[{"date_created":"2023-05-16T12:34:09Z","date_published":"2021-04-10T00:00:00Z","doi":"10.5061/DRYAD.ZGMSBCCB4","related_material":{"record":[{"relation":"used_in_publication","id":"9394","status":"public"}]},"day":"10","year":"2021","has_accepted_license":"1","month":"04","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.zgmsbccb4"}],"oa":1,"publisher":"Dryad","oa_version":"Published Version","abstract":[{"text":"Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions for adaptation requires confirmation of their influence on traits under divergent selection. Here, we studied a marine snail, Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab predation. These two types occur in close proximity on different parts of the shore. Gene flow between them exists in contact zones. However, they exhibit strong phenotypic divergence in several traits under habitat-specific selection, including size, shape and behaviour. We used crosses between these ecotypes to identify genomic regions that explain variation in these traits by using QTL analysis and variance partitioning across linkage groups. We could show that previously detected inversion regions contribute to adaptive divergence. Some inversions influenced multiple traits suggesting that they contain sets of locally adaptive alleles. Our study also identified regions without known inversions that are important for phenotypic divergence. Thus, we provide a more complete overview of the importance of inversions in relation to the remaining genome.","lang":"eng"}],"title":"Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","department":[{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"last_name":"Koch","full_name":"Koch, Eva","first_name":"Eva"},{"first_name":"Hernán E.","full_name":"Morales, Hernán E.","last_name":"Morales"},{"first_name":"Jenny","full_name":"Larsson, Jenny","last_name":"Larsson"},{"last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Lemmon, Alan R.","last_name":"Lemmon","first_name":"Alan R."},{"full_name":"Lemmon, E. Moriarty","last_name":"Lemmon","first_name":"E. Moriarty"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"}],"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Koch E, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis, Dryad, 10.5061/DRYAD.ZGMSBCCB4.","chicago":"Koch, Eva, Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Dryad, 2021. https://doi.org/10.5061/DRYAD.ZGMSBCCB4.","ama":"Koch E, Morales HE, Larsson J, et al. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. 2021. doi:10.5061/DRYAD.ZGMSBCCB4","apa":"Koch, E., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Dryad. https://doi.org/10.5061/DRYAD.ZGMSBCCB4","short":"E. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, (2021).","ieee":"E. Koch et al., “Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.","mla":"Koch, Eva, et al. Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis. Dryad, 2021, doi:10.5061/DRYAD.ZGMSBCCB4."},"date_updated":"2023-08-08T13:34:07Z","status":"public","tmp":{"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)","short":"CC0 (1.0)"},"type":"research_data_reference","_id":"12987"},{"publication_status":"published","publication_identifier":{"issn":["19410506"],"eissn":["10772626"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2021-05-25T15:08:49Z","file_size":6183002,"creator":"kschuh","date_created":"2021-05-25T15:08:49Z","file_name":"2021_TVCG_Feng.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9427","checksum":"a78e6ac94e33ade4ffaea66943d5f7dc","success":1}],"ec_funded":1,"volume":27,"issue":"6","abstract":[{"lang":"eng","text":"We present a computational design system that assists users to model, optimize, and fabricate quad-robots with soft skins. Our system addresses the challenging task of predicting their physical behavior by fully integrating the multibody dynamics of the mechanical skeleton and the elastic behavior of the soft skin. The developed motion control strategy uses an alternating optimization scheme to avoid expensive full space time-optimization, interleaving space-time optimization for the skeleton, and frame-by-frame optimization for the full dynamics. The output are motor torques to drive the robot to achieve a user prescribed motion trajectory. We also provide a collection of convenient engineering tools and empirical manufacturing guidance to support the fabrication of the designed quad-robot. We validate the feasibility of designs generated with our system through physics simulations and with a physically-fabricated prototype."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 27","month":"06","date_updated":"2023-08-08T13:45:46Z","ddc":["000"],"file_date_updated":"2021-05-25T15:08:49Z","department":[{"_id":"BeBi"}],"_id":"9408","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","year":"2021","isi":1,"has_accepted_license":"1","publication":"IEEE Transactions on Visualization and Computer Graphics","day":"01","date_created":"2021-05-23T22:01:42Z","doi":"10.1109/TVCG.2019.2957218","date_published":"2021-06-01T00:00:00Z","acknowledgement":"The authors would like to thank anonymous reviewers for their constructive comments. Weiwei Xu is partially supported by Zhejiang Lab. Yin Yang is partially spported by NSF under Grant Nos. CHS 1845024 and 1717972. Weiwei Xu and Hujun Bao are supported by Fundamental Research Funds for the Central Universities. This project has received funding from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation programme (Grant agreement No 715767).","oa":1,"publisher":"IEEE","quality_controlled":"1","citation":{"ama":"Feng X, Liu J, Wang H, et al. Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. 2021;27(6). doi:10.1109/TVCG.2019.2957218","apa":"Feng, X., Liu, J., Wang, H., Yang, Y., Bao, H., Bickel, B., & Xu, W. (2021). Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2019.2957218","ieee":"X. Feng et al., “Computational design of skinned Quad-Robots,” IEEE Transactions on Visualization and Computer Graphics, vol. 27, no. 6. IEEE, 2021.","short":"X. Feng, J. Liu, H. Wang, Y. Yang, H. Bao, B. Bickel, W. Xu, IEEE Transactions on Visualization and Computer Graphics 27 (2021).","mla":"Feng, Xudong, et al. “Computational Design of Skinned Quad-Robots.” IEEE Transactions on Visualization and Computer Graphics, vol. 27, no. 6, 2881–2895, IEEE, 2021, doi:10.1109/TVCG.2019.2957218.","ista":"Feng X, Liu J, Wang H, Yang Y, Bao H, Bickel B, Xu W. 2021. Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. 27(6), 2881–2895.","chicago":"Feng, Xudong, Jiafeng Liu, Huamin Wang, Yin Yang, Hujun Bao, Bernd Bickel, and Weiwei Xu. “Computational Design of Skinned Quad-Robots.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2021. https://doi.org/10.1109/TVCG.2019.2957218."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000649620700009"],"pmid":["31804937"]},"article_processing_charge":"No","author":[{"first_name":"Xudong","full_name":"Feng, Xudong","last_name":"Feng"},{"last_name":"Liu","full_name":"Liu, Jiafeng","first_name":"Jiafeng"},{"full_name":"Wang, Huamin","last_name":"Wang","first_name":"Huamin"},{"full_name":"Yang, Yin","last_name":"Yang","first_name":"Yin"},{"last_name":"Bao","full_name":"Bao, Hujun","first_name":"Hujun"},{"last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Weiwei","last_name":"Xu","full_name":"Xu, Weiwei"}],"title":"Computational design of skinned Quad-Robots","article_number":"2881-2895","project":[{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}]},{"day":"12","publication":"Biology letters","isi":1,"has_accepted_license":"1","year":"2021","doi":"10.1098/rsbl.2020.0913","date_published":"2021-05-12T00:00:00Z","date_created":"2021-05-23T22:01:43Z","acknowledgement":"We would like to thank Martin Ackermann, Camilo Barbosa, Nick Barton, Jonathan Bollback, Sebastian Bonhoeffer, Nick Colegrave, Calin Guet, Alex Hall, Sally Otto, Tiago Paixao, Srdjan Sarikas, Hinrich Schulenburg, Marjon de Vos and Michael Whitlock for insightful support.","quality_controlled":"1","publisher":"Royal Society of London","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic concentration gradients. Biology letters. 17(5), 20200913.","chicago":"Lagator, Mato, Hildegard Uecker, and Paul Neve. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters. Royal Society of London, 2021. https://doi.org/10.1098/rsbl.2020.0913.","short":"M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021).","ieee":"M. Lagator, H. Uecker, and P. Neve, “Adaptation at different points along antibiotic concentration gradients,” Biology letters, vol. 17, no. 5. Royal Society of London, 2021.","ama":"Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic concentration gradients. Biology letters. 2021;17(5). doi:10.1098/rsbl.2020.0913","apa":"Lagator, M., Uecker, H., & Neve, P. (2021). Adaptation at different points along antibiotic concentration gradients. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2020.0913","mla":"Lagator, Mato, et al. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters, vol. 17, no. 5, 20200913, Royal Society of London, 2021, doi:10.1098/rsbl.2020.0913."},"title":"Adaptation at different points along antibiotic concentration gradients","author":[{"first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato","last_name":"Lagator"},{"id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","first_name":"Hildegard","orcid":"0000-0001-9435-2813","full_name":"Uecker, Hildegard","last_name":"Uecker"},{"first_name":"Paul","last_name":"Neve","full_name":"Neve, Paul"}],"external_id":{"pmid":[" 33975485"],"isi":["000651501400001"]},"article_processing_charge":"No","article_number":"20200913","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"file":[{"success":1,"file_id":"9425","checksum":"9c13c1f5af7609c97c741f11d293188a","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_BiologyLetters_Lagator.pdf","date_created":"2021-05-25T14:09:03Z","creator":"kschuh","file_size":726759,"date_updated":"2021-05-25T14:09:03Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1744957X"]},"publication_status":"published","issue":"5","volume":17,"ec_funded":1,"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Antibiotic concentrations vary dramatically in the body and the environment. Hence, understanding the dynamics of resistance evolution along antibiotic concentration gradients is critical for predicting and slowing the emergence and spread of resistance. While it has been shown that increasing the concentration of an antibiotic slows resistance evolution, how adaptation to one antibiotic concentration correlates with fitness at other points along the gradient has not received much attention. Here, we selected populations of Escherichia coli at several points along a concentration gradient for three different antibiotics, asking how rapidly resistance evolved and whether populations became specialized to the antibiotic concentration they were selected on. Populations selected at higher concentrations evolved resistance more slowly but exhibited equal or higher fitness across the whole gradient. Populations selected at lower concentrations evolved resistance rapidly, but overall fitness in the presence of antibiotics was lower. However, these populations readily adapted to higher concentrations upon subsequent selection. Our results indicate that resistance management strategies must account not only for the rates of resistance evolution but also for the fitness of evolved strains.","lang":"eng"}],"month":"05","intvolume":" 17","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-08T13:44:35Z","department":[{"_id":"NiBa"}],"file_date_updated":"2021-05-25T14:09:03Z","_id":"9410","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"article_number":"24","title":"Fluctuation around the circular law for random matrices with real entries","external_id":{"isi":["000641855600001"],"arxiv":["2002.02438"]},"article_processing_charge":"No","author":[{"orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgio"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","last_name":"Schröder"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/21-EJP591","ama":"Cipolloni G, Erdös L, Schröder DJ. Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. 2021;26. doi:10.1214/21-EJP591","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Electronic Journal of Probability 26 (2021).","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Fluctuation around the circular law for random matrices with real entries,” Electronic Journal of Probability, vol. 26. Institute of Mathematical Statistics, 2021.","mla":"Cipolloni, Giorgio, et al. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” Electronic Journal of Probability, vol. 26, 24, Institute of Mathematical Statistics, 2021, doi:10.1214/21-EJP591.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. 26, 24.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2021. https://doi.org/10.1214/21-EJP591."},"oa":1,"publisher":"Institute of Mathematical Statistics","quality_controlled":"1","date_created":"2021-05-23T22:01:44Z","doi":"10.1214/21-EJP591","date_published":"2021-03-23T00:00:00Z","publication":"Electronic Journal of Probability","day":"23","year":"2021","has_accepted_license":"1","isi":1,"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"9412","file_date_updated":"2021-05-25T13:24:19Z","department":[{"_id":"LaEr"}],"ddc":["510"],"date_updated":"2023-08-08T13:39:19Z","intvolume":" 26","month":"03","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We extend our recent result [22] on the central limit theorem for the linear eigenvalue statistics of non-Hermitian matrices X with independent, identically distributed complex entries to the real symmetry class. We find that the expectation and variance substantially differ from their complex counterparts, reflecting (i) the special spectral symmetry of real matrices onto the real axis; and (ii) the fact that real i.i.d. matrices have many real eigenvalues. Our result generalizes the previously known special cases where either the test function is analytic [49] or the first four moments of the matrix elements match the real Gaussian [59, 44]. The key element of the proof is the analysis of several weakly dependent Dyson Brownian motions (DBMs). The conceptual novelty of the real case compared with [22] is that the correlation structure of the stochastic differentials in each individual DBM is non-trivial, potentially even jeopardising its well-posedness."}],"ec_funded":1,"volume":26,"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9423","checksum":"864ab003ad4cffea783f65aa8c2ba69f","success":1,"creator":"kschuh","date_updated":"2021-05-25T13:24:19Z","file_size":865148,"date_created":"2021-05-25T13:24:19Z","file_name":"2021_EJP_Cipolloni.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["10836489"]}},{"file_date_updated":"2021-05-25T14:18:40Z","department":[{"_id":"BjHo"}],"date_updated":"2023-08-08T13:45:13Z","ddc":["570"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9407","issue":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/smashing-the-covid-curve/","relation":"press_release","description":"News on IST Homepage"}]},"volume":12,"publication_identifier":{"eissn":["20411723"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9426","checksum":"fe26c1b8a7da1ae07a6c03f80ff06ea1","success":1,"date_updated":"2021-05-25T14:18:40Z","file_size":1176573,"creator":"kschuh","date_created":"2021-05-25T14:18:40Z","file_name":"2021_NatureCommunications_Scarselli.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 12","abstract":[{"text":"High impact epidemics constitute one of the largest threats humanity is facing in the 21st century. In the absence of pharmaceutical interventions, physical distancing together with testing, contact tracing and quarantining are crucial in slowing down epidemic dynamics. Yet, here we show that if testing capacities are limited, containment may fail dramatically because such combined countermeasures drastically change the rules of the epidemic transition: Instead of continuous, the response to countermeasures becomes discontinuous. Rather than following the conventional exponential growth, the outbreak that is initially strongly suppressed eventually accelerates and scales faster than exponential during an explosive growth period. As a consequence, containment measures either suffice to stop the outbreak at low total case numbers or fail catastrophically if marginally too weak, thus implying large uncertainties in reliably estimating overall epidemic dynamics, both during initial phases and during second wave scenarios.","lang":"eng"}],"oa_version":"Published Version","author":[{"id":"40315C30-F248-11E8-B48F-1D18A9856A87","first_name":"Davide","last_name":"Scarselli","full_name":"Scarselli, Davide","orcid":"0000-0001-5227-4271"},{"orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B","last_name":"Budanur","first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Timme, Marc","last_name":"Timme","first_name":"Marc"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"article_processing_charge":"No","external_id":{"isi":["000687305500044"]},"title":"Discontinuous epidemic transition due to limited testing","citation":{"ama":"Scarselli D, Budanur NB, Timme M, Hof B. Discontinuous epidemic transition due to limited testing. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-22725-9","apa":"Scarselli, D., Budanur, N. B., Timme, M., & Hof, B. (2021). Discontinuous epidemic transition due to limited testing. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-22725-9","ieee":"D. Scarselli, N. B. Budanur, M. Timme, and B. Hof, “Discontinuous epidemic transition due to limited testing,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","short":"D. Scarselli, N.B. Budanur, M. Timme, B. Hof, Nature Communications 12 (2021).","mla":"Scarselli, Davide, et al. “Discontinuous Epidemic Transition Due to Limited Testing.” Nature Communications, vol. 12, no. 1, 2586, Springer Nature, 2021, doi:10.1038/s41467-021-22725-9.","ista":"Scarselli D, Budanur NB, Timme M, Hof B. 2021. Discontinuous epidemic transition due to limited testing. Nature Communications. 12(1), 2586.","chicago":"Scarselli, Davide, Nazmi B Budanur, Marc Timme, and Björn Hof. “Discontinuous Epidemic Transition Due to Limited Testing.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-22725-9."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"2586","date_published":"2021-05-10T00:00:00Z","doi":"10.1038/s41467-021-22725-9","date_created":"2021-05-23T22:01:42Z","has_accepted_license":"1","isi":1,"year":"2021","day":"10","publication":"Nature Communications","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"The authors thank Malte Schröder for valuable discussions and creating the scale-free network topologies. B.H. thanks Mukund Vasudevan for helpful discussion. The research by M.T. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany´s Excellence Strategy–EXC-2068–390729961–Cluster of Excellence Physics of Life of TU Dresden."},{"article_number":"59","citation":{"ista":"Sukhov A, Hubert M, Grosjean GM, Trosman O, Ziegler S, Collard Y, Vandewalle N, Smith AS, Harting J. 2021. Regimes of motion of magnetocapillary swimmers. European Physical Journal E. 44(4), 59.","chicago":"Sukhov, Alexander, Maxime Hubert, Galien M Grosjean, Oleg Trosman, Sebastian Ziegler, Ylona Collard, Nicolas Vandewalle, Ana Sunčana Smith, and Jens Harting. “Regimes of Motion of Magnetocapillary Swimmers.” European Physical Journal E. Springer, 2021. https://doi.org/10.1140/epje/s10189-021-00065-2.","apa":"Sukhov, A., Hubert, M., Grosjean, G. M., Trosman, O., Ziegler, S., Collard, Y., … Harting, J. (2021). Regimes of motion of magnetocapillary swimmers. European Physical Journal E. Springer. https://doi.org/10.1140/epje/s10189-021-00065-2","ama":"Sukhov A, Hubert M, Grosjean GM, et al. Regimes of motion of magnetocapillary swimmers. European Physical Journal E. 2021;44(4). doi:10.1140/epje/s10189-021-00065-2","ieee":"A. Sukhov et al., “Regimes of motion of magnetocapillary swimmers,” European Physical Journal E, vol. 44, no. 4. Springer, 2021.","short":"A. Sukhov, M. Hubert, G.M. Grosjean, O. Trosman, S. Ziegler, Y. Collard, N. Vandewalle, A.S. Smith, J. Harting, European Physical Journal E 44 (2021).","mla":"Sukhov, Alexander, et al. “Regimes of Motion of Magnetocapillary Swimmers.” European Physical Journal E, vol. 44, no. 4, 59, Springer, 2021, doi:10.1140/epje/s10189-021-00065-2."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Sukhov","full_name":"Sukhov, Alexander","first_name":"Alexander"},{"first_name":"Maxime","full_name":"Hubert, Maxime","last_name":"Hubert"},{"first_name":"Galien M","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","full_name":"Grosjean, Galien M","orcid":"0000-0001-5154-417X","last_name":"Grosjean"},{"first_name":"Oleg","full_name":"Trosman, Oleg","last_name":"Trosman"},{"last_name":"Ziegler","full_name":"Ziegler, Sebastian","first_name":"Sebastian"},{"last_name":"Collard","full_name":"Collard, Ylona","first_name":"Ylona"},{"first_name":"Nicolas","full_name":"Vandewalle, Nicolas","last_name":"Vandewalle"},{"first_name":"Ana Sunčana","last_name":"Smith","full_name":"Smith, Ana Sunčana"},{"full_name":"Harting, Jens","last_name":"Harting","first_name":"Jens"}],"external_id":{"isi":["000643251300001"]},"article_processing_charge":"No","title":"Regimes of motion of magnetocapillary swimmers","acknowledgement":"This work was financially supported by the DFG Priority Programme SPP 1726 “Microswimmers–From Single Particle Motion to Collective Behaviour” (HA 4382/5-1). We further acknowledge the Jülich Supercomputing Centre (JSC) and the High Performance Computing Centre Stuttgart (HLRS) for the allocation of computing time.","quality_controlled":"1","publisher":"Springer","oa":1,"isi":1,"has_accepted_license":"1","year":"2021","day":"24","publication":"European Physical Journal E","date_published":"2021-04-24T00:00:00Z","doi":"10.1140/epje/s10189-021-00065-2","date_created":"2021-05-23T22:01:44Z","_id":"9411","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-08T13:36:28Z","ddc":["530"],"department":[{"_id":"ScWa"}],"file_date_updated":"2021-05-25T11:32:14Z","abstract":[{"text":"The dynamics of a triangular magnetocapillary swimmer is studied using the lattice Boltzmann method. We extend on our previous work, which deals with the self-assembly and a specific type of the swimmer motion characterized by the swimmer’s maximum velocity centred around the particle’s inverse viscous time. Here, we identify additional regimes of motion. First, modifying the ratio of surface tension and magnetic forces allows to study the swimmer propagation in the regime of significantly lower frequencies mainly defined by the strength of the magnetocapillary potential. Second, introducing a constant magnetic contribution in each of the particles in addition to their magnetic moment induced by external fields leads to another regime characterized by strong in-plane swimmer reorientations that resemble experimental observations.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 44","publication_identifier":{"issn":["12928941"],"eissn":["1292895X"]},"publication_status":"published","file":[{"success":1,"checksum":"0ef342d011afbe3c5cb058fda9a3f395","file_id":"9422","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_EPJE_Sukhov.pdf","date_created":"2021-05-25T11:32:14Z","file_size":2507870,"date_updated":"2021-05-25T11:32:14Z","creator":"kschuh"}],"language":[{"iso":"eng"}],"volume":44,"issue":"4"},{"page":"869-879","doi":"10.1091/MBC.E20-11-0723","date_published":"2021-04-19T00:00:00Z","date_created":"2021-05-23T22:01:45Z","isi":1,"year":"2021","day":"19","publication":"Molecular Biology of the Cell","quality_controlled":"1","publisher":"American Society for Cell Biology","oa":1,"acknowledgement":"The authors thank the members of Mitchison, Brugués, and Jay Gatlin groups (University of Wyoming) for discussions. We thank Heino Andreas (MPI-CBG) for frog maintenance. We thank Nikon for microscopy support at Marine Biological Laboratory (MBL). K.I. was supported by fellowships from the Honjo International Scholarship Foundation and Center of Systems Biology Dresden. F.D. was supported by the DIGGS-BB fellowship provided by the German Research Foundation (DFG). P.C. is supported by a Boehringer Ingelheim Fonds PhD fellowship. J.F.P. was supported by a fellowship from the Fannie and John Hertz Foundation. M.L.’s research is supported by European Research Council (ERC) Grant no. ERC-2015-StG-679239. J.B.’s research is supported by the Human Frontiers Science Program (CDA00074/2014). T.J.M.’s research is supported by National Institutes of Health Grant no. R35GM131753.","author":[{"first_name":"Keisuke","full_name":"Ishihara, Keisuke","last_name":"Ishihara"},{"last_name":"Decker","full_name":"Decker, Franziska","first_name":"Franziska"},{"first_name":"Paulo R","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6730-4461","full_name":"Dos Santos Caldas, Paulo R","last_name":"Dos Santos Caldas"},{"full_name":"Pelletier, James F.","last_name":"Pelletier","first_name":"James F."},{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose"},{"last_name":"Brugués","full_name":"Brugués, Jan","first_name":"Jan"},{"full_name":"Mitchison, Timothy J.","last_name":"Mitchison","first_name":"Timothy J."}],"article_processing_charge":"No","external_id":{"isi":["000641574700005"]},"title":"Spatial variation of microtubule depolymerization in large asters","citation":{"mla":"Ishihara, Keisuke, et al. “Spatial Variation of Microtubule Depolymerization in Large Asters.” Molecular Biology of the Cell, vol. 32, no. 9, American Society for Cell Biology, 2021, pp. 869–79, doi:10.1091/MBC.E20-11-0723.","apa":"Ishihara, K., Decker, F., Dos Santos Caldas, P. R., Pelletier, J. F., Loose, M., Brugués, J., & Mitchison, T. J. (2021). Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/MBC.E20-11-0723","ama":"Ishihara K, Decker F, Dos Santos Caldas PR, et al. Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. 2021;32(9):869-879. doi:10.1091/MBC.E20-11-0723","ieee":"K. Ishihara et al., “Spatial variation of microtubule depolymerization in large asters,” Molecular Biology of the Cell, vol. 32, no. 9. American Society for Cell Biology, pp. 869–879, 2021.","short":"K. Ishihara, F. Decker, P.R. Dos Santos Caldas, J.F. Pelletier, M. Loose, J. Brugués, T.J. Mitchison, Molecular Biology of the Cell 32 (2021) 869–879.","chicago":"Ishihara, Keisuke, Franziska Decker, Paulo R Dos Santos Caldas, James F. Pelletier, Martin Loose, Jan Brugués, and Timothy J. Mitchison. “Spatial Variation of Microtubule Depolymerization in Large Asters.” Molecular Biology of the Cell. American Society for Cell Biology, 2021. https://doi.org/10.1091/MBC.E20-11-0723.","ista":"Ishihara K, Decker F, Dos Santos Caldas PR, Pelletier JF, Loose M, Brugués J, Mitchison TJ. 2021. Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. 32(9), 869–879."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Self-Organization of the Bacterial Cell","grant_number":"679239","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"name":"Reconstitution of Bacterial Cell Division Using Purified Components","_id":"260D98C8-B435-11E9-9278-68D0E5697425"}],"issue":"9","volume":32,"license":"https://creativecommons.org/licenses/by-nc-sa/3.0/","ec_funded":1,"publication_identifier":{"eissn":["1939-4586"],"issn":["1059-1524"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.molbiolcell.org/doi/10.1091/mbc.E20-11-0723"}],"month":"04","intvolume":" 32","abstract":[{"lang":"eng","text":"Microtubule plus-end depolymerization rate is a potentially important target of physiological regulation, but it has been challenging to measure, so its role in spatial organization is poorly understood. Here we apply a method for tracking plus ends based on time difference imaging to measure depolymerization rates in large interphase asters growing in Xenopus egg extract. We observed strong spatial regulation of depolymerization rates, which were higher in the aster interior compared with the periphery, and much less regulation of polymerization or catastrophe rates. We interpret these data in terms of a limiting component model, where aster growth results in lower levels of soluble tubulin and microtubule-associated proteins (MAPs) in the interior cytosol compared with that at the periphery. The steady-state polymer fraction of tubulin was ∼30%, so tubulin is not strongly depleted in the aster interior. We propose that the limiting component for microtubule assembly is a MAP that inhibits depolymerization, and that egg asters are tuned to low microtubule density."