angelini, D. Ann, U.C. Anozie, M.Y. Ansari, P. Antas, A. Antebi, Z. Antón, T. Anwar, L. Apetoh, N. Apostolova, T. Araki, Y. Araki, K. Arasaki, W.L. Araújo, J. Araya, C. Arden, M.A. Arévalo, S. Arguelles, E. Arias, J. Arikkath, H. Arimoto, A.R. Ariosa, D. Armstrong-James, L. Arnauné-Pelloquin, A. Aroca, D.S. Arroyo, I. Arsov, R. Artero, D.M.L. Asaro, M. Aschner, M. Ashrafizadeh, O. Ashur-Fabian, A.G. Atanasov, A.K. Au, P. Auberger, H.W. Auner, L. Aurelian, R. Autelli, L. Avagliano, Y. Ávalos, S. Aveic, C.A. Aveleira, T. Avin-Wittenberg, Y. Aydin, S. Ayton, S. Ayyadevara, M. Azzopardi, M. Baba, J.M. Backer, S.K. Backues, D.H. Bae, O.N. Bae, S.H. Bae, E.H. Baehrecke, A. Baek, S.H. Baek, S.H. Baek, G. Bagetta, A. Bagniewska-Zadworna, H. Bai, J. Bai, X. Bai, Y. Bai, N. Bairagi, S. Baksi, T. Balbi, C.T. Baldari, W. Balduini, A. Ballabio, M. Ballester, S. Balazadeh, R. Balzan, R. Bandopadhyay, S. Banerjee, S. Banerjee, Á. Bánréti, Y. Bao, M.S. Baptista, A. Baracca, C. Barbati, A. Bargiela, D. Barilà, P.G. Barlow, S.J. Barmada, E. Barreiro, G.E. Barreto, J. Bartek, B. Bartel, A. Bartolome, G.R. Barve, S.H. Basagoudanavar, D.C. Bassham, R.C. Bast, A. Basu, H. Batoko, I. Batten, E.E. Baulieu, B.L. Baumgarner, J. Bayry, R. Beale, I. Beau, F. Beaumatin, L.R.G. Bechara, G.R. Beck, M.F. Beers, J. Begun, C. Behrends, G.M.N. Behrens, R. Bei, E. Bejarano, S. Bel, C. Behl, A. Belaid, N. Belgareh-Touzé, C. Bellarosa, F. Belleudi, M. Belló Pérez, R. Bello-Morales, J.S.D.O. Beltran, S. Beltran, D.M. Benbrook, M. Bendorius, B.A. Benitez, I. Benito-Cuesta, J. Bensalem, M.W. Berchtold, S. Berezowska, D. Bergamaschi, M. Bergami, A. Bergmann, L. Berliocchi, C. Berlioz-Torrent, A. Bernard, L. Berthoux, C.G. Besirli, S. Besteiro, V.M. Betin, R. Beyaert, J.S. Bezbradica, K. Bhaskar, I. Bhatia-Kissova, R. Bhattacharya, S. Bhattacharya, S. Bhattacharyya, M.S. Bhuiyan, S.K. Bhutia, L. Bi, X. Bi, T.J. Biden, K. Bijian, V.A. Billes, N. Binart, C. Bincoletto, A.B. Birgisdottir, G. Bjorkoy, G. Blanco, A. Blas-Garcia, J. Blasiak, R. Blomgran, K. Blomgren, J.S. Blum, E. Boada-Romero, M. Boban, K. Boesze-Battaglia, P. Boeuf, B. Boland, P. Bomont, P. Bonaldo, S.R. Bonam, L. Bonfili, J.S. Bonifacino, B.A. Boone, M.D. Bootman, M. Bordi, C. Borner, B.C. Bornhauser, G. Borthakur, J. Bosch, S. Bose, L.M. Botana, J. Botas, C.M. Boulanger, M.E. Boulton, M. Bourdenx, B. Bourgeois, N.M. Bourke, G. Bousquet, P. Boya, P.V. Bozhkov, L.H.M. Bozi, T.O. Bozkurt, D.E. Brackney, C.H. Brandts, R.J. Braun, G.H. Braus, R. Bravo-Sagua, J.M. Bravo-San Pedro, P. Brest, M.A. Bringer, A. Briones-Herrera, V.C. Broaddus, P. Brodersen, J.L. Brodsky, S.L. Brody, P.G. Bronson, J.M. Bronstein, C.N. Brown, R.E. Brown, P.C. Brum, J.H. Brumell, N. Brunetti-Pierri, D. Bruno, R.J. Bryson-Richardson, C. Bucci, C. Buchrieser, M. Bueno, L.E. Buitrago-Molina, S. Buraschi, S. Buch, J.R. Buchan, E.M. Buckingham, H. Budak, M. Budini, G. Bultynck, F. Burada, J.R. Burgoyne, M.I. Burón, V. Bustos, S. Büttner, E. Butturini, A. Byrd, I. Cabas, S. Cabrera-Benitez, K. Cadwell, J. Cai, L. Cai, Q. Cai, M. Cairó, J.A. Calbet, G.A. Caldwell, K.A. Caldwell, J.A. Call, R. Calvani, A.C. Calvo, M. Calvo-Rubio Barrera, N.O.S. Camara, J.H. Camonis, N. Camougrand, M. Campanella, E.M. Campbell, F.X. Campbell-Valois, S. Campello, I. Campesi, J.C. Campos, O. Camuzard, J. Cancino, D. Candido De Almeida, L. Canesi, I. Caniggia, B. Canonico, C. Cantí, B. Cao, M. Caraglia, B. Caramés, E.H. Carchman, E. Cardenal-Muñoz, C. Cardenas, L. Cardenas, S.M. Cardoso, J.S. Carew, G.F. Carle, G. Carleton, S. Carloni, D. Carmona-Gutierrez, L.A. Carneiro, O. Carnevali, J.M. Carosi, S. Carra, A. Carrier, L. Carrier, B. Carroll, A.B. Carter, A.N. Carvalho, M. Casanova, C. Casas, J. Casas, C. Cassioli, E.F. Castillo, K. Castillo, S. Castillo-Lluva, F. Castoldi, M. Castori, A.F. Castro, M. Castro-Caldas, J. Castro-Hernandez, S. Castro-Obregon, S.D. Catz, C. Cavadas, F. Cavaliere, G. Cavallini, M. Cavinato, M.L. Cayuela, P. Cebollada Rica, V. Cecarini, F. Cecconi, M. Cechowska-Pasko, S. Cenci, V. Ceperuelo-Mallafré, J.J. Cerqueira, J.M. Cerutti, D. Cervia, V.B. Cetintas, S. Cetrullo, H.J. Chae, A.S. Chagin, C.Y. Chai, G. Chakrabarti, O. Chakrabarti, T. Chakraborty, T. Chakraborty, M. Chami, G. Chamilos, D.W. Chan, E.Y.W. Chan, E.D. Chan, H.Y.E. Chan, H.H. Chan, H. Chan, M.T.V. Chan, Y.S. Chan, P.K. Chandra, C.P. Chang, C. Chang, H.C. Chang, K. Chang, J. Chao, T. Chapman, N. Charlet-Berguerand, S. Chatterjee, S.K. Chaube, A. Chaudhary, S. Chauhan, E. Chaum, F. Checler, M.E. Cheetham, C.S. Chen, G.C. Chen, J.F. Chen, L.L. Chen, L. Chen, L. Chen, M. Chen, M.K. Chen, N. Chen, Q. Chen, R.H. Chen, S. Chen, W. Chen, W. Chen, X.M. Chen, X.W. Chen, X. Chen, Y. Chen, Y.G. Chen, Y. Chen, Y. Chen, Y.J. Chen, Y.Q. Chen, Z.S. Chen, Z. Chen, Z.H. Chen, Z.J. Chen, Z. Chen, H. Cheng, J. Cheng, S.Y. Cheng, W. Cheng, X. Cheng, X.T. Cheng, Y. Cheng, Z. Cheng, Z. Chen, H. Cheong, J.K. Cheong, B.V. Chernyak, S. Cherry, C.F.R. Cheung, C.H.A. Cheung, K.H. Cheung, E. Chevet, R.J. Chi, A.K.S. Chiang, F. Chiaradonna, R. Chiarelli, M. Chiariello, N. Chica, S. Chiocca, M. Chiong, S.H. Chiou, A.I. Chiramel, V. Chiurchiù, D.H. Cho, S.K. Choe, A.M.K. Choi, M.E. Choi, K.R. Choudhury, N.S. Chow, C.T. Chu, J.P. Chua, J.J.E. Chua, H. Chung, K.P. Chung, S. 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Sluimer, C.L. Stallings, C.K. Tong, Autophagy 17 (2021) 1–382.","ista":"Klionsky DJ et al. 2021. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. 17(1), 1–382.","apa":"Klionsky, D. J., Abdel-Aziz, A. K., Abdelfatah, S., Abdellatif, M., Abdoli, A., Abel, S., … Tong, C. K. (2021). Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. Taylor & Francis. https://doi.org/10.1080/15548627.2020.1797280","ieee":"D. J. Klionsky et al., “Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition),” Autophagy, vol. 17, no. 1. Taylor & Francis, pp. 1–382, 2021.","ama":"Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, et al. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. 2021;17(1):1-382. doi:10.1080/15548627.2020.1797280"},"date_published":"2021-02-08T00:00:00Z","scopus_import":"1","day":"08","article_processing_charge":"No","title":"Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)","status":"public","intvolume":" 17","_id":"9298","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field. ","lang":"eng"}],"issue":"1","quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1080/15548627.2020.1797280"}],"external_id":{"isi":["000636121800001"],"pmid":["33634751"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1080/15548627.2020.1797280","month":"02","publication_identifier":{"eissn":["1554-8635"],"issn":["1554-8627"]},"publication_status":"published","department":[{"_id":"JiFr"},{"_id":"CaHe"}],"publisher":"Taylor & Francis","year":"2021","acknowledgement":"This work was supported by the National Institute of General Medical Sciences [GM131919]. Due to space and other limitations, it is not possible to include all other sources of financial support.","pmid":1,"date_created":"2021-03-28T22:01:44Z","date_updated":"2023-10-16T09:43:56Z","volume":17,"author":[{"full_name":"Klionsky, Daniel J.","last_name":"Klionsky","first_name":"Daniel J."},{"last_name":"Abdel-Aziz","first_name":"Amal Kamal","full_name":"Abdel-Aziz, Amal Kamal"},{"full_name":"Abdelfatah, Sara","first_name":"Sara","last_name":"Abdelfatah"},{"first_name":"Mahmoud","last_name":"Abdellatif","full_name":"Abdellatif, Mahmoud"},{"full_name":"Abdoli, Asghar","first_name":"Asghar","last_name":"Abdoli"},{"first_name":"Steffen","last_name":"Abel","full_name":"Abel, Steffen"},{"last_name":"Abeliovich","first_name":"Hagai","full_name":"Abeliovich, Hagai"},{"full_name":"Abildgaard, Marie H.","first_name":"Marie H.","last_name":"Abildgaard"},{"last_name":"Abudu","first_name":"Yakubu Princely","full_name":"Abudu, Yakubu Princely"},{"first_name":"Abraham","last_name":"Acevedo-Arozena","full_name":"Acevedo-Arozena, Abraham"},{"full_name":"Adamopoulos, Iannis E.","last_name":"Adamopoulos","first_name":"Iannis E."},{"full_name":"Adeli, Khosrow","first_name":"Khosrow","last_name":"Adeli"},{"full_name":"Adolph, Timon E.","first_name":"Timon E.","last_name":"Adolph"},{"full_name":"Adornetto, Annagrazia","first_name":"Annagrazia","last_name":"Adornetto"},{"first_name":"Elma","last_name":"Aflaki","full_name":"Aflaki, Elma"},{"full_name":"Agam, Galila","first_name":"Galila","last_name":"Agam"},{"first_name":"Anupam","last_name":"Agarwal","full_name":"Agarwal, Anupam"},{"full_name":"Aggarwal, Bharat B.","last_name":"Aggarwal","first_name":"Bharat B."},{"full_name":"Agnello, Maria","last_name":"Agnello","first_name":"Maria"},{"first_name":"Patrizia","last_name":"Agostinis","full_name":"Agostinis, Patrizia"},{"first_name":"Javed N.","last_name":"Agrewala","full_name":"Agrewala, Javed N."},{"full_name":"Agrotis, Alexander","last_name":"Agrotis","first_name":"Alexander"},{"first_name":"Patricia V.","last_name":"Aguilar","full_name":"Aguilar, Patricia V."},{"last_name":"Ahmad","first_name":"S. 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As one ranges over the zeros of such quadratic forms, we use the sieve to compute the density of coprime values of polynomials, and furthermore, to address a question about local solubility in families of varieties parameterised by the zeros."}],"issue":"1","type":"journal_article","date_published":"2021-01-01T00:00:00Z","article_type":"original","page":"147-165","publication":"Forum Mathematicum","citation":{"ieee":"T. D. Browning and R. Heath-Brown, “The geometric sieve for quadrics,” Forum Mathematicum, vol. 33, no. 1. De Gruyter, pp. 147–165, 2021.","apa":"Browning, T. D., & Heath-Brown, R. (2021). The geometric sieve for quadrics. Forum Mathematicum. De Gruyter. https://doi.org/10.1515/forum-2020-0074","ista":"Browning TD, Heath-Brown R. 2021. The geometric sieve for quadrics. Forum Mathematicum. 33(1), 147–165.","ama":"Browning TD, Heath-Brown R. The geometric sieve for quadrics. Forum Mathematicum. 2021;33(1):147-165. doi:10.1515/forum-2020-0074","chicago":"Browning, Timothy D, and Roger Heath-Brown. “The Geometric Sieve for Quadrics.” Forum Mathematicum. De Gruyter, 2021. https://doi.org/10.1515/forum-2020-0074.","short":"T.D. Browning, R. Heath-Brown, Forum Mathematicum 33 (2021) 147–165.","mla":"Browning, Timothy D., and Roger Heath-Brown. “The Geometric Sieve for Quadrics.” Forum Mathematicum, vol. 33, no. 1, De Gruyter, 2021, pp. 147–65, doi:10.1515/forum-2020-0074."},"day":"01","article_processing_charge":"No","scopus_import":"1","date_created":"2020-11-08T23:01:25Z","date_updated":"2023-10-17T07:39:01Z","volume":33,"author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning","full_name":"Browning, Timothy D"},{"full_name":"Heath-Brown, Roger","first_name":"Roger","last_name":"Heath-Brown"}],"publication_status":"published","publisher":"De Gruyter","department":[{"_id":"TiBr"}],"year":"2021","language":[{"iso":"eng"}],"doi":"10.1515/forum-2020-0074","isi":1,"quality_controlled":"1","project":[{"grant_number":"P32428","_id":"26AEDAB2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"New frontiers of the Manin conjecture"}],"main_file_link":[{"url":"https://arxiv.org/abs/2003.09593","open_access":"1"}],"external_id":{"arxiv":["2003.09593"],"isi":["000604750900008"]},"oa":1,"month":"01","publication_identifier":{"issn":["0933-7741"],"eissn":["1435-5337"]}},{"acknowledgement":"I want to acknowledge the funding by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).\r\n","year":"2021","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"publication_status":"published","related_material":{"record":[{"id":"10044","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"10049"},{"id":"637","status":"public","relation":"part_of_dissertation"},{"id":"10041","status":"public","relation":"part_of_dissertation"},{"id":"6430","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10048"}]},"author":[{"full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","last_name":"Klein","first_name":"Karen"}],"date_created":"2021-09-23T07:31:44Z","date_updated":"2023-10-17T09:24:07Z","ec_funded":1,"file_date_updated":"2022-03-10T12:15:18Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"doi":"10.15479/at:ista:10035","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"}],"publication_identifier":{"issn":["2663-337X"]},"month":"09","_id":"10035","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["519"],"title":"On the adaptive security of graph-based games","oa_version":"Published Version","file":[{"file_name":"thesis_pdfa.pdf","access_level":"open_access","creator":"cchlebak","file_size":2104726,"content_type":"application/pdf","file_id":"10082","relation":"main_file","date_created":"2021-10-04T12:22:33Z","date_updated":"2021-10-04T12:22:33Z","success":1,"checksum":"73a44345c683e81f3e765efbf86fdcc5"},{"file_id":"10085","relation":"source_file","checksum":"7b80df30a0e686c3ef6a56d4e1c59e29","date_created":"2021-10-05T07:04:37Z","date_updated":"2022-03-10T12:15:18Z","access_level":"closed","file_name":"thesis_final (1).zip","creator":"cchlebak","file_size":9538359,"content_type":"application/x-zip-compressed"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Many security definitions come in two flavors: a stronger “adaptive” flavor, where the adversary can arbitrarily make various choices during the course of the attack, and a weaker “selective” flavor where the adversary must commit to some or all of their choices a-priori. For example, in the context of identity-based encryption, selective security requires the adversary to decide on the identity of the attacked party at the very beginning of the game whereas adaptive security allows the attacker to first see the master public key and some secret keys before making this choice. Often, it appears to be much easier to achieve selective security than it is to achieve adaptive security. A series of several recent works shows how to cleverly achieve adaptive security in several such scenarios including generalized selective decryption [Pan07][FJP15], constrained PRFs [FKPR14], and Yao’s garbled circuits [JW16]. Although the above works expressed vague intuition that they share a common technique, the connection was never made precise. In this work we present a new framework (published at Crypto ’17 [JKK+17a]) that connects all of these works and allows us to present them in a unified and simplified fashion. Having the framework in place, we show how to achieve adaptive security for proxy re-encryption schemes (published at PKC ’19 [FKKP19]) and provide the first adaptive security proofs for continuous group key agreement protocols (published at S&P ’21 [KPW+21]). Questioning optimality of our framework, we then show that currently used proof techniques cannot lead to significantly better security guarantees for \"graph-building\" games (published at TCC ’21 [KKPW21a]). These games cover generalized selective decryption, as well as the security of prominent constructions for constrained PRFs, continuous group key agreement, and proxy re-encryption. Finally, we revisit the adaptive security of Yao’s garbled circuits and extend the analysis of Jafargholi and Wichs in two directions: While they prove adaptive security only for a modified construction with increased online complexity, we provide the first positive results for the original construction by Yao (published at TCC ’21 [KKP21a]). On the negative side, we prove that the results of Jafargholi and Wichs are essentially optimal by showing that no black-box reduction can provide a significantly better security bound (published at Crypto ’21 [KKPW21c]).","lang":"eng"}],"citation":{"ama":"Klein K. On the adaptive security of graph-based games. 