[{"year":"2021","_id":"10598","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"conference","volume":130,"page":"397-405","publication_identifier":{"issn":["2640-3498"]},"citation":{"chicago":"Mondelli, Marco, and Ramji Venkataramanan. “Approximate Message Passing with Spectral Initialization for Generalized Linear Models.” In <i>Proceedings of The 24th International Conference on Artificial Intelligence and Statistics</i>, edited by Arindam Banerjee and Kenji Fukumizu, 130:397–405. ML Research Press, 2021.","ieee":"M. Mondelli and R. Venkataramanan, “Approximate message passing with spectral initialization for generalized linear models,” in <i>Proceedings of The 24th International Conference on Artificial Intelligence and Statistics</i>, Virtual, San Diego, CA, United States, 2021, vol. 130, pp. 397–405.","apa":"Mondelli, M., &#38; Venkataramanan, R. (2021). Approximate message passing with spectral initialization for generalized linear models. In A. Banerjee &#38; K. Fukumizu (Eds.), <i>Proceedings of The 24th International Conference on Artificial Intelligence and Statistics</i> (Vol. 130, pp. 397–405). Virtual, San Diego, CA, United States: ML Research Press.","ama":"Mondelli M, Venkataramanan R. Approximate message passing with spectral initialization for generalized linear models. In: Banerjee A, Fukumizu K, eds. <i>Proceedings of The 24th International Conference on Artificial Intelligence and Statistics</i>. Vol 130. ML Research Press; 2021:397-405.","ista":"Mondelli M, Venkataramanan R. 2021. Approximate message passing with spectral initialization for generalized linear models. Proceedings of The 24th International Conference on Artificial Intelligence and Statistics. AISTATS: Artificial Intelligence and Statistics, Proceedings of Machine Learning Research, vol. 130, 397–405.","mla":"Mondelli, Marco, and Ramji Venkataramanan. “Approximate Message Passing with Spectral Initialization for Generalized Linear Models.” <i>Proceedings of The 24th International Conference on Artificial Intelligence and Statistics</i>, edited by Arindam Banerjee and Kenji Fukumizu, vol. 130, ML Research Press, 2021, pp. 397–405.","short":"M. Mondelli, R. Venkataramanan, in:, A. Banerjee, K. Fukumizu (Eds.), Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, ML Research Press, 2021, pp. 397–405."},"external_id":{"arxiv":["2010.03460"]},"status":"public","acknowledgement":"The authors would like to thank Andrea Montanari for helpful discussions. M. Mondelli was partially supported by the 2019 Lopez-Loreta Prize. R. Venkataramanan was partially supported by the Alan Turing Institute under the EPSRC grant EP/N510129/1.","oa":1,"date_created":"2022-01-03T11:34:22Z","oa_version":"Preprint","publisher":"ML Research Press","publication":"Proceedings of The 24th International Conference on Artificial Intelligence and Statistics","department":[{"_id":"MaMo"}],"title":"Approximate message passing with spectral initialization for generalized linear models","abstract":[{"lang":"eng","text":" We consider the problem of estimating a signal from measurements obtained via a generalized linear model. We focus on estimators based on approximate message passing (AMP), a family of iterative algorithms with many appealing features: the performance of AMP in the high-dimensional limit can be succinctly characterized under suitable model assumptions; AMP can also be tailored to the empirical distribution of the signal entries, and for a wide class of estimation problems, AMP is conjectured to be optimal among all polynomial-time algorithms. However, a major issue of AMP is that in many models (such as phase retrieval), it requires an initialization correlated with the ground-truth signal and independent from the measurement matrix. Assuming that such an initialization is available is typically not realistic. In this paper, we solve this problem by proposing an AMP algorithm initialized with a spectral estimator. With such an initialization, the standard AMP analysis fails since the spectral estimator depends in a complicated way on the design matrix. Our main contribution is a rigorous characterization of the performance of AMP with spectral initialization in the high-dimensional limit. The key technical idea is to define and analyze a two-phase artificial AMP algorithm that first produces the spectral estimator, and then closely approximates the iterates of the true AMP. We also provide numerical results that demonstrate the validity of the proposed approach. "}],"arxiv":1,"publication_status":"published","intvolume":"       