}],"oa_version":"Published Version","department":[{"_id":"MaLo"}],"date_updated":"2023-08-08T13:36:02Z","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-SA (3.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)"},"status":"public","_id":"9414"},{"quality_controlled":"1","publisher":"Institute of Electrical and Electronics Engineers","oa":1,"acknowledgement":"We thank the anonymous reviewers for their helpful comments. This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","date_published":"2021-06-29T00:00:00Z","doi":"10.1109/LICS52264.2021.9470547","date_created":"2021-04-30T17:30:47Z","day":"29","publication":"Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science","isi":1,"has_accepted_license":"1","year":"2021","project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"article_number":"9470547","title":"Quantitative and approximate monitoring","author":[{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","full_name":"Sarac, Naci E","last_name":"Sarac"}],"article_processing_charge":"No","external_id":{"isi":["000947350400021"],"arxiv":["2105.08353"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Henzinger, T. A., & Sarac, N. E. (2021). Quantitative and approximate monitoring. In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Online: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LICS52264.2021.9470547","ama":"Henzinger TA, Sarac NE. Quantitative and approximate monitoring. In: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Institute of Electrical and Electronics Engineers; 2021. doi:10.1109/LICS52264.2021.9470547","ieee":"T. A. Henzinger and N. E. Sarac, “Quantitative and approximate monitoring,” in Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Online, 2021.","short":"T.A. Henzinger, N.E. Sarac, in:, Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021.","mla":"Henzinger, Thomas A., and Naci E. Sarac. “Quantitative and Approximate Monitoring.” Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, 9470547, Institute of Electrical and Electronics Engineers, 2021, doi:10.1109/LICS52264.2021.9470547.","ista":"Henzinger TA, Sarac NE. 2021. Quantitative and approximate monitoring. Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 9470547.","chicago":"Henzinger, Thomas A, and Naci E Sarac. “Quantitative and Approximate Monitoring.” In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/LICS52264.2021.9470547."},"month":"06","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"In runtime verification, a monitor watches a trace of a system and, if possible, decides after observing each finite prefix whether or not the unknown infinite trace satisfies a given specification. We generalize the theory of runtime verification to monitors that attempt to estimate numerical values of quantitative trace properties (instead of attempting to conclude boolean values of trace specifications), such as maximal or average response time along a trace. Quantitative monitors are approximate: with every finite prefix, they can improve their estimate of the infinite trace's unknown property value. Consequently, quantitative monitors can be compared with regard to a precision-cost trade-off: better approximations of the property value require more monitor resources, such as states (in the case of finite-state monitors) or registers, and additional resources yield better approximations. We introduce a formal framework for quantitative and approximate monitoring, show how it conservatively generalizes the classical boolean setting for monitoring, and give several precision-cost trade-offs for monitors. For example, we prove that there are quantitative properties for which every additional register improves monitoring precision."}],"file":[{"creator":"esarac","date_updated":"2021-06-16T08:23:54Z","file_size":641990,"date_created":"2021-06-16T08:23:54Z","file_name":"qam.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9557","checksum":"6e4cba3f72775f479c5b1b75d1a4a0c4","success":1}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"conference","conference":{"name":"LICS: Symposium on Logic in Computer Science","start_date":"2021-06-29","end_date":"2021-07-02","location":"Online"},"_id":"9356","file_date_updated":"2021-06-16T08:23:54Z","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2023-08-08T13:52:56Z"},{"publication":"Nature Neuroscience","day":"20","year":"2021","isi":1,"date_created":"2021-05-30T22:01:24Z","doi":"10.1038/s41593-021-00846-0","date_published":"2021-05-20T00:00:00Z","page":"998-1009","acknowledgement":"We thank D. Kastner and T. Münch for generously providing figures from their work. We also thank V. Jayaraman, M. Noorman, T. Ma, and K. Krishnamurthy for useful discussions and feedback on the manuscript. W.F.M. was funded by the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie Grant Agreement No. 754411. A.M.H. was supported by the Howard Hughes Medical Institute.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"W. F. Mlynarski and A. M. Hermundstad, “Efficient and adaptive sensory codes,” Nature Neuroscience, vol. 24. Springer Nature, pp. 998–1009, 2021.","short":"W.F. Mlynarski, A.M. Hermundstad, Nature Neuroscience 24 (2021) 998–1009.","apa":"Mlynarski, W. F., & Hermundstad, A. M. (2021). Efficient and adaptive sensory codes. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-021-00846-0","ama":"Mlynarski WF, Hermundstad AM. Efficient and adaptive sensory codes. Nature Neuroscience. 2021;24:998-1009. doi:10.1038/s41593-021-00846-0","mla":"Mlynarski, Wiktor F., and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience, vol. 24, Springer Nature, 2021, pp. 998–1009, doi:10.1038/s41593-021-00846-0.","ista":"Mlynarski WF, Hermundstad AM. 2021. Efficient and adaptive sensory codes. Nature Neuroscience. 24, 998–1009.","chicago":"Mlynarski, Wiktor F, and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience. Springer Nature, 2021. https://doi.org/10.1038/s41593-021-00846-0."},"title":"Efficient and adaptive sensory codes","external_id":{"isi":["000652577300003"]},"article_processing_charge":"No","author":[{"last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F","first_name":"Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ann M.","last_name":"Hermundstad","full_name":"Hermundstad, Ann M."}],"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"ec_funded":1,"volume":24,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The ability to adapt to changes in stimulus statistics is a hallmark of sensory systems. Here, we developed a theoretical framework that can account for the dynamics of adaptation from an information processing perspective. We use this framework to optimize and analyze adaptive sensory codes, and we show that codes optimized for stationary environments can suffer from prolonged periods of poor performance when the environment changes. To mitigate the adversarial effects of these environmental changes, sensory systems must navigate tradeoffs between the ability to accurately encode incoming stimuli and the ability to rapidly detect and adapt to changes in the distribution of these stimuli. We derive families of codes that balance these objectives, and we demonstrate their close match to experimentally observed neural dynamics during mean and variance adaptation. Our results provide a unifying perspective on adaptation across a range of sensory systems, environments, and sensory tasks."}],"intvolume":" 24","month":"05","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/669200 "}],"scopus_import":"1","date_updated":"2023-08-08T13:51:14Z","department":[{"_id":"GaTk"}],"_id":"9439","status":"public","article_type":"original","type":"journal_article"},{"citation":{"mla":"Ruiz-Lopez, N., et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.” Plant Cell, vol. 33, no. 7, American Society of Plant Biologists, 2021, pp. 2431–53, doi:10.1093/plcell/koab122.","ieee":"N. Ruiz-Lopez et al., “Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress,” Plant Cell, vol. 33, no. 7. American Society of Plant Biologists, pp. 2431–2453, 2021.","short":"N. Ruiz-Lopez, J. Pérez-Sancho, A. Esteban Del Valle, R. Haslam, S. Vanneste, R. Catalá, C. Perea-Resa, D. Van Damme, S. García-Hernández, A. Albert, J. Vallarino, J. Lin, J. Friml, A. Macho, J. Salinas, A. Rosado, J. Napier, V. Amorim-Silva, M. Botella, Plant Cell 33 (2021) 2431–2453.","ama":"Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, et al. Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. 2021;33(7):2431-2453. doi:10.1093/plcell/koab122","apa":"Ruiz-Lopez, N., Pérez-Sancho, J., Esteban Del Valle, A., Haslam, R., Vanneste, S., Catalá, R., … Botella, M. (2021). Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab122","chicago":"Ruiz-Lopez, N, J Pérez-Sancho, A Esteban Del Valle, RP Haslam, S Vanneste, R Catalá, C Perea-Resa, et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.” Plant Cell. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab122.","ista":"Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, Haslam R, Vanneste S, Catalá R, Perea-Resa C, Van Damme D, García-Hernández S, Albert A, Vallarino J, Lin J, Friml J, Macho A, Salinas J, Rosado A, Napier J, Amorim-Silva V, Botella M. 2021. Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. 33(7), 2431–2453."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"N","last_name":"Ruiz-Lopez","full_name":"Ruiz-Lopez, N"},{"first_name":"J","full_name":"Pérez-Sancho, J","last_name":"Pérez-Sancho"},{"last_name":"Esteban Del Valle","full_name":"Esteban Del Valle, A","first_name":"A"},{"last_name":"Haslam","full_name":"Haslam, RP","first_name":"RP"},{"last_name":"Vanneste","full_name":"Vanneste, S","first_name":"S"},{"first_name":"R","last_name":"Catalá","full_name":"Catalá, R"},{"first_name":"C","last_name":"Perea-Resa","full_name":"Perea-Resa, C"},{"first_name":"D","full_name":"Van Damme, D","last_name":"Van Damme"},{"full_name":"García-Hernández, S","last_name":"García-Hernández","first_name":"S"},{"full_name":"Albert, A","last_name":"Albert","first_name":"A"},{"first_name":"J","last_name":"Vallarino","full_name":"Vallarino, J"},{"last_name":"Lin","full_name":"Lin, J","first_name":"J"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"AP","full_name":"Macho, AP","last_name":"Macho"},{"first_name":"J","last_name":"Salinas","full_name":"Salinas, J"},{"first_name":"A","full_name":"Rosado, A","last_name":"Rosado"},{"last_name":"Napier","full_name":"Napier, JA","first_name":"JA"},{"last_name":"Amorim-Silva","full_name":"Amorim-Silva, V","first_name":"V"},{"first_name":"MA","last_name":"Botella","full_name":"Botella, MA"}],"external_id":{"isi":["000703938100026"],"pmid":["33944955"]},"article_processing_charge":"No","title":"Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"isi":1,"has_accepted_license":"1","year":"2021","day":"01","publication":"Plant Cell","page":"2431-2453","doi":"10.1093/plcell/koab122","date_published":"2021-07-01T00:00:00Z","date_created":"2021-06-02T13:13:58Z","acknowledgement":"We would also like to thank Lothar Willmitzer for the lipidomic analysis at the Max Planck Institute of Molecular Plant Physiology (Potsdam, Germany). We thank Manuela Vega from SCI for her technical assistance in image analysis. We thank John R. Pearson and the Bionand Nanoimaging Unit, F. David Navas Fernández and the SCAI Imaging Facility and The Plant Cell Biology facility at the Shanghai Center for Plant Stress Biology for assistance with confocal microscopy. The FaFAH1 clone was a gift from Iraida Amaya Saavedra (IFAPA-Centro de Churriana, Málaga, Spain). The AHA3 antibody against the H+-ATPase was a gift from Ramón Serrano Salom (Instituto de Biología Molecular y Celular de Plantas, Valencia, Spain). The MAP-mTU2-SAC1 construct was provided by Yvon Jaillais (Laboratoire Reproduction et Développement des Plantes, Univ Lyon, France). The pGWB5 from the pGWB vector series, was provided by Tsuyoshi Nakagawa (Department of Molecular and Functional Genomics, Shimane University). We thank Plan Propio from the University of Málaga for financial support.\r\nFunding","publisher":"American Society of Plant Biologists","quality_controlled":"1","oa":1,"date_updated":"2023-08-08T13:54:32Z","ddc":["580"],"department":[{"_id":"JiFr"}],"file_date_updated":"2021-10-14T13:36:38Z","_id":"9443","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298x"]},"publication_status":"published","file":[{"date_updated":"2021-10-14T13:36:38Z","file_size":2952028,"creator":"cchlebak","date_created":"2021-10-14T13:36:38Z","file_name":"2021_PlantCell_RuizLopez.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"22d596678d00310d793611864a6d0fcd","file_id":"10141","success":1}],"language":[{"iso":"eng"}],"volume":33,"issue":"7","ec_funded":1,"abstract":[{"text":"Endoplasmic reticulum–plasma membrane contact sites (ER–PM CS) play fundamental roles in all eukaryotic cells. Arabidopsis thaliana mutants lacking the ER–PM protein tether synaptotagmin1 (SYT1) exhibit decreased PM integrity under multiple abiotic stresses, such as freezing, high salt, osmotic stress, and mechanical damage. Here, we show that, together with SYT1, the stress-induced SYT3 is an ER–PM tether that also functions in maintaining PM integrity. The ER–PM CS localization of SYT1 and SYT3 is dependent on PM phosphatidylinositol-4-phosphate and is regulated by abiotic stress. Lipidomic analysis revealed that cold stress increased the accumulation of diacylglycerol at the PM in a syt1/3 double mutant relative to wild-type while the levels of most glycerolipid species remain unchanged. In addition, the SYT1-green fluorescent protein fusion preferentially binds diacylglycerol in vivo with little affinity for polar glycerolipids. Our work uncovers a SYT-dependent mechanism of stress adaptation counteracting the detrimental accumulation of diacylglycerol at the PM produced during episodes of abiotic stress.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"07","intvolume":" 33"},{"project":[{"name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445","call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"article_number":"3226","author":[{"first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Obr, Martin","last_name":"Obr"},{"first_name":"Clifton L.","full_name":"Ricana, Clifton L.","last_name":"Ricana"},{"full_name":"Nikulin, Nadia","last_name":"Nikulin","first_name":"Nadia"},{"last_name":"Feathers","full_name":"Feathers, Jon-Philip R.","first_name":"Jon-Philip R."},{"full_name":"Klanschnig, Marco","last_name":"Klanschnig","first_name":"Marco"},{"full_name":"Thader, Andreas","last_name":"Thader","first_name":"Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Johnson","full_name":"Johnson, Marc C.","first_name":"Marc C."},{"first_name":"Volker M.","full_name":"Vogt, Volker M.","last_name":"Vogt"},{"last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dick","full_name":"Dick, Robert A.","first_name":"Robert A."}],"article_processing_charge":"No","external_id":{"isi":["000659145000011"]},"title":"Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer","citation":{"apa":"Obr, M., Ricana, C. L., Nikulin, N., Feathers, J.-P. R., Klanschnig, M., Thader, A., … Dick, R. A. (2021). Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. Nature Research. https://doi.org/10.1038/s41467-021-23506-0","ama":"Obr M, Ricana CL, Nikulin N, et al. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23506-0","ieee":"M. Obr et al., “Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer,” Nature Communications, vol. 12, no. 1. Nature Research, 2021.","short":"M. Obr, C.L. Ricana, N. Nikulin, J.-P.R. Feathers, M. Klanschnig, A. Thader, M.C. Johnson, V.M. Vogt, F.K. Schur, R.A. Dick, Nature Communications 12 (2021).","mla":"Obr, Martin, et al. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications, vol. 12, no. 1, 3226, Nature Research, 2021, doi:10.1038/s41467-021-23506-0.","ista":"Obr M, Ricana CL, Nikulin N, Feathers J-PR, Klanschnig M, Thader A, Johnson MC, Vogt VM, Schur FK, Dick RA. 2021. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 12(1), 3226.","chicago":"Obr, Martin, Clifton L. Ricana, Nadia Nikulin, Jon-Philip R. Feathers, Marco Klanschnig, Andreas Thader, Marc C. Johnson, Volker M. Vogt, Florian KM Schur, and Robert A. Dick. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications. Nature Research, 2021. https://doi.org/10.1038/s41467-021-23506-0."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"Nature Research","oa":1,"acknowledgement":"This work was funded by the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D., R01AI150454 to V.M.V, R35GM136258 in support of J-P.R.F, and the Austrian Science Fund (FWF) grant P31445 to F.K.M.S. Access to high-resolution cryo-ET data acquisition at EMBL Heidelberg was supported by iNEXT (grant no. 653706), funded by the Horizon 2020 program of the European Union (PID 4246). We thank Wim Hagen and Felix Weis at EMBL Heidelberg for support in cryo-ET data acquisition. This work made use of the Cornell Center for Materials Research Shared Facilities, which are supported through the NSF MRSEC program (DMR-179875). This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF).","date_published":"2021-05-28T00:00:00Z","doi":"10.1038/s41467-021-23506-0","date_created":"2021-05-28T14:25:50Z","has_accepted_license":"1","isi":1,"year":"2021","day":"28","publication":"Nature Communications","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"_id":"9431","department":[{"_id":"FlSc"}],"file_date_updated":"2021-06-09T15:21:14Z","date_updated":"2023-08-08T13:53:53Z","ddc":["570"],"scopus_import":"1","month":"05","intvolume":" 12","abstract":[{"lang":"eng","text":"Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles."}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"oa_version":"Published Version","volume":12,"issue":"1","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-retroviruses-become-infectious/","relation":"press_release"}]},"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","file":[{"date_updated":"2021-06-09T15:21:14Z","file_size":6166295,"creator":"kschuh","date_created":"2021-06-09T15:21:14Z","file_name":"2021_NatureCommunications_Obr.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"53ccc53d09a9111143839dbe7784e663","file_id":"9538","success":1}],"language":[{"iso":"eng"}]},{"acknowledgement":"The anonymous referees are kindly acknowledged for their useful suggestions andcomments.","quality_controlled":"1","publisher":"Cambridge University Press","oa":1,"isi":1,"has_accepted_license":"1","year":"2021","day":"25","publication":"Journal of Fluid Mechanics","doi":"10.1017/jfm.2021.371","date_published":"2021-07-25T00:00:00Z","date_created":"2021-06-06T22:01:30Z","article_number":"A17","citation":{"ista":"Marensi E, He S, Willis AP. 2021. Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. 919, A17.","chicago":"Marensi, Elena, Shuisheng He, and Ashley P. Willis. “Suppression of Turbulence and Travelling Waves in a Vertical Heated Pipe.” Journal of Fluid Mechanics. Cambridge University Press, 2021. https://doi.org/10.1017/jfm.2021.371.","ama":"Marensi E, He S, Willis AP. Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. 2021;919. doi:10.1017/jfm.2021.371","apa":"Marensi, E., He, S., & Willis, A. P. (2021). Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2021.371","ieee":"E. Marensi, S. He, and A. P. Willis, “Suppression of turbulence and travelling waves in a vertical heated pipe,” Journal of Fluid Mechanics, vol. 919. Cambridge University Press, 2021.","short":"E. Marensi, S. He, A.P. Willis, Journal of Fluid Mechanics 919 (2021).","mla":"Marensi, Elena, et al. “Suppression of Turbulence and Travelling Waves in a Vertical Heated Pipe.” Journal of Fluid Mechanics, vol. 919, A17, Cambridge University Press, 2021, doi:10.1017/jfm.2021.371."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Marensi","full_name":"Marensi, Elena","id":"0BE7553A-1004-11EA-B805-18983DDC885E","first_name":"Elena"},{"full_name":"He, Shuisheng","last_name":"He","first_name":"Shuisheng"},{"first_name":"Ashley P.","last_name":"Willis","full_name":"Willis, Ashley P."}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2008.13486"],"isi":["000653785000001"]},"title":"Suppression of turbulence and travelling waves in a vertical heated pipe","abstract":[{"text":"Turbulence in the flow of fluid through a pipe can be suppressed by buoyancy forces. As the suppression of turbulence leads to severe heat transfer deterioration, this is an important and undesirable phenomenon in both heating and cooling applications. Vertical flow is often considered, as the axial buoyancy force can help drive the flow. With heating measured by the buoyancy parameter 𝐶, our direct numerical simulations show that shear-driven turbulence may either be completely laminarised or it transitions to a relatively quiescent convection-driven state. Buoyancy forces cause a flattening of the base flow profile, which in isothermal pipe flow has recently been linked to complete suppression of turbulence (Kühnen et al., Nat. Phys., vol. 14, 2018, pp. 386–390), and the flattened laminar base profile has enhanced nonlinear stability (Marensi et al., J. Fluid Mech., vol. 863, 2019, pp. 50–875). In agreement with these findings, the nonlinear lower-branch travelling-wave solution analysed here, which is believed to mediate transition to turbulence in isothermal pipe flow, is shown to be suppressed by buoyancy. A linear instability of the laminar base flow is responsible for the appearance of the relatively quiescent convection driven state for 𝐶≳4 across the range of Reynolds numbers considered. In the suppression of turbulence, however, i.e. in the transition from turbulence, we find clearer association with the analysis of He et al. (J. Fluid Mech., vol. 809, 2016, pp. 31–71) than with the above dynamical systems approach, which describes better the transition to turbulence. The laminarisation criterion He et al. propose, based on an apparent Reynolds number of the flow as measured by its driving pressure gradient, is found to capture the critical 𝐶=𝐶𝑐𝑟(𝑅𝑒) above which the flow will be laminarised or switch to the convection-driven type. Our analysis suggests that it is the weakened rolls, rather than the streaks, which appear to be critical for laminarisation.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"07","intvolume":" 919","publication_identifier":{"issn":["00221120"],"eissn":["14697645"]},"publication_status":"published","file":[{"creator":"kschuh","file_size":4087358,"date_updated":"2021-08-03T09:53:28Z","file_name":"2021_JournalFluidMechanics_Marensi.pdf","date_created":"2021-08-03T09:53:28Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"867ad077e45c181c2c5ec1311ba27c41","file_id":"9766"}],"language":[{"iso":"eng"}],"volume":919,"_id":"9467","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-08T13:58:41Z","ddc":["530"],"file_date_updated":"2021-08-03T09:53:28Z","department":[{"_id":"BjHo"}]},{"page":"2710-2723","date_created":"2021-06-06T22:01:31Z","date_published":"2021-06-01T00:00:00Z","doi":"10.1111/mec.15936","year":"2021","isi":1,"has_accepted_license":"1","publication":"Molecular Ecology","day":"01","oa":1,"quality_controlled":"1","publisher":"Wiley","acknowledgement":"We thank the editor, two helpful reviewers, Roger Butlin, Kerstin Johannesson, Valentina Peona, Rike Stelkens, Julie Blommaert, Nick Barton, and João Alpedrinha for helpful comments that improved the manuscript. The authors acknowledge funding from the Swedish Research Council Formas (2017-01597 to AS), the Swedish Research Council Vetenskapsrådet (2016-05139 to AS, 2019-04452 to TS) and from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 757451 to TS). ELB was funded by a Carl Tryggers grant awarded to Tanja Slotte. Anja M. Westram was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 797747. Inês Fragata was funded by a Junior Researcher contract from FCT (CEECIND/02616/2018).","external_id":{"isi":["000652056400001"]},"article_processing_charge":"No","author":[{"last_name":"Berdan","full_name":"Berdan, Emma L.","first_name":"Emma L."},{"first_name":"Alexandre","full_name":"Blanckaert, Alexandre","last_name":"Blanckaert"},{"first_name":"Tanja","last_name":"Slotte","full_name":"Slotte, Tanja"},{"first_name":"Alexander","full_name":"Suh, Alexander","last_name":"Suh"},{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Inês","last_name":"Fragata","full_name":"Fragata, Inês"}],"title":"Unboxing mutations: Connecting mutation types with evolutionary consequences","citation":{"mla":"Berdan, Emma L., et al. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” Molecular Ecology, vol. 30, no. 12, Wiley, 2021, pp. 2710–23, doi:10.1111/mec.15936.","apa":"Berdan, E. L., Blanckaert, A., Slotte, T., Suh, A., Westram, A. M., & Fragata, I. (2021). Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15936","ama":"Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 2021;30(12):2710-2723. doi:10.1111/mec.15936","ieee":"E. L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A. M. Westram, and I. Fragata, “Unboxing mutations: Connecting mutation types with evolutionary consequences,” Molecular Ecology, vol. 30, no. 12. Wiley, pp. 2710–2723, 2021.","short":"E.L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A.M. Westram, I. Fragata, Molecular Ecology 30 (2021) 2710–2723.","chicago":"Berdan, Emma L., Alexandre Blanckaert, Tanja Slotte, Alexander Suh, Anja M Westram, and Inês Fragata. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” Molecular Ecology. Wiley, 2021. https://doi.org/10.1111/mec.15936.","ista":"Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. 2021. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 30(12), 2710–2723."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"797747","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020","_id":"265B41B8-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"volume":30,"issue":"12","publication_status":"published","publication_identifier":{"eissn":["1365294X"],"issn":["09621083"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9545","checksum":"e6f4731365bde2614b333040a08265d8","success":1,"creator":"kschuh","date_updated":"2021-06-11T15:34:53Z","file_size":1031978,"date_created":"2021-06-11T15:34:53Z","file_name":"2021_MolecularEcology_Berdan.pdf"}],"scopus_import":"1","intvolume":" 30","month":"06","abstract":[{"text":"A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types (e.g., SNPs, translocations and inversions). To do this we must simultaneously consider different mutation types in an evolutionary framework. Here, we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance in a given scenario. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2021-06-11T15:34:53Z","department":[{"_id":"NiBa"}],"date_updated":"2023-08-08T13:59:18Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","status":"public","_id":"9470"},{"_id":"9468","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-08T13:58:12Z","department":[{"_id":"UlWa"}],"oa_version":"Preprint","abstract":[{"text":"Motivated by the successful application of geometry to proving the Harary--Hill conjecture for “pseudolinear” drawings of $K_n$, we introduce “pseudospherical” drawings of graphs. A spherical drawing of a graph $G$ is a drawing in the unit sphere $\\mathbb{S}^2$ in which the vertices of $G$ are represented as points---no three on a great circle---and the edges of $G$ are shortest-arcs in $\\mathbb{S}^2$ connecting pairs of vertices. Such a drawing has three properties: (1) every edge $e$ is contained in a simple closed curve $\\gamma_e$ such that the only vertices in $\\gamma_e$ are the ends of $e$; (2) if $e\\ne f$, then $\\gamma_e\\cap\\gamma_f$ has precisely two crossings; and (3) if $e\\ne f$, then $e$ intersects $\\gamma_f$ at most once, in either a crossing or an end of $e$. We use properties (1)--(3) to define a pseudospherical drawing of $G$. Our main result is that for the complete graph, properties (1)--(3) are equivalent to the same three properties but with “precisely two crossings” in (2) replaced by “at most two crossings.” The proof requires a result in the geometric transversal theory of arrangements of pseudocircles. This is proved using the surprising result that the absence of special arcs (coherent spirals) in an arrangement of simple closed curves characterizes the fact that any two curves in the arrangement have at most two crossings. Our studies provide the necessary ideas for exhibiting a drawing of $K_{10}$ that has no extension to an arrangement of pseudocircles and a drawing of $K_9$ that does extend to an arrangement of pseudocircles, but no such extension has all pairs of pseudocircles crossing twice.