2021. doi:10.15479/at:ista:10035","apa":"Klein, K. (2021). On the adaptive security of graph-based games. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10035","ieee":"K. Klein, “On the adaptive security of graph-based games,” Institute of Science and Technology Austria, 2021.","ista":"Klein K. 2021. On the adaptive security of graph-based games. Institute of Science and Technology Austria.","short":"K. Klein, On the Adaptive Security of Graph-Based Games, Institute of Science and Technology Austria, 2021.","mla":"Klein, Karen. On the Adaptive Security of Graph-Based Games. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10035.","chicago":"Klein, Karen. “On the Adaptive Security of Graph-Based Games.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10035."},"page":"276","date_published":"2021-09-23T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"23"},{"abstract":[{"lang":"eng","text":"The security of cryptographic primitives and protocols against adversaries that are allowed to make adaptive choices (e.g., which parties to corrupt or which queries to make) is notoriously difficult to establish. A broad theoretical framework was introduced by Jafargholi et al. [Crypto’17] for this purpose. In this paper we initiate the study of lower bounds on loss in adaptive security for certain cryptographic protocols considered in the framework. We prove lower bounds that almost match the upper bounds (proven using the framework) for proxy re-encryption, prefix-constrained PRFs and generalized selective decryption, a security game that captures the security of certain group messaging and broadcast encryption schemes. Those primitives have in common that their security game involves an underlying graph that can be adaptively built by the adversary. Some of our lower bounds only apply to a restricted class of black-box reductions which we term “oblivious” (the existing upper bounds are of this restricted type), some apply to the broader but still restricted class of non-rewinding reductions, while our lower bound for proxy re-encryption applies to all black-box reductions. The fact that some of our lower bounds seem to crucially rely on obliviousness or at least a non-rewinding reduction hints to the exciting possibility that the existing upper bounds can be improved by using more sophisticated reductions. Our main conceptual contribution is a two-player multi-stage game called the Builder-Pebbler Game. We can translate bounds on the winning probabilities for various instantiations of this game into cryptographic lower bounds for the above-mentioned primitives using oracle separation techniques."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10410","intvolume":" 13043","status":"public","title":"The cost of adaptivity in security games on graphs","article_processing_charge":"No","day":"04","scopus_import":"1","date_published":"2021-11-04T00:00:00Z","citation":{"chicago":"Kamath Hosdurg, Chethan, Karen Klein, Krzysztof Z Pietrzak, and Michael Walter. “The Cost of Adaptivity in Security Games on Graphs.” In 19th International Conference, 13043:550–81. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90453-1_19.","short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:, 19th International Conference, Springer Nature, 2021, pp. 550–581.","mla":"Kamath Hosdurg, Chethan, et al. “The Cost of Adaptivity in Security Games on Graphs.” 19th International Conference, vol. 13043, Springer Nature, 2021, pp. 550–81, doi:10.1007/978-3-030-90453-1_19.","apa":"Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., & Walter, M. (2021). The cost of adaptivity in security games on graphs. In 19th International Conference (Vol. 13043, pp. 550–581). Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90453-1_19","ieee":"C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and M. Walter, “The cost of adaptivity in security games on graphs,” in 19th International Conference, Raleigh, NC, United States, 2021, vol. 13043, pp. 550–581.","ista":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. 2021. The cost of adaptivity in security games on graphs. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol. 13043, 550–581.","ama":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. The cost of adaptivity in security games on graphs. In: 19th International Conference. Vol 13043. Springer Nature; 2021:550-581. doi:10.1007/978-3-030-90453-1_19"},"publication":"19th International Conference","page":"550-581","ec_funded":1,"related_material":{"record":[{"id":"10048","relation":"earlier_version","status":"public"}]},"author":[{"full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","last_name":"Kamath Hosdurg","first_name":"Chethan"},{"full_name":"Klein, Karen","first_name":"Karen","last_name":"Klein","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"},{"last_name":"Walter","first_name":"Michael","orcid":"0000-0003-3186-2482","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","full_name":"Walter, Michael"}],"volume":13043,"date_updated":"2023-10-17T09:24:07Z","date_created":"2021-12-05T23:01:43Z","year":"2021","acknowledgement":"C. Kamath—Supported by Azrieli International Postdoctoral Fellowship. Most of the work was done while the author was at Northeastern University and Charles University, funded by the IARPA grant IARPA/2019-19-020700009 and project PRIMUS/17/SCI/9, respectively. K. Klein—Supported in part by ERC CoG grant 724307. Most of the work was done while the author was at IST Austria funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT). K. Pietrzak—Funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).","publisher":"Springer Nature","department":[{"_id":"KrPi"}],"publication_status":"published","publication_identifier":{"eissn":["1611-3349"],"isbn":["9-783-0309-0452-4"],"issn":["0302-9743"]},"month":"11","doi":"10.1007/978-3-030-90453-1_19","conference":{"end_date":"2021-11-11","start_date":"2021-11-08","location":"Raleigh, NC, United States","name":"TCC: Theory of Cryptography"},"language":[{"iso":"eng"}],"external_id":{"isi":["000728364000019"]},"oa":1,"main_file_link":[{"url":"https://ia.cr/2021/059","open_access":"1"}],"project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"quality_controlled":"1","isi":1},{"abstract":[{"text":"The security of cryptographic primitives and protocols against adversaries that are allowed to make adaptive choices (e.g., which parties to corrupt or which queries to make) is notoriously difficult to establish. A broad theoretical\r\nframework was introduced by Jafargholi et al. [Crypto’17] for this purpose. In this paper we initiate the study of lower bounds on loss in adaptive security for certain cryptographic protocols considered in the framework. We prove lower\r\nbounds that almost match the upper bounds (proven using the framework) for proxy re-encryption, prefix-constrained PRFs and generalized selective decryption, a security game that captures the security of certain group messaging and\r\nbroadcast encryption schemes. Those primitives have in common that their security game involves an underlying graph that can be adaptively built by the adversary. Some of our lower bounds only apply to a restricted class of black-box reductions which we term “oblivious” (the existing upper bounds are of this restricted type), some apply to the broader but still restricted class of non-rewinding reductions, while our lower bound for proxy re-encryption applies to all black-box reductions. The fact that some of our lower bounds seem to crucially rely on obliviousness or at least a non-rewinding reduction hints to the exciting possibility that the existing upper bounds can be improved by using more sophisticated reductions. Our main conceptual contribution is a two-player multi-stage game called the Builder-Pebbler Game. We can translate bounds on the winning probabilities for various instantiations of this game into cryptographic lower bounds for the above-mentioned primitives using oracle separation techniques.\r\n","lang":"eng"}],"type":"conference","oa_version":"Preprint","date_updated":"2023-10-17T09:24:08Z","date_created":"2021-09-27T12:52:05Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"10410"},{"relation":"dissertation_contains","status":"public","id":"10035"}]},"author":[{"last_name":"Kamath Hosdurg","first_name":"Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","full_name":"Kamath Hosdurg, Chethan"},{"full_name":"Klein, Karen","last_name":"Klein","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak"},{"id":"488F98B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3186-2482","first_name":"Michael","last_name":"Walter","full_name":"Walter, Michael"}],"department":[{"_id":"KrPi"}],"publisher":"International Association for Cryptologic Research","title":"The cost of adaptivity in security games on graphs","status":"public","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10048","year":"2021","article_processing_charge":"No","day":"08","month":"07","language":[{"iso":"eng"}],"date_published":"2021-07-08T00:00:00Z","conference":{"location":"Raleigh, NC, United States","start_date":"2021-11-08","end_date":"2021-11-11","name":"TCC: Theory of Cryptography Conference"},"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://ia.cr/2021/059","open_access":"1"}],"citation":{"ama":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. The cost of adaptivity in security games on graphs. In: 19th Theory of Cryptography Conference 2021. International Association for Cryptologic Research; 2021.","ista":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. 2021. The cost of adaptivity in security games on graphs. 19th Theory of Cryptography Conference 2021. TCC: Theory of Cryptography Conference.","apa":"Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., & Walter, M. (2021). The cost of adaptivity in security games on graphs. In 19th Theory of Cryptography Conference 2021. Raleigh, NC, United States: International Association for Cryptologic Research.","ieee":"C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and M. Walter, “The cost of adaptivity in security games on graphs,” in 19th Theory of Cryptography Conference 2021, Raleigh, NC, United States, 2021.","mla":"Kamath Hosdurg, Chethan, et al. “The Cost of Adaptivity in Security Games on Graphs.” 19th Theory of Cryptography Conference 2021, International Association for Cryptologic Research, 2021.","short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:, 19th Theory of Cryptography Conference 2021, International Association for Cryptologic Research, 2021.","chicago":"Kamath Hosdurg, Chethan, Karen Klein, Krzysztof Z Pietrzak, and Michael Walter. “The Cost of Adaptivity in Security Games on Graphs.” In 19th Theory of Cryptography Conference 2021. International Association for Cryptologic Research, 2021."},"publication":"19th Theory of Cryptography Conference 2021"},{"article_processing_charge":"No","day":"10","scopus_import":"1","date_published":"2021-11-10T00:00:00Z","citation":{"apa":"Leopold, N. K., Rademacher, S. A. E., Schlein, B., & Seiringer, R. (2021). The Landau–Pekar equations: Adiabatic theorem and accuracy. Analysis and PDE. Mathematical Sciences Publishers. https://doi.org/10.2140/APDE.2021.14.2079","ieee":"N. K. Leopold, S. A. E. Rademacher, B. Schlein, and R. Seiringer, “ The Landau–Pekar equations: Adiabatic theorem and accuracy,” Analysis and PDE, vol. 14, no. 7. Mathematical Sciences Publishers, pp. 2079–2100, 2021.","ista":"Leopold NK, Rademacher SAE, Schlein B, Seiringer R. 2021. The Landau–Pekar equations: Adiabatic theorem and accuracy. Analysis and PDE. 14(7), 2079–2100.","ama":"Leopold NK, Rademacher SAE, Schlein B, Seiringer R. The Landau–Pekar equations: Adiabatic theorem and accuracy. Analysis and PDE. 2021;14(7):2079-2100. doi:10.2140/APDE.2021.14.2079","chicago":"Leopold, Nikolai K, Simone Anna Elvira Rademacher, Benjamin Schlein, and Robert Seiringer. “ The Landau–Pekar Equations: Adiabatic Theorem and Accuracy.” Analysis and PDE. Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/APDE.2021.14.2079.","short":"N.K. Leopold, S.A.E. Rademacher, B. Schlein, R. Seiringer, Analysis and PDE 14 (2021) 2079–2100.","mla":"Leopold, Nikolai K., et al. “ The Landau–Pekar Equations: Adiabatic Theorem and Accuracy.” Analysis and PDE, vol. 14, no. 7, Mathematical Sciences Publishers, 2021, pp. 2079–100, doi:10.2140/APDE.2021.14.2079."},"publication":"Analysis and PDE","page":"2079-2100","article_type":"original","issue":"7","abstract":[{"text":"We prove an adiabatic theorem for the Landau–Pekar equations. This allows us to derive new results on the accuracy of their use as effective equations for the time evolution generated by the Fröhlich Hamiltonian with large coupling constant α. In particular, we show that the time evolution of Pekar product states with coherent phonon field and the electron being trapped by the phonons is well approximated by the Landau–Pekar equations until times short compared to α2.