130","main_file_link":[{"open_access":"1","url":"https://proceedings.mlr.press/v130/mondelli21a.html"}],"month":"04","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"language":[{"iso":"eng"}],"day":"01","conference":{"end_date":"2021-04-15","name":"AISTATS: Artificial Intelligence and Statistics","start_date":"2021-04-13","location":"Virtual, San Diego, CA, United States"},"quality_controlled":"1","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","related_material":{"record":[{"id":"12480","status":"public","relation":"later_version"}]},"alternative_title":["Proceedings of Machine Learning Research"],"date_updated":"2024-03-07T10:36:53Z","date_published":"2021-04-01T00:00:00Z","author":[{"first_name":"Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"first_name":"Ramji","last_name":"Venkataramanan","full_name":"Venkataramanan, Ramji"}],"editor":[{"full_name":"Banerjee, Arindam","first_name":"Arindam","last_name":"Banerjee"},{"first_name":"Kenji","last_name":"Fukumizu","full_name":"Fukumizu, Kenji"}]},{"publication_status":"published","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2112.00057"}],"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"language":[{"iso":"eng"}],"month":"11","day":"01","conference":{"name":"ACSSC: Asilomar Conference on Signals, Systems, and Computers","end_date":"2021-11-03","location":"Virtual, Pacific Grove, CA, United States","start_date":"2021-10-31"},"quality_controlled":"1","scopus_import":"1","doi":"10.1109/IEEECONF53345.2021.9723394","date_updated":"2024-09-10T13:03:17Z","article_processing_charge":"No","date_published":"2021-11-01T00:00:00Z","author":[{"last_name":"Hashemi","first_name":"Seyyed Ali","full_name":"Hashemi, Seyyed Ali"},{"orcid":"0000-0002-3242-7020","last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco"},{"full_name":"Cioffi, John","last_name":"Cioffi","first_name":"John"},{"full_name":"Goldsmith, Andrea","first_name":"Andrea","last_name":"Goldsmith"}],"year":"2021","_id":"10599","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"943-947","volume":"2021-October","publication_identifier":{"isbn":["9781665458283"],"issn":["1058-6393"]},"citation":{"chicago":"Hashemi, Seyyed Ali, Marco Mondelli, John Cioffi, and Andrea Goldsmith. “Successive Syndrome-Check Decoding of Polar Codes.” In <i>Proceedings of the 55th Asilomar Conference on Signals, Systems, and Computers</i>, 2021–October:943–47. Institute of Electrical and Electronics Engineers, 2021. <a href=\"https://doi.org/10.1109/IEEECONF53345.2021.9723394\">https://doi.org/10.1109/IEEECONF53345.2021.9723394</a>.","ieee":"S. A. Hashemi, M. Mondelli, J. Cioffi, and A. Goldsmith, “Successive syndrome-check decoding of polar codes,” in <i>Proceedings of the 55th Asilomar Conference on Signals, Systems, and Computers</i>, Virtual, Pacific Grove, CA, United States, 2021, vol. 2021–October, pp. 943–947.","apa":"Hashemi, S. A., Mondelli, M., Cioffi, J., &#38; Goldsmith, A. (2021). Successive syndrome-check decoding of polar codes. In <i>Proceedings of the 55th Asilomar Conference on Signals, Systems, and Computers</i> (Vol. 2021–October, pp. 943–947). Virtual, Pacific Grove, CA, United States: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/IEEECONF53345.2021.9723394\">https://doi.org/10.1109/IEEECONF53345.2021.9723394</a>","ama":"Hashemi SA, Mondelli M, Cioffi J, Goldsmith A. Successive syndrome-check decoding of polar codes. In: <i>Proceedings of the 55th Asilomar Conference on Signals, Systems, and Computers</i>. Vol 2021-October. Institute of Electrical and Electronics Engineers; 2021:943-947. doi:<a href=\"https://doi.org/10.1109/IEEECONF53345.2021.9723394\">10.1109/IEEECONF53345.2021.9723394</a>","mla":"Hashemi, Seyyed Ali, et al. “Successive Syndrome-Check Decoding of Polar Codes.” <i>Proceedings of the 55th Asilomar Conference on Signals, Systems, and Computers</i>, vol. 2021–October, Institute of Electrical and Electronics Engineers, 2021, pp. 943–47, doi:<a href=\"https://doi.org/10.1109/IEEECONF53345.2021.9723394\">10.1109/IEEECONF53345.2021.9723394</a>.","ista":"Hashemi SA, Mondelli M, Cioffi J, Goldsmith A. 2021. Successive syndrome-check decoding of polar codes. Proceedings of the 55th Asilomar Conference on Signals, Systems, and Computers. ACSSC: Asilomar Conference on Signals, Systems, and Computers vol. 2021–October, 943–947.","short":"S.A. Hashemi, M. Mondelli, J. Cioffi, A. Goldsmith, in:, Proceedings of the 55th Asilomar Conference on Signals, Systems, and Computers, Institute of Electrical and Electronics Engineers, 2021, pp. 943–947."