\r\n","lang":"eng"}],"month":"05","intvolume":" 35","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2001.06053","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["08954801"]},"publication_status":"published","volume":35,"issue":"2","ec_funded":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"A. M. Arroyo Guevara, R. B. Richter, and M. Sunohara, “Extending drawings of complete graphs into arrangements of pseudocircles,” SIAM Journal on Discrete Mathematics, vol. 35, no. 2. Society for Industrial and Applied Mathematics, pp. 1050–1076, 2021.","short":"A.M. Arroyo Guevara, R.B. Richter, M. Sunohara, SIAM Journal on Discrete Mathematics 35 (2021) 1050–1076.","ama":"Arroyo Guevara AM, Richter RB, Sunohara M. Extending drawings of complete graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics. 2021;35(2):1050-1076. doi:10.1137/20M1313234","apa":"Arroyo Guevara, A. M., Richter, R. B., & Sunohara, M. (2021). Extending drawings of complete graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/20M1313234","mla":"Arroyo Guevara, Alan M., et al. “Extending Drawings of Complete Graphs into Arrangements of Pseudocircles.” SIAM Journal on Discrete Mathematics, vol. 35, no. 2, Society for Industrial and Applied Mathematics, 2021, pp. 1050–76, doi:10.1137/20M1313234.","ista":"Arroyo Guevara AM, Richter RB, Sunohara M. 2021. Extending drawings of complete graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics. 35(2), 1050–1076.","chicago":"Arroyo Guevara, Alan M, R. Bruce Richter, and Matthew Sunohara. “Extending Drawings of Complete Graphs into Arrangements of Pseudocircles.” SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics, 2021. https://doi.org/10.1137/20M1313234."},"title":"Extending drawings of complete graphs into arrangements of pseudocircles","author":[{"first_name":"Alan M","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","full_name":"Arroyo Guevara, Alan M","orcid":"0000-0003-2401-8670","last_name":"Arroyo Guevara"},{"first_name":"R. Bruce","full_name":"Richter, R. Bruce","last_name":"Richter"},{"last_name":"Sunohara","full_name":"Sunohara, Matthew","first_name":"Matthew"}],"article_processing_charge":"No","external_id":{"isi":["000674142200022"],"arxiv":["2001.06053"]},"publisher":"Society for Industrial and Applied Mathematics","quality_controlled":"1","oa":1,"day":"20","publication":"SIAM Journal on Discrete Mathematics","isi":1,"year":"2021","doi":"10.1137/20M1313234","date_published":"2021-05-20T00:00:00Z","date_created":"2021-06-06T22:01:30Z","page":"1050-1076"},{"acknowledgement":"Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 (R.S.) and under the Marie Sklodowska-Curie grant agreement No 836146 (A.D.) is gratefully acknowledged. A.D. acknowledges support of the Swiss National Science Foundation through the Ambizione grant PZ00P2 185851.","quality_controlled":"1","publisher":"Elsevier","oa":1,"day":"15","publication":"Journal of Functional Analysis","isi":1,"year":"2021","date_published":"2021-09-15T00:00:00Z","doi":"10.1016/j.jfa.2021.109096","date_created":"2021-06-06T22:01:28Z","article_number":"109096","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and Critical Temperature Shift for Weakly Interacting Trapped Bosons.” Journal of Functional Analysis. Elsevier, 2021. https://doi.org/10.1016/j.jfa.2021.109096.","ista":"Deuchert A, Seiringer R. 2021. Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. 281(6), 109096.","mla":"Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and Critical Temperature Shift for Weakly Interacting Trapped Bosons.” Journal of Functional Analysis, vol. 281, no. 6, 109096, Elsevier, 2021, doi:10.1016/j.jfa.2021.109096.","ama":"Deuchert A, Seiringer R. Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. 2021;281(6). doi:10.1016/j.jfa.2021.109096","apa":"Deuchert, A., & Seiringer, R. (2021). Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2021.109096","short":"A. Deuchert, R. Seiringer, Journal of Functional Analysis 281 (2021).","ieee":"A. Deuchert and R. Seiringer, “Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons,” Journal of Functional Analysis, vol. 281, no. 6. Elsevier, 2021."},"title":"Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons","author":[{"first_name":"Andreas","full_name":"Deuchert, Andreas","last_name":"Deuchert"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"external_id":{"arxiv":["2009.00992"],"isi":["000656508600008"]},"article_processing_charge":"No","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider a system of N trapped bosons with repulsive interactions in a combined semiclassical mean-field limit at positive temperature. We show that the free energy is well approximated by the minimum of the Hartree free energy functional – a natural extension of the Hartree energy functional to positive temperatures. The Hartree free energy functional converges in the same limit to a semiclassical free energy functional, and we show that the system displays Bose–Einstein condensation if and only if it occurs in the semiclassical free energy functional. This allows us to show that for weak coupling the critical temperature decreases due to the repulsive interactions."}],"month":"09","intvolume":" 281","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2009.00992"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"publication_status":"published","issue":"6","volume":281,"ec_funded":1,"_id":"9462","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-08-08T13:56:27Z","department":[{"_id":"RoSe"}]},{"project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Iyiola OS, Enyi CD, Shehu Y. 2021. Reflected three-operator splitting method for monotone inclusion problem. Optimization Methods and Software.","chicago":"Iyiola, Olaniyi S., Cyril D. Enyi, and Yekini Shehu. “Reflected Three-Operator Splitting Method for Monotone Inclusion Problem.” Optimization Methods and Software. Taylor and Francis, 2021. https://doi.org/10.1080/10556788.2021.1924715.","apa":"Iyiola, O. S., Enyi, C. D., & Shehu, Y. (2021). Reflected three-operator splitting method for monotone inclusion problem. Optimization Methods and Software. Taylor and Francis. https://doi.org/10.1080/10556788.2021.1924715","ama":"Iyiola OS, Enyi CD, Shehu Y. Reflected three-operator splitting method for monotone inclusion problem. Optimization Methods and Software. 2021. doi:10.1080/10556788.2021.1924715","ieee":"O. S. Iyiola, C. D. Enyi, and Y. Shehu, “Reflected three-operator splitting method for monotone inclusion problem,” Optimization Methods and Software. Taylor and Francis, 2021.","short":"O.S. Iyiola, C.D. Enyi, Y. Shehu, Optimization Methods and Software (2021).","mla":"Iyiola, Olaniyi S., et al. “Reflected Three-Operator Splitting Method for Monotone Inclusion Problem.” Optimization Methods and Software, Taylor and Francis, 2021, doi:10.1080/10556788.2021.1924715."},"title":"Reflected three-operator splitting method for monotone inclusion problem","article_processing_charge":"No","external_id":{"isi":["000650507600001"]},"author":[{"last_name":"Iyiola","full_name":"Iyiola, Olaniyi S.","first_name":"Olaniyi S."},{"first_name":"Cyril D.","full_name":"Enyi, Cyril D.","last_name":"Enyi"},{"first_name":"Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","full_name":"Shehu, Yekini","orcid":"0000-0001-9224-7139","last_name":"Shehu"}],"acknowledgement":"The authors are grateful to the anonymous referees and the handling Editor for their insightful comments which have improved the earlier version of the manuscript greatly. The second author is grateful to the University of Hafr Al Batin. The last 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).","quality_controlled":"1","publisher":"Taylor and Francis","publication":"Optimization Methods and Software","day":"12","year":"2021","isi":1,"date_created":"2021-06-06T22:01:30Z","date_published":"2021-05-12T00:00:00Z","doi":"10.1080/10556788.2021.1924715","_id":"9469","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-08-08T13:57:43Z","department":[{"_id":"VlKo"}],"oa_version":"None","abstract":[{"lang":"eng","text":"In this paper, we consider reflected three-operator splitting methods for monotone inclusion problems in real Hilbert spaces. To do this, we first obtain weak convergence analysis and nonasymptotic O(1/n) convergence rate of the reflected Krasnosel'skiĭ-Mann iteration for finding a fixed point of nonexpansive mapping in real Hilbert spaces under some seemingly easy to implement conditions on the iterative parameters. We then apply our results to three-operator splitting for the monotone inclusion problem and consequently obtain the corresponding convergence analysis. Furthermore, we derive reflected primal-dual algorithms for highly structured monotone inclusion problems. Some numerical implementations are drawn from splitting methods to support the theoretical analysis."}],"month":"05","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1055-6788"],"eissn":["1029-4937"]},"ec_funded":1},{"acknowledgement":"We are deeply grateful to the late Gregor Högenauer who built the foundation for this study with his visionary work on the inhibitor diazaborine and its bacterial target. We thank Rolf Breinbauer for insightful discussions on boron chemistry. We thank Anton Meinhart and Tim Clausen for the valuable discussion of the manuscript. We are indebted to Thomas Köcher for the MS measurement of the diazaborine-ATPγS adduct. We thank the team of the VBCF for support during early phases of this work and the IST Austria Electron Microscopy Facility for providing equipment. The lab of D.H. is supported by Boehringer Ingelheim. The work was funded by FWF projects P32536 and P32977 (to H.B.).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2021","has_accepted_license":"1","isi":1,"publication":"Nature Communications","day":"09","date_created":"2021-06-10T14:57:45Z","doi":"10.1038/s41467-021-23854-x","date_published":"2021-06-09T00:00:00Z","article_number":"3483","citation":{"ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23854-x","apa":"Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Rössler, I., Klein, I., Hetzmannseder, C., … Bergler, H. (2021). Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23854-x","short":"M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, I. Rössler, I. Klein, C. Hetzmannseder, G. Zisser, C.C. Gruber, K. Gruber, D. Haselbach, H. Bergler, Nature Communications 12 (2021).","ieee":"M. Prattes et al., “Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","mla":"Prattes, Michael, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” Nature Communications, vol. 12, no. 1, 3483, Springer Nature, 2021, doi:10.1038/s41467-021-23854-x.","ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Rössler I, Klein I, Hetzmannseder C, Zisser G, Gruber CC, Gruber K, Haselbach D, Bergler H. 2021. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 12(1), 3483.","chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Ingrid Rössler, Isabella Klein, Christina Hetzmannseder, Gertrude Zisser, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23854-x."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000664874700014"],"pmid":["34108481"]},"article_processing_charge":"No","author":[{"first_name":"Michael","last_name":"Prattes","full_name":"Prattes, Michael"},{"first_name":"Irina","last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina"},{"last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin"},{"first_name":"Ingrid","last_name":"Rössler","full_name":"Rössler, Ingrid"},{"first_name":"Isabella","full_name":"Klein, Isabella","last_name":"Klein"},{"last_name":"Hetzmannseder","full_name":"Hetzmannseder, Christina","first_name":"Christina"},{"full_name":"Zisser, Gertrude","last_name":"Zisser","first_name":"Gertrude"},{"first_name":"Christian C.","last_name":"Gruber","full_name":"Gruber, Christian C."},{"last_name":"Gruber","full_name":"Gruber, Karl","first_name":"Karl"},{"last_name":"Haselbach","full_name":"Haselbach, David","first_name":"David"},{"first_name":"Helmut","last_name":"Bergler","full_name":"Bergler, Helmut"}],"title":"Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine","acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","text":"The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases."}],"oa_version":"Published Version","pmid":1,"intvolume":" 12","month":"06","publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2021-06-15T18:55:59Z","file_size":3397292,"creator":"cziletti","date_created":"2021-06-15T18:55:59Z","file_name":"2021_NatureComm_Prattes.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9556","checksum":"40fc24c1310930990b52a8ad1142ee97","success":1}],"issue":"1","volume":12,"_id":"9540","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"status":"public","date_updated":"2023-08-08T14:05:26Z","ddc":["570"],"department":[{"_id":"EM-Fac"}],"file_date_updated":"2021-06-15T18:55:59Z"},{"pmid":1,"oa_version":"Published Version","abstract":[{"text":"AMPA receptors (AMPARs) mediate the majority of excitatory transmission in the brain and enable the synaptic plasticity that underlies learning1. A diverse array of AMPAR signalling complexes are established by receptor auxiliary subunits, which associate with the AMPAR in various combinations to modulate trafficking, gating and synaptic strength2. However, their mechanisms of action are poorly understood. Here we determine cryo-electron microscopy structures of the heteromeric GluA1–GluA2 receptor assembled with both TARP-γ8 and CNIH2, the predominant AMPAR complex in the forebrain, in both resting and active states. Two TARP-γ8 and two CNIH2 subunits insert at distinct sites beneath the ligand-binding domains of the receptor, with site-specific lipids shaping each interaction and affecting the gating regulation of the AMPARs. Activation of the receptor leads to asymmetry between GluA1 and GluA2 along the ion conduction path and an outward expansion of the channel triggers counter-rotations of both auxiliary subunit pairs, promoting the active-state conformation. In addition, both TARP-γ8 and CNIH2 pivot towards the pore exit upon activation, extending their reach for cytoplasmic receptor elements. CNIH2 achieves this through its uniquely extended M2 helix, which has transformed this endoplasmic reticulum-export factor into a powerful AMPAR modulator that is capable of providing hippocampal pyramidal neurons with their integrative synaptic properties. ","lang":"eng"}],"intvolume":" 594","month":"06","main_file_link":[{"url":"https://doi.org/10.1038/s41586-021-03613-0","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"volume":594,"_id":"9549","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-08T13:59:51Z","department":[{"_id":"PeJo"}],"acknowledgement":"We thank members of the Greger laboratory, B. Herguedas, J. Krieger and J.-N. Dohrke for comments on the manuscript; J. Krieger and J.-N. Dohrke for discussion, J. Krieger for help with the normal mode analysis, B. Köhegyi for help with cryo-EM imaging, V. Chang and K. Suzuki for helping to generate the CNIH2-1D4-HA stable cell line, M. Carvalho for assistance at early stages of this project, the LMB scientific computing and the cryo-EM facility for support, P. Emsley for help with model building, T. Nakane for helpful comments with RELION 3.1 and R. Warshamanage for helping with EMDA cryo-EM-map processing. We acknowledge the Diamond Light Source for access and support of the Cryo-EM facilities at the UK national electron bio10 imaging centre (eBIC), proposal EM17434, funded by the Wellcome Trust, MRC and BBSRC. This work was supported by grants from the Medical Research Council, as part of United Kingdom Research and Innovation (also known as UK Research and Innovation) (MC_U105174197) and BBSRC (BB/N002113/1) to I.H.G.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"Nature","day":"02","year":"2021","isi":1,"date_created":"2021-06-13T22:01:33Z","doi":"10.1038/s41586-021-03613-0","date_published":"2021-06-02T00:00:00Z","page":"454-458","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Zhang, Danyang, Jake Watson, Peter M. Matthews, Ondrej Cais, and Ingo H. Greger. “Gating and Modulation of a Hetero-Octameric AMPA Glutamate Receptor.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03613-0.","ista":"Zhang D, Watson J, Matthews PM, Cais O, Greger IH. 2021. Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature. 594, 454–458.","mla":"Zhang, Danyang, et al. “Gating and Modulation of a Hetero-Octameric AMPA Glutamate Receptor.” Nature, vol. 594, Springer Nature, 2021, pp. 454–58, doi:10.1038/s41586-021-03613-0.","apa":"Zhang, D., Watson, J., Matthews, P. M., Cais, O., & Greger, I. H. (2021). Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-03613-0","ama":"Zhang D, Watson J, Matthews PM, Cais O, Greger IH. Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature. 2021;594:454-458. doi:10.1038/s41586-021-03613-0","ieee":"D. Zhang, J. Watson, P. M. Matthews, O. Cais, and I. H. Greger, “Gating and modulation of a hetero-octameric AMPA glutamate receptor,” Nature, vol. 594. Springer Nature, pp. 454–458, 2021.","short":"D. Zhang, J. Watson, P.M. Matthews, O. Cais, I.H. Greger, Nature 594 (2021) 454–458."},"title":"Gating and modulation of a hetero-octameric AMPA glutamate receptor","article_processing_charge":"No","external_id":{"isi":["000657238100003"],"pmid":["34079129"]},"author":[{"last_name":"Zhang","full_name":"Zhang, Danyang","first_name":"Danyang"},{"last_name":"Watson","orcid":"0000-0002-8698-3823","full_name":"Watson, Jake","first_name":"Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"first_name":"Peter M.","full_name":"Matthews, Peter M.","last_name":"Matthews"},{"first_name":"Ondrej","last_name":"Cais","full_name":"Cais, Ondrej"},{"last_name":"Greger","full_name":"Greger, Ingo H.","first_name":"Ingo H."}]},{"year":"2021","isi":1,"has_accepted_license":"1","publication":"Forum of Mathematics, Sigma","day":"27","date_created":"2021-06-13T22:01:33Z","doi":"10.1017/fms.2021.38","date_published":"2021-05-27T00:00:00Z","acknowledgement":"The first author is supported in part by Hong Kong RGC Grant GRF 16301519 and NSFC 11871425. The second author is supported in part by ERC Advanced Grant RANMAT 338804. The third author is supported in part by Swedish Research Council Grant VR-2017-05195 and the Knut and Alice Wallenberg Foundation","oa":1,"quality_controlled":"1","publisher":"Cambridge University Press","citation":{"chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Equipartition Principle for Wigner Matrices.” Forum of Mathematics, Sigma. Cambridge University Press, 2021. https://doi.org/10.1017/fms.2021.38.","ista":"Bao Z, Erdös L, Schnelli K. 2021. Equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 9, e44.","mla":"Bao, Zhigang, et al. “Equipartition Principle for Wigner Matrices.” Forum of Mathematics, Sigma, vol. 9, e44, Cambridge University Press, 2021, doi:10.1017/fms.2021.38.","ama":"Bao Z, Erdös L, Schnelli K. Equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 2021;9. doi:10.1017/fms.2021.38","apa":"Bao, Z., Erdös, L., & Schnelli, K. (2021). Equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2021.38","short":"Z. Bao, L. Erdös, K. Schnelli, Forum of Mathematics, Sigma 9 (2021).","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Equipartition principle for Wigner matrices,” Forum of Mathematics, Sigma, vol. 9. Cambridge University Press, 2021."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["2008.07061"],"isi":["000654960800001"]},"article_processing_charge":"No","author":[{"id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","first_name":"Zhigang","orcid":"0000-0003-3036-1475","full_name":"Bao, Zhigang","last_name":"Bao"},{"last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin","last_name":"Schnelli"}],"title":"Equipartition principle for Wigner matrices","article_number":"e44","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","publication_identifier":{"eissn":["20505094"]},"language":[{"iso":"eng"}],"file":[{"file_id":"9555","checksum":"47c986578de132200d41e6d391905519","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-06-15T14:40:45Z","file_name":"2021_ForumMath_Bao.pdf","creator":"cziletti","date_updated":"2021-06-15T14:40:45Z","file_size":483458}],"ec_funded":1,"volume":9,"abstract":[{"lang":"eng","text":"We prove that the energy of any eigenvector of a sum of several independent large Wigner matrices is equally distributed among these matrices with very high precision. This shows a particularly strong microcanonical form of the equipartition principle for quantum systems whose components are modelled by Wigner matrices. "}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 9","month":"05","date_updated":"2023-08-08T14:03:40Z","ddc":["510"],"department":[{"_id":"LaEr"}],"file_date_updated":"2021-06-15T14:40:45Z","_id":"9550","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public"},{"acknowledgement":"We acknowledge insightful discussions with K. Flensberg, E. B. Hansen, T. Karzig, R. Lutchyn, D. Pikulin, E. Prada, and R. Aguado. This work was supported by Microsoft Project Q and the Danmarks Grundforskningsfond. C.M.M. acknowledges support from the Villum Fonden. A.P.H. and L.C. contributed equally to this work.","publisher":"American Physical Society","quality_controlled":"1","oa":1,"isi":1,"year":"2021","day":"15","publication":"Physical Review B","doi":"10.1103/PhysRevB.103.235201","date_published":"2021-06-15T00:00:00Z","date_created":"2021-06-20T22:01:33Z","article_number":"235201","citation":{"ista":"Puglia D, Martinez EA, Ménard GC, Pöschl A, Gronin S, Gardner GC, Kallaher R, Manfra MJ, Marcus CM, Higginbotham AP, Casparis L. 2021. Closing of the induced gap in a hybrid superconductor-semiconductor nanowire. Physical Review B. 103(23), 235201.","chicago":"Puglia, Denise, E. A. Martinez, G. C. Ménard, A. Pöschl, S. Gronin, G. C. Gardner, R. Kallaher, et al. “Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Physical Review B. American Physical Society, 2021. https://doi.org/10.1103/PhysRevB.103.235201.","ieee":"D. Puglia et al., “Closing of the induced gap in a hybrid superconductor-semiconductor nanowire,” Physical Review B, vol. 103, no. 23. American Physical Society, 2021.","short":"D. Puglia, E.A. Martinez, G.C. Ménard, A. Pöschl, S. Gronin, G.C. Gardner, R. Kallaher, M.J. Manfra, C.M. Marcus, A.P. Higginbotham, L. Casparis, Physical Review B 103 (2021).","ama":"Puglia D, Martinez EA, Ménard GC, et al. Closing of the induced gap in a hybrid superconductor-semiconductor nanowire. Physical Review B. 2021;103(23). doi:10.1103/PhysRevB.103.235201","apa":"Puglia, D., Martinez, E. A., Ménard, G. C., Pöschl, A., Gronin, S., Gardner, G. C., … Casparis, L. (2021). Closing of the induced gap in a hybrid superconductor-semiconductor nanowire. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.103.235201","mla":"Puglia, Denise, et al. “Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Physical Review B, vol. 103, no. 23, 235201, American Physical Society, 2021, doi:10.1103/PhysRevB.103.235201."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Denise","id":"4D495994-AE37-11E9-AC72-31CAE5697425","full_name":"Puglia, Denise","last_name":"Puglia"},{"last_name":"Martinez","full_name":"Martinez, E. A.","first_name":"E. A."},{"first_name":"G. C.","full_name":"Ménard, G. C.","last_name":"Ménard"},{"first_name":"A.","last_name":"Pöschl","full_name":"Pöschl, A."},{"full_name":"Gronin, S.","last_name":"Gronin","first_name":"S."},{"full_name":"Gardner, G. C.","last_name":"Gardner","first_name":"G. C."},{"full_name":"Kallaher, R.","last_name":"Kallaher","first_name":"R."},{"last_name":"Manfra","full_name":"Manfra, M. J.","first_name":"M. J."},{"last_name":"Marcus","full_name":"Marcus, C. M.","first_name":"C. M."},{"first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P"},{"first_name":"L.","last_name":"Casparis","full_name":"Casparis, L."}],"article_processing_charge":"No","external_id":{"arxiv":["2006.01275"],"isi":["000661512500002"]},"title":"Closing of the induced gap in a hybrid superconductor-semiconductor nanowire","abstract":[{"lang":"eng","text":"We present conductance-matrix measurements in long, three-terminal hybrid superconductor-semiconductor nanowires, and compare with theoretical predictions of a magnetic-field-driven, topological quantum phase transition. By examining the nonlocal conductance, we identify the closure of the excitation gap in the bulk of the semiconductor before the emergence of zero-bias peaks, ruling out spurious gap-closure signatures from localized states. We observe that after the gap closes, nonlocal signals and zero-bias peaks fluctuate strongly at both ends, inconsistent with a simple picture of clean topological superconductivity."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2006.01275"}],"month":"06","intvolume":" 103","publication_identifier":{"eissn":["24699969"],"issn":["24699950"]},"publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"13080"}]},"issue":"23","volume":103,"_id":"9570","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-08T14:08:08Z","department":[{"_id":"AnHi"}]},{"doi":"10.1007/s12220-021-00691-4","date_published":"2021-05-31T00:00:00Z","date_created":"2021-06-13T22:01:32Z","page":"11493-11528","day":"31","publication":"Journal of Geometric Analysis","isi":1,"year":"2021","publisher":"Springer","quality_controlled":"1","oa":1,"acknowledgement":"The authors acknowledge the support of the grant of the Russian Government N 075-15-2019-1926.","title":"Functional Löwner ellipsoids","author":[{"full_name":"Ivanov, Grigory","last_name":"Ivanov","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","first_name":"Grigory"},{"full_name":"Tsiutsiurupa, Igor","last_name":"Tsiutsiurupa","first_name":"Igor"}],"article_processing_charge":"No","external_id":{"arxiv":["2008.09543"],"isi":["000656507500001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Ivanov, Grigory, and Igor Tsiutsiurupa. “Functional Löwner Ellipsoids.” Journal of Geometric Analysis. Springer, 2021. https://doi.org/10.1007/s12220-021-00691-4.","ista":"Ivanov G, Tsiutsiurupa I. 2021. Functional Löwner ellipsoids. Journal of Geometric Analysis. 31, 11493–11528.","mla":"Ivanov, Grigory, and Igor Tsiutsiurupa. “Functional Löwner Ellipsoids.” Journal of Geometric Analysis, vol. 31, Springer, 2021, pp. 11493–528, doi:10.1007/s12220-021-00691-4.","ieee":"G. Ivanov and I. Tsiutsiurupa, “Functional Löwner ellipsoids,” Journal of Geometric Analysis, vol. 31. Springer, pp. 11493–11528, 2021.","short":"G. Ivanov, I. Tsiutsiurupa, Journal of Geometric Analysis 31 (2021) 11493–11528.","ama":"Ivanov G, Tsiutsiurupa I. Functional Löwner ellipsoids. Journal of Geometric Analysis. 