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10738","intvolume":" 14","title":" The Landau–Pekar equations: Adiabatic theorem and accuracy","status":"public","publication_identifier":{"eissn":["1948-206X"],"issn":["2157-5045"]},"month":"11","doi":"10.2140/APDE.2021.14.2079","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000733976600004"],"arxiv":["1904.12532"]},"main_file_link":[{"url":"https://arxiv.org/abs/1904.12532","open_access":"1"}],"project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","ec_funded":1,"author":[{"id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0495-6822","first_name":"Nikolai K","last_name":"Leopold","full_name":"Leopold, Nikolai K"},{"full_name":"Rademacher, Simone Anna Elvira","last_name":"Rademacher","first_name":"Simone Anna Elvira","orcid":"0000-0001-5059-4466","id":"856966FE-A408-11E9-977E-802DE6697425"},{"last_name":"Schlein","first_name":"Benjamin","full_name":"Schlein, Benjamin"},{"last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"volume":14,"date_created":"2022-02-06T23:01:33Z","date_updated":"2023-10-17T11:26:45Z","acknowledgement":"N. L. and R. S. gratefully acknowledge financial support by the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (grant\r\nagreement No 694227). B. S. acknowledges support from the Swiss National Science Foundation (grant 200020_172623) and from the NCCR SwissMAP. N. L. would like to thank\r\nAndreas Deuchert and David Mitrouskas for interesting discussions. B. S. and R. S. would\r\nlike to thank Rupert Frank for stimulating discussions about the time-evolution of a polaron.\r\n","year":"2021","department":[{"_id":"RoSe"}],"publisher":"Mathematical Sciences Publishers","publication_status":"published"},{"day":"09","has_accepted_license":"1","article_processing_charge":"No","date_published":"2021-12-09T00:00:00Z","page":"132","citation":{"ama":"Nadiradze G. On achieving scalability through relaxation. 2021. doi:10.15479/at:ista:10429","ista":"Nadiradze G. 2021. On achieving scalability through relaxation. Institute of Science and Technology Austria.","apa":"Nadiradze, G. (2021). On achieving scalability through relaxation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10429","ieee":"G. Nadiradze, “On achieving scalability through relaxation,” Institute of Science and Technology Austria, 2021.","mla":"Nadiradze, Giorgi. On Achieving Scalability through Relaxation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10429.","short":"G. Nadiradze, On Achieving Scalability through Relaxation, Institute of Science and Technology Austria, 2021.","chicago":"Nadiradze, Giorgi. “On Achieving Scalability through Relaxation.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10429."},"abstract":[{"text":"The scalability of concurrent data structures and distributed algorithms strongly depends on\r\nreducing the contention for shared resources and the costs of synchronization and communication. We show how such cost reductions can be attained by relaxing the strict consistency conditions required by sequential implementations. In the first part of the thesis, we consider relaxation in the context of concurrent data structures. Specifically, in data structures \r\nsuch as priority queues, imposing strong semantics renders scalability impossible, since a correct implementation of the remove operation should return only the element with highest priority. Intuitively, attempting to invoke remove operations concurrently creates a race condition. This bottleneck can be circumvented by relaxing semantics of the affected data structure, thus allowing removal of the elements which are no longer required to have the highest priority. We prove that the randomized implementations of relaxed data structures provide provable guarantees on the priority of the removed elements even under concurrency. Additionally, we show that in some cases the relaxed data structures can be used to scale the classical algorithms which are usually implemented with the exact ones. In the second part, we study parallel variants of the stochastic gradient descent (SGD) algorithm, which distribute computation among the multiple processors, thus reducing the running time. Unfortunately, in order for standard parallel SGD to succeed, each processor has to maintain a local copy of the necessary model parameter, which is identical to the local copies of other processors; the overheads from this perfect consistency in terms of communication and synchronization can negate the speedup gained by distributing the computation. We show that the consistency conditions required by SGD can be relaxed, allowing the algorithm to be more flexible in terms of tolerating quantized communication, asynchrony, or even crash faults, while its convergence remains asymptotically the same.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"checksum":"6bf14e9a523387328f016c0689f5e10e","success":1,"date_updated":"2021-12-09T17:47:49Z","date_created":"2021-12-09T17:47:49Z","relation":"main_file","file_id":"10436","file_size":2370859,"content_type":"application/pdf","creator":"gnadirad","access_level":"open_access","file_name":"Thesis_Final_09_12_2021.pdf"},{"date_created":"2021-12-09T17:47:49Z","date_updated":"2022-03-28T12:55:12Z","checksum":"914d6c5ca86bd0add471971a8f4c4341","file_id":"10437","relation":"source_file","creator":"gnadirad","content_type":"application/zip","file_size":2596924,"file_name":"Thesis_Final_09_12_2021.zip","access_level":"closed"}],"status":"public","ddc":["000"],"title":"On achieving scalability through relaxation","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10429","month":"12","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","supervisor":[{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:10429","project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"}],"oa":1,"file_date_updated":"2022-03-28T12:55:12Z","ec_funded":1,"date_created":"2021-12-08T21:52:28Z","date_updated":"2023-10-17T11:48:55Z","author":[{"full_name":"Nadiradze, Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5634-0731","first_name":"Giorgi","last_name":"Nadiradze"}],"related_material":{"record":[{"id":"10432","status":"public","relation":"part_of_dissertation"},{"id":"6673","relation":"part_of_dissertation","status":"public"},{"id":"5965","relation":"part_of_dissertation","status":"public"},{"id":"10435","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"DaAl"}],"year":"2021"},{"abstract":[{"lang":"eng","text":"Decentralized optimization is emerging as a viable alternative for scalable distributed machine learning, but also introduces new challenges in terms of synchronization costs. To this end, several communication-reduction techniques, such as non-blocking communication, quantization, and local steps, have been explored in the decentralized setting. Due to the complexity of analyzing optimization in such a relaxed setting, this line of work often assumes \\emph{global} communication rounds, which require additional synchronization. In this paper, we consider decentralized optimization in the simpler, but harder to analyze, \\emph{asynchronous gossip} model, in which communication occurs in discrete, randomly chosen pairings among nodes. Perhaps surprisingly, we show that a variant of SGD called \\emph{SwarmSGD} still converges in this setting, even if \\emph{non-blocking communication}, \\emph{quantization}, and \\emph{local steps} are all applied \\emph{in conjunction}, and even if the node data distributions and underlying graph topology are both \\emph{heterogenous}. Our analysis is based on a new connection with multi-dimensional load-balancing processes. We implement this algorithm and deploy it in a super-computing environment, showing that it can outperform previous decentralized methods in terms of end-to-end training time, and that it can even rival carefully-tuned large-batch SGD for certain tasks."}],"ec_funded":1,"type":"conference","author":[{"id":"3279A00C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5634-0731","first_name":"Giorgi","last_name":"Nadiradze","full_name":"Nadiradze, Giorgi"},{"id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67","first_name":"Amirmojtaba","last_name":"Sabour","full_name":"Sabour, Amirmojtaba"},{"id":"11396234-BB50-11E9-B24C-90FCE5697425","orcid":"0000-0002-5646-9524","first_name":"Peter","last_name":"Davies","full_name":"Davies, Peter"},{"first_name":"Shigang","last_name":"Li","full_name":"Li, Shigang"},{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10429"}]},"date_created":"2021-12-09T10:59:12Z","date_updated":"2023-10-17T11:48:56Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10435","year":"2021","acknowledgement":"We gratefully acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). PD partly conducted this work while at IST Austria and was supported by the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No. 754411. SL was funded in part by European Research Council (ERC) under the European Union’s Horizon 2020 programme (grant agreement DAPP, No. 678880, and EPiGRAM-HS, No. 801039).\r\n","publication_status":"published","title":"Asynchronous decentralized SGD with quantized and local updates","status":"public","department":[{"_id":"DaAl"}],"publisher":"Neural Information Processing Systems Foundation","day":"01","month":"12","article_processing_charge":"No","conference":{"end_date":"2021-12-14","location":"Sydney, Australia","start_date":"2021-12-06","name":"NeurIPS: Neural Information Processing Systems"},"date_published":"2021-12-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"35th Conference on Neural Information Processing Systems","citation":{"short":"G. Nadiradze, A. Sabour, P. Davies, S. Li, D.-A. Alistarh, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021.","mla":"Nadiradze, Giorgi, et al. “Asynchronous Decentralized SGD with Quantized and Local Updates.” 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021.","chicago":"Nadiradze, Giorgi, Amirmojtaba Sabour, Peter Davies, Shigang Li, and Dan-Adrian Alistarh. “Asynchronous Decentralized SGD with Quantized and Local Updates.” In 35th Conference on Neural Information Processing Systems. Neural Information Processing Systems Foundation, 2021.","ama":"Nadiradze G, Sabour A, Davies P, Li S, Alistarh D-A. Asynchronous decentralized SGD with quantized and local updates. In: 35th Conference on Neural Information Processing Systems. Neural Information Processing Systems Foundation; 2021.","apa":"Nadiradze, G., Sabour, A., Davies, P., Li, S., & Alistarh, D.-A. (2021). Asynchronous decentralized SGD with quantized and local updates. In 35th Conference on Neural Information Processing Systems. Sydney, Australia: Neural Information Processing Systems Foundation.","ieee":"G. Nadiradze, A. Sabour, P. Davies, S. Li, and D.-A. Alistarh, “Asynchronous decentralized SGD with quantized and local updates,” in 35th Conference on Neural Information Processing Systems, Sydney, Australia, 2021.","ista":"Nadiradze G, Sabour A, Davies P, Li S, Alistarh D-A. 2021. Asynchronous decentralized SGD with quantized and local updates. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems."},"oa":1,"main_file_link":[{"url":"https://papers.nips.cc/paper/2021/hash/362c99307cdc3f2d8b410652386a9dd1-Abstract.html","open_access":"1"}],"external_id":{"arxiv":["1910.12308"]},"quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"}]},{"oa_version":"Preprint","_id":"10593","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"PCA initialization for approximate message passing in rotationally invariant models","status":"public","intvolume":" 35","abstract":[{"lang":"eng","text":"We study the problem of estimating a rank-$1$ signal in the presence of rotationally invariant noise-a class of perturbations more general than Gaussian noise. Principal Component Analysis (PCA) provides a natural estimator, and sharp results on its performance have been obtained in the high-dimensional regime. Recently, an Approximate Message Passing (AMP) algorithm has been proposed as an alternative estimator with the potential to improve the accuracy of PCA. However, the existing analysis of AMP requires an initialization that is both correlated with the signal and independent of the noise, which is often unrealistic in practice. In this work, we combine the two methods, and propose to initialize AMP with PCA. Our main result is a rigorous asymptotic characterization of the performance of this estimator. Both the AMP algorithm and its analysis differ from those previously derived in the Gaussian setting: at every iteration, our AMP algorithm requires a specific term to account for PCA initialization, while in the Gaussian case, PCA initialization affects only the first iteration of AMP. The proof is based on a two-phase artificial AMP that first approximates the PCA estimator and then mimics the true AMP. Our numerical simulations show an excellent agreement between AMP results and theoretical predictions, and suggest an interesting open direction on achieving Bayes-optimal performance."}],"type":"conference","date_published":"2021-12-01T00:00:00Z","publication":"35th Conference on Neural Information Processing Systems","citation":{"short":"M. Mondelli, R. Venkataramanan, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021, pp. 29616–29629.","mla":"Mondelli, Marco, and Ramji Venkataramanan. “PCA Initialization for Approximate Message Passing in Rotationally Invariant Models.” 35th Conference on Neural Information Processing Systems, vol. 35, Neural Information Processing Systems Foundation, 2021, pp. 29616–29.","chicago":"Mondelli, Marco, and Ramji Venkataramanan. “PCA Initialization for Approximate Message Passing in Rotationally Invariant Models.” In 35th Conference on Neural Information Processing Systems, 35:29616–29. Neural Information Processing Systems Foundation, 2021.","ama":"Mondelli M, Venkataramanan R. PCA initialization for approximate message passing in rotationally invariant models. In: 35th Conference on Neural Information Processing Systems. Vol 35. Neural Information Processing Systems Foundation; 2021:29616-29629.","ieee":"M. Mondelli and R. Venkataramanan, “PCA initialization for approximate message passing in rotationally invariant models,” in 35th Conference on Neural Information Processing Systems, Virtual, 2021, vol. 35, pp. 29616–29629.","apa":"Mondelli, M., & Venkataramanan, R. (2021). PCA initialization for approximate message passing in rotationally invariant models. In 35th Conference on Neural Information Processing Systems (Vol. 35, pp. 29616–29629). Virtual: Neural Information Processing Systems Foundation.","ista":"Mondelli M, Venkataramanan R. 2021. PCA initialization for approximate message passing in rotationally invariant models. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 35, 29616–29629."},"page":"29616-29629","day":"01","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","first_name":"Marco","last_name":"Mondelli"},{"last_name":"Venkataramanan","first_name":"Ramji","full_name":"Venkataramanan, Ramji"}],"date_updated":"2023-10-17T11:48:23Z","date_created":"2022-01-03T10:50:02Z","volume":35,"acknowledgement":"M. Mondelli would like to thank László Erdős for helpful discussions. M. Mondelli was partially supported by the 2019 Lopez-Loreta Prize. R. Venkataramanan was partially supported by the Alan Turing Institute under the EPSRC grant EP/N510129/1.\r\n","year":"2021","publication_status":"published","department":[{"_id":"MaMo"}],"publisher":"Neural Information Processing Systems Foundation","conference":{"location":"Virtual","start_date":"2021-12-06","end_date":"2021-12-14","name":"NeurIPS: Neural Information Processing Systems"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2106.02356"}],"external_id":{"arxiv":["2106.02356"]},"oa":1,"quality_controlled":"1","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"month":"12","publication_identifier":{"isbn":["9781713845393"],"issn":["1049-5258"]}},{"_id":"10594","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"When are solutions connected in deep networks?","status":"public","intvolume":" 35","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"The question of how and why the phenomenon of mode connectivity occurs in training deep neural networks has gained remarkable attention in the research community. From a theoretical perspective, two possible explanations have been proposed: (i) the loss function has connected sublevel sets, and (ii) the solutions found by stochastic gradient descent are dropout stable. While these explanations provide insights into the phenomenon, their assumptions are not always satisfied in practice. In particular, the first approach requires the network to have one layer with order of N neurons (N being the number of training samples), while the second one requires the loss to be almost invariant after removing half of the neurons at each layer (up to some rescaling of the remaining ones). In this work, we improve both conditions by exploiting the quality of the features at every intermediate layer together with a milder over-parameterization condition. More specifically, we show that: (i) under generic assumptions on the features of intermediate layers, it suffices that the last two hidden layers have order of N−−√ neurons, and (ii) if subsets of features at each layer are linearly separable, then no over-parameterization is needed to show the connectivity. Our experiments confirm that the proposed condition ensures the connectivity of solutions found by stochastic gradient descent, even in settings where the previous requirements do not hold."}],"publication":"35th Conference on Neural Information Processing Systems","citation":{"ista":"Nguyen Q, Bréchet P, Mondelli M. 2021. When are solutions connected in deep networks? 35th Conference on Neural Information Processing Systems. 35th Conference on Neural Information Processing Systems vol. 35.","ieee":"Q. Nguyen, P. Bréchet, and M. Mondelli, “When are solutions connected in deep networks?,” in 35th Conference on Neural Information Processing Systems, Virtual, 2021, vol. 35.","apa":"Nguyen, Q., Bréchet, P., & Mondelli, M. (2021). When are solutions connected in deep networks? In 35th Conference on Neural Information Processing Systems (Vol. 35). Virtual: Neural Information Processing Systems Foundation.","ama":"Nguyen Q, Bréchet P, Mondelli M. When are solutions connected in deep networks? In: 35th Conference on Neural Information Processing Systems. Vol 35. Neural Information Processing Systems Foundation; 2021.","chicago":"Nguyen, Quynh, Pierre Bréchet, and Marco Mondelli. “When Are Solutions Connected in Deep Networks?” In 35th Conference on Neural Information Processing Systems, Vol. 35. Neural Information Processing Systems Foundation, 2021.","mla":"Nguyen, Quynh, et al. “When Are Solutions Connected in Deep Networks?” 35th Conference on Neural Information Processing Systems, vol. 35, Neural Information Processing Systems Foundation, 2021.","short":"Q. Nguyen, P. Bréchet, M. Mondelli, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021."},"date_published":"2021-12-01T00:00:00Z","day":"01","article_processing_charge":"No","acknowledgement":"MM was partially supported by the 2019 Lopez-Loreta Prize. QN and PB acknowledge support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no 757983).","year":"2021","publication_status":"published","department":[{"_id":"MaMo"}],"publisher":"Neural Information Processing Systems Foundation","author":[{"full_name":"Nguyen, Quynh","first_name":"Quynh","last_name":"Nguyen"},{"full_name":"Bréchet, Pierre","last_name":"Bréchet","first_name":"Pierre"},{"first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"}],"date_created":"2022-01-03T10:56:20Z","date_updated":"2023-10-17T11:48:40Z","volume":35,"external_id":{"arxiv":["2102.09671"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.09671"}],"quality_controlled":"1","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"conference":{"name":"35th Conference on Neural Information Processing Systems","end_date":"2021-12-14","location":"Virtual","start_date":"2021-12-06"},"language":[{"iso":"eng"}],"month":"12","publication_identifier":{"isbn":["9781713845393"],"issn":["1049-5258"]}},{"date_published":"2021-07-15T00:00:00Z","citation":{"ama":"Mobassem S, Lambert NJ, Rueda Sanchez AR, Fink JM, Leuchs G, Schwefel HGL. Thermal noise in electro-optic devices at cryogenic temperatures. Quantum Science and Technology. 2021;6(4). doi:10.1088/2058-9565/ac0f36","apa":"Mobassem, S., Lambert, N. J., Rueda Sanchez, A. R., Fink, J. M., Leuchs, G., & Schwefel, H. G. L. (2021). Thermal noise in electro-optic devices at cryogenic temperatures. Quantum Science and Technology. IOP Publishing. https://doi.org/10.1088/2058-9565/ac0f36","ieee":"S. Mobassem, N. J. Lambert, A. R. Rueda Sanchez, J. M. Fink, G. Leuchs, and H. G. L. Schwefel, “Thermal noise in electro-optic devices at cryogenic temperatures,” Quantum Science and Technology, vol. 6, no. 4. IOP Publishing, 2021.","ista":"Mobassem S, Lambert NJ, Rueda Sanchez AR, Fink JM, Leuchs G, Schwefel HGL. 2021. Thermal noise in electro-optic devices at cryogenic temperatures. Quantum Science and Technology. 6(4), 045005.","short":"S. Mobassem, N.J. Lambert, A.R. Rueda Sanchez, J.M. Fink, G. Leuchs, H.G.L. Schwefel, Quantum Science and Technology 6 (2021).","mla":"Mobassem, Sonia, et al. “Thermal Noise in Electro-Optic Devices at Cryogenic Temperatures.” Quantum Science and Technology, vol. 6, no. 4, 045005, IOP Publishing, 2021, doi:10.1088/2058-9565/ac0f36.","chicago":"Mobassem, Sonia, Nicholas J. Lambert, Alfredo R Rueda Sanchez, Johannes M Fink, Gerd Leuchs, and Harald G.L. Schwefel. “Thermal Noise in Electro-Optic Devices at Cryogenic Temperatures.” Quantum Science and Technology. IOP Publishing, 2021. https://doi.org/10.1088/2058-9565/ac0f36."},"publication":"Quantum Science and Technology","article_type":"original","has_accepted_license":"1","article_processing_charge":"Yes","day":"15","scopus_import":"1","file":[{"checksum":"b15c2c228487a75002c3b52d56f23d5c","date_created":"2021-08-09T12:23:13Z","date_updated":"2021-08-09T12:23:13Z","file_id":"9836","relation":"main_file","creator":"cchlebak","file_size":2366118,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_QuantumScienceTechnology_Mobassem.pdf"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9815","intvolume":" 6","ddc":["530"],"status":"public","title":"Thermal noise in electro-optic devices at cryogenic temperatures","issue":"4","abstract":[{"text":"The quantum bits (qubits) on which superconducting quantum computers are based have energy scales corresponding to photons with GHz frequencies. The energy of photons in the gigahertz domain is too low to allow transmission through the noisy room-temperature environment, where the signal would be lost in thermal noise. Optical photons, on the other hand, have much higher energies, and signals can be detected using highly efficient single-photon detectors. Transduction from microwave to optical frequencies is therefore a potential enabling technology for quantum devices. However, in such a device the optical pump can be a source of thermal noise and thus degrade the fidelity; the similarity of input microwave state to the output optical state. In order to investigate the magnitude of this effect we model the sub-Kelvin thermal behavior of an electro-optic transducer based on a lithium niobate whispering gallery mode resonator. We find that there is an optimum power level for a continuous pump, whilst pulsed operation of the pump increases the fidelity of the conversion.","lang":"eng"}],"type":"journal_article","doi":"10.1088/2058-9565/ac0f36","language":[{"iso":"eng"}],"external_id":{"arxiv":["2008.08764"],"isi":["000673081500001"]},"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,"publication_identifier":{"eissn":["2058-9565"]},"month":"07","author":[{"last_name":"Mobassem","first_name":"Sonia","full_name":"Mobassem, Sonia"},{"full_name":"Lambert, Nicholas J.","first_name":"Nicholas J.","last_name":"Lambert"},{"full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M"},{"full_name":"Leuchs, Gerd","first_name":"Gerd","last_name":"Leuchs"},{"first_name":"Harald G.L.","last_name":"Schwefel","full_name":"Schwefel, Harald G.L."}],"volume":6,"date_updated":"2023-10-17T12:54:54Z","date_created":"2021-08-08T22:01:25Z","year":"2021","acknowledgement":"NJL is supported by the MBIE Endeavour Fund (UOOX1805) and GL is by the Julius von Haast Fellowship of New Zealand. SM acknowledges stimulating discussions with T M Jensen.","publisher":"IOP Publishing","department":[{"_id":"JoFi"}],"publication_status":"published","file_date_updated":"2021-08-09T12:23:13Z","article_number":"045005"},{"doi":"10.21203/rs.3.rs-750965/v1","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,"publication_identifier":{"eissn":["2693-5015"]},"month":"08","related_material":{"record":[{"relation":"later_version","status":"public","id":"10813"}]},"author":[{"last_name":"Cao","first_name":"Deqing","full_name":"Cao, Deqing"},{"first_name":"Xiaoxiao","last_name":"Shen","full_name":"Shen, Xiaoxiao"},{"first_name":"Aiping","last_name":"Wang","full_name":"Wang, Aiping"},{"first_name":"Fengjiao","last_name":"Yu","full_name":"Yu, Fengjiao"},{"last_name":"Wu","first_name":"Yuping","full_name":"Wu, Yuping"},{"last_name":"Shi","first_name":"Siqi","full_name":"Shi, Siqi"},{"full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"last_name":"Chen","first_name":"Yuhui","full_name":"Chen, Yuhui"}],"date_updated":"2023-10-17T13:06:29Z","date_created":"2021-08-31T12:54:16Z","year":"2021","acknowledgement":"This work was financially supported by the National Natural Science Foundation of China (51773092, 21975124, 11874254, 51802187, U2030206). S.A.F. is indebted to IST Austria for support. ","publisher":"Research Square","department":[{"_id":"StFr"}],"publication_status":"submitted","file_date_updated":"2021-08-31T14:02:19Z","date_published":"2021-08-18T00:00:00Z","citation":{"ista":"Cao D, Shen X, Wang A, Yu F, Wu Y, Shi S, Freunberger SA, Chen Y. Sharp kinetic acceleration potentials during mediated redox catalysis of insulators. Research Square, 10.21203/rs.3.rs-750965/v1.","apa":"Cao, D., Shen, X., Wang, A., Yu, F., Wu, Y., Shi, S., … Chen, Y. (n.d.). Sharp kinetic acceleration potentials during mediated redox catalysis of insulators. Research Square. Research Square. https://doi.org/10.21203/rs.3.rs-750965/v1","ieee":"D. Cao et al., “Sharp kinetic acceleration potentials during mediated redox catalysis of insulators,” Research Square. Research Square.","ama":"Cao D, Shen X, Wang A, et al. Sharp kinetic acceleration potentials during mediated redox catalysis of insulators. Research Square. doi:10.21203/rs.3.rs-750965/v1","chicago":"Cao, Deqing, Xiaoxiao Shen, Aiping Wang, Fengjiao Yu, Yuping Wu, Siqi Shi, Stefan Alexander Freunberger, and Yuhui Chen. “Sharp Kinetic Acceleration Potentials during Mediated Redox Catalysis of Insulators.” Research Square. Research Square, n.d. https://doi.org/10.21203/rs.3.rs-750965/v1.","mla":"Cao, Deqing, et al. “Sharp Kinetic Acceleration Potentials during Mediated Redox Catalysis of Insulators.” Research Square, Research Square, doi:10.21203/rs.3.rs-750965/v1.","short":"D. Cao, X. Shen, A. Wang, F. Yu, Y. Wu, S. Shi, S.A. Freunberger, Y. Chen, Research Square (n.d.)."},"publication":"Research Square","page":"21","has_accepted_license":"1","article_processing_charge":"No","day":"18","keyword":["Catalysis","Energy engineering","Materials theory and modeling"],"oa_version":"Preprint","file":[{"success":1,"checksum":"1878e91c29d5769ed5a827b0b7addf00","date_updated":"2021-08-31T14:02:19Z","date_created":"2021-08-31T14:02:19Z","file_id":"9979","relation":"main_file","creator":"cchlebak","content_type":"application/pdf","file_size":1019662,"access_level":"open_access","file_name":"2021_ResearchSquare_Cao.pdf"}],"_id":"9978","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Sharp kinetic acceleration potentials during mediated redox catalysis of insulators","ddc":["541"],"abstract":[{"lang":"eng","text":"Redox mediators could catalyse otherwise slow and energy-inefficient cycling of Li-S and Li-O 2 batteries by shuttling electrons/holes between the electrode and the solid insulating storage materials. For mediators to work efficiently they need to oxidize the solid with fast kinetics yet the lowest possible overpotential. Here, we found that when the redox potentials of mediators are tuned via, e.g., Li + concentration in the electrolyte, they exhibit distinct threshold potentials, where the kinetics accelerate several-fold within a range as small as 10 mV. This phenomenon is independent of types of mediators and electrolyte. The acceleration originates from the overpotentials required to activate fast Li + /e – extraction and the following chemical step at specific abundant surface facets. Efficient redox catalysis at insulating solids requires therefore carefully considering the surface conditions of the storage materials and electrolyte-dependent redox potentials, which may be tuned by salt concentrations or solvents."