},"external_id":{"arxiv":["2112.00057"]},"acknowledgement":"This work is supported in part by ONR grant N00014-18-1-2191. S. A. Hashemi was supported by a Postdoctoral Fellowship from the Natural Sciences and Engineering Research Council of Canada (NSERC) and by Huawei. M. Mondelli was partially supported by the 2019 Lopez-Loreta Prize.","oa":1,"status":"public","oa_version":"Preprint","date_created":"2022-01-03T11:39:51Z","publisher":"Institute of Electrical and Electronics Engineers","department":[{"_id":"MaMo"}],"title":"Successive syndrome-check decoding of polar codes","publication":"Proceedings of the 55th Asilomar Conference on Signals, Systems, and Computers","abstract":[{"lang":"eng","text":"A two-part successive syndrome-check decoding of polar codes is proposed with the first part successively refining the received codeword and the second part checking its syndrome. A new formulation of the successive-cancellation (SC) decoding algorithm is presented that allows for successively refining the received codeword by comparing the log-likelihood ratio value of a frozen bit with its predefined value. The syndrome of the refined received codeword is then checked for possible errors. In case there are no errors, the decoding process is terminated. Otherwise, the decoder continues to refine the received codeword. The proposed method is extended to the case of SC list (SCL) decoding by terminating the decoding process when the syndrome of the best candidate in the list indicates no errors. Simulation results show that the proposed method reduces the time-complexity of SC and SCL decoders and their fast variants, especially at high signal-to-noise ratios."}],"arxiv":1},{"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"e75639","file_date_updated":"2022-01-10T09:40:37Z","quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","doi":"10.7554/eLife.75639","date_updated":"2023-08-17T06:32:44Z","author":[{"last_name":"Godard","first_name":"Benoit G","id":"33280250-F248-11E8-B48F-1D18A9856A87","full_name":"Godard, Benoit G"},{"last_name":"Dumollard","first_name":"Remi","full_name":"Dumollard, Remi"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"},{"last_name":"Mcdougall","first_name":"Alex","full_name":"Mcdougall, Alex"}],"date_published":"2021-12-21T00:00:00Z","file":[{"success":1,"date_created":"2022-01-10T09:40:37Z","content_type":"application/pdf","access_level":"open_access","creator":"alisjak","relation":"main_file","file_name":"2021_eLife_Godard.pdf","checksum":"759c7a873d554c48a6639e6350746ca6","file_size":7769934,"file_id":"10611","date_updated":"2022-01-10T09:40:37Z"}],"publication_status":"published","intvolume":"        10","isi":1,"month":"12","project":[{"call_identifier":"FWF","name":"Control of embryonic cleavage pattern","grant_number":"I03601","_id":"2646861A-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"ddc":["570"],"day":"21","date_created":"2022-01-09T23:01:26Z","oa_version":"Published Version","publisher":"eLife Sciences Publications","publication":"eLife","title":"Combined effect of cell geometry and polarity domains determines the orientation of unequal division","department":[{"_id":"CaHe"}],"abstract":[{"lang":"eng","text":"Cell division orientation is thought to result from a competition between cell geometry and polarity domains controlling the position of the mitotic spindle during mitosis. Depending on the level of cell shape anisotropy or the strength of the polarity domain, one dominates the other and determines the orientation of the spindle. Whether and how such competition is also at work to determine unequal cell division (UCD), producing daughter cells of different size, remains unclear. Here, we show that cell geometry and polarity domains cooperate, rather than compete, in positioning the cleavage plane during UCDs in early ascidian embryos. We found that the UCDs and their orientation at the ascidian third cleavage rely on the spindle tilting in an anisotropic cell shape, and cortical polarity domains exerting different effects on spindle astral microtubules. By systematically varying mitotic cell shape, we could modulate the effect of attractive and repulsive polarity domains and consequently generate predicted daughter cell size asymmetries and position. We therefore propose that the spindle position during UCD is set by the combined activities of cell geometry and polarity domains, where cell geometry modulates the effect of cortical polarity domain(s)."}],"year":"2021","has_accepted_license":"1","_id":"10606","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":10,"publication_identifier":{"eissn":["2050-084X"]},"citation":{"short":"B.G. Godard, R. Dumollard, C.-P.J. Heisenberg, A. Mcdougall, ELife 10 (2021).","ista":"Godard BG, Dumollard R, Heisenberg C-PJ, Mcdougall A. 2021. Combined effect of cell geometry and polarity domains determines the orientation of unequal division. eLife. 