2021;31:11493-11528. doi:10.1007/s12220-021-00691-4","apa":"Ivanov, G., & Tsiutsiurupa, I. (2021). Functional Löwner ellipsoids. Journal of Geometric Analysis. Springer. https://doi.org/10.1007/s12220-021-00691-4"},"volume":31,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1559-002X"],"issn":["1050-6926"]},"publication_status":"published","month":"05","intvolume":" 31","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2008.09543"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We extend the notion of the minimal volume ellipsoid containing a convex body in Rd to the setting of logarithmically concave functions. We consider a vast class of logarithmically concave functions whose superlevel sets are concentric ellipsoids. For a fixed function from this class, we consider the set of all its “affine” positions. For any log-concave function f on Rd, we consider functions belonging to this set of “affine” positions, and find the one with the minimal integral under the condition that it is pointwise greater than or equal to f. We study the properties of existence and uniqueness of the solution to this problem. For any s∈[0,+∞), we consider the construction dual to the recently defined John s-function (Ivanov and Naszódi in Functional John ellipsoids. arXiv preprint: arXiv:2006.09934, 2020). We prove that such a construction determines a unique function and call it the Löwner s-function of f. We study the Löwner s-functions as s tends to zero and to infinity. Finally, extending the notion of the outer volume ratio, we define the outer integral ratio of a log-concave function and give an asymptotically tight bound on it."}],"department":[{"_id":"UlWa"}],"date_updated":"2023-08-08T14:04:49Z","status":"public","article_type":"original","type":"journal_article","_id":"9548"},{"_id":"13080","type":"research_data_reference","status":"public","citation":{"mla":"Puglia, Denise, et al. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. Zenodo, 2021, doi:10.5281/ZENODO.4592435.","short":"D. Puglia, E. Martinez, G. Menard, A. Pöschl, S. Gronin, G. Gardner, R. Kallaher, M. Manfra, C. Marcus, A.P. Higginbotham, L. Casparis, (2021).","ieee":"D. Puglia et al., “Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Zenodo, 2021.","ama":"Puglia D, Martinez E, Menard G, et al. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. 2021. doi:10.5281/ZENODO.4592435","apa":"Puglia, D., Martinez, E., Menard, G., Pöschl, A., Gronin, S., Gardner, G., … Casparis, L. (2021). Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. Zenodo. https://doi.org/10.5281/ZENODO.4592435","chicago":"Puglia, Denise, Esteban Martinez, Gerbold Menard, Andreas Pöschl, Sergei Gronin, Geoffrey Gardner, Ray Kallaher, et al. “Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.4592435.","ista":"Puglia D, Martinez E, Menard G, Pöschl A, Gronin S, Gardner G, Kallaher R, Manfra M, Marcus C, Higginbotham AP, Casparis L. 2021. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire, Zenodo, 10.5281/ZENODO.4592435."},"date_updated":"2023-08-08T14:08:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"author":[{"id":"4D495994-AE37-11E9-AC72-31CAE5697425","first_name":"Denise","full_name":"Puglia, Denise","last_name":"Puglia"},{"first_name":"Esteban","last_name":"Martinez","full_name":"Martinez, Esteban"},{"first_name":"Gerbold","last_name":"Menard","full_name":"Menard, Gerbold"},{"full_name":"Pöschl, Andreas","last_name":"Pöschl","first_name":"Andreas"},{"full_name":"Gronin, Sergei","last_name":"Gronin","first_name":"Sergei"},{"first_name":"Geoffrey","last_name":"Gardner","full_name":"Gardner, Geoffrey"},{"first_name":"Ray","full_name":"Kallaher, Ray","last_name":"Kallaher"},{"first_name":"Michael","last_name":"Manfra","full_name":"Manfra, Michael"},{"first_name":"Charles","last_name":"Marcus","full_name":"Marcus, Charles"},{"orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P"},{"first_name":"Lucas","last_name":"Casparis","full_name":"Casparis, Lucas"}],"article_processing_charge":"No","department":[{"_id":"AnHi"}],"title":"Data for 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire","abstract":[{"lang":"eng","text":"Data for the manuscript 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire' ([2006.01275] Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire (arxiv.org))\r\n\r\nWe upload a pdf with extended data sets, and the raw data for these extended datasets as well."}],"oa_version":"Published Version","publisher":"Zenodo","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.4592460"}],"oa":1,"month":"03","year":"2021","day":"09","doi":"10.5281/ZENODO.4592435","related_material":{"link":[{"relation":"software","url":"https://github.com/caslu85/Induced-Gap-Closing-Shared/tree/1.1.3"}],"record":[{"status":"public","id":"9570","relation":"used_in_publication"}]},"date_published":"2021-03-09T00:00:00Z","date_created":"2023-05-23T17:11:28Z"},{"page":"21702-21715","date_created":"2021-06-19T07:27:45Z","doi":"10.1039/d1ra03428f","date_published":"2021-06-18T00:00:00Z","year":"2021","has_accepted_license":"1","isi":1,"publication":"RSC Advances","day":"18","oa":1,"quality_controlled":"1","publisher":"Royal Society of Chemistry","acknowledgement":"The research is funded by Higher Education Commission (HEC) Pakistan under start-up research grant program (SRGP) Project no. 2454.","article_processing_charge":"No","external_id":{"isi":["000665644000048"]},"author":[{"first_name":"M. S.","last_name":"Dar","full_name":"Dar, M. S."},{"last_name":"Akram","full_name":"Akram, Khush Bakhat","first_name":"Khush Bakhat"},{"full_name":"Sohail, Ayesha","last_name":"Sohail","first_name":"Ayesha"},{"full_name":"Arif, Fatima","last_name":"Arif","first_name":"Fatima"},{"first_name":"Fatemeh","full_name":"Zabihi, Fatemeh","last_name":"Zabihi"},{"first_name":"Shengyuan","last_name":"Yang","full_name":"Yang, Shengyuan"},{"first_name":"Shamsa","last_name":"Munir","full_name":"Munir, Shamsa"},{"last_name":"Zhu","full_name":"Zhu, Meifang","first_name":"Meifang"},{"last_name":"Abid","full_name":"Abid, M.","first_name":"M."},{"id":"32c21954-2022-11eb-9d5f-af9f93c24e71","first_name":"Muhammad","last_name":"Nauman","full_name":"Nauman, Muhammad","orcid":"0000-0002-2111-4846"}],"title":"Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling","citation":{"chicago":"Dar, M. S., Khush Bakhat Akram, Ayesha Sohail, Fatima Arif, Fatemeh Zabihi, Shengyuan Yang, Shamsa Munir, Meifang Zhu, M. Abid, and Muhammad Nauman. “Heat Induction in Two-Dimensional Graphene–Fe3O4 Nanohybrids for Magnetic Hyperthermia Applications with Artificial Neural Network Modeling.” RSC Advances. Royal Society of Chemistry, 2021. https://doi.org/10.1039/d1ra03428f.","ista":"Dar MS, Akram KB, Sohail A, Arif F, Zabihi F, Yang S, Munir S, Zhu M, Abid M, Nauman M. 2021. Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling. RSC Advances. 11(35), 21702–21715.","mla":"Dar, M. S., et al. “Heat Induction in Two-Dimensional Graphene–Fe3O4 Nanohybrids for Magnetic Hyperthermia Applications with Artificial Neural Network Modeling.” RSC Advances, vol. 11, no. 35, Royal Society of Chemistry, 2021, pp. 21702–15, doi:10.1039/d1ra03428f.","apa":"Dar, M. S., Akram, K. B., Sohail, A., Arif, F., Zabihi, F., Yang, S., … Nauman, M. (2021). Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling. RSC Advances. Royal Society of Chemistry. https://doi.org/10.1039/d1ra03428f","ama":"Dar MS, Akram KB, Sohail A, et al. Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling. RSC Advances. 2021;11(35):21702-21715. doi:10.1039/d1ra03428f","short":"M.S. Dar, K.B. Akram, A. Sohail, F. Arif, F. Zabihi, S. Yang, S. Munir, M. Zhu, M. Abid, M. Nauman, RSC Advances 11 (2021) 21702–21715.","ieee":"M. S. Dar et al., “Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling,” RSC Advances, vol. 11, no. 35. Royal Society of Chemistry, pp. 21702–21715, 2021."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"35","volume":11,"publication_status":"published","publication_identifier":{"eissn":["2046-2069"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2021-06-23T13:09:34Z","file_size":2114557,"creator":"asandaue","date_created":"2021-06-23T13:09:34Z","file_name":"2021_RSCAdvances_Dar.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"cd582d67ace7151078e46b3a896871a9","file_id":"9596","success":1}],"intvolume":" 11","month":"06","abstract":[{"lang":"eng","text":"We report the synthesis and characterization of graphene functionalized with iron (Fe3+) oxide (G-Fe3O4) nanohybrids for radio-frequency magnetic hyperthermia application. We adopted the wet chemical procedure, using various contents of Fe3O4 (magnetite) from 0–100% for making two-dimensional graphene–Fe3O4 nanohybrids. The homogeneous dispersal of Fe3O4 nanoparticles decorated on the graphene surface combined with their biocompatibility and high thermal conductivity make them an excellent material for magnetic hyperthermia. The morphological and magnetic properties of the nanohybrids were studied using scanning electron microscopy (SEM) and a vibrating sample magnetometer (VSM), respectively. The smart magnetic platforms were exposed to an alternating current (AC) magnetic field of 633 kHz and of strength 9.1 mT for studying their hyperthermic performance. The localized antitumor effects were investigated with artificial neural network modeling. A neural net time-series model was developed for the assessment of the best nanohybrid composition to serve the purpose with an accuracy close to 100%. Six Nonlinear Autoregressive with External Input (NARX) models were obtained, one for each of the components. The assessment of the accuracy of the predicted results has been done on the basis of Mean Squared Error (MSE). The highest Mean Squared Error value was obtained for the nanohybrid containing 45% magnetite and 55% graphene (F45G55) in the training phase i.e., 0.44703, which is where the model achieved optimal results after 71 epochs. The F45G55 nanohybrid was found to be the best for hyperthermia applications in low dosage with the highest specific absorption rate (SAR) and mean squared error values."}],"oa_version":"Published Version","file_date_updated":"2021-06-23T13:09:34Z","department":[{"_id":"KiMo"}],"date_updated":"2023-08-08T14:23:21Z","ddc":["540"],"tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"9569"},{"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/turbulent-flow-simplified/","relation":"press_release"}]},"volume":126,"issue":"24","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/2007.02584","open_access":"1"}],"month":"06","intvolume":" 126","abstract":[{"text":"We show that turbulent dynamics that arise in simulations of the three-dimensional Navier--Stokes equations in a triply-periodic domain under sinusoidal forcing can be described as transient visits to the neighborhoods of unstable time-periodic solutions. Based on this description, we reduce the original system with more than 10^5 degrees of freedom to a 17-node Markov chain where each node corresponds to the neighborhood of a periodic orbit. The model accurately reproduces long-term averages of the system's observables as weighted sums over the periodic orbits.\r\n","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Preprint","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"date_updated":"2023-08-08T14:08:36Z","article_type":"letter_note","type":"journal_article","status":"public","_id":"9558","date_published":"2021-06-18T00:00:00Z","doi":"10.1103/PhysRevLett.126.244502","date_created":"2021-06-16T15:45:36Z","isi":1,"year":"2021","day":"18","publication":"Physical Review Letters","publisher":"American Physical Society","quality_controlled":"1","oa":1,"acknowledgement":"We thank the referees for improving this Letter with their comments. We acknowledge stimulating discussions with\r\nH. Edelsbrunner. This work was supported by Grant No. 662960 from the Simons Foundation (B. H.). The numerical calculations were performed at TUBITAK ULAKBIM High Performance and Grid Computing Center (TRUBA resources) and IST Austria High Performance Computing cluster.","author":[{"last_name":"Yalniz","orcid":"0000-0002-8490-9312","full_name":"Yalniz, Gökhan","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","first_name":"Gökhan"},{"last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"},{"last_name":"Budanur","orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B","first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000663310100008"],"arxiv":["2007.02584"]},"title":"Coarse graining the state space of a turbulent flow using periodic orbits","citation":{"ista":"Yalniz G, Hof B, Budanur NB. 2021. Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. 126(24), 244502.","chicago":"Yalniz, Gökhan, Björn Hof, and Nazmi B Budanur. “Coarse Graining the State Space of a Turbulent Flow Using Periodic Orbits.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/PhysRevLett.126.244502.","apa":"Yalniz, G., Hof, B., & Budanur, N. B. (2021). Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.126.244502","ama":"Yalniz G, Hof B, Budanur NB. Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. 2021;126(24). doi:10.1103/PhysRevLett.126.244502","short":"G. Yalniz, B. Hof, N.B. Budanur, Physical Review Letters 126 (2021).","ieee":"G. Yalniz, B. Hof, and N. B. Budanur, “Coarse graining the state space of a turbulent flow using periodic orbits,” Physical Review Letters, vol. 126, no. 24. American Physical Society, 2021.","mla":"Yalniz, Gökhan, et al. “Coarse Graining the State Space of a Turbulent Flow Using Periodic Orbits.” Physical Review Letters, vol. 126, no. 24, 244502, American Physical Society, 2021, doi:10.1103/PhysRevLett.126.244502."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","grant_number":"662960"}],"article_number":"244502"},{"publication_status":"published","publication_identifier":{"eissn":["2050084X"]},"language":[{"iso":"eng"}],"file":[{"creator":"asandaue","date_updated":"2021-06-28T11:35:30Z","file_size":2500720,"date_created":"2021-06-28T11:35:30Z","file_name":"2021_ELife_Bespalov.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"885b746051a7a6b6e24e3d2781a48fde","file_id":"9609","success":1}],"volume":10,"abstract":[{"lang":"eng","text":"While high risk of failure is an inherent part of developing innovative therapies, it can be reduced by adherence to evidence-based rigorous research practices. Numerous analyses conducted to date have clearly identified measures that need to be taken to improve research rigor. Supported through the European Union's Innovative Medicines Initiative, the EQIPD consortium has developed a novel preclinical research quality system that can be applied in both public and private sectors and is free for anyone to use. The EQIPD Quality System was designed to be suited to boost innovation by ensuring the generation of robust and reliable preclinical data while being lean, effective and not becoming a burden that could negatively impact the freedom to explore scientific questions. EQIPD defines research quality as the extent to which research data are fit for their intended use. Fitness, in this context, is defined by the stakeholders, who are the scientists directly involved in the research, but also their funders, sponsors, publishers, research tool manufacturers and collaboration partners such as peers in a multi-site research project. The essence of the EQIPD Quality System is the set of 18 core requirements that can be addressed flexibly, according to user-specific needs and following a user-defined trajectory. The EQIPD Quality System proposes guidance on expectations for quality-related measures, defines criteria for adequate processes (i.e., performance standards) and provides examples of how such measures can be developed and implemented. However, it does not prescribe any pre-determined solutions. EQIPD has also developed tools (for optional use) to support users in implementing the system and assessment services for those research units that successfully implement the quality system and seek formal accreditation. Building upon the feedback from users and continuous improvement, a sustainable EQIPD Quality System will ultimately serve the entire community of scientists conducting non-regulated preclinical research, by helping them generate reliable data that are fit for their intended use."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 10","month":"05","date_updated":"2023-08-10T13:36:50Z","ddc":["570"],"department":[{"_id":"PreCl"}],"file_date_updated":"2021-06-28T11:35:30Z","_id":"9607","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","year":"2021","has_accepted_license":"1","isi":1,"publication":"eLife","day":"24","date_created":"2021-06-27T22:01:49Z","date_published":"2021-05-24T00:00:00Z","doi":"10.7554/eLife.63294","acknowledgement":"This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA. The authors are very grateful to Martin Heinrich (Abbvie, Ludwigshafen, Germany) for the exceptional IT support and programming the EQIPD Planning Tool and the Creator Tool and to Dr Shai Silberberg (NINDS, USA), Dr. Renza Roncarati (PAASP Italy) and Dr Judith Homberg (Radboud University, Nijmegen) for highly stimulating contributions to the discussions and comments on earlier versions of this manuscript. We also wish to express our thanks to Dr. Sara Stöber (concentris research management GmbH, Fürstenfeldbruck, Germany) for excellent and continuous support of this project. Creation of the EQIPD Stakeholder group was supported by Noldus Information Technology bv (Wageningen, the Netherlands).","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","citation":{"ama":"Bespalov A, Bernard R, Gilis A, et al. Introduction to the EQIPD quality system. eLife. 2021;10. doi:10.7554/eLife.63294","apa":"Bespalov, A., Bernard, R., Gilis, A., Gerlach, B., Guillén, J., Castagné, V., … Steckler, T. (2021). Introduction to the EQIPD quality system. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.63294","ieee":"A. Bespalov et al., “Introduction to the EQIPD quality system,” eLife, vol. 10. eLife Sciences Publications, 2021.","short":"A. Bespalov, R. Bernard, A. Gilis, B. Gerlach, J. Guillén, V. Castagné, I.A. Lefevre, F. Ducrey, L. Monk, S. Bongiovanni, B. Altevogt, M. Arroyo-Araujo, L. Bikovski, N. De Bruin, E. Castaños-Vélez, A. Dityatev, C.H. Emmerich, R. Fares, C. Ferland-Beckham, C. Froger-Colléaux, V. Gailus-Durner, S.M. Hölter, M.C. Hofmann, P. Kabitzke, M.J. Kas, C. Kurreck, P. Moser, M. Pietraszek, P. Popik, H. Potschka, E. Prado Montes De Oca, L. Restivo, G. Riedel, M. Ritskes-Hoitinga, J. Samardzic, M. Schunn, C. Stöger, V. Voikar, J. Vollert, K.E. Wever, K. Wuyts, M.R. Macleod, U. Dirnagl, T. Steckler, ELife 10 (2021).","mla":"Bespalov, Anton, et al. “Introduction to the EQIPD Quality System.” ELife, vol. 10, eLife Sciences Publications, 2021, doi:10.7554/eLife.63294.","ista":"Bespalov A, Bernard R, Gilis A, Gerlach B, Guillén J, Castagné V, Lefevre IA, Ducrey F, Monk L, Bongiovanni S, Altevogt B, Arroyo-Araujo M, Bikovski L, De Bruin N, Castaños-Vélez E, Dityatev A, Emmerich CH, Fares R, Ferland-Beckham C, Froger-Colléaux C, Gailus-Durner V, Hölter SM, Hofmann MC, Kabitzke P, Kas MJ, Kurreck C, Moser P, Pietraszek M, Popik P, Potschka H, Prado Montes De Oca E, Restivo L, Riedel G, Ritskes-Hoitinga M, Samardzic J, Schunn M, Stöger C, Voikar V, Vollert J, Wever KE, Wuyts K, Macleod MR, Dirnagl U, Steckler T. 2021. Introduction to the EQIPD quality system. eLife. 10.","chicago":"Bespalov, Anton, René Bernard, Anja Gilis, Björn Gerlach, Javier Guillén, Vincent Castagné, Isabel A. Lefevre, et al. “Introduction to the EQIPD Quality System.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.63294."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"pmid":["34028353"],"isi":["000661272000001"]},"author":[{"last_name":"Bespalov","full_name":"Bespalov, Anton","first_name":"Anton"},{"first_name":"René","last_name":"Bernard","full_name":"Bernard, René"},{"last_name":"Gilis","full_name":"Gilis, Anja","first_name":"Anja"},{"first_name":"Björn","last_name":"Gerlach","full_name":"Gerlach, Björn"},{"first_name":"Javier","last_name":"Guillén","full_name":"Guillén, Javier"},{"first_name":"Vincent","full_name":"Castagné, Vincent","last_name":"Castagné"},{"first_name":"Isabel A.","full_name":"Lefevre, Isabel A.","last_name":"Lefevre"},{"full_name":"Ducrey, Fiona","last_name":"Ducrey","first_name":"Fiona"},{"full_name":"Monk, Lee","last_name":"Monk","first_name":"Lee"},{"first_name":"Sandrine","full_name":"Bongiovanni, Sandrine","last_name":"Bongiovanni"},{"first_name":"Bruce","full_name":"Altevogt, Bruce","last_name":"Altevogt"},{"full_name":"Arroyo-Araujo, María","last_name":"Arroyo-Araujo","first_name":"María"},{"last_name":"Bikovski","full_name":"Bikovski, Lior","first_name":"Lior"},{"last_name":"De Bruin","full_name":"De Bruin, Natasja","first_name":"Natasja"},{"first_name":"Esmeralda","full_name":"Castaños-Vélez, Esmeralda","last_name":"Castaños-Vélez"},{"last_name":"Dityatev","full_name":"Dityatev, Alexander","first_name":"Alexander"},{"first_name":"Christoph H.","last_name":"Emmerich","full_name":"Emmerich, Christoph H."},{"full_name":"Fares, Raafat","last_name":"Fares","first_name":"Raafat"},{"first_name":"Chantelle","last_name":"Ferland-Beckham","full_name":"Ferland-Beckham, Chantelle"},{"full_name":"Froger-Colléaux, Christelle","last_name":"Froger-Colléaux","first_name":"Christelle"},{"full_name":"Gailus-Durner, Valerie","last_name":"Gailus-Durner","first_name":"Valerie"},{"full_name":"Hölter, Sabine M.","last_name":"Hölter","first_name":"Sabine M."},{"last_name":"Hofmann","full_name":"Hofmann, Martine Cj","first_name":"Martine Cj"},{"first_name":"Patricia","full_name":"Kabitzke, Patricia","last_name":"Kabitzke"},{"first_name":"Martien Jh","last_name":"Kas","full_name":"Kas, Martien Jh"},{"first_name":"Claudia","full_name":"Kurreck, Claudia","last_name":"Kurreck"},{"last_name":"Moser","full_name":"Moser, Paul","first_name":"Paul"},{"first_name":"Malgorzata","last_name":"Pietraszek","full_name":"Pietraszek, Malgorzata"},{"first_name":"Piotr","last_name":"Popik","full_name":"Popik, Piotr"},{"first_name":"Heidrun","last_name":"Potschka","full_name":"Potschka, Heidrun"},{"last_name":"Prado Montes De Oca","full_name":"Prado Montes De Oca, Ernesto","first_name":"Ernesto"},{"last_name":"Restivo","full_name":"Restivo, Leonardo","first_name":"Leonardo"},{"first_name":"Gernot","full_name":"Riedel, Gernot","last_name":"Riedel"},{"last_name":"Ritskes-Hoitinga","full_name":"Ritskes-Hoitinga, Merel","first_name":"Merel"},{"full_name":"Samardzic, Janko","last_name":"Samardzic","first_name":"Janko"},{"id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","full_name":"Schunn, Michael","orcid":"0000-0003-4326-5300","last_name":"Schunn"},{"full_name":"Stöger, Claudia","last_name":"Stöger","first_name":"Claudia"},{"first_name":"Vootele","full_name":"Voikar, Vootele","last_name":"Voikar"},{"first_name":"Jan","last_name":"Vollert","full_name":"Vollert, Jan"},{"full_name":"Wever, Kimberley E.","last_name":"Wever","first_name":"Kimberley E."},{"first_name":"Kathleen","last_name":"Wuyts","full_name":"Wuyts, Kathleen"},{"first_name":"Malcolm R.","last_name":"Macleod","full_name":"Macleod, Malcolm R."},{"full_name":"Dirnagl, Ulrich","last_name":"Dirnagl","first_name":"Ulrich"},{"full_name":"Steckler, Thomas","last_name":"Steckler","first_name":"Thomas"}],"title":"Introduction to the EQIPD quality system"},{"citation":{"chicago":"Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Xiaoyan Ma, Julia Ramesmayer, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23510-4.","ista":"Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ma X, Ramesmayer J, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. 2021. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. 12(1), 3804.","mla":"Santini, Laura, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” Nature Communications, vol. 12, no. 1, 3804, Springer Nature, 2021, doi:10.1038/s41467-021-23510-4.","apa":"Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ma, X., … Leeb, M. (2021). Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23510-4","ama":"Santini L, Halbritter F, Titz-Teixeira F, et al. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23510-4","ieee":"L. Santini et al., “Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","short":"L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, X. Ma, J. Ramesmayer, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, Nature Communications 12 (2021)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000667248600005"]},"author":[{"first_name":"Laura","last_name":"Santini","full_name":"Santini, Laura"},{"full_name":"Halbritter, Florian","last_name":"Halbritter","first_name":"Florian"},{"last_name":"Titz-Teixeira","full_name":"Titz-Teixeira, Fabian","first_name":"Fabian"},{"last_name":"Suzuki","full_name":"Suzuki, Toru","first_name":"Toru"},{"first_name":"Maki","last_name":"Asami","full_name":"Asami, Maki"},{"last_name":"Ma","full_name":"Ma, Xiaoyan","first_name":"Xiaoyan"},{"full_name":"Ramesmayer, Julia","last_name":"Ramesmayer","first_name":"Julia"},{"last_name":"Lackner","full_name":"Lackner, Andreas","first_name":"Andreas"},{"first_name":"Nick","last_name":"Warr","full_name":"Warr, Nick"},{"first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"},{"first_name":"Ernest","full_name":"Laue, Ernest","last_name":"Laue"},{"first_name":"Matthias","full_name":"Farlik, Matthias","last_name":"Farlik"},{"first_name":"Christoph","last_name":"Bock","full_name":"Bock, Christoph"},{"first_name":"Andreas","full_name":"Beyer, Andreas","last_name":"Beyer"},{"full_name":"Perry, Anthony C.F.","last_name":"Perry","first_name":"Anthony C.F."},{"full_name":"Leeb, Martin","last_name":"Leeb","first_name":"Martin"}],"title":"Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3","article_number":"3804","year":"2021","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"12","date_created":"2021-06-27T22:01:46Z","date_published":"2021-07-12T00:00:00Z","doi":"10.1038/s41467-021-23510-4","acknowledgement":"The authors thank Robert Feil and Anton Wutz for helpful discussions and comments, Samuel Collombet and Peter Fraser for sharing embryo TAD coordinates, and Andy Riddel at the Cambridge Stem Cell Institute and Thomas Sauer at the Max Perutz Laboratories FACS facility for flow-sorting. We thank the team of the Biomedical Sequencing Facility at the CeMM and the Vienna Biocenter Core Facilities (VBCF) for support with next-generation sequencing. We are grateful to animal care teams at the University of Bath and MRC Harwell. A.C.F.P. acknowledges support from the UK Medical Research Council (MR/N000080/1 and MR/N020294/1) and Biotechnology and Biological Sciences Research Council (BB/P009506/1). L.S. is part of the FWF doctoral programme SMICH and supported by an Austrian Academy of Sciences DOC Fellowship. M.L. is funded by a Vienna Research Group for Young Investigators grant (VRG14-006) by the Vienna Science and Technology Fund (WWTF) and by the Austrian Science Fund FWF (I3786 and P31334).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","date_updated":"2023-08-10T13:53:23Z","ddc":["570"],"file_date_updated":"2021-06-28T08:04:22Z","department":[{"_id":"SiHi"}],"_id":"9601","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"eissn":["20411723"]},"language":[{"iso":"eng"}],"file":[{"file_size":2156554,"date_updated":"2021-06-28T08:04:22Z","creator":"asandaue","file_name":"2021_NatureCommunications_Santini.pdf","date_created":"2021-06-28T08:04:22Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9608","checksum":"75dd89d09945185b2d14b2434a0bcb50"}],"volume":12,"issue":"1","abstract":[{"lang":"eng","text":"In mammalian genomes, differentially methylated regions (DMRs) and histone marks including trimethylation of histone 3 lysine 27 (H3K27me3) at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. However, neither parent-of-origin-specific transcription nor imprints have been comprehensively mapped at the blastocyst stage of preimplantation development. Here, we address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos. We find that seventy-one genes exhibit previously unreported parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expressed). Uniparental expression of nBiX genes disappears soon after implantation. Micro-whole-genome bisulfite sequencing (µWGBS) of individual uniparental blastocysts detects 859 DMRs. We further find that 16% of nBiX genes are associated with a DMR, whereas most are associated with parentally-biased H3K27me3, suggesting a role for Polycomb-mediated imprinting in blastocysts. nBiX genes are clustered: five clusters contained at least one published imprinted gene, and five clusters exclusively contained nBiX genes. These data suggest that early development undergoes a complex program of stage-specific imprinting involving different tiers of regulation."