}],"type":"preprint"},{"page":"1634-1646","article_type":"original","citation":{"mla":"Tournier, N., et al. “Complete Inhibition of ABCB1 and ABCG2 at the Blood-Brain Barrier by Co-Infusion of Erlotinib and Tariquidar to Improve Brain Delivery of the Model ABCB1/ABCG2 Substrate [11C]Erlotinib.” Journal of Cerebral Blood Flow and Metabolism, vol. 41, no. 7, SAGE Publications, 2021, pp. 1634–46, doi:10.1177/0271678X20965500.","short":"N. Tournier, S. Goutal, S. Mairinger, I. Lozano, T. Filip, M. Sauberer, F. Caillé, L. Breuil, J. Stanek, A. Freeman, G. Novarino, C. Truillet, T. Wanek, O. Langer, Journal of Cerebral Blood Flow and Metabolism 41 (2021) 1634–1646.","chicago":"Tournier, N, S Goutal, S Mairinger, IH Lozano, T Filip, M Sauberer, F Caillé, et al. “Complete Inhibition of ABCB1 and ABCG2 at the Blood-Brain Barrier by Co-Infusion of Erlotinib and Tariquidar to Improve Brain Delivery of the Model ABCB1/ABCG2 Substrate [11C]Erlotinib.” Journal of Cerebral Blood Flow and Metabolism. SAGE Publications, 2021. https://doi.org/10.1177/0271678X20965500.","ama":"Tournier N, Goutal S, Mairinger S, et al. Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Journal of Cerebral Blood Flow and Metabolism. 2021;41(7):1634-1646. doi:10.1177/0271678X20965500","ista":"Tournier N, Goutal S, Mairinger S, Lozano I, Filip T, Sauberer M, Caillé F, Breuil L, Stanek J, Freeman A, Novarino G, Truillet C, Wanek T, Langer O. 2021. Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Journal of Cerebral Blood Flow and Metabolism. 41(7), 1634–1646.","apa":"Tournier, N., Goutal, S., Mairinger, S., Lozano, I., Filip, T., Sauberer, M., … Langer, O. (2021). Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Journal of Cerebral Blood Flow and Metabolism. SAGE Publications. https://doi.org/10.1177/0271678X20965500","ieee":"N. Tournier et al., “Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib,” Journal of Cerebral Blood Flow and Metabolism, vol. 41, no. 7. SAGE Publications, pp. 1634–1646, 2021."},"publication":"Journal of Cerebral Blood Flow and Metabolism","date_published":"2021-07-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 41","status":"public","title":"Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8730","oa_version":"Published Version","type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"P-glycoprotein (ABCB1) and breast cancer resistance protein (ABCG2) restrict at the blood–brain barrier (BBB) the brain distribution of the majority of currently known molecularly targeted anticancer drugs. To improve brain delivery of dual ABCB1/ABCG2 substrates, both ABCB1 and ABCG2 need to be inhibited simultaneously at the BBB. We examined the feasibility of simultaneous ABCB1/ABCG2 inhibition with i.v. co-infusion of erlotinib and tariquidar by studying brain distribution of the model ABCB1/ABCG2 substrate [11C]erlotinib in mice and rhesus macaques with PET. Tolerability of the erlotinib/tariquidar combination was assessed in human embryonic stem cell-derived cerebral organoids. In mice and macaques, baseline brain distribution of [11C]erlotinib was low (brain distribution volume, VT,brain < 0.3 mL/cm3). Co-infusion of erlotinib and tariquidar increased VT,brain in mice by 3.0-fold and in macaques by 3.4- to 5.0-fold, while infusion of erlotinib alone or tariquidar alone led to less pronounced VT,brain increases in both species. Treatment of cerebral organoids with erlotinib/tariquidar led to an induction of Caspase-3-dependent apoptosis. Co-infusion of erlotinib/tariquidar may potentially allow for complete ABCB1/ABCG2 inhibition at the BBB, while simultaneously achieving brain-targeted EGFR inhibition. Our protocol may be applicable to enhance brain delivery of molecularly targeted anticancer drugs for a more effective treatment of brain tumors."}],"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8221757/","open_access":"1"}],"external_id":{"isi":["000664214100012"],"pmid":["33081568"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1177/0271678X20965500","publication_identifier":{"issn":["0271-678x"],"eissn":["1559-7016"]},"month":"07","publisher":"SAGE Publications","department":[{"_id":"GaNo"}],"publication_status":"published","pmid":1,"year":"2021","volume":41,"date_created":"2020-11-06T08:39:01Z","date_updated":"2023-10-18T06:45:30Z","author":[{"full_name":"Tournier, N","last_name":"Tournier","first_name":"N"},{"last_name":"Goutal","first_name":"S","full_name":"Goutal, S"},{"first_name":"S","last_name":"Mairinger","full_name":"Mairinger, S"},{"full_name":"Lozano, IH","first_name":"IH","last_name":"Lozano"},{"first_name":"T","last_name":"Filip","full_name":"Filip, T"},{"full_name":"Sauberer, M","first_name":"M","last_name":"Sauberer"},{"last_name":"Caillé","first_name":"F","full_name":"Caillé, F"},{"full_name":"Breuil, L","last_name":"Breuil","first_name":"L"},{"first_name":"J","last_name":"Stanek","full_name":"Stanek, J"},{"full_name":"Freeman, AF","last_name":"Freeman","first_name":"AF"},{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino"},{"full_name":"Truillet, C","last_name":"Truillet","first_name":"C"},{"full_name":"Wanek, T","first_name":"T","last_name":"Wanek"},{"last_name":"Langer","first_name":"O","full_name":"Langer, O"}]},{"oa_version":"Published Version","file":[{"file_name":"2021_Evolution_Stankowski.pdf","access_level":"open_access","creator":"kschuh","file_size":719991,"content_type":"application/pdf","file_id":"10921","relation":"main_file","date_updated":"2022-03-25T12:02:04Z","date_created":"2022-03-25T12:02:04Z","success":1,"checksum":"96f6ccf15d95a4e9f7c0b27eee570fa6"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9383","title":"Defining the speciation continuum","status":"public","ddc":["570"],"intvolume":" 75","abstract":[{"text":"A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present‐day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us.","lang":"eng"}],"issue":"6","type":"journal_article","date_published":"2021-03-22T00:00:00Z","publication":"Evolution","citation":{"ama":"Stankowski S, Ravinet M. Defining the speciation continuum. Evolution. 2021;75(6):1256-1273. doi:10.1111/evo.14215","ista":"Stankowski S, Ravinet M. 2021. Defining the speciation continuum. Evolution. 75(6), 1256–1273.","apa":"Stankowski, S., & Ravinet, M. (2021). Defining the speciation continuum. Evolution. Oxford University Press. https://doi.org/10.1111/evo.14215","ieee":"S. Stankowski and M. Ravinet, “Defining the speciation continuum,” Evolution, vol. 75, no. 6. Oxford University Press, pp. 1256–1273, 2021.","mla":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution, vol. 75, no. 6, Oxford University Press, 2021, pp. 1256–73, doi:10.1111/evo.14215.","short":"S. Stankowski, M. Ravinet, Evolution 75 (2021) 1256–1273.","chicago":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution. Oxford University Press, 2021. https://doi.org/10.1111/evo.14215."},"article_type":"original","page":"1256-1273","day":"22","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"}],"date_created":"2021-05-09T22:01:39Z","date_updated":"2023-10-18T08:16:01Z","volume":75,"acknowledgement":"We thank M. Garlovsky, S. Martin, C. Cooney, C. Roux, J. Larson, and J. Mallet for critical feedback and for discussion. K. Lohse, M. de la Cámara, J. Cerca, M. A. Chase, C. Baskett, A. M. Westram, and N. H. Barton gave feedback on a draft of the manuscript. O. Seehausen, two anonymous reviewers, and the AE (Michael Kopp) provided comments that greatly improved the manuscript. V. Holzmann made many corrections to the proofs. G. Bisschop and K. Lohse kindly contributed the simulations and analyses presented in Box 3. We would also like to extend our thanks to everyone who took part in the speciation survey, which received ethical approval through the University of Sheffield Ethics Review Procedure (Application 029768). We are especially grateful to R. K. Butlin for stimulating discussion throughout the writing of the manuscript and for feedback on an earlier draft.","year":"2021","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"NiBa"}],"file_date_updated":"2022-03-25T12:02:04Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","doi":"10.1111/evo.14215","language":[{"iso":"eng"}],"external_id":{"isi":["000647226400001"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"isi":1,"quality_controlled":"1","month":"03","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]}},{"acknowledgement":"We thank N. Gnyliukh and L. Hörmayer for technical assistance and N. Paris for sharing PM-Cyto seeds. We gratefully acknowledge the Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) under I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001), Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R. and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., and the China Scholarship Council to J.C.","year":"2021","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"author":[{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","first_name":"Lanxin","last_name":"Li","full_name":"Li, Lanxin"},{"full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","first_name":"Inge","last_name":"Verstraeten"},{"first_name":"Mark","last_name":"Roosjen","full_name":"Roosjen, Mark"},{"last_name":"Takahashi","first_name":"Koji","full_name":"Takahashi, Koji"},{"full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey","first_name":"Lesia"},{"last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"},{"full_name":"Chen, Jian","first_name":"Jian","last_name":"Chen"},{"full_name":"Shabala, Lana","first_name":"Lana","last_name":"Shabala"},{"first_name":"Wouter","last_name":"Smet","full_name":"Smet, Wouter"},{"first_name":"Hong","last_name":"Ren","full_name":"Ren, Hong"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"full_name":"Shabala, Sergey","last_name":"Shabala","first_name":"Sergey"},{"last_name":"De Rybel","first_name":"Bert","full_name":"De Rybel, Bert"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"},{"full_name":"Kinoshita, Toshinori","last_name":"Kinoshita","first_name":"Toshinori"},{"first_name":"William M.","last_name":"Gray","full_name":"Gray, William M."},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"related_material":{"record":[{"id":"10095","status":"public","relation":"earlier_version"}],"link":[{"url":"https://ist.ac.at/en/news/stop-and-grow/","relation":"press_release","description":"News on IST Webpage"}]},"date_created":"2021-11-07T23:01:25Z","date_updated":"2023-10-18T08:30:53Z","volume":599,"ec_funded":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3"}],"external_id":{"isi":["000713338100006"],"pmid":["34707283"]},"isi":1,"quality_controlled":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"doi":"10.1038/s41586-021-04037-6","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"month":"11","publication_identifier":{"issn":["00280836"],"eissn":["14764687"]},"_id":"10223","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Cell surface and intracellular auxin signalling for H+ fluxes in root growth","status":"public","intvolume":" 599","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Growth regulation tailors development in plants to their environment. A prominent example of this is the response to gravity, in which shoots bend up and roots bend down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phosphoproteomics in Arabidopsis thaliana, we advance understanding of how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on rapid regulation of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+ influx, causing apoplast alkalinization. Simultaneous activation of these two counteracting mechanisms poises roots for rapid, fine-tuned growth modulation in navigating complex soil environments."}],"issue":"7884","publication":"Nature","citation":{"chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+ Fluxes in Root Growth.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-04037-6.","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+ Fluxes in Root Growth.” Nature, vol. 599, no. 7884, Springer Nature, 2021, pp. 273–77, doi:10.1038/s41586-021-04037-6.","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Nature 599 (2021) 273–277.","ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. 2021. Cell surface and intracellular auxin signalling for H+ fluxes in root growth. Nature. 599(7884), 273–277.","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (2021). Cell surface and intracellular auxin signalling for H+ fluxes in root growth. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-04037-6","ieee":"L. Li et al., “Cell surface and intracellular auxin signalling for H+ fluxes in root growth,” Nature, vol. 599, no. 7884. Springer Nature, pp. 273–277, 2021.","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+ fluxes in root growth. Nature. 2021;599(7884):273-277. doi:10.1038/s41586-021-04037-6"},"article_type":"original","page":"273-277","date_published":"2021-11-11T00:00:00Z","scopus_import":"1","keyword":["Multidisciplinary"],"day":"11","article_processing_charge":"No"},{"doi":"10.3389/fcell.2021.649433","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":["000644419500001"],"pmid":["33928084"]},"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["2296-634X"]},"month":"04","author":[{"last_name":"Bolger-Munro","first_name":"Madison","orcid":"0000-0002-8176-4824","id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E","full_name":"Bolger-Munro, Madison"},{"last_name":"Choi","first_name":"Kate","full_name":"Choi, Kate"},{"last_name":"Cheung","first_name":"Faith","full_name":"Cheung, Faith"},{"full_name":"Liu, Yi Tian","first_name":"Yi Tian","last_name":"Liu"},{"full_name":"Dang-Lawson, May","first_name":"May","last_name":"Dang-Lawson"},{"first_name":"Nikola","last_name":"Deretic","full_name":"Deretic, Nikola"},{"last_name":"Keane","first_name":"Connor","full_name":"Keane, Connor"},{"last_name":"Gold","first_name":"Michael R.","full_name":"Gold, Michael R."}],"volume":9,"date_created":"2021-05-09T22:01:37Z","date_updated":"2023-10-18T08:19:49Z","pmid":1,"acknowledgement":"We thank the UBC Life Sciences Institute Imaging Facility andthe UBC Flow Cytometry Facility.","year":"2021","department":[{"_id":"CaHe"}],"publisher":"Frontiers Media","publication_status":"published","file_date_updated":"2021-05-11T15:09:23Z","article_number":"649433","date_published":"2021-04-13T00:00:00Z","citation":{"ama":"Bolger-Munro M, Choi K, Cheung F, et al. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental Biology. 