10, e75639.","mla":"Godard, Benoit G., et al. “Combined Effect of Cell Geometry and Polarity Domains Determines the Orientation of Unequal Division.” <i>ELife</i>, vol. 10, e75639, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.75639\">10.7554/eLife.75639</a>.","ama":"Godard BG, Dumollard R, Heisenberg C-PJ, Mcdougall A. Combined effect of cell geometry and polarity domains determines the orientation of unequal division. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.75639\">10.7554/eLife.75639</a>","apa":"Godard, B. G., Dumollard, R., Heisenberg, C.-P. J., &#38; Mcdougall, A. (2021). Combined effect of cell geometry and polarity domains determines the orientation of unequal division. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.75639\">https://doi.org/10.7554/eLife.75639</a>","chicago":"Godard, Benoit G, Remi Dumollard, Carl-Philipp J Heisenberg, and Alex Mcdougall. “Combined Effect of Cell Geometry and Polarity Domains Determines the Orientation of Unequal Division.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.75639\">https://doi.org/10.7554/eLife.75639</a>.","ieee":"B. G. Godard, R. Dumollard, C.-P. J. Heisenberg, and A. Mcdougall, “Combined effect of cell geometry and polarity domains determines the orientation of unequal division,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021."},"external_id":{"isi":["000733610100001"]},"article_type":"original","acknowledgement":"We thank members of the Heisenberg and McDougall groups for technical advice and discussion. We are grateful to the Bioimaging and Nanofabrication facilities of IST Austria and the Imaging Platform (PIM) and animal facility (CRB) of Institut de la Mer de Villefranche (IMEV), which is supported by EMBRC-France, whose French state funds are managed by the ANR within the Investments of the Future program under reference ANR-10-INBS-0, for continuous support. This work was supported by a collaborative grant from the French Government funding agency Agence National de la Recherche to McDougall (ANR 'MorCell': ANR-17-CE 13-0028) and the Austrian Science Fund to Heisenberg (FWF: I 3601-B27).","status":"public","oa":1},{"intvolume":"        91","publication_status":"published","file":[{"date_updated":"2022-01-10T13:41:40Z","file_id":"10612","file_size":6848513,"file_name":"2021_Parkinsonism_Venezia.pdf","checksum":"360681585acb51e80d17c6b213c56b55","relation":"main_file","creator":"alisjak","access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2022-01-10T13:41:40Z"}],"language":[{"iso":"eng"}],"isi":1,"month":"10","pmid":1,"day":"01","ddc":["610"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2022-01-10T13:41:40Z","scopus_import":"1","quality_controlled":"1","author":[{"first_name":"Serena","last_name":"Venezia","full_name":"Venezia, Serena"},{"last_name":"Kaufmann","orcid":"0000-0001-9735-5315","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter"},{"full_name":"Wenning, Gregor K.","last_name":"Wenning","first_name":"Gregor K."},{"last_name":"Stefanova","first_name":"Nadia","full_name":"Stefanova, Nadia"}],"date_published":"2021-10-01T00:00:00Z","doi":"10.1016/j.parkreldis.2021.09.007","date_updated":"2023-08-17T06:36:01Z","article_processing_charge":"No","_id":"10607","has_accepted_license":"1","year":"2021","page":"59-65","volume":91,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Venezia, Serena, Walter Kaufmann, Gregor K. Wenning, and Nadia Stefanova. “Toll-like Receptor 4 Deficiency Facilitates α-Synuclein Propagation and Neurodegeneration in a Mouse Model of Prodromal Parkinson’s Disease.” <i>Parkinsonism &#38; Related Disorders</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.parkreldis.2021.09.007\">https://doi.org/10.1016/j.parkreldis.2021.09.007</a>.","ieee":"S. Venezia, W. Kaufmann, G. K. Wenning, and N. Stefanova, “Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease,” <i>Parkinsonism &#38; Related Disorders</i>, vol. 91. Elsevier, pp. 59–65, 2021.","apa":"Venezia, S., Kaufmann, W., Wenning, G. K., &#38; Stefanova, N. (2021). Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease. <i>Parkinsonism &#38; Related Disorders</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.parkreldis.2021.09.007\">https://doi.org/10.1016/j.parkreldis.2021.09.007</a>","ama":"Venezia S, Kaufmann W, Wenning GK, Stefanova N. Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease. <i>Parkinsonism &#38; Related Disorders</i>. 