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 12","month":"07"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"An ordered graph is a graph with a linear ordering on its vertex set. We prove that for every positive integer k, there exists a constant ck > 0 such that any ordered graph G on n vertices with the property that neither G nor its complement contains an induced monotone path of size k, has either a clique or an independent set of size at least n^ck . This strengthens a result of Bousquet, Lagoutte, and Thomassé, who proved the analogous result for unordered graphs.\r\nA key idea of the above paper was to show that any unordered graph on n vertices that does not contain an induced path of size k, and whose maximum degree is at most c(k)n for some small c(k) > 0, contains two disjoint linear size subsets with no edge between them. This approach fails for ordered graphs, because the analogous statement is false for k ≥ 3, by a construction of Fox. We provide some further examples showing that this statement also fails for ordered graphs avoiding other ordered trees."}],"intvolume":" 151","month":"06","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"15fbc9064cd9d1c777ac0043b78c8f12","file_id":"9612","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_JournalOfCombinatorialTheory_Pach.pdf","date_created":"2021-06-28T13:33:23Z","creator":"asandaue","file_size":418168,"date_updated":"2021-06-28T13:33:23Z"}],"publication_status":"published","publication_identifier":{"issn":["0095-8956"]},"volume":151,"_id":"9602","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["510"],"date_updated":"2023-08-10T13:38:00Z","file_date_updated":"2021-06-28T13:33:23Z","department":[{"_id":"HeEd"}],"acknowledgement":"We would like to thank the anonymous referees for their useful comments and suggestions. János Pach is partially supported by Austrian Science Fund (FWF) grant Z 342-N31 and by ERC Advanced grant “GeoScape.” István Tomon is partially supported by Swiss National Science Foundation grant no. 200021_196965, and thanks the support of MIPT Moscow. Both authors are partially supported by The Russian Government in the framework of MegaGrant no. 075-15-2019-1926.","oa":1,"publisher":"Elsevier","quality_controlled":"1","publication":"Journal of Combinatorial Theory. Series B","day":"09","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-06-27T22:01:47Z","date_published":"2021-06-09T00:00:00Z","doi":"10.1016/j.jctb.2021.05.004","page":"21-37","project":[{"_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z00342"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Pach, J., & Tomon, I. (2021). Erdős-Hajnal-type results for monotone paths. Journal of Combinatorial Theory. Series B. Elsevier. https://doi.org/10.1016/j.jctb.2021.05.004","ama":"Pach J, Tomon I. Erdős-Hajnal-type results for monotone paths. Journal of Combinatorial Theory Series B. 2021;151:21-37. doi:10.1016/j.jctb.2021.05.004","short":"J. Pach, I. Tomon, Journal of Combinatorial Theory. Series B 151 (2021) 21–37.","ieee":"J. Pach and I. Tomon, “Erdős-Hajnal-type results for monotone paths,” Journal of Combinatorial Theory. Series B, vol. 151. Elsevier, pp. 21–37, 2021.","mla":"Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone Paths.” Journal of Combinatorial Theory. Series B, vol. 151, Elsevier, 2021, pp. 21–37, doi:10.1016/j.jctb.2021.05.004.","ista":"Pach J, Tomon I. 2021. Erdős-Hajnal-type results for monotone paths. Journal of Combinatorial Theory. Series B. 151, 21–37.","chicago":"Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone Paths.” Journal of Combinatorial Theory. Series B. Elsevier, 2021. https://doi.org/10.1016/j.jctb.2021.05.004."},"title":"Erdős-Hajnal-type results for monotone paths","article_processing_charge":"No","external_id":{"isi":["000702280800002"]},"author":[{"id":"E62E3130-B088-11EA-B919-BF823C25FEA4","first_name":"János","full_name":"Pach, János","last_name":"Pach"},{"full_name":"Tomon, István","last_name":"Tomon","first_name":"István"}]},{"month":"06","intvolume":" 103","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2009.06491"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Sound propagation is a macroscopic manifestation of the interplay between the equilibrium thermodynamics and the dynamical transport properties of fluids. Here, for a two-dimensional system of ultracold fermions, we calculate the first and second sound velocities across the whole BCS-BEC crossover, and we analyze the system response to an external perturbation. In the low-temperature regime we reproduce the recent measurements [Phys. Rev. Lett. 124, 240403 (2020)] of the first sound velocity, which, due to the decoupling of density and entropy fluctuations, is the sole mode excited by a density probe. Conversely, a heat perturbation excites only the second sound, which, being sensitive to the superfluid depletion, vanishes in the deep BCS regime and jumps discontinuously to zero at the Berezinskii-Kosterlitz-Thouless superfluid transition. A mixing between the modes occurs only in the finite-temperature BEC regime, where our theory converges to the purely bosonic results."}],"volume":103,"issue":"6","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["24699934"],"issn":["24699926"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"letter_note","_id":"9606","department":[{"_id":"MiLe"}],"date_updated":"2023-08-10T13:37:25Z","publisher":"American Physical Society","quality_controlled":"1","oa":1,"acknowledgement":"G.B. acknowledges support from the Austrian Science Fund (FWF), under Project No. M2641-N27. This work was\r\npartially supported by the University of Padua, BIRD project “Superfluid properties of Fermi gases in optical potentials.”\r\nThe authors thank Miki Ota, Tomoki Ozawa, Sandro Stringari, Tilman Enss, Hauke Biss, Henning Moritz, and Nicolò Defenu for fruitful discussions. The authors thank Henning Moritz and Markus Bohlen for providing their experimental\r\ndata.","doi":"10.1103/PhysRevA.103.L061303","date_published":"2021-06-01T00:00:00Z","date_created":"2021-06-27T22:01:49Z","day":"01","publication":"Physical Review A","isi":1,"year":"2021","article_number":"L061303","title":"Propagation of first and second sound in a two-dimensional Fermi superfluid","author":[{"last_name":"Tononi","full_name":"Tononi, A.","first_name":"A."},{"first_name":"Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","last_name":"Cappellaro","orcid":"0000-0001-6110-2359","full_name":"Cappellaro, Alberto"},{"id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo","last_name":"Bighin"},{"first_name":"L.","full_name":"Salasnich, L.","last_name":"Salasnich"}],"article_processing_charge":"No","external_id":{"isi":["000662296700014"],"arxiv":["2009.06491"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Tononi, A., Cappellaro, A., Bighin, G., & Salasnich, L. (2021). Propagation of first and second sound in a two-dimensional Fermi superfluid. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.103.L061303","ama":"Tononi A, Cappellaro A, Bighin G, Salasnich L. Propagation of first and second sound in a two-dimensional Fermi superfluid. Physical Review A. 2021;103(6). doi:10.1103/PhysRevA.103.L061303","short":"A. Tononi, A. Cappellaro, G. Bighin, L. Salasnich, Physical Review A 103 (2021).","ieee":"A. Tononi, A. Cappellaro, G. Bighin, and L. Salasnich, “Propagation of first and second sound in a two-dimensional Fermi superfluid,” Physical Review A, vol. 103, no. 6. American Physical Society, 2021.","mla":"Tononi, A., et al. “Propagation of First and Second Sound in a Two-Dimensional Fermi Superfluid.” Physical Review A, vol. 103, no. 6, L061303, American Physical Society, 2021, doi:10.1103/PhysRevA.103.L061303.","ista":"Tononi A, Cappellaro A, Bighin G, Salasnich L. 2021. Propagation of first and second sound in a two-dimensional Fermi superfluid. Physical Review A. 103(6), L061303.","chicago":"Tononi, A., Alberto Cappellaro, Giacomo Bighin, and L. Salasnich. “Propagation of First and Second Sound in a Two-Dimensional Fermi Superfluid.” Physical Review A. American Physical Society, 2021. https://doi.org/10.1103/PhysRevA.103.L061303."}},{"oa":1,"quality_controlled":"1","publisher":"Elsevier","acknowledgement":"We thank the scientific service units at IST Austria, especially the IST bioimaging facility, the preclinical facility, and, specifically, Michael Schunn and Sonja Haslinger for excellent support; Plexxikon for the PLX food; the Csicsvari group for advice and equipment for in vivo recording; Jürgen Siegert for the light-entrainment design; Marco Benevento, Soledad Gonzalo Cogno, Pat King, and all Siegert group members for constant feedback on the project and manuscript; Lorena Pantano (PILM Bioinformatics Core) for assisting with sample-size determination for OD plasticity experiments; and Ana Morello from MIT for technical assistance with VEPs recordings. This research was supported by a DOC Fellowship from the Austrian Academy of Sciences at the Institute of Science and Technology Austria to R.S., from the European Union Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Actions program (grants 665385 to G.C.; 754411 to R.J.A.C.), the European Research Council (grant 715571 to S.S.), and the National Eye Institute of the National Institutes of Health under award numbers R01EY029245 (to M.F.B.) and R01EY023037 (diversity supplement to H.D.J-C.).","date_created":"2021-07-11T22:01:16Z","doi":"10.1016/j.celrep.2021.109313","date_published":"2021-07-06T00:00:00Z","publication":"Cell Reports","day":"06","year":"2021","isi":1,"has_accepted_license":"1","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"name":"Microglia action towards neuronal circuit formation and function in health and disease","grant_number":"715571","call_identifier":"H2020","_id":"25D4A630-B435-11E9-9278-68D0E5697425"}],"article_number":"109313","title":"Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain","article_processing_charge":"No","external_id":{"isi":["000670188500004"],"pmid":["34233180"]},"author":[{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","first_name":"Alessandro","last_name":"Venturino","orcid":"0000-0003-2356-9403","full_name":"Venturino, Alessandro"},{"last_name":"Schulz","full_name":"Schulz, Rouven","orcid":"0000-0001-5297-733X","first_name":"Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87"},{"last_name":"De Jesús-Cortés","full_name":"De Jesús-Cortés, Héctor","first_name":"Héctor"},{"id":"3838F452-F248-11E8-B48F-1D18A9856A87","first_name":"Margaret E","full_name":"Maes, Margaret E","orcid":"0000-0001-9642-1085","last_name":"Maes"},{"full_name":"Nagy, Balint","last_name":"Nagy","id":"93C65ECC-A6F2-11E9-8DF9-9712E6697425","first_name":"Balint"},{"full_name":"Reilly-Andújar, Francis","last_name":"Reilly-Andújar","first_name":"Francis"},{"first_name":"Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","full_name":"Colombo, Gloria","orcid":"0000-0001-9434-8902","last_name":"Colombo"},{"first_name":"Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425","full_name":"Cubero, Ryan J","orcid":"0000-0003-0002-1867","last_name":"Cubero"},{"id":"3526230C-F248-11E8-B48F-1D18A9856A87","first_name":"Florianne E","full_name":"Schoot Uiterkamp, Florianne E","last_name":"Schoot Uiterkamp"},{"full_name":"Bear, Mark F.","last_name":"Bear","first_name":"Mark F."},{"first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Venturino, Alessandro, Rouven Schulz, Héctor De Jesús-Cortés, Margaret E Maes, Balint Nagy, Francis Reilly-Andújar, Gloria Colombo, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” Cell Reports. Elsevier, 2021. https://doi.org/10.1016/j.celrep.2021.109313.","ista":"Venturino A, Schulz R, De Jesús-Cortés H, Maes ME, Nagy B, Reilly-Andújar F, Colombo G, Cubero RJ, Schoot Uiterkamp FE, Bear MF, Siegert S. 2021. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. 36(1), 109313.","mla":"Venturino, Alessandro, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” Cell Reports, vol. 36, no. 1, 109313, Elsevier, 2021, doi:10.1016/j.celrep.2021.109313.","apa":"Venturino, A., Schulz, R., De Jesús-Cortés, H., Maes, M. E., Nagy, B., Reilly-Andújar, F., … Siegert, S. (2021). Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2021.109313","ama":"Venturino A, Schulz R, De Jesús-Cortés H, et al. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. 2021;36(1). doi:10.1016/j.celrep.2021.109313","ieee":"A. Venturino et al., “Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain,” Cell Reports, vol. 36, no. 1. Elsevier, 2021.","short":"A. Venturino, R. Schulz, H. De Jesús-Cortés, M.E. Maes, B. Nagy, F. Reilly-Andújar, G. Colombo, R.J. Cubero, F.E. Schoot Uiterkamp, M.F. Bear, S. Siegert, Cell Reports 36 (2021)."},"intvolume":" 36","month":"07","scopus_import":"1","pmid":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"abstract":[{"lang":"eng","text":"Perineuronal nets (PNNs), components of the extracellular matrix, preferentially coat parvalbumin-positive interneurons and constrain critical-period plasticity in the adult cerebral cortex. Current strategies to remove PNN are long-lasting, invasive, and trigger neuropsychiatric symptoms. Here, we apply repeated anesthetic ketamine as a method with minimal behavioral effect. We find that this paradigm strongly reduces PNN coating in the healthy adult brain and promotes juvenile-like plasticity. Microglia are critically involved in PNN loss because they engage with parvalbumin-positive neurons in their defined cortical layer. We identify external 60-Hz light-flickering entrainment to recapitulate microglia-mediated PNN removal. Importantly, 40-Hz frequency, which is known to remove amyloid plaques, does not induce PNN loss, suggesting microglia might functionally tune to distinct brain frequencies. Thus, our 60-Hz light-entrainment strategy provides an alternative form of PNN intervention in the healthy adult brain."}],"ec_funded":1,"issue":"1","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/the-twinkle-and-the-brain/"}]},"volume":36,"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"f056255f6d01fd9a86b5387635928173","file_id":"9693","creator":"cziletti","file_size":56388540,"date_updated":"2021-07-19T13:32:17Z","file_name":"2021_CellReports_Venturino.pdf","date_created":"2021-07-19T13:32:17Z"}],"publication_status":"published","publication_identifier":{"eissn":["22111247"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"9642","department":[{"_id":"SaSi"}],"file_date_updated":"2021-07-19T13:32:17Z","ddc":["570"],"date_updated":"2023-08-10T14:09:39Z"},{"year":"2021","has_accepted_license":"1","isi":1,"publication":"Cell Reports","day":"22","date_created":"2021-06-27T22:01:48Z","date_published":"2021-06-22T00:00:00Z","doi":"10.1016/j.celrep.2021.109274","acknowledgement":"We thank the Bioimaging, Life Science, and Pre-Clinical Facilities at IST Austria; M.P. Postiglione, C. Simbriger, K. Valoskova, C. Schwayer, T. Hussain, M. Pieber, and V. Wimmer for initial experiments, technical support, and/or assistance; R. Shigemoto for sharing iv (Dnah11 mutant) mice; and M. Sixt and all members of the Hippenmeyer lab for discussion. This work was supported by National Institutes of Health grants ( R01-NS050580 to L.L. and F32MH096361 to L.A.S.). L.L. is an investigator of HHMI. N.A. received support from FWF Firnberg-Programm ( T 1031 ). A.H.H. is a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences . This work also received support from IST Austria institutional funds , FWF SFB F78 to S.H., the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme ( FP7/2007-2013 ) under REA grant agreement no 618444 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.","oa":1,"quality_controlled":"1","publisher":"Cell Press","citation":{"ama":"Contreras X, Amberg N, Davaatseren A, et al. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. 2021;35(12). doi:10.1016/j.celrep.2021.109274","apa":"Contreras, X., Amberg, N., Davaatseren, A., Hansen, A. H., Sonntag, J., Andersen, L., … Hippenmeyer, S. (2021). A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2021.109274","ieee":"X. Contreras et al., “A genome-wide library of MADM mice for single-cell genetic mosaic analysis,” Cell Reports, vol. 35, no. 12. Cell Press, 2021.","short":"X. Contreras, N. Amberg, A. Davaatseren, A.H. Hansen, J. Sonntag, L. Andersen, T. Bernthaler, C. Streicher, A.-M. Heger, R.L. Johnson, L.A. Schwarz, L. Luo, T. Rülicke, S. Hippenmeyer, Cell Reports 35 (2021).","mla":"Contreras, Ximena, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” Cell Reports, vol. 35, no. 12, 109274, Cell Press, 2021, doi:10.1016/j.celrep.2021.109274.","ista":"Contreras X, Amberg N, Davaatseren A, Hansen AH, Sonntag J, Andersen L, Bernthaler T, Streicher C, Heger A-M, Johnson RL, Schwarz LA, Luo L, Rülicke T, Hippenmeyer S. 2021. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. 35(12), 109274.","chicago":"Contreras, Ximena, Nicole Amberg, Amarbayasgalan Davaatseren, Andi H Hansen, Johanna Sonntag, Lill Andersen, Tina Bernthaler, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” Cell Reports. Cell Press, 2021. https://doi.org/10.1016/j.celrep.2021.109274."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000664463600016"]},"article_processing_charge":"No","author":[{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","full_name":"Contreras, Ximena","last_name":"Contreras"},{"last_name":"Amberg","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole"},{"first_name":"Amarbayasgalan","id":"70ADC922-B424-11E9-99E3-BA18E6697425","full_name":"Davaatseren, Amarbayasgalan","last_name":"Davaatseren"},{"last_name":"Hansen","full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H"},{"last_name":"Sonntag","full_name":"Sonntag, Johanna","first_name":"Johanna","id":"32FE7D7C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lill","last_name":"Andersen","full_name":"Andersen, Lill"},{"full_name":"Bernthaler, Tina","last_name":"Bernthaler","first_name":"Tina"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher","full_name":"Streicher, Carmen"},{"last_name":"Heger","full_name":"Heger, Anna-Magdalena","id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87","first_name":"Anna-Magdalena"},{"first_name":"Randy L.","last_name":"Johnson","full_name":"Johnson, Randy L."},{"full_name":"Schwarz, Lindsay A.","last_name":"Schwarz","first_name":"Lindsay A."},{"full_name":"Luo, Liqun","last_name":"Luo","first_name":"Liqun"},{"full_name":"Rülicke, Thomas","last_name":"Rülicke","first_name":"Thomas"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"}],"title":"A genome-wide library of MADM mice for single-cell genetic mosaic analysis","article_number":"109274","project":[{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812"},{"name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444","call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"}],"publication_status":"published","publication_identifier":{"eissn":["22111247"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9613","checksum":"d49520fdcbbb5c2f883bddb67cee5d77","success":1,"creator":"asandaue","date_updated":"2021-06-28T14:06:24Z","file_size":7653149,"date_created":"2021-06-28T14:06:24Z","file_name":"2021_CellReports_Contreras.pdf"}],"ec_funded":1,"volume":35,"issue":"12","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/boost-for-mouse-genetic-analysis/","relation":"press_release"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"abstract":[{"text":"Mosaic analysis with double markers (MADM) offers one approach to visualize and concomitantly manipulate genetically defined cells in mice with single-cell resolution. MADM applications include the analysis of lineage, single-cell morphology and physiology, genomic imprinting phenotypes, and dissection of cell-autonomous gene functions in vivo in health and disease. Yet, MADM can only be applied to <25% of all mouse genes on select chromosomes to date. To overcome this limitation, we generate transgenic mice with knocked-in MADM cassettes near the centromeres of all 19 autosomes and validate their use across organs. With this resource, >96% of the entire mouse genome can now be subjected to single-cell genetic mosaic analysis. Beyond a proof of principle, we apply our MADM library to systematically trace sister chromatid segregation in distinct mitotic cell lineages. We find striking chromosome-specific biases in segregation patterns, reflecting a putative mechanism for the asymmetric segregation of genetic determinants in somatic stem cell division.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 35","month":"06","date_updated":"2023-08-10T13:55:00Z","ddc":["570"],"department":[{"_id":"SiHi"},{"_id":"LoSw"},{"_id":"PreCl"}],"file_date_updated":"2021-06-28T14:06:24Z","_id":"9603","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","status":"public"},{"scopus_import":"1","month":"03","intvolume":" 371","abstract":[{"text":"The control of nonequilibrium quantum dynamics in many-body systems is challenging because interactions typically lead to thermalization and a chaotic spreading throughout Hilbert space. We investigate nonequilibrium dynamics after rapid quenches in a many-body system composed of 3 to 200 strongly interacting qubits in one and two spatial dimensions. Using a programmable quantum simulator based on Rydberg atom arrays, we show that coherent revivals associated with so-called quantum many-body scars can be stabilized by periodic driving, which generates a robust subharmonic response akin to discrete time-crystalline order. We map Hilbert space dynamics, geometry dependence, phase diagrams, and system-size dependence of this emergent phenomenon, demonstrating new ways to steer complex dynamics in many-body systems and enabling potential applications in quantum information science.","lang":"eng"}],"oa_version":"Preprint","pmid":1,"issue":"6536","volume":371,"ec_funded":1,"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"publication_status":"published","file":[{"date_created":"2021-09-23T14:00:05Z","file_name":"scars_subharmonic_combined_manuscript_2_11_2021 (2)-1.pdf","creator":"patrickd","date_updated":"2021-09-23T14:00:05Z","file_size":3671159,"checksum":"0b356fd10ab9bb95177d4c047d4e9c1a","file_id":"10040","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","keyword":["Multidisciplinary"],"_id":"9618","file_date_updated":"2021-09-23T14:00:05Z","department":[{"_id":"MaSe"}],"date_updated":"2023-08-10T13:57:07Z","ddc":["539"],"quality_controlled":"1","publisher":"AAAS","oa":1,"acknowledgement":"We thank many members of the Harvard AMO community, particularly E. Urbach, S. Dakoulas, and J. Doyle for their efforts enabling safe and productive operation of our laboratories during 2020. We thank D. Abanin, I. Cong, F. Machado, H. Pichler, N. Yao, B. Ye, and H. Zhou for stimulating discussions. Funding: We acknowledge financial support from the Center for Ultracold Atoms, the National Science Foundation, the Vannevar Bush Faculty Fellowship, the U.S. Department of Energy (LBNL QSA Center and grant no. DE-SC0021013), the Office of Naval Research, the Army Research Office MURI, the DARPA DRINQS program (grant no. D18AC00033), and the DARPA ONISQ program (grant no. W911NF2010021). The authors acknowledge support from the NSF Graduate Research Fellowship Program (grant DGE1745303) and The Fannie and John Hertz Foundation (D.B.); a National Defense Science and Engineering Graduate (NDSEG) fellowship (H.L.); a fellowship from the Max Planck/Harvard Research Center for Quantum Optics (G.S.); Gordon College (T.T.W.); the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 850899) (A.A.M. and M.S.); a Department of Energy Computational Science Graduate Fellowship under award number DE-SC0021110 (N.M.); the Moore Foundation’s EPiQS Initiative grant no. GBMF4306, the NUS Development grant AY2019/2020, and the Stanford Institute of Theoretical Physics (W.W.H.); and the Miller Institute for Basic Research in Science (S.C.). Author contributions: D.B., A.O., H.L., A.K., G.S., S.E., and T.T.W. contributed to the building of the experimental setup, performed the measurements, and analyzed the data. A.A.M., N.M., W.W.H., S.C., and M.S. performed theoretical analysis. All work was supervised by M.G., V.V., and M.D.L. All authors discussed the results and contributed to the manuscript. Competing interests: M.G., V.V., and M.D.L. are co-founders and shareholders of QuEra Computing. A.O. is a shareholder of QuEra Computing. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and the supplementary materials.","page":"1355-1359","date_published":"2021-03-26T00:00:00Z","doi":"10.1126/science.abg2530","date_created":"2021-06-29T12:04:05Z","has_accepted_license":"1","isi":1,"year":"2021","day":"26","publication":"Science","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"author":[{"full_name":"Bluvstein, D.","last_name":"Bluvstein","first_name":"D."},{"first_name":"A.","full_name":"Omran, A.","last_name":"Omran"},{"full_name":"Levine, H.","last_name":"Levine","first_name":"H."},{"first_name":"A.","full_name":"Keesling, A.","last_name":"Keesling"},{"last_name":"Semeghini","full_name":"Semeghini, G.","first_name":"G."},{"full_name":"Ebadi, S.","last_name":"Ebadi","first_name":"S."},{"full_name":"Wang, T. T.","last_name":"Wang","first_name":"T. T."},{"orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios","last_name":"Michailidis","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","first_name":"Alexios"},{"first_name":"N.","full_name":"Maskara, N.","last_name":"Maskara"},{"first_name":"W. W.","last_name":"Ho","full_name":"Ho, W. W."},{"last_name":"Choi","full_name":"Choi, S.","first_name":"S."},{"last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"},{"first_name":"M.","full_name":"Greiner, M.","last_name":"Greiner"},{"last_name":"Vuletić","full_name":"Vuletić, V.","first_name":"V."},{"last_name":"Lukin","full_name":"Lukin, M. D.","first_name":"M. D."}],"external_id":{"arxiv":["2012.12276"],"isi":["000636043400048"],"pmid":["33632894"]},"article_processing_charge":"No","title":"Controlling quantum many-body dynamics in driven Rydberg atom arrays","citation":{"chicago":"Bluvstein, D., A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi, T. T. Wang, et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg Atom Arrays.” Science. AAAS, 2021. https://doi.org/10.1126/science.abg2530.","ista":"Bluvstein D, Omran A, Levine H, Keesling A, Semeghini G, Ebadi S, Wang TT, Michailidis A, Maskara N, Ho WW, Choi S, Serbyn M, Greiner M, Vuletić V, Lukin MD. 2021. Controlling quantum many-body dynamics in driven Rydberg atom arrays. Science. 371(6536), 1355–1359.","mla":"Bluvstein, D., et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg Atom Arrays.” Science, vol. 371, no. 6536, AAAS, 2021, pp. 1355–59, doi:10.1126/science.abg2530.","short":"D. Bluvstein, A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi, T.T. Wang, A. Michailidis, N. Maskara, W.W. Ho, S. Choi, M. Serbyn, M. Greiner, V. Vuletić, M.D. Lukin, Science 371 (2021) 1355–1359.","ieee":"D. Bluvstein et al., “Controlling quantum many-body dynamics in driven Rydberg atom arrays,” Science, vol. 371, no. 6536. AAAS, pp. 1355–1359, 2021.","apa":"Bluvstein, D., Omran, A., Levine, H., Keesling, A., Semeghini, G., Ebadi, S., … Lukin, M. D. (2021). Controlling quantum many-body dynamics in driven Rydberg atom arrays. Science. AAAS. https://doi.org/10.1126/science.abg2530","ama":"Bluvstein D, Omran A, Levine H, et al. Controlling quantum many-body dynamics in driven Rydberg atom arrays. Science. 