2021;9. doi:10.3389/fcell.2021.649433","apa":"Bolger-Munro, M., Choi, K., Cheung, F., Liu, Y. T., Dang-Lawson, M., Deretic, N., … Gold, M. R. (2021). The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental Biology. Frontiers Media. https://doi.org/10.3389/fcell.2021.649433","ieee":"M. Bolger-Munro et al., “The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse,” Frontiers in Cell and Developmental Biology, vol. 9. Frontiers Media, 2021.","ista":"Bolger-Munro M, Choi K, Cheung F, Liu YT, Dang-Lawson M, Deretic N, Keane C, Gold MR. 2021. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental Biology. 9, 649433.","short":"M. Bolger-Munro, K. Choi, F. Cheung, Y.T. Liu, M. Dang-Lawson, N. Deretic, C. Keane, M.R. Gold, Frontiers in Cell and Developmental Biology 9 (2021).","mla":"Bolger-Munro, Madison, et al. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” Frontiers in Cell and Developmental Biology, vol. 9, 649433, Frontiers Media, 2021, doi:10.3389/fcell.2021.649433.","chicago":"Bolger-Munro, Madison, Kate Choi, Faith Cheung, Yi Tian Liu, May Dang-Lawson, Nikola Deretic, Connor Keane, and Michael R. Gold. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” Frontiers in Cell and Developmental Biology. Frontiers Media, 2021. https://doi.org/10.3389/fcell.2021.649433."},"publication":"Frontiers in Cell and Developmental Biology","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"13","scopus_import":"1","keyword":["B cell","actin","immune synapse","cell spreading","cofilin","WDR1 (AIP1)","LIM domain kinase","B cell receptor (BCR)"],"oa_version":"Published Version","file":[{"creator":"kschuh","file_size":4076024,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_Frontiers_Cell_Bolger-Munro.pdf","success":1,"checksum":"8c8a03575d2f7583f88dc3b658b0976b","date_updated":"2021-05-11T15:09:23Z","date_created":"2021-05-11T15:09:23Z","file_id":"9386","relation":"main_file"}],"_id":"9379","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 9","title":"The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse","ddc":["570"],"status":"public","abstract":[{"text":"When B cells encounter membrane-bound antigens, the formation and coalescence of B cell antigen receptor (BCR) microclusters amplifies BCR signaling. The ability of B cells to probe the surface of antigen-presenting cells (APCs) and respond to APC-bound antigens requires remodeling of the actin cytoskeleton. Initial BCR signaling stimulates actin-related protein (Arp) 2/3 complex-dependent actin polymerization, which drives B cell spreading as well as the centripetal movement and coalescence of BCR microclusters at the B cell-APC synapse. Sustained actin polymerization depends on concomitant actin filament depolymerization, which enables the recycling of actin monomers and Arp2/3 complexes. Cofilin-mediated severing of actin filaments is a rate-limiting step in the morphological changes that occur during immune synapse formation. Hence, regulators of cofilin activity such as WD repeat-containing protein 1 (Wdr1), LIM domain kinase (LIMK), and coactosin-like 1 (Cotl1) may also be essential for actin-dependent processes in B cells. Wdr1 enhances cofilin-mediated actin disassembly. Conversely, Cotl1 competes with cofilin for binding to actin and LIMK phosphorylates cofilin and prevents it from binding to actin filaments. We now show that Wdr1 and LIMK have distinct roles in BCR-induced assembly of the peripheral actin structures that drive B cell spreading, and that cofilin, Wdr1, and LIMK all contribute to the actin-dependent amplification of BCR signaling at the immune synapse. Depleting Cotl1 had no effect on these processes. Thus, the Wdr1-LIMK-cofilin axis is critical for BCR-induced actin remodeling and for B cell responses to APC-bound antigens.","lang":"eng"}],"type":"journal_article"},{"article_number":"e0248940","file_date_updated":"2021-05-04T13:22:19Z","pmid":1,"acknowledgement":"The authors would like to thank Ulisse Ferrari for useful discussions and feedback.","year":"2021","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"publication_status":"published","author":[{"full_name":"Chalk, Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436","first_name":"Matthew J","last_name":"Chalk"},{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"}],"volume":16,"date_created":"2021-05-02T22:01:28Z","date_updated":"2023-10-18T08:17:42Z","publication_identifier":{"eissn":["19326203"]},"month":"04","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["33857170"],"isi":["000641474900072"]},"isi":1,"quality_controlled":"1","doi":"10.1371/journal.pone.0248940","language":[{"iso":"eng"}],"type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"A central goal in systems neuroscience is to understand the functions performed by neural circuits. Previous top-down models addressed this question by comparing the behaviour of an ideal model circuit, optimised to perform a given function, with neural recordings. However, this requires guessing in advance what function is being performed, which may not be possible for many neural systems. To address this, we propose an inverse reinforcement learning (RL) framework for inferring the function performed by a neural network from data. We assume that the responses of each neuron in a network are optimised so as to drive the network towards ‘rewarded’ states, that are desirable for performing a given function. We then show how one can use inverse RL to infer the reward function optimised by the network from observing its responses. This inferred reward function can be used to predict how the neural network should adapt its dynamics to perform the same function when the external environment or network structure changes. This could lead to theoretical predictions about how neural network dynamics adapt to deal with cell death and/or varying sensory stimulus statistics."}],"_id":"9362","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 16","ddc":["570"],"status":"public","title":"Inferring the function performed by a recurrent neural network","oa_version":"Published Version","file":[{"file_name":"2021_pone_Chalk.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2768282,"creator":"kschuh","relation":"main_file","file_id":"9371","date_updated":"2021-05-04T13:22:19Z","date_created":"2021-05-04T13:22:19Z","checksum":"c52da133850307d2031f552d998f00e8","success":1}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"15","citation":{"mla":"Chalk, Matthew J., et al. “Inferring the Function Performed by a Recurrent Neural Network.” PLoS ONE, vol. 16, no. 4, e0248940, Public Library of Science, 2021, doi:10.1371/journal.pone.0248940.","short":"M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021).","chicago":"Chalk, Matthew J, Gašper Tkačik, and Olivier Marre. “Inferring the Function Performed by a Recurrent Neural Network.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0248940.","ama":"Chalk MJ, Tkačik G, Marre O. Inferring the function performed by a recurrent neural network. PLoS ONE. 2021;16(4). doi:10.1371/journal.pone.0248940","ista":"Chalk MJ, Tkačik G, Marre O. 2021. Inferring the function performed by a recurrent neural network. PLoS ONE. 16(4), e0248940.","ieee":"M. J. Chalk, G. Tkačik, and O. Marre, “Inferring the function performed by a recurrent neural network,” PLoS ONE, vol. 16, no. 4. Public Library of Science, 2021.","apa":"Chalk, M. J., Tkačik, G., & Marre, O. (2021). Inferring the function performed by a recurrent neural network. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0248940"},"publication":"PLoS ONE","article_type":"original","date_published":"2021-04-15T00:00:00Z"},{"has_accepted_license":"1","article_processing_charge":"Yes","day":"26","keyword":["auxin","growth","cell wall","xyloglucans","hypocotyls","gravitropism"],"scopus_import":"1","date_published":"2021-08-26T00:00:00Z","article_type":"original","citation":{"apa":"Velasquez, S. M., Guo, X., Gallemi, M., Aryal, B., Venhuizen, P., Barbez, E., … Kleine-Vehn, J. (2021). Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms22179222","ieee":"S. M. Velasquez et al., “Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants,” International Journal of Molecular Sciences, vol. 22, no. 17. MDPI, 2021.","ista":"Velasquez SM, Guo X, Gallemi M, Aryal B, Venhuizen P, Barbez E, Dünser KA, Darino M, Pӗnčík A, Novák O, Kalyna M, Mouille G, Benková E, Bhalerao RP, Mravec J, Kleine-Vehn J. 2021. Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. International Journal of Molecular Sciences. 22(17), 9222.","ama":"Velasquez SM, Guo X, Gallemi M, et al. Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. International Journal of Molecular Sciences. 2021;22(17). doi:10.3390/ijms22179222","chicago":"Velasquez, Silvia Melina, Xiaoyuan Guo, Marçal Gallemi, Bibek Aryal, Peter Venhuizen, Elke Barbez, Kai Alexander Dünser, et al. “Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants.” International Journal of Molecular Sciences. MDPI, 2021. https://doi.org/10.3390/ijms22179222.","short":"S.M. Velasquez, X. Guo, M. Gallemi, B. Aryal, P. Venhuizen, E. Barbez, K.A. Dünser, M. Darino, A. Pӗnčík, O. Novák, M. Kalyna, G. Mouille, E. Benková, R.P. Bhalerao, J. Mravec, J. Kleine-Vehn, International Journal of Molecular Sciences 22 (2021).","mla":"Velasquez, Silvia Melina, et al. “Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants.” International Journal of Molecular Sciences, vol. 22, no. 17, 9222, MDPI, 2021, doi:10.3390/ijms22179222."},"publication":"International Journal of Molecular Sciences","issue":"17","abstract":[{"text":"Size control is a fundamental question in biology, showing incremental complexity in plants, whose cells possess a rigid cell wall. The phytohormone auxin is a vital growth regulator with central importance for differential growth control. Our results indicate that auxin-reliant growth programs affect the molecular complexity of xyloglucans, the major type of cell wall hemicellulose in eudicots. Auxin-dependent induction and repression of growth coincide with reduced and enhanced molecular complexity of xyloglucans, respectively. In agreement with a proposed function in growth control, genetic interference with xyloglucan side decorations distinctly modulates auxin-dependent differential growth rates. Our work proposes that auxin-dependent growth programs have a spatially defined effect on xyloglucan’s molecular structure, which in turn affects cell wall mechanics and specifies differential, gravitropic hypocotyl growth.","lang":"eng"}],"type":"journal_article","file":[{"creator":"cchlebak","file_size":2162247,"content_type":"application/pdf","file_name":"2021_IntJMolecularSciences_Velasquez.pdf","access_level":"open_access","date_updated":"2021-09-07T09:04:53Z","date_created":"2021-09-06T12:50:19Z","checksum":"6b7055cf89f1b7ed8594c3fdf56f000b","file_id":"9988","relation":"main_file"}],"oa_version":"Published Version","intvolume":" 22","status":"public","ddc":["575"],"title":"Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9986","publication_identifier":{"eissn":["1422-0067"],"issn":["1661-6596"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.3390/ijms22179222","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":{"pmid":["34502129"],"isi":["000694347100001"]},"oa":1,"file_date_updated":"2021-09-07T09:04:53Z","article_number":"9222","volume":22,"date_created":"2021-09-05T22:01:24Z","date_updated":"2023-10-31T19:29:38Z","author":[{"full_name":"Velasquez, Silvia Melina","last_name":"Velasquez","first_name":"Silvia Melina"},{"last_name":"Guo","first_name":"Xiaoyuan","full_name":"Guo, Xiaoyuan"},{"full_name":"Gallemi, Marçal","id":"460C6802-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4675-6893","first_name":"Marçal","last_name":"Gallemi"},{"last_name":"Aryal","first_name":"Bibek","full_name":"Aryal, Bibek"},{"last_name":"Venhuizen","first_name":"Peter","full_name":"Venhuizen, Peter"},{"last_name":"Barbez","first_name":"Elke","full_name":"Barbez, Elke"},{"full_name":"Dünser, Kai Alexander","first_name":"Kai Alexander","last_name":"Dünser"},{"full_name":"Darino, Martin","first_name":"Martin","last_name":"Darino"},{"full_name":"Pӗnčík, Aleš","first_name":"Aleš","last_name":"Pӗnčík"},{"last_name":"Novák","first_name":"Ondřej","full_name":"Novák, Ondřej"},{"first_name":"Maria","last_name":"Kalyna","full_name":"Kalyna, Maria"},{"full_name":"Mouille, Gregory","first_name":"Gregory","last_name":"Mouille"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva"},{"full_name":"Bhalerao, Rishikesh P.","first_name":"Rishikesh P.","last_name":"Bhalerao"},{"first_name":"Jozef","last_name":"Mravec","full_name":"Mravec, Jozef"},{"full_name":"Kleine-Vehn, Jürgen","first_name":"Jürgen","last_name":"Kleine-Vehn"}],"publisher":"MDPI","department":[{"_id":"EvBe"}],"publication_status":"published","pmid":1,"year":"2021","acknowledgement":"We are grateful to Paul Knox, Markus Pauly, Malcom O’Neill, and Ignacio Zarra for providing published material; the BOKU-VIBT Imaging Center for access and M. Debreczeny for expertise; J.I. Thaker and Georg Seifert for critical reading.\r\n"},{"issue":"6","abstract":[{"text":"Transposable elements exist widely throughout plant genomes and play important roles in plant evolution. Auxin is an important regulator that is traditionally associated with root development and drought stress adaptation. The DEEPER ROOTING 1 (DRO1) gene is a key component of rice drought avoidance. Here, we identified a transposon that acts as an autonomous auxin‐responsive promoter and its presence at specific genome positions conveys physiological adaptations related to drought avoidance. Rice varieties with high and auxin‐mediated transcription of DRO1 in the root tip show deeper and longer root phenotypes and are thus better adapted to drought. The INDITTO2 transposon contains an auxin response element and displays auxin‐responsive promoter activity; it is thus able to convey auxin regulation of transcription to genes in its proximity. In the rice Acuce, which displays DRO1‐mediated drought adaptation, the INDITTO2 transposon was found to be inserted at the promoter region of the DRO1 locus. Transgenesis‐based insertion of the INDITTO2 transposon into the DRO1 promoter of the non‐adapted rice variety Nipponbare was sufficient to promote its drought avoidance. Our data identify an example of how transposons can act as promoters and convey hormonal regulation to nearby loci, improving plant fitness in response to different abiotic stresses.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"14481","date_created":"2023-11-02T17:02:11Z","date_updated":"2023-11-02T17:02:11Z","checksum":"a812418fede076741c9c4dc07f317068","success":1,"file_name":"Zhao PlantCellEnv 2021_accepted.pdf","access_level":"open_access","file_size":8437528,"content_type":"application/pdf","creator":"amally"}],"_id":"9189","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 44","status":"public","title":"INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance","ddc":["580"],"has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2021-06-01T00:00:00Z","citation":{"apa":"Zhao, Y., Wu, L., Fu, Q., Wang, D., Li, J., Yao, B., … Du, Y. (2021). INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant, Cell & Environment. Wiley. https://doi.org/10.1111/pce.14029","ieee":"Y. Zhao et al., “INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance,” Plant, Cell & Environment, vol. 44, no. 6. Wiley, pp. 1846–1857, 2021.","ista":"Zhao Y, Wu L, Fu Q, Wang D, Li J, Yao B, Yu S, Jiang L, Qian J, Zhou X, Han L, Zhao S, Ma C, Zhang Y, Luo C, Dong Q, Li S, Zhang L, Jiang X, Li Y, Luo H, Li K, Yang J, Luo Q, Li L, Peng S, Huang H, Zuo Z, Liu C, Wang L, Li C, He X, Friml J, Du Y. 2021. INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant, Cell & Environment. 44(6), 1846–1857.","ama":"Zhao Y, Wu L, Fu Q, et al. INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant, Cell & Environment. 2021;44(6):1846-1857. doi:10.1111/pce.14029","chicago":"Zhao, Y, L Wu, Q Fu, D Wang, J Li, B Yao, S Yu, et al. “INDITTO2 Transposon Conveys Auxin-Mediated DRO1 Transcription for Rice Drought Avoidance.” Plant, Cell & Environment. Wiley, 2021. https://doi.org/10.1111/pce.14029.","short":"Y. Zhao, L. Wu, Q. Fu, D. Wang, J. Li, B. Yao, S. Yu, L. Jiang, J. Qian, X. Zhou, L. Han, S. Zhao, C. Ma, Y. Zhang, C. Luo, Q. Dong, S. Li, L. Zhang, X. Jiang, Y. Li, H. Luo, K. Li, J. Yang, Q. Luo, L. Li, S. Peng, H. Huang, Z. Zuo, C. Liu, L. Wang, C. Li, X. He, J. Friml, Y. Du, Plant, Cell & Environment 44 (2021) 1846–1857.","mla":"Zhao, Y., et al. “INDITTO2 Transposon Conveys Auxin-Mediated DRO1 Transcription for Rice Drought Avoidance.” Plant, Cell & Environment, vol. 44, no. 6, Wiley, 2021, pp. 1846–57, doi:10.1111/pce.14029."},"publication":"Plant, Cell & Environment","page":"1846-1857","article_type":"original","file_date_updated":"2023-11-02T17:02:11Z","author":[{"last_name":"Zhao","first_name":"Y","full_name":"Zhao, Y"},{"last_name":"Wu","first_name":"L","full_name":"Wu, L"},{"full_name":"Fu, Q","first_name":"Q","last_name":"Fu"},{"full_name":"Wang, D","last_name":"Wang","first_name":"D"},{"full_name":"Li, J","last_name":"Li","first_name":"J"},{"last_name":"Yao","first_name":"B","full_name":"Yao, B"},{"first_name":"S","last_name":"Yu","full_name":"Yu, S"},{"full_name":"Jiang, L","last_name":"Jiang","first_name":"L"},{"full_name":"Qian, J","first_name":"J","last_name":"Qian"},{"full_name":"Zhou, X","last_name":"Zhou","first_name":"X"},{"last_name":"Han","first_name":"L","full_name":"Han, L"},{"first_name":"S","last_name":"Zhao","full_name":"Zhao, S"},{"full_name":"Ma, C","last_name":"Ma","first_name":"C"},{"first_name":"Y","last_name":"Zhang","full_name":"Zhang, Y"},{"first_name":"C","last_name":"Luo","full_name":"Luo, C"},{"full_name":"Dong, Q","first_name":"Q","last_name":"Dong"},{"full_name":"Li, S","last_name":"Li","first_name":"S"},{"full_name":"Zhang, L","last_name":"Zhang","first_name":"L"},{"full_name":"Jiang, X","first_name":"X","last_name":"Jiang"},{"first_name":"Y","last_name":"Li","full_name":"Li, Y"},{"last_name":"Luo","first_name":"H","full_name":"Luo, H"},{"first_name":"K","last_name":"Li","full_name":"Li, K"},{"full_name":"Yang, J","last_name":"Yang","first_name":"J"},{"first_name":"Q","last_name":"Luo","full_name":"Luo, Q"},{"first_name":"L","last_name":"Li","full_name":"Li, L"},{"first_name":"S","last_name":"Peng","full_name":"Peng, S"},{"full_name":"Huang, H","last_name":"Huang","first_name":"H"},{"full_name":"Zuo, Z","first_name":"Z","last_name":"Zuo"},{"full_name":"Liu, C","first_name":"C","last_name":"Liu"},{"first_name":"L","last_name":"Wang","full_name":"Wang, L"},{"full_name":"Li, C","last_name":"Li","first_name":"C"},{"full_name":"He, X","first_name":"X","last_name":"He"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"first_name":"Y","last_name":"Du","full_name":"Du, Y"}],"volume":44,"date_updated":"2023-11-07T08:18:36Z","date_created":"2021-02-24T10:07:21Z","pmid":1,"year":"2021","publisher":"Wiley","department":[{"_id":"JiFr"}],"publication_status":"published","publication_identifier":{"eissn":["1365-3040"],"issn":["0140-7791"]},"month":"06","doi":"10.1111/pce.14029","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["33576018"],"isi":["000625398600001"]},"isi":1,"quality_controlled":"1"},{"ddc":["510"],"title":"A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9792","oa_version":"Preprint","type":"preprint","abstract":[{"text":"This paper establishes new connections between many-body quantum systems, One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport (OT), by interpreting the problem of computing the ground-state energy of a finite dimensional composite quantum system at positive temperature as a non-commutative entropy regularized Optimal Transport problem. We develop a new approach to fully characterize the dual-primal solutions in such non-commutative setting. The mathematical formalism is particularly relevant in quantum chemistry: numerical realizations of the many-electron ground state energy can be computed via a non-commutative version of Sinkhorn algorithm. Our approach allows to prove convergence and robustness of this algorithm, which, to our best knowledge, were unknown even in the two marginal case. Our methods are based on careful a priori estimates in the dual problem, which we believe to be of independent interest. Finally, the above results are extended in 1RDMFT setting, where bosonic or fermionic symmetry conditions are enforced on the problem.","lang":"eng"}],"citation":{"ieee":"D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature,” arXiv. .","apa":"Feliciangeli, D., Gerolin, A., & Portinale, L. (n.d.). A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. arXiv. https://doi.org/10.48550/arXiv.2106.11217","ista":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. arXiv, 2106.11217.","ama":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. arXiv. doi:10.48550/arXiv.2106.11217","chicago":"Feliciangeli, Dario, Augusto Gerolin, and Lorenzo Portinale. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2106.11217.","short":"D. Feliciangeli, A. Gerolin, L. Portinale, ArXiv (n.d.).","mla":"Feliciangeli, Dario, et al. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” ArXiv, 2106.11217, doi:10.48550/arXiv.2106.11217."},"publication":"arXiv","date_published":"2021-07-21T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"21","department":[{"_id":"RoSe"},{"_id":"JaMa"}],"publication_status":"submitted","acknowledgement":"This work started when A.G. was visiting the Erwin Schrödinger Institute and then continued when D.F. and L.P visited the Theoretical Chemistry Department of the Vrije Universiteit Amsterdam. The authors thanks the hospitality of both places and, especially, P. Gori-Giorgi and K. Giesbertz for fruitful discussions and literature suggestions in the early state of the project. Finally, the authors also thanks J. Maas and R. Seiringer for their feedback and useful comments to a first draft of the article. L.P. acknowledges support by the Austrian Science Fund (FWF), grants No W1245 and NoF65. D.F acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 716117 and No 694227). A.G. acknowledges funding by the European Research Council under H2020/MSCA-IF “OTmeetsDFT” [grant ID: 795942].","year":"2021","date_created":"2021-08-06T09:07:12Z","date_updated":"2023-11-14T13:21:01Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9733"},{"status":"public","relation":"dissertation_contains","id":"10030"},{"status":"public","relation":"later_version","id":"12911"}]},"author":[{"full_name":"Feliciangeli, Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0754-8530","first_name":"Dario","last_name":"Feliciangeli"},{"first_name":"Augusto","last_name":"Gerolin","full_name":"Gerolin, Augusto"},{"full_name":"Portinale, Lorenzo","first_name":"Lorenzo","last_name":"Portinale","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87"}],"article_number":"2106.11217","ec_funded":1,"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"external_id":{"arxiv":["2106.11217"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2106.11217"}],"language":[{"iso":"eng"}],"doi":"10.48550/arXiv.2106.11217","month":"07"},{"article_type":"original","page":"210-224","publication":"Molecular Therapy - Methods and Clinical Development","citation":{"chicago":"Maes, Margaret E, Gabriele M. Wögenstein, Gloria Colombo, Raquel Casado Polanco, and Sandra Siegert. “Optimizing AAV2/6 Microglial Targeting Identified Enhanced Efficiency in the Photoreceptor Degenerative Environment.” Molecular Therapy - Methods and Clinical Development. Elsevier, 2021. https://doi.org/10.1016/j.omtm.2021.09.006.","short":"M.E. Maes, G.M. Wögenstein, G. Colombo, R. Casado Polanco, S. Siegert, Molecular Therapy - Methods and Clinical Development 23 (2021) 210–224.","mla":"Maes, Margaret E., et al. “Optimizing AAV2/6 Microglial Targeting Identified Enhanced Efficiency in the Photoreceptor Degenerative Environment.” Molecular Therapy - Methods and Clinical Development, vol. 23, Elsevier, 2021, pp. 210–24, doi:10.1016/j.omtm.2021.09.006.","apa":"Maes, M. E., Wögenstein, G. M., Colombo, G., Casado Polanco, R., & Siegert, S. (2021). Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. Molecular Therapy - Methods and Clinical Development. Elsevier. https://doi.org/10.1016/j.omtm.2021.09.006","ieee":"M. E. Maes, G. M. Wögenstein, G. Colombo, R. Casado Polanco, and S. Siegert, “Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment,” Molecular Therapy - Methods and Clinical Development, vol. 23. Elsevier, pp. 210–224, 2021.","ista":"Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. 2021. Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. Molecular Therapy - Methods and Clinical Development. 23, 210–224.","ama":"Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. Molecular Therapy - Methods and Clinical Development. 2021;23:210-224. doi:10.1016/j.omtm.2021.09.006"},"date_published":"2021-12-10T00:00:00Z","scopus_import":"1","day":"10","article_processing_charge":"Yes","has_accepted_license":"1","status":"public","title":"Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment","ddc":["570"],"intvolume":" 23","_id":"10655","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"10657","date_created":"2022-01-24T07:43:09Z","date_updated":"2022-01-24T07:43:09Z","checksum":"77dc540e8011c5475031bdf6ccef20a6","success":1,"file_name":"2021_MolTherMethodsClinDev_Maes.pdf","access_level":"open_access","file_size":4794147,"content_type":"application/pdf","creator":"cchlebak"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Adeno-associated viruses (AAVs) are widely used to deliver genetic material in vivo to distinct cell types such as neurons or glial cells, allowing for targeted manipulation. Transduction of microglia is mostly excluded from this strategy, likely due to the cells’ heterogeneous state upon environmental changes, which makes AAV design challenging. Here, we established the retina as a model system for microglial AAV validation and optimization. First, we show that AAV2/6 transduced microglia in both synaptic layers, where layer preference corresponds to the intravitreal or subretinal delivery method. Surprisingly, we observed significantly enhanced microglial transduction during photoreceptor degeneration. Thus, we modified the AAV6 capsid to reduce heparin binding by introducing four point mutations (K531E, R576Q, K493S, and K459S), resulting in increased microglial transduction in the outer plexiform layer. Finally, to improve microglial-specific transduction, we validated a Cre-dependent transgene delivery cassette for use in combination with the Cx3cr1CreERT2 mouse line. Together, our results provide a foundation for future studies optimizing AAV-mediated microglia transduction and highlight that environmental conditions influence microglial transduction efficiency.\r\n"}],"isi":1,"quality_controlled":"1","project":[{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571","name":"Microglia action towards neuronal circuit formation and function in health and disease","call_identifier":"H2020"}],"external_id":{"isi":["000748748500019"]},"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,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.omtm.2021.09.006","month":"12","publication_identifier":{"eissn":["2329-0501"]},"publication_status":"published","department":[{"_id":"SaSi"},{"_id":"SiHi"}],"publisher":"Elsevier","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. 715571). The research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility, the Life Science Facility, and the Pre-Clinical Facility, namely Sonja Haslinger and Michael Schunn for their animal colony management and support. We would also like to thank Chakrabarty Lab for sharing the plasmids for AAV2/6 production. Finally, we would like to thank the Siegert team members for discussion about the manuscript.","year":"2021","date_created":"2022-01-23T23:01:28Z","date_updated":"2023-11-16T13:12:03Z","volume":23,"author":[{"last_name":"Maes","first_name":"Margaret E","orcid":"0000-0001-9642-1085","id":"3838F452-F248-11E8-B48F-1D18A9856A87","full_name":"Maes, Margaret E"},{"full_name":"Wögenstein, Gabriele M.","first_name":"Gabriele M.","last_name":"Wögenstein"},{"id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9434-8902","first_name":"Gloria","last_name":"Colombo","full_name":"Colombo, Gloria"},{"first_name":"Raquel","last_name":"Casado Polanco","id":"15240fc1-dbcd-11ea-9d1d-ac5a786425fd","orcid":"0000-0001-8293-4568","full_name":"Casado Polanco, Raquel"},{"orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","first_name":"Sandra","full_name":"Siegert, Sandra"}],"file_date_updated":"2022-01-24T07:43:09Z","ec_funded":1},{"date_published":"2021-12-17T00:00:00Z","article_type":"original","citation":{"ista":"Venturino A, Siegert S. 2021. Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. 