2021;371(6536):1355-1359. doi:10.1126/science.abg2530"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"quality_controlled":"1","publisher":"American Society of Plant Biologists","oa":1,"page":"2981–3003","doi":"10.1093/plcell/koab183","date_published":"2021-07-07T00:00:00Z","date_created":"2021-07-14T15:32:43Z","has_accepted_license":"1","isi":1,"year":"2021","day":"07","publication":"Plant Cell","author":[{"first_name":"Z","full_name":"Gao, Z","last_name":"Gao"},{"first_name":"Z","last_name":"Chen","full_name":"Chen, Z"},{"full_name":"Cui, Y","last_name":"Cui","first_name":"Y"},{"last_name":"Ke","full_name":"Ke, M","first_name":"M"},{"first_name":"H","full_name":"Xu, H","last_name":"Xu"},{"last_name":"Xu","full_name":"Xu, Q","first_name":"Q"},{"last_name":"Chen","full_name":"Chen, J","first_name":"J"},{"full_name":"Li, Y","last_name":"Li","first_name":"Y"},{"first_name":"L","full_name":"Huang, L","last_name":"Huang"},{"full_name":"Zhao, H","last_name":"Zhao","first_name":"H"},{"first_name":"D","last_name":"Huang","full_name":"Huang, D"},{"last_name":"Mai","full_name":"Mai, S","first_name":"S"},{"last_name":"Xu","full_name":"Xu, T","first_name":"T"},{"full_name":"Liu, X","last_name":"Liu","first_name":"X"},{"last_name":"Li","full_name":"Li, S","first_name":"S"},{"last_name":"Guan","full_name":"Guan, Y","first_name":"Y"},{"last_name":"Yang","full_name":"Yang, W","first_name":"W"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"first_name":"J","full_name":"Petrášek, J","last_name":"Petrášek"},{"first_name":"J","full_name":"Zhang, J","last_name":"Zhang"},{"full_name":"Chen, X","last_name":"Chen","first_name":"X"}],"article_processing_charge":"No","external_id":{"pmid":["34240197"],"isi":["000702165300012"]},"title":"GmPIN-dependent polar auxin transport is involved in soybean nodule development","citation":{"chicago":"Gao, Z, Z Chen, Y Cui, M Ke, H Xu, Q Xu, J Chen, et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” Plant Cell. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab183.","ista":"Gao Z, Chen Z, Cui Y, Ke M, Xu H, Xu Q, Chen J, Li Y, Huang L, Zhao H, Huang D, Mai S, Xu T, Liu X, Li S, Guan Y, Yang W, Friml J, Petrášek J, Zhang J, Chen X. 2021. GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. 33(9), 2981–3003.","mla":"Gao, Z., et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” Plant Cell, vol. 33, no. 9, American Society of Plant Biologists, 2021, pp. 2981–3003, doi:10.1093/plcell/koab183.","ieee":"Z. Gao et al., “GmPIN-dependent polar auxin transport is involved in soybean nodule development,” Plant Cell, vol. 33, no. 9. American Society of Plant Biologists, pp. 2981–3003, 2021.","short":"Z. Gao, Z. Chen, Y. Cui, M. Ke, H. Xu, Q. Xu, J. Chen, Y. Li, L. Huang, H. Zhao, D. Huang, S. Mai, T. Xu, X. Liu, S. Li, Y. Guan, W. Yang, J. Friml, J. Petrášek, J. Zhang, X. Chen, Plant Cell 33 (2021) 2981–3003.","apa":"Gao, Z., Chen, Z., Cui, Y., Ke, M., Xu, H., Xu, Q., … Chen, X. (2021). GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab183","ama":"Gao Z, Chen Z, Cui Y, et al. GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. 2021;33(9):2981–3003. doi:10.1093/plcell/koab183"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"07","intvolume":" 33","abstract":[{"lang":"eng","text":"To overcome nitrogen deficiency, legume roots establish symbiotic interactions with nitrogen-fixing rhizobia that is fostered in specialized organs (nodules). Similar to other organs, nodule formation is determined by a local maximum of the phytohormone auxin at the primordium site. However, how auxin regulates nodule development remains poorly understood. Here, we found that in soybean, (Glycine max), dynamic auxin transport driven by PIN-FORMED (PIN) transporter GmPIN1 is involved in nodule primordium formation. GmPIN1 was specifically expressed in nodule primordium cells and GmPIN1 was polarly localized in these cells. Two nodulation regulators, (iso)flavonoids trigger expanded distribution of GmPIN1b to root cortical cells, and cytokinin rearranges GmPIN1b polarity. Gmpin1abc triple mutants generated with CRISPR-Cas9 showed impaired establishment of auxin maxima in nodule meristems and aberrant divisions in the nodule primordium cells. Moreover, overexpression of GmPIN1 suppressed nodule primordium initiation. GmPIN9d, an ortholog of Arabidopsis thaliana PIN2, acts together with GmPIN1 later in nodule development to acropetally transport auxin in vascular bundles, fine-tuning the auxin supply for nodule enlargement. Our findings reveal how PIN-dependent auxin transport modulates different aspects of soybean nodule development and suggest that establishment of auxin gradient is a prerequisite for the proper interaction between legumes and rhizobia."}],"pmid":1,"oa_version":"Published Version","volume":33,"issue":"9","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298x"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"6715712ec306c321f0204c817b7f8ae7","file_id":"9691","file_size":10566921,"date_updated":"2021-07-19T12:13:34Z","creator":"cziletti","file_name":"2021_PlantCell_Gao.pdf","date_created":"2021-07-19T12:13:34Z"}],"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"9657","department":[{"_id":"JiFr"}],"file_date_updated":"2021-07-19T12:13:34Z","date_updated":"2023-08-10T14:01:41Z","ddc":["580"]},{"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9640","file_date_updated":"2021-07-19T13:02:20Z","department":[{"_id":"KrCh"}],"date_updated":"2023-08-10T14:05:09Z","ddc":["510"],"scopus_import":"1","month":"06","intvolume":" 12","abstract":[{"text":"Selection and random drift determine the probability that novel mutations fixate in a population. Population structure is known to affect the dynamics of the evolutionary process. Amplifiers of selection are population structures that increase the fixation probability of beneficial mutants compared to well-mixed populations. Over the past 15 years, extensive research has produced remarkable structures called strong amplifiers which guarantee that every beneficial mutation fixates with high probability. But strong amplification has come at the cost of considerably delaying the fixation event, which can slow down the overall rate of evolution. However, the precise relationship between fixation probability and time has remained elusive. Here we characterize the slowdown effect of strong amplification. First, we prove that all strong amplifiers must delay the fixation event at least to some extent. Second, we construct strong amplifiers that delay the fixation event only marginally as compared to the well-mixed populations. Our results thus establish a tight relationship between fixation probability and time: Strong amplification always comes at a cost of a slowdown, but more than a marginal slowdown is not needed.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"issue":"1","volume":12,"ec_funded":1,"publication_identifier":{"eissn":["20411723"]},"publication_status":"published","file":[{"creator":"cziletti","date_updated":"2021-07-19T13:02:20Z","file_size":628992,"date_created":"2021-07-19T13:02:20Z","file_name":"2021_NatCoom_Tkadlec.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9692","checksum":"5767418926a7f7fb76151de29473dae0","success":1}],"language":[{"iso":"eng"}],"project":[{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"article_number":"4009","author":[{"first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"external_id":{"isi":["000671752100003"],"pmid":["34188036"]},"article_processing_charge":"No","title":"Fast and strong amplifiers of natural selection","citation":{"mla":"Tkadlec, Josef, et al. “Fast and Strong Amplifiers of Natural Selection.” Nature Communications, vol. 12, no. 1, 4009, Springer Nature, 2021, doi:10.1038/s41467-021-24271-w.","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Nature Communications 12 (2021).","ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Fast and strong amplifiers of natural selection,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2021). Fast and strong amplifiers of natural selection. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-24271-w","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Fast and strong amplifiers of natural selection. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-24271-w","chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Fast and Strong Amplifiers of Natural Selection.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-24271-w.","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2021. Fast and strong amplifiers of natural selection. Nature Communications. 12(1), 4009."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"K.C. acknowledges support from ERC Start grant no. (279307: Graph Games), ERC Consolidator grant no. (863818: ForM-SMart), Austrian Science Fund (FWF) grant no. P23499-N23 and S11407-N23 (RiSE). M.A.N. acknowledges support from Office of Naval Research grant N00014-16-1-2914 and from the John Templeton Foundation.","doi":"10.1038/s41467-021-24271-w","date_published":"2021-06-29T00:00:00Z","date_created":"2021-07-11T22:01:15Z","has_accepted_license":"1","isi":1,"year":"2021","day":"29","publication":"Nature Communications"},{"citation":{"ista":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. 2021. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. 232(2), 510–522.","chicago":"Han, Huibin, Maciek Adamowski, Linlin Qi, SS Alotaibi, and Jiří Friml. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17617.","apa":"Han, H., Adamowski, M., Qi, L., Alotaibi, S., & Friml, J. (2021). PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. Wiley. https://doi.org/10.1111/nph.17617","ama":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. 2021;232(2):510-522. doi:10.1111/nph.17617","ieee":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, and J. Friml, “PIN-mediated polar auxin transport regulations in plant tropic responses,” New Phytologist, vol. 232, no. 2. Wiley, pp. 510–522, 2021.","short":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, J. Friml, New Phytologist 232 (2021) 510–522.","mla":"Han, Huibin, et al. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” New Phytologist, vol. 232, no. 2, Wiley, 2021, pp. 510–22, doi:10.1111/nph.17617."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Han","full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin"},{"last_name":"Adamowski","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek"},{"first_name":"Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","full_name":"Qi, Linlin","orcid":"0000-0001-5187-8401","last_name":"Qi"},{"first_name":"SS","last_name":"Alotaibi","full_name":"Alotaibi, SS"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"external_id":{"pmid":["34254313"],"isi":["000680587100001"]},"article_processing_charge":"Yes (via OA deal)","title":"PIN-mediated polar auxin transport regulations in plant tropic responses","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","isi":1,"year":"2021","day":"01","publication":"New Phytologist","page":"510-522","doi":"10.1111/nph.17617","date_published":"2021-10-01T00:00:00Z","date_created":"2021-07-14T15:29:14Z","acknowledgement":"We are grateful to Lukas Fiedler, Alexandra Mally (IST Austria) and Dr. Bartel Vanholme (VIB, Ghent) for their critical comments on the manuscript. We apologize to those researchers whose great work was not cited. This work is supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship, 201506870018) and a starting grant from Jiangxi Agriculture University (9232308314).","publisher":"Wiley","quality_controlled":"1","oa":1,"date_updated":"2023-08-10T14:02:41Z","ddc":["580"],"file_date_updated":"2021-10-07T13:42:47Z","department":[{"_id":"JiFr"}],"_id":"9656","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"publication_status":"published","file":[{"date_created":"2021-10-07T13:42:47Z","file_name":"2021_NewPhytologist_Han.pdf","creator":"kschuh","date_updated":"2021-10-07T13:42:47Z","file_size":1939800,"file_id":"10105","checksum":"6422a6eb329b52d96279daaee0fcf189","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"issue":"2","volume":232,"ec_funded":1,"abstract":[{"text":"Tropisms, growth responses to environmental stimuli such as light or gravity, are spectacular examples of adaptive plant development. The plant hormone auxin serves as a major coordinative signal. The PIN auxin exporters, through their dynamic polar subcellular localizations, redirect auxin fluxes in response to environmental stimuli and the resulting auxin gradients across organs underly differential cell elongation and bending. In this review, we discuss recent advances concerning regulations of PIN polarity during tropisms, focusing on PIN phosphorylation and trafficking. We also cover how environmental cues regulate PIN actions during tropisms, and a crucial role of auxin feedback on PIN polarity during bending termination. Finally, the interactions between different tropisms are reviewed to understand plant adaptive growth in the natural environment.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"10","intvolume":" 232"},{"_id":"9679","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["530"],"date_updated":"2023-08-10T13:58:09Z","file_date_updated":"2021-07-19T11:47:16Z","department":[{"_id":"MiLe"}],"oa_version":"Published Version","abstract":[{"text":"The relative motion of three impenetrable particles on a ring, in our case two identical fermions and one impurity, is isomorphic to a triangular quantum billiard. Depending on the ratio κ of the impurity and fermion masses, the billiards can be integrable or non-integrable (also referred to in the main text as chaotic). To set the stage, we first investigate the energy level distributions of the billiards as a function of 1/κ ∈ [0, 1] and find no evidence of integrable cases beyond the limiting values 1/κ = 1 and 1/κ = 0. Then, we use machine learning tools to analyze properties of probability distributions of individual quantum states. We find that convolutional neural networks can correctly classify integrable and non-integrable states. The decisive features of the wave functions are the normalization and a large number of zero elements, corresponding to the existence of a nodal line. The network achieves typical accuracies of 97%, suggesting that machine learning tools can be used to analyze and classify the morphology of probability densities obtained in theory or experiment.","lang":"eng"}],"intvolume":" 23","month":"06","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"e39164ce7ea228d287cf8924e1a0f9fe","file_id":"9690","creator":"cziletti","file_size":3868445,"date_updated":"2021-07-19T11:47:16Z","file_name":"2021_NewJPhys_Huber.pdf","date_created":"2021-07-19T11:47:16Z"}],"publication_status":"published","publication_identifier":{"eissn":["13672630"]},"ec_funded":1,"volume":23,"issue":"6","article_number":"065009","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Huber D, Marchukov OV, Hammer HW, Volosniev A. 2021. Morphology of three-body quantum states from machine learning. New Journal of Physics. 23(6), 065009.","chicago":"Huber, David, Oleksandr V. Marchukov, Hans Werner Hammer, and Artem Volosniev. “Morphology of Three-Body Quantum States from Machine Learning.” New Journal of Physics. IOP Publishing, 2021. https://doi.org/10.1088/1367-2630/ac0576.","apa":"Huber, D., Marchukov, O. V., Hammer, H. W., & Volosniev, A. (2021). Morphology of three-body quantum states from machine learning. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac0576","ama":"Huber D, Marchukov OV, Hammer HW, Volosniev A. Morphology of three-body quantum states from machine learning. New Journal of Physics. 2021;23(6). doi:10.1088/1367-2630/ac0576","ieee":"D. Huber, O. V. Marchukov, H. W. Hammer, and A. Volosniev, “Morphology of three-body quantum states from machine learning,” New Journal of Physics, vol. 23, no. 6. IOP Publishing, 2021.","short":"D. Huber, O.V. Marchukov, H.W. Hammer, A. Volosniev, New Journal of Physics 23 (2021).","mla":"Huber, David, et al. “Morphology of Three-Body Quantum States from Machine Learning.” New Journal of Physics, vol. 23, no. 6, 065009, IOP Publishing, 2021, doi:10.1088/1367-2630/ac0576."},"title":"Morphology of three-body quantum states from machine learning","external_id":{"arxiv":["2102.04961"],"isi":["000664736300001"]},"article_processing_charge":"Yes","author":[{"first_name":"David","full_name":"Huber, David","last_name":"Huber"},{"full_name":"Marchukov, Oleksandr V.","last_name":"Marchukov","first_name":"Oleksandr V."},{"full_name":"Hammer, Hans Werner","last_name":"Hammer","first_name":"Hans Werner"},{"last_name":"Volosniev","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"We thank Aidan Tracy for his input during the initial stages of this project. We thank Nathan Harshman, Achim Richter, Wojciech Rzadkowski, and Dane Hudson Smith for helpful discussions and comments on the manuscript. This work has been supported by European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411 (AGV); by the German Aeronautics and Space Administration (DLR) through Grant No. 50 WM 1957 (OVM); by the Deutsche Forschungsgemeinschaft through Project VO 2437/1-1 (Project No. 413495248) (AGV and HWH); by the Deutsche Forschungsgemeinschaft through Collaborative Research Center SFB 1245 (Project No. 279384907) and by the Bundesministerium für Bildung und Forschung under Contract 05P18RDFN1 (HWH). HWH also thanks the ECT* for hospitality during the workshop 'Universal physics in Many-Body Quantum Systems—From Atoms to Quarks'. This infrastructure is part of a project that has received funding from the European Union's Horizon 2020 research and innovation program under Grant Agreement No. 824093. We acknowledge support by the Deutsche Forschungsgemeinschaft and the Open Access Publishing Fund of Technische Universität Darmstadt.","oa":1,"quality_controlled":"1","publisher":"IOP Publishing","publication":"New Journal of Physics","day":"23","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-07-18T22:01:22Z","date_published":"2021-06-23T00:00:00Z","doi":"10.1088/1367-2630/ac0576"},{"date_updated":"2023-08-10T13:57:36Z","department":[{"_id":"EdHa"}],"_id":"9629","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1476-4679"],"issn":["1465-7392"]},"publication_status":"published","volume":23,"ec_funded":1,"pmid":1,"oa_version":"Preprint","abstract":[{"text":"Intestinal organoids derived from single cells undergo complex crypt–villus patterning and morphogenesis. However, the nature and coordination of the underlying forces remains poorly characterized. Here, using light-sheet microscopy and large-scale imaging quantification, we demonstrate that crypt formation coincides with a stark reduction in lumen volume. We develop a 3D biophysical model to computationally screen different mechanical scenarios of crypt morphogenesis. Combining this with live-imaging data and multiple mechanical perturbations, we show that actomyosin-driven crypt apical contraction and villus basal tension work synergistically with lumen volume reduction to drive crypt morphogenesis, and demonstrate the existence of a critical point in differential tensions above which crypt morphology becomes robust to volume changes. Finally, we identified a sodium/glucose cotransporter that is specific to differentiated enterocytes that modulates lumen volume reduction through cell swelling in the villus region. Together, our study uncovers the cellular basis of how cell fate modulates osmotic and actomyosin forces to coordinate robust morphogenesis.","lang":"eng"}],"month":"06","intvolume":" 23","scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.05.13.094359","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Yang, Qiutan, Shi-lei Xue, Chii Jou Chan, Markus Rempfler, Dario Vischi, Francisca Maurer-Gutierrez, Takashi Hiiragi, Edouard B Hannezo, and Prisca Liberali. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.” Nature Cell Biology. Springer Nature, 2021. https://doi.org/10.1038/s41556-021-00700-2.","ista":"Yang Q, Xue S, Chan CJ, Rempfler M, Vischi D, Maurer-Gutierrez F, Hiiragi T, Hannezo EB, Liberali P. 2021. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. 23, 733–744.","mla":"Yang, Qiutan, et al. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.” Nature Cell Biology, vol. 23, Springer Nature, 2021, pp. 733–744, doi:10.1038/s41556-021-00700-2.","ieee":"Q. Yang et al., “Cell fate coordinates mechano-osmotic forces in intestinal crypt formation,” Nature Cell Biology, vol. 23. Springer Nature, pp. 733–744, 2021.","short":"Q. Yang, S. Xue, C.J. Chan, M. Rempfler, D. Vischi, F. Maurer-Gutierrez, T. Hiiragi, E.B. Hannezo, P. Liberali, Nature Cell Biology 23 (2021) 733–744.","ama":"Yang Q, Xue S, Chan CJ, et al. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. 2021;23:733–744. doi:10.1038/s41556-021-00700-2","apa":"Yang, Q., Xue, S., Chan, C. J., Rempfler, M., Vischi, D., Maurer-Gutierrez, F., … Liberali, P. (2021). Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-021-00700-2"},"title":"Cell fate coordinates mechano-osmotic forces in intestinal crypt formation","author":[{"first_name":"Qiutan","last_name":"Yang","full_name":"Yang, Qiutan"},{"first_name":"Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87","full_name":"Xue, Shi-lei","last_name":"Xue"},{"first_name":"Chii Jou","last_name":"Chan","full_name":"Chan, Chii Jou"},{"full_name":"Rempfler, Markus","last_name":"Rempfler","first_name":"Markus"},{"first_name":"Dario","last_name":"Vischi","full_name":"Vischi, Dario"},{"last_name":"Maurer-Gutierrez","full_name":"Maurer-Gutierrez, Francisca","first_name":"Francisca"},{"first_name":"Takashi","full_name":"Hiiragi, Takashi","last_name":"Hiiragi"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"full_name":"Liberali, Prisca","last_name":"Liberali","first_name":"Prisca"}],"external_id":{"isi":["000664016300003"],"pmid":["34155381"]},"article_processing_charge":"No","project":[{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"},{"grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425"}],"day":"21","publication":"Nature Cell Biology","isi":1,"year":"2021","date_published":"2021-06-21T00:00:00Z","doi":"10.1038/s41556-021-00700-2","date_created":"2021-07-04T22:01:25Z","page":"733–744","acknowledgement":"We acknowledge the members of the Lennon-Duménil laboratory for sharing the mouse line of Myh9-GFP. We are grateful to the members of the Liberali laboratory and the FMI facilities for their support. We thank E. Tagliavini for IT support; L. Gelman for assistance and training; S. Bichet and A. Bogucki for helping with histology of mouse tissues; H. Kohler for fluorescence-activated cell sorting; G. Q. G. de Medeiros for maintenance of light-sheet microscopy; M. G. Stadler for scRNA-seq analysis; G. Gay for discussions on the 3D vertex model; the members of the Liberali laboratory, C. P. Heisenberg and C. Tsiairis for reading and providing feedback on the manuscript. Funding: Q.Y. is supported by a Postdoc fellowship from Peter und Taul Engelhorn Stiftung (PTES). This work received funding from the European Research Council (ERC) under the EU Horizon 2020 research and Innovation Programme Grant Agreement no. 758617 (to P.L.), the Swiss National Foundation (SNF) (POOP3_157531, to P.L.) and from the ERC under the EU Horizon 2020 Research and Innovation Program Grant Agreements 851288 (to E.H.) and the Austrian Science Fund (FWF) (P31639, to E.H.).","quality_controlled":"1","publisher":"Springer Nature","oa":1},{"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"This work was supported by National Natural Science Foundation of China (51772012), National Key Research and Development Program of China (2018YFA0702100 and 2018YFB0703600), the Beijing Natural Science Foundation (JQ18004). This work was also supported by Lise Meitner Project (M2889-N) and the National Postdoctoral Program for Innovative Talents (BX20200028). L.D.Z. appreciates the support of the High Performance Computing (HPC) resources at Beihang University, the National Science Fund for Distinguished Young Scholars (51925101), and center for High Pressure Science and Technology Advanced Research (HPSTAR) for SEM measurements.","date_created":"2021-07-04T22:01:24Z","date_published":"2021-06-03T00:00:00Z","doi":"10.1016/j.mtphys.2021.100452","publication":"Materials Today Physics","day":"03","year":"2021","isi":1,"article_number":"100452","title":"Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation","article_processing_charge":"No","external_id":{"isi":["000703159600010"]},"author":[{"first_name":"Lizhong","full_name":"Su, Lizhong","last_name":"Su"},{"last_name":"Hong","full_name":"Hong, Tao","first_name":"Tao"},{"first_name":"Dongyang","last_name":"Wang","full_name":"Wang, Dongyang"},{"first_name":"Sining","full_name":"Wang, Sining","last_name":"Wang"},{"full_name":"Qin, Bingchao","last_name":"Qin","first_name":"Bingchao"},{"first_name":"Mengmeng","last_name":"Zhang","full_name":"Zhang, Mengmeng"},{"last_name":"Gao","full_name":"Gao, Xiang","first_name":"Xiang"},{"full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277","last_name":"Chang","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","first_name":"Cheng"},{"first_name":"Li Dong","last_name":"Zhao","full_name":"Zhao, Li Dong"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Su L, Hong T, Wang D, et al. Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. Materials Today Physics. 2021;20. doi:10.1016/j.mtphys.2021.100452","apa":"Su, L., Hong, T., Wang, D., Wang, S., Qin, B., Zhang, M., … Zhao, L. D. (2021). Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. Materials Today Physics. Elsevier. https://doi.org/10.1016/j.mtphys.2021.100452","short":"L. Su, T. Hong, D. Wang, S. Wang, B. Qin, M. Zhang, X. Gao, C. Chang, L.D. Zhao, Materials Today Physics 20 (2021).","ieee":"L. Su et al., “Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation,” Materials Today Physics, vol. 20. Elsevier, 2021.","mla":"Su, Lizhong, et al. “Realizing High Doping Efficiency and Thermoelectric Performance in N-Type SnSe Polycrystals via Bandgap Engineering and Vacancy Compensation.” Materials Today Physics, vol. 20, 100452, Elsevier, 2021, doi:10.1016/j.mtphys.2021.100452.","ista":"Su L, Hong T, Wang D, Wang S, Qin B, Zhang M, Gao X, Chang C, Zhao LD. 2021. Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. Materials Today Physics. 20, 100452.","chicago":"Su, Lizhong, Tao Hong, Dongyang Wang, Sining Wang, Bingchao Qin, Mengmeng Zhang, Xiang Gao, Cheng Chang, and Li Dong Zhao. “Realizing High Doping Efficiency and Thermoelectric Performance in N-Type SnSe Polycrystals via Bandgap Engineering and Vacancy Compensation.” Materials Today Physics. Elsevier, 2021. https://doi.org/10.1016/j.mtphys.2021.100452."},"intvolume":" 20","month":"06","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"SnSe, a wide-bandgap semiconductor, has attracted significant attention from the thermoelectric (TE) community due to its outstanding TE performance deriving from the ultralow thermal conductivity and advantageous electronic structures. Here, we promoted the TE performance of n-type SnSe polycrystals through bandgap engineering and vacancy compensation. We found that PbTe can significantly reduce the wide bandgap of SnSe to reduce the impurity transition energy, largely enhancing the carrier concentration. Also, PbTe-induced crystal symmetry promotion increases the carrier mobility, preserving large Seebeck coefficient. Consequently, a maximum ZT of ∼1.4 at 793 K is obtained in Br doped SnSe–13%PbTe. Furthermore, we found that extra Sn in n-type SnSe can compensate for the intrinsic Sn vacancies and form electron donor-like metallic Sn nanophases. The Sn nanophases near the grain boundary could also reduce the intergrain energy barrier which largely enhances the carrier mobility. As a result, a maximum ZT value of ∼1.7 at 793 K and an average ZT (ZTave) of ∼0.58 in 300–793 K are achieved in Br doped Sn1.08Se–13%PbTe. Our findings provide a novel strategy to promote the TE performance in wide-bandgap semiconductors."}],"volume":20,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2542-5293"]},"status":"public","type":"journal_article","article_type":"original","_id":"9626","department":[{"_id":"MaIb"}],"date_updated":"2023-08-10T13:56:31Z"},{"file_date_updated":"2021-12-17T11:34:50Z","department":[{"_id":"PeJo"}],"ddc":["570"],"date_updated":"2023-08-10T14:16:16Z","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"9778","ec_funded":1,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/synaptic-transmission-not-a-one-way-street/"}]},"volume":12,"issue":"1","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"6036a8cdae95e1707c2a04d54e325ff4","file_id":"10563","creator":"kschuh","file_size":3108845,"date_updated":"2021-12-17T11:34:50Z","file_name":"2021_NatureCommunications_Vandael.pdf","date_created":"2021-12-17T11:34:50Z"}],"publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"intvolume":" 12","month":"05","scopus_import":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"SSU"}],"abstract":[{"lang":"eng","text":"The hippocampal mossy fiber synapse is a key synapse of the trisynaptic circuit. Post-tetanic potentiation (PTP) is the most powerful form of plasticity at this synaptic connection. It is widely believed that mossy fiber PTP is an entirely presynaptic phenomenon, implying that PTP induction is input-specific, and requires neither activity of multiple inputs nor stimulation of postsynaptic neurons. To directly test cooperativity and associativity, we made paired recordings between single mossy fiber terminals and postsynaptic CA3 pyramidal neurons in rat brain slices. By stimulating non-overlapping mossy fiber inputs converging onto single CA3 neurons, we confirm that PTP is input-specific and non-cooperative. Unexpectedly, mossy fiber PTP exhibits anti-associative induction properties. EPSCs show only minimal PTP after combined pre- and postsynaptic high-frequency stimulation with intact postsynaptic Ca2+ signaling, but marked PTP in the absence of postsynaptic spiking and after suppression of postsynaptic Ca2+ signaling (10 mM EGTA). PTP is largely recovered by inhibitors of voltage-gated R- and L-type Ca2+ channels, group II mGluRs, and vacuolar-type H+-ATPase, suggesting the involvement of retrograde vesicular glutamate signaling. Transsynaptic regulation of PTP extends the repertoire of synaptic computations, implementing a brake on mossy fiber detonation and a “smart teacher” function of hippocampal mossy fiber synapses."}],"title":"Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses","article_processing_charge":"No","external_id":{"isi":["000655481800014"]},"author":[{"orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","last_name":"Vandael","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H"},{"last_name":"Okamoto","orcid":"0000-0003-0408-6094","full_name":"Okamoto, Yuji","first_name":"Yuji","id":"3337E116-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Vandael DH, Okamoto Y, Jonas PM. 2021. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. 12(1), 2912.","chicago":"Vandael, David H, Yuji Okamoto, and Peter M Jonas. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” Nature Communications. Springer, 2021. https://doi.org/10.1038/s41467-021-23153-5.","short":"D.H. Vandael, Y. Okamoto, P.M. Jonas, Nature Communications 12 (2021).","ieee":"D. H. Vandael, Y. Okamoto, and P. M. Jonas, “Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses,” Nature Communications, vol. 12, no. 1. Springer, 2021.","apa":"Vandael, D. H., Okamoto, Y., & Jonas, P. M. (2021). Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. Springer. https://doi.org/10.1038/s41467-021-23153-5","ama":"Vandael DH, Okamoto Y, Jonas PM. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23153-5","mla":"Vandael, David H., et al. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” Nature Communications, vol. 12, no. 1, 2912, Springer, 2021, doi:10.1038/s41467-021-23153-5."},"project":[{"call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z00312"}],"article_number":"2912","date_created":"2021-08-06T07:22:55Z","date_published":"2021-05-18T00:00:00Z","doi":"10.1038/s41467-021-23153-5","publication":"Nature Communications","day":"18","year":"2021","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"We thank Drs. Carolina Borges-Merjane and Jose Guzman for critically reading the manuscript, and Pablo Castillo for discussions. We are grateful to Alois Schlögl for help with analysis, Florian Marr for excellent technical assistance and cell reconstruction, Christina Altmutter for technical help, Eleftheria Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for support. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award), both to P.J."},{"status":"public","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"_id":"9647","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"file_date_updated":"2022-05-12T12:13:27Z","ddc":["004"],"date_updated":"2023-08-10T14:11:19Z","month":"06","intvolume":" 893","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Gene expression is regulated by the set of transcription factors (TFs) that bind to the promoter. The ensuing regulating function is often represented as a combinational logic circuit, where output (gene expression) is determined by current input values (promoter bound TFs) only. However, the simultaneous arrival of TFs is a strong assumption, since transcription and translation of genes introduce intrinsic time delays and there is no global synchronisation among the arrival times of different molecular species at their targets. We present an experimentally implementable genetic circuit with two inputs and one output, which in the presence of small delays in input arrival, exhibits qualitatively distinct population-level phenotypes, over timescales that are longer than typical cell doubling times. From a dynamical systems point of view, these phenotypes represent long-lived transients: although they converge to the same value eventually, they do so after a very long time span. The key feature of this toy model genetic circuit is that, despite having only two inputs and one output, it is regulated by twenty-three distinct DNA-TF configurations, two of which are more stable than others (DNA looped states), one promoting and another blocking the expression of the output gene. Small delays in input arrival time result in a majority of cells in the population quickly reaching the stable state associated with the first input, while exiting of this stable state occurs at a slow timescale. In order to mechanistically model the behaviour of this genetic circuit, we used a rule-based modelling language, and implemented a grid-search to find parameter combinations giving rise to long-lived transients. Our analysis shows that in the absence of feedback, there exist path-dependent gene regulatory mechanisms based on the long timescale of transients. The behaviour of this toy model circuit suggests that gene regulatory networks can exploit event timing to create phenotypes, and it opens the possibility that they could use event timing to memorise events, without regulatory feedback. The model reveals the importance of (i) mechanistically modelling the transitions between the different DNA-TF states, and (ii) employing transient analysis thereof.","lang":"eng"}],"volume":893,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"11364","checksum":"d3aef34cfb13e53bba4cf44d01680793","creator":"dernst","file_size":2566504,"date_updated":"2022-05-12T12:13:27Z","file_name":"2021_TheoreticalComputerScience_Petrov.pdf","date_created":"2022-05-12T12:13:27Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0304-3975"]},"publication_status":"published","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"}],"title":"Long lived transients in gene regulation","author":[{"first_name":"Tatjana","full_name":"Petrov, Tatjana","last_name":"Petrov"},{"full_name":"Igler, Claudia","last_name":"Igler","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sezgin, Ali","last_name":"Sezgin","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","first_name":"Ali"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000710180500002"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Petrov, Tatjana, et al. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science, vol. 893, Elsevier, 2021, pp. 1–16, doi:10.1016/j.tcs.2021.05.023.","short":"T. Petrov, C. Igler, A. Sezgin, T.A. Henzinger, C.C. Guet, Theoretical Computer Science 893 (2021) 1–16.","ieee":"T. Petrov, C. Igler, A. Sezgin, T. A. Henzinger, and C. C. Guet, “Long lived transients in gene regulation,” Theoretical Computer Science, vol. 893. Elsevier, pp. 1–16, 2021.","ama":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. Long lived transients in gene regulation. Theoretical Computer Science. 2021;893:1-16. doi:10.1016/j.tcs.2021.05.023","apa":"Petrov, T., Igler, C., Sezgin, A., Henzinger, T. A., & Guet, C. C. (2021). Long lived transients in gene regulation. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2021.05.023","chicago":"Petrov, Tatjana, Claudia Igler, Ali Sezgin, Thomas A Henzinger, and Calin C Guet. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science. Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.05.023.","ista":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. 2021. Long lived transients in gene regulation. Theoretical Computer Science. 893, 1–16."},"publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"Tatjana Petrov’s research was supported in part by SNSF Advanced Postdoctoral Mobility Fellowship grant number P300P2 161067, the Ministry of Science, Research and the Arts of the state of Baden-Wurttemberg, and the DFG Centre of Excellence 2117 ‘Centre for the Advanced Study of Collective Behaviour’ (ID: 422037984). Claudia Igler is the recipient of a DOC Fellowship of the Austrian Academy of Sciences. Thomas A. Henzinger’s research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","date_published":"2021-06-04T00:00:00Z","doi":"10.1016/j.tcs.2021.05.023","date_created":"2021-07-11T22:01:18Z","page":"1-16","day":"04","publication":"Theoretical Computer Science","isi":1,"has_accepted_license":"1","year":"2021"},{"publisher":"MDPI","quality_controlled":"1","oa":1,"acknowledgement":"The authors are grateful to Kazuya Oikawa and Gillian McLellan for generously sharing some of their data for this review, and to Janis Eells for helpful comments on the manuscript.","date_published":"2021-06-25T00:00:00Z","doi":"10.3390/cells10071593","date_created":"2021-08-01T22:01:22Z","day":"25","publication":"Cells","has_accepted_license":"1","isi":1,"year":"2021","article_number":"1593","title":"The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease","author":[{"first_name":"Nicole A.","full_name":"Muench, Nicole A.","last_name":"Muench"},{"full_name":"Patel, Sonia","last_name":"Patel","first_name":"Sonia"},{"full_name":"Maes, Margaret E","orcid":"0000-0001-9642-1085","last_name":"Maes","first_name":"Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ryan J.","last_name":"Donahue","full_name":"Donahue, Ryan J."},{"last_name":"Ikeda","full_name":"Ikeda, Akihiro","first_name":"Akihiro"},{"first_name":"Robert W.","full_name":"Nickells, Robert W.","last_name":"Nickells"}],"external_id":{"isi":["000678193300001"],"pmid":["34201955"]},"article_processing_charge":"Yes","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Muench, Nicole A., Sonia Patel, Margaret E Maes, Ryan J. Donahue, Akihiro Ikeda, and Robert W. Nickells. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells. MDPI, 2021. https://doi.org/10.3390/cells10071593.","ista":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. 2021. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. 10(7), 1593.","mla":"Muench, Nicole A., et al. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells, vol. 10, no. 7, 1593, MDPI, 2021, doi:10.3390/cells10071593.","short":"N.A. Muench, S. Patel, M.E. Maes, R.J. Donahue, A. Ikeda, R.W. Nickells, Cells 10 (2021).","ieee":"N. A. Muench, S. Patel, M. E. Maes, R. J. Donahue, A. Ikeda, and R. W. Nickells, “The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease,” Cells, vol. 10, no. 7. MDPI, 2021.","ama":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. 2021;10(7). doi:10.3390/cells10071593","apa":"Muench, N. A., Patel, S., Maes, M. E., Donahue, R. J., Ikeda, A., & Nickells, R. W. (2021). The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. MDPI. https://doi.org/10.3390/cells10071593"},"month":"06","intvolume":" 10","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"The important roles of mitochondrial function and dysfunction in the process of neurodegeneration are widely acknowledged. Retinal ganglion cells (RGCs) appear to be a highly vulnerable neuronal cell type in the central nervous system with respect to mitochondrial dysfunction but the actual reasons for this are still incompletely understood. These cells have a unique circumstance where unmyelinated axons must bend nearly 90° to exit the eye and then cross a translaminar pressure gradient before becoming myelinated in the optic nerve. This region, the optic nerve head, contains some of the highest density of mitochondria present in these cells. Glaucoma represents a perfect storm of events occurring at this location, with a combination of changes in the translaminar pressure gradient and reassignment of the metabolic support functions of supporting glia, which appears to apply increased metabolic stress to the RGC axons leading to a failure of axonal transport mechanisms. However, RGCs themselves are also extremely sensitive to genetic mutations, particularly in genes affecting mitochondrial dynamics and mitochondrial clearance. These mutations, which systemically affect the mitochondria in every cell, often lead to an optic neuropathy as the sole pathologic defect in affected patients. This review summarizes knowledge of mitochondrial structure and function, the known energy demands of neurons in general, and places these in the context of normal and pathological characteristics of mitochondria attributed to RGCs. ","lang":"eng"}],"issue":"7","volume":10,"file":[{"checksum":"e0497ce5c77fa3b65a538c7d6e0f6c66","file_id":"9768","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-08-04T14:01:30Z","file_name":"2021_Cells_Muench.pdf","creator":"cziletti","date_updated":"2021-08-04T14:01:30Z","file_size":4555611}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20734409"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"9761","file_date_updated":"2021-08-04T14:01:30Z","department":[{"_id":"SaSi"}],"ddc":["570"],"date_updated":"2023-08-10T14:14:53Z"},{"intvolume":" 183","month":"06","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"At the encounter with a novel environment, contextual memory formation is greatly enhanced, accompanied with increased arousal and active exploration. Although this phenomenon has been widely observed in animal and human daily life, how the novelty in the environment is detected and contributes to contextual memory formation has lately started to be unveiled. The hippocampus has been studied for many decades for its largely known roles in encoding spatial memory, and a growing body of evidence indicates a differential involvement of dorsal and ventral hippocampal divisions in novelty detection. In this brief review article, we discuss the recent findings of the role of mossy cells in the ventral hippocampal moiety in novelty detection and put them in perspective with other novelty-related pathways in the hippocampus. We propose a mechanism for novelty-driven memory acquisition in the dentate gyrus by the direct projection of ventral mossy cells to dorsal dentate granule cells. By this projection, the ventral hippocampus sends novelty signals to the dorsal hippocampus, opening a gate for memory encoding in dentate granule cells based on information coming from the entorhinal cortex. We conclude that, contrary to the presently accepted functional independence, the dorsal and ventral hippocampi cooperate to link the novelty and contextual information, and this dorso-ventral interaction is crucial for the novelty-dependent memory formation."}],"ec_funded":1,"volume":183,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9694","checksum":"8e8298a9e8c7df146ad23f32c2a63929","success":1,"date_updated":"2021-07-19T13:46:06Z","file_size":1994793,"creator":"cziletti","date_created":"2021-07-19T13:46:06Z","file_name":"2021_NeurobLearnMemory_Fredes.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["10959564"],"issn":["10747427"]},"status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","_id":"9641","department":[{"_id":"RySh"}],"file_date_updated":"2021-07-19T13:46:06Z","ddc":["610"],"date_updated":"2023-08-10T14:10:37Z","oa":1,"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"This work was supported by a European Research Council Advanced Grant 694539 to Ryuichi Shigemoto.","date_created":"2021-07-11T22:01:16Z","doi":"10.1016/j.nlm.2021.107486","date_published":"2021-06-30T00:00:00Z","publication":"Neurobiology of Learning and Memory","day":"30","year":"2021","isi":1,"has_accepted_license":"1","project":[{"call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"}],"article_number":"107486","title":"The role of hippocampal mossy cells in novelty detection","external_id":{"pmid":["34214666"],"isi":["000677694900004"]},"article_processing_charge":"No","author":[{"first_name":"Felipe","last_name":"Fredes","full_name":"Fredes, Felipe"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” Neurobiology of Learning and Memory, vol. 183, 107486, Elsevier, 2021, doi:10.1016/j.nlm.2021.107486.","ama":"Fredes F, Shigemoto R. The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. 2021;183. doi:10.1016/j.nlm.2021.107486","apa":"Fredes, F., & Shigemoto, R. (2021). The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. Elsevier. https://doi.org/10.1016/j.nlm.2021.107486","ieee":"F. Fredes and R. Shigemoto, “The role of hippocampal mossy cells in novelty detection,” Neurobiology of Learning and Memory, vol. 183. Elsevier, 2021.","short":"F. Fredes, R. Shigemoto, Neurobiology of Learning and Memory 183 (2021).","chicago":"Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” Neurobiology of Learning and Memory. Elsevier, 2021. https://doi.org/10.1016/j.nlm.2021.107486.","ista":"Fredes F, Shigemoto R. 2021. The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. 183, 107486."}},{"conference":{"name":"PLDI: Programming Language Design and Implementation","start_date":"2021-06-20","end_date":"2021-06-26","location":"Online"},"type":"conference","status":"public","_id":"9646","department":[{"_id":"KrCh"}],"date_updated":"2023-08-10T14:14:08Z","main_file_link":[{"url":"https://arxiv.org/abs/2011.14617","open_access":"1"}],"scopus_import":"1","month":"06","abstract":[{"text":"We consider the fundamental problem of deriving quantitative bounds on the probability that a given assertion is violated in a probabilistic program. We provide automated algorithms that obtain both lower and upper bounds on the assertion violation probability. The main novelty of our approach is that we prove new and dedicated fixed-point theorems which serve as the theoretical basis of our algorithms and enable us to reason about assertion violation bounds in terms of pre and post fixed-point functions. To synthesize such fixed-points, we devise algorithms that utilize a wide range of mathematical tools, including repulsing ranking supermartingales, Hoeffding's lemma, Minkowski decompositions, Jensen's inequality, and convex optimization. On the theoretical side, we provide (i) the first automated algorithm for lower-bounds on assertion violation probabilities, (ii) the first complete algorithm for upper-bounds of exponential form in affine programs, and (iii) provably and significantly tighter upper-bounds than the previous approaches. On the practical side, we show our algorithms can handle a wide variety of programs from the literature and synthesize bounds that are remarkably tighter than previous results, in some cases by thousands of orders of magnitude.","lang":"eng"}],"oa_version":"Preprint","ec_funded":1,"publication_status":"published","publication_identifier":{"isbn":["9781450383912"]},"language":[{"iso":"eng"}],"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","external_id":{"isi":["000723661700076"],"arxiv":["2011.14617"]},"author":[{"first_name":"Jinyi","full_name":"Wang, Jinyi","last_name":"Wang"},{"last_name":"Sun","full_name":"Sun, Yican","first_name":"Yican"},{"last_name":"Fu","full_name":"Fu, Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"}],"title":"Quantitative analysis of assertion violations in probabilistic programs","citation":{"mla":"Wang, Jinyi, et al. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1171–86, doi:10.1145/3453483.3454102.","short":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1171–1186.","ieee":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Quantitative analysis of assertion violations in probabilistic programs,” in Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Online, 2021, pp. 1171–1186.","apa":"Wang, J., Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2021). Quantitative analysis of assertion violations in probabilistic programs. In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation (pp. 1171–1186). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454102","ama":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. Quantitative analysis of assertion violations in probabilistic programs. In: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2021:1171-1186. doi:10.1145/3453483.3454102","chicago":"Wang, Jinyi, Yican Sun, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, 1171–86. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453483.3454102.","ista":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. 2021. Quantitative analysis of assertion violations in probabilistic programs. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 1171–1186."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","acknowledgement":"We are very thankful to the anonymous reviewers for the helpful and valuable comments. The work was partially supported by the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the ERC CoG 863818 (ForM-SMArt), the Facebook PhD Fellowship Program and DOC Fellowship #24956 of the Austrian Academy of Sciences (ÖAW).","page":"1171-1186","date_created":"2021-07-11T22:01:18Z","doi":"10.1145/3453483.3454102","date_published":"2021-06-01T00:00:00Z","year":"2021","isi":1,"publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","day":"01"},{"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"}],"external_id":{"isi":["000723661700050"]},"article_processing_charge":"No","author":[{"first_name":"Ali","last_name":"Asadi","full_name":"Asadi, Ali"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584"},{"first_name":"Mohammad","full_name":"Mahdavi, Mohammad","last_name":"Mahdavi"}],"title":"Polynomial reachability witnesses via Stellensätze","citation":{"short":"A. Asadi, K. Chatterjee, H. Fu, A.K. Goharshady, M. Mahdavi, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 772–787.","ieee":"A. Asadi, K. Chatterjee, H. Fu, A. K. Goharshady, and M. Mahdavi, “Polynomial reachability witnesses via Stellensätze,” in Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Online, 2021, pp. 772–787.","apa":"Asadi, A., Chatterjee, K., Fu, H., Goharshady, A. K., & Mahdavi, M. (2021). Polynomial reachability witnesses via Stellensätze. In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation (pp. 772–787). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454076","ama":"Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. Polynomial reachability witnesses via Stellensätze. In: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2021:772-787. doi:10.1145/3453483.3454076","mla":"Asadi, Ali, et al. “Polynomial Reachability Witnesses via Stellensätze.” Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 772–87, doi:10.1145/3453483.3454076.","ista":"Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. 2021. Polynomial reachability witnesses via Stellensätze. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 772–787.","chicago":"Asadi, Ali, Krishnendu Chatterjee, Hongfei Fu, Amir Kafshdar Goharshady, and Mohammad Mahdavi. “Polynomial Reachability Witnesses via Stellensätze.” In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, 772–87. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453483.3454076."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt), the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the Facebook PhD Fellowship Program, and DOC Fellowship No. 24956 of the Austrian Academy of Sciences (ÖAW).","page":"772-787","date_created":"2021-07-11T22:01:17Z","doi":"10.1145/3453483.3454076","date_published":"2021-06-01T00:00:00Z","year":"2021","isi":1,"publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","day":"01","conference":{"name":" PLDI: Programming Language Design and Implementation","start_date":"2021-06-20","location":"Online","end_date":"2021-06-26"},"type":"conference","status":"public","_id":"9645","department":[{"_id":"KrCh"}],"date_updated":"2023-08-10T14:13:39Z","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-03183862/","open_access":"1"}],"scopus_import":"1","month":"06","abstract":[{"lang":"eng","text":"We consider the fundamental problem of reachability analysis over imperative programs with real variables. Previous works that tackle reachability are either unable to handle programs consisting of general loops (e.g. symbolic execution), or lack completeness guarantees (e.g. abstract interpretation), or are not automated (e.g. incorrectness logic). In contrast, we propose a novel approach for reachability analysis that can handle general and complex loops, is complete, and can be entirely automated for a wide family of programs. Through the notion of Inductive Reachability Witnesses (IRWs), our approach extends ideas from both invariant generation and termination to reachability analysis.\r\n\r\nWe first show that our IRW-based approach is sound and complete for reachability analysis of imperative programs. Then, we focus on linear and polynomial programs and develop automated methods for synthesizing linear and polynomial IRWs. In the linear case, we follow the well-known approaches using Farkas' Lemma. Our main contribution is in the polynomial case, where we present a push-button semi-complete algorithm. We achieve this using a novel combination of classical theorems in real algebraic geometry, such as Putinar's Positivstellensatz and Hilbert's Strong Nullstellensatz. Finally, our experimental results show we can prove complex reachability objectives over various benchmarks that were beyond the reach of previous methods."}],"oa_version":"Submitted Version","ec_funded":1,"publication_status":"published","publication_identifier":{"isbn":["9781450383912"]},"language":[{"iso":"eng"}]},{"publisher":"Public Library of Science","oa":1,"acknowledgement":"The authors thank Inez Lam of Johns Hopkins University for valuable comments on an earlier version of the manuscript. We also thank the facilitators of the 2019–2020 eLife Community Ambassador program.","doi":"10.1371/journal.pcbi.1009124","date_published":"2021-07-15T00:00:00Z","date_created":"2021-08-01T22:01:21Z","day":"15","publication":"PLoS Computational Biology","has_accepted_license":"1","isi":1,"year":"2021","article_number":"e1009124","title":"Ten simple rules to improve academic work- life balance","author":[{"full_name":"Bartlett, Michael John","last_name":"Bartlett","first_name":"Michael John"},{"first_name":"Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N","last_name":"Arslan"},{"last_name":"Bankston","full_name":"Bankston, Adriana","first_name":"Adriana"},{"full_name":"Sarabipour, Sarvenaz","last_name":"Sarabipour","first_name":"Sarvenaz"}],"article_processing_charge":"Yes","external_id":{"pmid":["34264932"],"isi":["000677713500008"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. 2021. Ten simple rules to improve academic work- life balance. PLoS Computational Biology. 17(7), e1009124.","chicago":"Bartlett, Michael John, Feyza N Arslan, Adriana Bankston, and Sarvenaz Sarabipour. “Ten Simple Rules to Improve Academic Work- Life Balance.” PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009124.","apa":"Bartlett, M. J., Arslan, F. N., Bankston, A., & Sarabipour, S. (2021). Ten simple rules to improve academic work- life balance. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009124","ama":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. Ten simple rules to improve academic work- life balance. PLoS Computational Biology. 