2(4), 101012.","ieee":"A. Venturino and S. Siegert, “Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain,” STAR Protocols, vol. 2, no. 4. Elsevier ; Cell Press, 2021.","apa":"Venturino, A., & Siegert, S. (2021). Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. Elsevier ; Cell Press. https://doi.org/10.1016/j.xpro.2021.101012","ama":"Venturino A, Siegert S. Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. 2021;2(4). doi:10.1016/j.xpro.2021.101012","chicago":"Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.” STAR Protocols. Elsevier ; Cell Press, 2021. https://doi.org/10.1016/j.xpro.2021.101012.","mla":"Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.” STAR Protocols, vol. 2, no. 4, 101012, Elsevier ; Cell Press, 2021, doi:10.1016/j.xpro.2021.101012.","short":"A. Venturino, S. Siegert, STAR Protocols 2 (2021)."},"publication":"STAR Protocols","article_processing_charge":"Yes","has_accepted_license":"1","day":"17","scopus_import":"1","file":[{"checksum":"9ea2501056c5df99e84726b845e9b976","success":1,"date_created":"2021-12-20T08:58:40Z","date_updated":"2021-12-20T08:58:40Z","relation":"main_file","file_id":"10570","file_size":6207060,"content_type":"application/pdf","creator":"cchlebak","access_level":"open_access","file_name":"2021_STARProt_Venturino.pdf"}],"oa_version":"Published Version","intvolume":" 2","status":"public","ddc":["573"],"title":"Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"10565","issue":"4","abstract":[{"text":"Enzymatic digestion of the extracellular matrix with chondroitinase-ABC reinstates juvenile-like plasticity in the adult cortex as it also disassembles the perineuronal nets (PNNs). The disadvantage of the enzyme is that it must be applied intracerebrally and it degrades the ECM for several weeks. Here, we provide two minimally invasive and transient protocols for microglia-enabled PNN disassembly in mouse cortex: repeated treatment with ketamine-xylazine-acepromazine (KXA) anesthesia and 60-Hz light entrainment. We also discuss how to analyze PNNs within microglial endosomes-lysosomes. For complete details on the use and execution of this protocol, please refer to Venturino et al. (2021).","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"doi":"10.1016/j.xpro.2021.101012","project":[{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571","call_identifier":"H2020","name":"Microglia action towards neuronal circuit formation and function in health and disease"}],"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":["2666-1667"]},"month":"12","volume":2,"date_updated":"2023-11-16T13:11:04Z","date_created":"2021-12-19T23:01:32Z","author":[{"full_name":"Venturino, Alessandro","first_name":"Alessandro","last_name":"Venturino","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2356-9403"},{"full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","first_name":"Sandra"}],"department":[{"_id":"SaSi"}],"publisher":"Elsevier ; Cell Press","publication_status":"published","acknowledgement":"This research was supported by the European Research Council (grant 715571 to S.S.). We thank Rouven Schulz, Michael Schunn, Claudia Gold, Gabriel Krens, Sarah Gorkiewicz, Margaret Maes, Jürgen Siegert, Marco Benevento, and Sara Oakeley for comments on the manuscript and the IST Austria Bioimaging Facility for the technical support.","year":"2021","ec_funded":1,"file_date_updated":"2021-12-20T08:58:40Z","article_number":"101012"},{"day":"10","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","date_published":"2021-11-10T00:00:00Z","publication":"STAR Protocols","citation":{"ama":"Amberg N, Hippenmeyer S. Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. STAR Protocols. 2021;2(4). doi:10.1016/j.xpro.2021.100939","ieee":"N. Amberg and S. Hippenmeyer, “Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers,” STAR Protocols, vol. 2, no. 4. Cell Press, 2021.","apa":"Amberg, N., & Hippenmeyer, S. (2021). Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. STAR Protocols. Cell Press. https://doi.org/10.1016/j.xpro.2021.100939","ista":"Amberg N, Hippenmeyer S. 2021. Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. STAR Protocols. 2(4), 100939.","short":"N. Amberg, S. Hippenmeyer, STAR Protocols 2 (2021).","mla":"Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate Genes in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols, vol. 2, no. 4, 100939, Cell Press, 2021, doi:10.1016/j.xpro.2021.100939.","chicago":"Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate Genes in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols. Cell Press, 2021. https://doi.org/10.1016/j.xpro.2021.100939."},"article_type":"original","abstract":[{"text":"Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice. MADM enables concomitant fluorescent cell labeling and introduction of a mutation of a gene of interest with single-cell resolution. This protocol highlights major steps for the generation of genetic mosaic tissue and the isolation and processing of respective tissues for downstream histological analysis. For complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).","lang":"eng"}],"issue":"4","type":"journal_article","file":[{"relation":"main_file","file_id":"10329","date_created":"2021-11-22T08:23:58Z","date_updated":"2021-11-22T08:23:58Z","checksum":"9e3f6d06bf583e7a8b6a9e9a60500a28","success":1,"file_name":"2021_STARProtocols_Amberg.pdf","access_level":"open_access","content_type":"application/pdf","file_size":7309464,"creator":"cchlebak"}],"oa_version":"Published Version","_id":"10321","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers","ddc":["573"],"status":"public","intvolume":" 2","month":"11","publication_identifier":{"eissn":["2666-1667"]},"doi":"10.1016/j.xpro.2021.100939","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780"},{"_id":"268F8446-B435-11E9-9278-68D0E5697425","grant_number":"T0101031","name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF"},{"name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F07805"}],"file_date_updated":"2021-11-22T08:23:58Z","ec_funded":1,"article_number":"100939","author":[{"first_name":"Nicole","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole"},{"last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"}],"date_created":"2021-11-21T23:01:28Z","date_updated":"2023-11-16T13:08:03Z","volume":2,"year":"2021","acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Bioimaging (BIF) and Preclinical Facilities (PCF). We particularly thank Mohammad Goudarzi for assistance with photography of mouse perfusion and dissection. N.A. received support from FWF Firnberg-Programm (T 1031). This work was also supported by IST Austria institutional funds; FWF SFB F78 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"Cell Press"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10290","intvolume":" 213","title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","status":"public","ddc":["572"],"oa_version":"Published Version","file":[{"date_updated":"2021-11-15T13:11:27Z","date_created":"2021-11-15T13:11:27Z","checksum":"6b209e4d44775d4e02b50f78982c15fa","success":1,"relation":"main_file","file_id":"10291","content_type":"application/pdf","file_size":16818304,"creator":"cchlebak","file_name":"2021_JournalStructBiol_Dimchev.pdf","access_level":"open_access"}],"type":"journal_article","issue":"4","abstract":[{"text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized filamentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner.","lang":"eng"}],"citation":{"ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 2021;213(4). doi:10.1016/j.jsb.2021.107808","ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2021. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 213(4), 107808.","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2021). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. Elsevier . https://doi.org/10.1016/j.jsb.2021.107808","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data,” Journal of Structural Biology, vol. 213, no. 4. Elsevier , 2021.","mla":"Dimchev, Georgi A., et al. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology, vol. 213, no. 4, 107808, Elsevier , 2021, doi:10.1016/j.jsb.2021.107808.","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural Biology 213 (2021).","chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology. Elsevier , 2021. https://doi.org/10.1016/j.jsb.2021.107808."},"publication":"Journal of Structural Biology","article_type":"original","date_published":"2021-11-03T00:00:00Z","scopus_import":"1","keyword":["Structural Biology"],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"03","acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Victor-Valentin Hodirnau for help with cryo-ET data acquisition. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S.","year":"2021","publisher":"Elsevier ","department":[{"_id":"FlSc"}],"publication_status":"published","related_material":{"record":[{"id":"14502","relation":"software","status":"public"}]},"author":[{"first_name":"Georgi A","last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161","full_name":"Dimchev, Georgi A"},{"first_name":"Behnam","last_name":"Amiri","full_name":"Amiri, Behnam"},{"full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","first_name":"Florian"},{"first_name":"Martin","last_name":"Falcke","full_name":"Falcke, Martin"},{"full_name":"Schur, Florian KM","last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"volume":213,"date_created":"2021-11-15T12:21:42Z","date_updated":"2023-11-21T08:36:02Z","article_number":"107808","file_date_updated":"2021-11-15T13:11:27Z","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":["000720259500002"]},"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"},{"name":"Protein structure and function in filopodia across scales","call_identifier":"FWF","grant_number":"M02495","_id":"2674F658-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","doi":"10.1016/j.jsb.2021.107808","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"publication_identifier":{"issn":["1047-8477"]},"month":"11"},{"month":"06","publication_identifier":{"eissn":["1861-2288"],"isbn":["978-1-6654-4501-6"],"eisbn":["978-3-9031-7639-3"]},"conference":{"name":"2021 IFIP Networking Conference (IFIP Networking)","end_date":"2021-06-24","location":"Espoo and Helsinki, Finland","start_date":"2021-06-21"},"doi":"10.23919/IFIPNetworking52078.2021.9472205","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2104.04293"}],"external_id":{"isi":["000853016800008"],"arxiv":["2104.04293"]},"isi":1,"quality_controlled":"1","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"author":[{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Salem, Iosif","first_name":"Iosif","last_name":"Salem"},{"first_name":"Stefan","last_name":"Schmid","full_name":"Schmid, Stefan"},{"id":"2D82B818-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle X","last_name":"Yeo","full_name":"Yeo, Michelle X"}],"related_material":{"record":[{"id":"14506","status":"public","relation":"dissertation_contains"}]},"date_created":"2021-08-29T22:01:16Z","date_updated":"2023-11-30T10:54:50Z","year":"2021","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"IEEE","day":"21","article_processing_charge":"No","scopus_import":"1","date_published":"2021-06-21T00:00:00Z","citation":{"ieee":"K. Z. Pietrzak, I. Salem, S. Schmid, and M. X. Yeo, “LightPIR: Privacy-preserving route discovery for payment channel networks,” presented at the 2021 IFIP Networking Conference (IFIP Networking), Espoo and Helsinki, Finland, 2021.","apa":"Pietrzak, K. Z., Salem, I., Schmid, S., & Yeo, M. X. (2021). LightPIR: Privacy-preserving route discovery for payment channel networks. Presented at the 2021 IFIP Networking Conference (IFIP Networking), Espoo and Helsinki, Finland: IEEE. https://doi.org/10.23919/IFIPNetworking52078.2021.9472205","ista":"Pietrzak KZ, Salem I, Schmid S, Yeo MX. 2021. LightPIR: Privacy-preserving route discovery for payment channel networks. 2021 IFIP Networking Conference (IFIP Networking).","ama":"Pietrzak KZ, Salem I, Schmid S, Yeo MX. LightPIR: Privacy-preserving route discovery for payment channel networks. In: IEEE; 2021. doi:10.23919/IFIPNetworking52078.2021.9472205","chicago":"Pietrzak, Krzysztof Z, Iosif Salem, Stefan Schmid, and Michelle X Yeo. “LightPIR: Privacy-Preserving Route Discovery for Payment Channel Networks.” IEEE, 2021. https://doi.org/10.23919/IFIPNetworking52078.2021.9472205.","short":"K.Z. Pietrzak, I. Salem, S. Schmid, M.X. Yeo, in:, IEEE, 2021.","mla":"Pietrzak, Krzysztof Z., et al. LightPIR: Privacy-Preserving Route Discovery for Payment Channel Networks. IEEE, 2021, doi:10.23919/IFIPNetworking52078.2021.9472205."},"abstract":[{"lang":"eng","text":"Payment channel networks are a promising approach to improve the scalability of cryptocurrencies: they allow to perform transactions in a peer-to-peer fashion, along multihop routes in the network, without requiring consensus on the blockchain. However, during the discovery of cost-efficient routes for the transaction, critical information may be revealed about the transacting entities. This paper initiates the study of privacy-preserving route discovery mechanisms for payment channel networks. In particular, we present LightPIR, an approach which allows a client to learn the shortest (or cheapest in terms of fees) path between two nodes without revealing any information about the endpoints of the transaction to the servers. The two main observations which allow for an efficient solution in LightPIR are that: (1) surprisingly, hub labelling algorithms – which were developed to preprocess “street network like” graphs so one can later efficiently compute shortest paths – also perform well for the graphs underlying payment channel networks, and that (2) hub labelling algorithms can be conveniently combined with private information retrieval. LightPIR relies on a simple hub labeling heuristic on top of existing hub labeling algorithms which leverages the specific topological features of cryptocurrency networks to further minimize storage and bandwidth overheads. In a case study considering the Lightning network, we show that our approach is an order of magnitude more efficient compared to a privacy-preserving baseline based on using private information retrieval on a database that stores all pairs shortest paths."}],"type":"conference","oa_version":"Submitted Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9969","status":"public","title":"LightPIR: Privacy-preserving route discovery for payment channel networks"}]