2021;17(7). doi:10.1371/journal.pcbi.1009124","ieee":"M. J. Bartlett, F. N. Arslan, A. Bankston, and S. Sarabipour, “Ten simple rules to improve academic work- life balance,” PLoS Computational Biology, vol. 17, no. 7. Public Library of Science, 2021.","short":"M.J. Bartlett, F.N. Arslan, A. Bankston, S. Sarabipour, PLoS Computational Biology 17 (2021).","mla":"Bartlett, Michael John, et al. “Ten Simple Rules to Improve Academic Work- Life Balance.” PLoS Computational Biology, vol. 17, no. 7, e1009124, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1009124."},"month":"07","intvolume":" 17","scopus_import":"1","oa_version":"Published Version","pmid":1,"issue":"7","volume":17,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"9771","checksum":"e56d91f0eeadb36f143a90e2c1b3ab63","creator":"cchlebak","file_size":693633,"date_updated":"2021-08-05T12:06:49Z","file_name":"2021_PlosCompBio_Bartlett.pdf","date_created":"2021-08-05T12:06:49Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1553734X"],"eissn":["15537358"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"letter_note","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"9759","department":[{"_id":"CaHe"}],"file_date_updated":"2021-08-05T12:06:49Z","ddc":["613"],"date_updated":"2023-08-10T14:16:46Z"},{"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9833","checksum":"b043a91d9f9200e467b970b692687ed3","success":1,"date_updated":"2021-08-09T09:44:03Z","file_size":7123293,"creator":"asandaue","date_created":"2021-08-09T09:44:03Z","file_name":"2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["19448252"],"issn":["19448244"]},"ec_funded":1,"issue":"30","volume":13,"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Attachment of adhesive molecules on cell culture surfaces to restrict cell adhesion to defined areas and shapes has been vital for the progress of in vitro research. In currently existing patterning methods, a combination of pattern properties such as stability, precision, specificity, high-throughput outcome, and spatiotemporal control is highly desirable but challenging to achieve. Here, we introduce a versatile and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent patterning step and a subsequent functionalization of the pattern via click chemistry. This two-step process is feasible on arbitrary surfaces and allows for generation of sustainable patterns and gradients. The method is validated in different biological systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining the growth and migration of cells to the designated areas. We then implement a sequential photopatterning approach by adding a second switchable patterning step, allowing for spatiotemporal control over two distinct surface patterns. As a proof of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis. Our results show that the spatiotemporal control provided by our “sequential photopatterning” system is essential for mimicking dynamic biological processes and that our innovative approach has great potential for further applications in cell science.","lang":"eng"}],"intvolume":" 13","month":"08","scopus_import":"1","ddc":["620","570"],"date_updated":"2023-08-10T14:22:48Z","file_date_updated":"2021-08-09T09:44:03Z","department":[{"_id":"MiSi"},{"_id":"GaTk"},{"_id":"Bio"},{"_id":"CaGu"}],"_id":"9822","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","publication":"ACS Applied Materials and Interfaces","day":"04","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-08-08T22:01:28Z","doi":"10.1021/acsami.1c09850","date_published":"2021-08-04T00:00:00Z","page":"35545–35560","acknowledgement":"We would like to thank Charlott Leu for the production of our chromium wafers, Louise Ritter for her contribution of the IF stainings in Figure 4, Shokoufeh Teymouri for her help with the Bioinert coated slides, and finally Prof. Dr. Joachim Rädler for his valuable scientific guidance.","oa":1,"publisher":"American Chemical Society","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait, R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials and Interfaces 13 (2021) 35545–35560.","ieee":"T. Zisis et al., “Sequential and switchable patterning for studying cellular processes under spatiotemporal control,” ACS Applied Materials and Interfaces, vol. 13, no. 30. American Chemical Society, pp. 35545–35560, 2021.","ama":"Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 2021;13(30):35545–35560. doi:10.1021/acsami.1c09850","apa":"Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R. P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.1c09850","mla":"Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560, doi:10.1021/acsami.1c09850.","ista":"Zisis T, Schwarz J, Balles M, Kretschmer M, Nemethova M, Chait RP, Hauschild R, Lange J, Guet CC, Sixt MK, Zahler S. 2021. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 13(30), 35545–35560.","chicago":"Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces. American Chemical Society, 2021. https://doi.org/10.1021/acsami.1c09850."},"title":"Sequential and switchable patterning for studying cellular processes under spatiotemporal control","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000683741400026"],"pmid":["34283577"]},"author":[{"last_name":"Zisis","full_name":"Zisis, Themistoklis","first_name":"Themistoklis"},{"full_name":"Schwarz, Jan","last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"first_name":"Miriam","full_name":"Balles, Miriam","last_name":"Balles"},{"first_name":"Maibritt","full_name":"Kretschmer, Maibritt","last_name":"Kretschmer"},{"first_name":"Maria","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","last_name":"Nemethova","full_name":"Nemethova, Maria"},{"orcid":"0000-0003-0876-3187","full_name":"Chait, Remy P","last_name":"Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","first_name":"Remy P"},{"last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"full_name":"Lange, Janina","last_name":"Lange","first_name":"Janina"},{"last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-4561-241X","full_name":"Sixt, Michael K","last_name":"Sixt"},{"first_name":"Stefan","full_name":"Zahler, Stefan","last_name":"Zahler"}],"project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Cellular navigation along spatial gradients","grant_number":"724373"}]},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"9819","file_date_updated":"2021-08-09T11:41:50Z","department":[{"_id":"BeBi"}],"ddc":["000"],"date_updated":"2023-08-10T14:25:08Z","intvolume":" 40","month":"08","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Photorealistic editing of head portraits is a challenging task as humans are very sensitive to inconsistencies in faces. We present an approach for high-quality intuitive editing of the camera viewpoint and scene illumination (parameterised with an environment map) in a portrait image. This requires our method to capture and control the full reflectance field of the person in the image. Most editing approaches rely on supervised learning using training data captured with setups such as light and camera stages. Such datasets are expensive to acquire, not readily available and do not capture all the rich variations of in-the-wild portrait images. In addition, most supervised approaches only focus on relighting, and do not allow camera viewpoint editing. Thus, they only capture and control a subset of the reflectance field. Recently, portrait editing has been demonstrated by operating in the generative model space of StyleGAN. While such approaches do not require direct supervision, there is a significant loss of quality when compared to the supervised approaches. In this paper, we present a method which learns from limited supervised training data. The training images only include people in a fixed neutral expression with eyes closed, without much hair or background variations. Each person is captured under 150 one-light-at-a-time conditions and under 8 camera poses. Instead of training directly in the image space, we design a supervised problem which learns transformations in the latent space of StyleGAN. This combines the best of supervised learning and generative adversarial modeling. We show that the StyleGAN prior allows for generalisation to different expressions, hairstyles and backgrounds. This produces high-quality photorealistic results for in-the-wild images and significantly outperforms existing methods. Our approach can edit the illumination and pose simultaneously, and runs at interactive rates."}],"volume":40,"issue":"4","language":[{"iso":"eng"}],"file":[{"creator":"asandaue","file_size":49840741,"date_updated":"2021-08-09T11:41:50Z","file_name":"2021_ACMTransactionsOnGraphics_Mallikarjun.pdf","date_created":"2021-08-09T11:41:50Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"9834","checksum":"51b61b7e5c175e2d7ed8fa3b35f7525a"}],"publication_status":"published","publication_identifier":{"issn":["07300301"],"eissn":["15577368"]},"article_number":"44","title":"PhotoApp: Photorealistic appearance editing of head portraits","external_id":{"arxiv":["2103.07658"],"isi":["000674930900011"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"first_name":"B. R.","full_name":"Mallikarjun, B. R.","last_name":"Mallikarjun"},{"first_name":"Ayush","full_name":"Tewari, Ayush","last_name":"Tewari"},{"first_name":"Abdallah","last_name":"Dib","full_name":"Dib, Abdallah"},{"full_name":"Weyrich, Tim","last_name":"Weyrich","first_name":"Tim"},{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hans Peter","last_name":"Seidel","full_name":"Seidel, Hans Peter"},{"last_name":"Pfister","full_name":"Pfister, Hanspeter","first_name":"Hanspeter"},{"last_name":"Matusik","full_name":"Matusik, Wojciech","first_name":"Wojciech"},{"full_name":"Chevallier, Louis","last_name":"Chevallier","first_name":"Louis"},{"first_name":"Mohamed A.","full_name":"Elgharib, Mohamed A.","last_name":"Elgharib"},{"full_name":"Theobalt, Christian","last_name":"Theobalt","first_name":"Christian"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Mallikarjun, B. R., Ayush Tewari, Abdallah Dib, Tim Weyrich, Bernd Bickel, Hans Peter Seidel, Hanspeter Pfister, et al. “PhotoApp: Photorealistic Appearance Editing of Head Portraits.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459765.","ista":"Mallikarjun BR, Tewari A, Dib A, Weyrich T, Bickel B, Seidel HP, Pfister H, Matusik W, Chevallier L, Elgharib MA, Theobalt C. 2021. PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. 40(4), 44.","mla":"Mallikarjun, B. R., et al. “PhotoApp: Photorealistic Appearance Editing of Head Portraits.” ACM Transactions on Graphics, vol. 40, no. 4, 44, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459765.","ama":"Mallikarjun BR, Tewari A, Dib A, et al. PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459765","apa":"Mallikarjun, B. R., Tewari, A., Dib, A., Weyrich, T., Bickel, B., Seidel, H. P., … Theobalt, C. (2021). PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3450626.3459765","ieee":"B. R. Mallikarjun et al., “PhotoApp: Photorealistic appearance editing of head portraits,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021.","short":"B.R. Mallikarjun, A. Tewari, A. Dib, T. Weyrich, B. Bickel, H.P. Seidel, H. Pfister, W. Matusik, L. Chevallier, M.A. Elgharib, C. Theobalt, ACM Transactions on Graphics 40 (2021)."},"oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery","acknowledgement":"This work was supported by the ERC Consolidator Grant 4DReply (770784). We also acknowledge support from Technicolor and InterDigital. We thank Tiancheng Sun for kindly helping us with the comparisons with Sun et al. [2019].","date_created":"2021-08-08T22:01:27Z","date_published":"2021-08-01T00:00:00Z","doi":"10.1145/3450626.3459765","publication":"ACM Transactions on Graphics","day":"01","year":"2021","isi":1,"has_accepted_license":"1"},{"isi":1,"has_accepted_license":"1","year":"2021","day":"29","publication":"PLoS ONE","date_published":"2021-07-29T00:00:00Z","doi":"10.1371/journal.pone.0255267","date_created":"2021-08-08T22:01:26Z","acknowledgement":"We would like to thank Alfred Uhl, Richard Kollár and Katarína Bod’ová for very helpful comments. We also thank Matej Mišík for discussion and information regarding the Slovak testing data and Ag-Test used.","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"citation":{"chicago":"Hledik, Michal, Jitka Polechova, Mathias Beiglböck, Anna Nele Herdina, Robert Strassl, and Martin Posch. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0255267.","ista":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 16(7), e0255267.","mla":"Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE, vol. 16, no. 7, e0255267, Public Library of Science, 2021, doi:10.1371/journal.pone.0255267.","ama":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 2021;16(7). doi:10.1371/journal.pone.0255267","apa":"Hledik, M., Polechova, J., Beiglböck, M., Herdina, A. N., Strassl, R., & Posch, M. (2021). Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0255267","ieee":"M. Hledik, J. Polechova, M. Beiglböck, A. N. Herdina, R. Strassl, and M. Posch, “Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program,” PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021.","short":"M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch, PLoS ONE 16 (2021)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal","last_name":"Hledik"},{"id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","first_name":"Jitka","last_name":"Polechova","full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112"},{"first_name":"Mathias","full_name":"Beiglböck, Mathias","last_name":"Beiglböck"},{"first_name":"Anna Nele","last_name":"Herdina","full_name":"Herdina, Anna Nele"},{"first_name":"Robert","last_name":"Strassl","full_name":"Strassl, Robert"},{"first_name":"Martin","full_name":"Posch, Martin","last_name":"Posch"}],"external_id":{"pmid":["34324553"],"isi":["000685248200095"]},"article_processing_charge":"Yes","title":"Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program","article_number":"e0255267","publication_identifier":{"eissn":["1932-6203"]},"publication_status":"published","file":[{"date_updated":"2021-08-09T11:52:14Z","file_size":773921,"creator":"asandaue","date_created":"2021-08-09T11:52:14Z","file_name":"2021_PLoSONE_Hledík.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"ae4df60eb62f4491278588548d0c1f93","file_id":"9835","success":1}],"language":[{"iso":"eng"}],"issue":"7","volume":16,"abstract":[{"lang":"eng","text":"Aims: Mass antigen testing programs have been challenged because of an alleged insufficient specificity, leading to a large number of false positives. The objective of this study is to derive a lower bound of the specificity of the SD Biosensor Standard Q Ag-Test in large scale practical use.\r\nMethods: Based on county data from the nationwide tests for SARS-CoV-2 in Slovakia between 31.10.–1.11. 2020 we calculate a lower confidence bound for the specificity. As positive test results were not systematically verified by PCR tests, we base the lower bound on a worst case assumption, assuming all positives to be false positives.\r\nResults: 3,625,332 persons from 79 counties were tested. The lowest positivity rate was observed in the county of Rožňava where 100 out of 34307 (0.29%) tests were positive. This implies a test specificity of at least 99.6% (97.5% one-sided lower confidence bound, adjusted for multiplicity).\r\nConclusion: The obtained lower bound suggests a higher specificity compared to earlier studies in spite of the underlying worst case assumption and the application in a mass testing setting. The actual specificity is expected to exceed 99.6% if the prevalence in the respective regions was non-negligible at the time of testing. To our knowledge, this estimate constitutes the first bound obtained from large scale practical use of an antigen test."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"07","intvolume":" 16","date_updated":"2023-08-10T14:26:32Z","ddc":["610"],"department":[{"_id":"NiBa"}],"file_date_updated":"2021-08-09T11:52:14Z","_id":"9816","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Graff, Grzegorz, Beata Graff, Pawel Pilarczyk, Grzegorz Jablonski, Dariusz Gąsecki, and Krzysztof Narkiewicz. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0253851.","ista":"Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. 2021. Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. 16(7), e0253851.","mla":"Graff, Grzegorz, et al. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” PLoS ONE, vol. 16, no. 7, e0253851, Public Library of Science, 2021, doi:10.1371/journal.pone.0253851.","ieee":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, and K. Narkiewicz, “Persistent homology as a new method of the assessment of heart rate variability,” PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021.","short":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, K. Narkiewicz, PLoS ONE 16 (2021).","apa":"Graff, G., Graff, B., Pilarczyk, P., Jablonski, G., Gąsecki, D., & Narkiewicz, K. (2021). Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0253851","ama":"Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. 2021;16(7). doi:10.1371/journal.pone.0253851"},"title":"Persistent homology as a new method of the assessment of heart rate variability","author":[{"full_name":"Graff, Grzegorz","last_name":"Graff","first_name":"Grzegorz"},{"first_name":"Beata","last_name":"Graff","full_name":"Graff, Beata"},{"last_name":"Pilarczyk","full_name":"Pilarczyk, Pawel","first_name":"Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Grzegorz","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","last_name":"Jablonski","full_name":"Jablonski, Grzegorz","orcid":"0000-0002-3536-9866"},{"last_name":"Gąsecki","full_name":"Gąsecki, Dariusz","first_name":"Dariusz"},{"full_name":"Narkiewicz, Krzysztof","last_name":"Narkiewicz","first_name":"Krzysztof"}],"external_id":{"isi":["000678124900050"],"pmid":["34292957"]},"article_processing_charge":"Yes","article_number":"e0253851","day":"01","publication":"PLoS ONE","has_accepted_license":"1","isi":1,"year":"2021","date_published":"2021-07-01T00:00:00Z","doi":"10.1371/journal.pone.0253851","date_created":"2021-08-08T22:01:28Z","acknowledgement":"We express our gratitude to the anonymous referees who provided constructive comments that helped us improve the quality of the paper.","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"ddc":["006"],"date_updated":"2023-08-10T14:21:42Z","department":[{"_id":"HeEd"}],"file_date_updated":"2021-08-09T09:25:41Z","_id":"9821","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_id":"9832","checksum":"0277aa155d5db1febd2cb384768bba5f","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-08-09T09:25:41Z","file_name":"2021_PLoSONE_Graff.pdf","date_updated":"2021-08-09T09:25:41Z","file_size":2706919,"creator":"asandaue"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["19326203"]},"publication_status":"published","issue":"7","volume":16,"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Heart rate variability (hrv) is a physiological phenomenon of the variation in the length of the time interval between consecutive heartbeats. In many cases it could be an indicator of the development of pathological states. The classical approach to the analysis of hrv includes time domain methods and frequency domain methods. However, attempts are still being made to define new and more effective hrv assessment tools. Persistent homology is a novel data analysis tool developed in the recent decades that is rooted at algebraic topology. The Topological Data Analysis (TDA) approach focuses on examining the shape of the data in terms of connectedness and holes, and has recently proved to be very effective in various fields of research. In this paper we propose the use of persistent homology to the hrv analysis. We recall selected topological descriptors used in the literature and we introduce some new topological descriptors that reflect the specificity of hrv, and we discuss their relation to the standard hrv measures. In particular, we show that this novel approach provides a collection of indices that might be at least as useful as the classical parameters in differentiating between series of beat-to-beat intervals (RR-intervals) in healthy subjects and patients suffering from a stroke episode.","lang":"eng"}],"month":"07","intvolume":" 16","scopus_import":"1"},{"title":"The effect of shape and illumination on material perception: Model and applications","author":[{"first_name":"Ana","full_name":"Serrano, Ana","last_name":"Serrano"},{"last_name":"Chen","full_name":"Chen, Bin","first_name":"Bin"},{"last_name":"Wang","full_name":"Wang, Chao","first_name":"Chao"},{"orcid":"0000-0002-5062-4474","full_name":"Piovarci, Michael","last_name":"Piovarci","first_name":"Michael","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E"},{"first_name":"Hans Peter","full_name":"Seidel, Hans Peter","last_name":"Seidel"},{"full_name":"Didyk, Piotr","last_name":"Didyk","first_name":"Piotr"},{"first_name":"Karol","last_name":"Myszkowski","full_name":"Myszkowski, Karol"}],"external_id":{"isi":["000674930900090"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Serrano, Ana, Bin Chen, Chao Wang, Michael Piovarci, Hans Peter Seidel, Piotr Didyk, and Karol Myszkowski. “The Effect of Shape and Illumination on Material Perception: Model and Applications.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459813.","ista":"Serrano A, Chen B, Wang C, Piovarci M, Seidel HP, Didyk P, Myszkowski K. 2021. The effect of shape and illumination on material perception: Model and applications. ACM Transactions on Graphics. 40(4), 125.","mla":"Serrano, Ana, et al. “The Effect of Shape and Illumination on Material Perception: Model and Applications.” ACM Transactions on Graphics, vol. 40, no. 4, 125, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459813.","ama":"Serrano A, Chen B, Wang C, et al. The effect of shape and illumination on material perception: Model and applications. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459813","apa":"Serrano, A., Chen, B., Wang, C., Piovarci, M., Seidel, H. P., Didyk, P., & Myszkowski, K. (2021). The effect of shape and illumination on material perception: Model and applications. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3450626.3459813","ieee":"A. Serrano et al., “The effect of shape and illumination on material perception: Model and applications,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021.","short":"A. Serrano, B. Chen, C. Wang, M. Piovarci, H.P. Seidel, P. Didyk, K. Myszkowski, ACM Transactions on Graphics 40 (2021)."},"article_number":"125","date_published":"2021-08-01T00:00:00Z","doi":"10.1145/3450626.3459813","date_created":"2021-08-08T22:01:28Z","day":"01","publication":"ACM Transactions on Graphics","isi":1,"year":"2021","publisher":"Association for Computing Machinery","quality_controlled":"1","oa":1,"acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie, grant agreement Nº 765911 (RealVision) and from the European Research Council (ERC), grant agreement Nº 804226 (PERDY).","department":[{"_id":"BeBi"}],"date_updated":"2023-08-10T14:20:10Z","status":"public","type":"journal_article","article_type":"original","_id":"9820","issue":"4","volume":40,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["15577368"],"issn":["07300301"]},"publication_status":"published","month":"08","intvolume":" 40","scopus_import":"1","main_file_link":[{"url":"https://zaguan.unizar.es/record/110704/files/texto_completo.pdf","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"text":"Material appearance hinges on material reflectance properties but also surface geometry and illumination. The unlimited number of potential combinations between these factors makes understanding and predicting material appearance a very challenging task. In this work, we collect a large-scale dataset of perceptual ratings of appearance attributes with more than 215,680 responses for 42,120 distinct combinations of material, shape, and illumination. The goal of this dataset is twofold. First, we analyze for the first time the effects of illumination and geometry in material perception across such a large collection of varied appearances. We connect our findings to those of the literature, discussing how previous knowledge generalizes across very diverse materials, shapes, and illuminations. Second, we use the collected dataset to train a deep learning architecture for predicting perceptual attributes that correlate with human judgments. We demonstrate the consistent and robust behavior of our predictor in various challenging scenarios, which, for the first time, enables estimating perceived material attributes from general 2D images. Since our predictor relies on the final appearance in an image, it can compare appearance properties across different geometries and illumination conditions. Finally, we demonstrate several applications that use our predictor, including appearance reproduction using 3D printing, BRDF editing by integrating our predictor in a differentiable renderer, illumination design, or material recommendations for scene design.","lang":"eng"}]},{"article_number":"168","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459816.","ista":"Sperl G, Narain R, Wojtan C. 2021. Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. 40(4), 168.","mla":"Sperl, Georg, et al. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” ACM Transactions on Graphics, vol. 40, no. 4, 168, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459816.","apa":"Sperl, G., Narain, R., & Wojtan, C. (2021). Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3450626.3459816","ama":"Sperl G, Narain R, Wojtan C. Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459816","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Mechanics-aware deformation of yarn pattern geometry,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021.","short":"G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 40 (2021)."},"title":"Mechanics-aware deformation of yarn pattern geometry","author":[{"full_name":"Sperl, Georg","last_name":"Sperl","first_name":"Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rahul","last_name":"Narain","full_name":"Narain, Rahul"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000674930900132"]},"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. We also thank Seddi Labs for providing the garment model with fold-over seams.\r\nThis research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific\r\nComputing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176. Rahul Narain is supported by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc.","publisher":"Association for Computing Machinery","quality_controlled":"1","oa":1,"day":"01","publication":"ACM Transactions on Graphics","isi":1,"year":"2021","date_published":"2021-08-01T00:00:00Z","doi":"10.1145/3450626.3459816","date_created":"2021-08-08T22:01:27Z","_id":"9818","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-10T14:24:36Z","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Triangle mesh-based simulations are able to produce satisfying animations of knitted and woven cloth; however, they lack the rich geometric detail of yarn-level simulations. Naive texturing approaches do not consider yarn-level physics, while full yarn-level simulations may become prohibitively expensive for large garments. We propose a method to animate yarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware fashion. Using triangle strains to interpolate precomputed yarn geometry, we are able to reproduce effects such as knit loops tightening under stretching. In combination with precomputed mesh animation or real-time mesh simulation, our method is able to animate yarn-level cloth in real-time at large scales."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"month":"08","intvolume":" 40","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1145/3450626.3459816","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["15577368"],"issn":["07300301"]},"publication_status":"published","related_material":{"record":[{"id":"12358","status":"public","relation":"dissertation_contains"},{"status":"public","id":"9327","relation":"software"}],"link":[{"description":"News on IST Webpage","url":"https://ist.ac.at/en/news/knitting-virtual-yarn/","relation":"press_release"}]},"issue":"4","volume":40,"ec_funded":1}]