2021;91:59-65. doi:<a href=\"https://doi.org/10.1016/j.parkreldis.2021.09.007\">10.1016/j.parkreldis.2021.09.007</a>","short":"S. Venezia, W. Kaufmann, G.K. Wenning, N. Stefanova, Parkinsonism &#38; Related Disorders 91 (2021) 59–65.","mla":"Venezia, Serena, et al. “Toll-like Receptor 4 Deficiency Facilitates α-Synuclein Propagation and Neurodegeneration in a Mouse Model of Prodromal Parkinson’s Disease.” <i>Parkinsonism &#38; Related Disorders</i>, vol. 91, Elsevier, 2021, pp. 59–65, doi:<a href=\"https://doi.org/10.1016/j.parkreldis.2021.09.007\">10.1016/j.parkreldis.2021.09.007</a>.","ista":"Venezia S, Kaufmann W, Wenning GK, Stefanova N. 2021. Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease. Parkinsonism &#38; Related Disorders. 91, 59–65."},"publication_identifier":{"issn":["1353-8020"],"eissn":["1873-5126"]},"oa":1,"acknowledgement":"This study was supported by grants of the Austrian Science Fund (FWF) F4414 and W1206-08. Electron microscopy was performed at the Scientific Service Units (SSU) of IST-Austria through resources provided by the Electron Microscopy Facility.","status":"public","article_type":"original","external_id":{"isi":["000701142900012"],"pmid":["34530328"]},"oa_version":"Published Version","date_created":"2022-01-09T23:01:26Z","department":[{"_id":"EM-Fac"}],"title":"Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson's disease","publication":"Parkinsonism & Related Disorders","publisher":"Elsevier","abstract":[{"lang":"eng","text":"The evidence linking innate immunity mechanisms and neurodegenerative diseases is growing, but the specific mechanisms are incompletely understood. Experimental data suggest that microglial TLR4 mediates the uptake and clearance of α-synuclein also termed synucleinophagy. The accumulation of misfolded α-synuclein throughout the brain is central to Parkinson's disease (PD). The distribution and progression of the pathology is often attributed to the propagation of α-synuclein. Here, we apply a classical α-synuclein propagation model of prodromal PD in wild type and TLR4 deficient mice to study the role of TLR4 in the progression of the disease. Our data suggest that TLR4 deficiency facilitates the α-synuclein seed spreading associated with reduced lysosomal activity of microglia. Three months after seed inoculation, more pronounced proteinase K-resistant α-synuclein inclusion pathology is observed in mice with TLR4 deficiency. The facilitated propagation of α-synuclein is associated with early loss of dopamine transporter (DAT) signal in the striatum and loss of dopaminergic neurons in substantia nigra pars compacta of TLR4 deficient mice. These new results support TLR4 signaling as a putative target for disease modification to slow the progression of PD and related disorders."}]},{"type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10608","year":"2021","has_accepted_license":"1","oa":1,"acknowledgement":"We would like to thank the referees for their careful reading and the comments that improved our work. The third named author would like to thank the Division of Mathematics, Physics and Earth Sciences of the Graduate School of Science and Engineering of Ehime University and the second named author for hosting his visit in June 2018. Open access funding provided by Institute of Science and Technology (IST Austria).","status":"public","article_type":"original","citation":{"ista":"Weighill T, Yamauchi T, Zava N. 2021. Coarse infinite-dimensionality of hyperspaces of finite subsets. European Journal of Mathematics.","mla":"Weighill, Thomas, et al. “Coarse Infinite-Dimensionality of Hyperspaces of Finite Subsets.” <i>European Journal of Mathematics</i>, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s40879-021-00515-3\">10.1007/s40879-021-00515-3</a>.","short":"T. Weighill, T. Yamauchi, N. Zava, European Journal of Mathematics (2021).","ama":"Weighill T, Yamauchi T, Zava N. Coarse infinite-dimensionality of hyperspaces of finite subsets. <i>European Journal of Mathematics</i>. 2021. doi:<a href=\"https://doi.org/10.1007/s40879-021-00515-3\">10.1007/s40879-021-00515-3</a>","apa":"Weighill, T., Yamauchi, T., &#38; Zava, N. (2021). Coarse infinite-dimensionality of hyperspaces of finite subsets. <i>European Journal of Mathematics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40879-021-00515-3\">https://doi.org/10.1007/s40879-021-00515-3</a>","chicago":"Weighill, Thomas, Takamitsu Yamauchi, and Nicolò Zava. “Coarse Infinite-Dimensionality of Hyperspaces of Finite Subsets.” <i>European Journal of Mathematics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s40879-021-00515-3\">https://doi.org/10.1007/s40879-021-00515-3</a>.","ieee":"T. Weighill, T. Yamauchi, and N. Zava, “Coarse infinite-dimensionality of hyperspaces of finite subsets,” <i>European Journal of Mathematics</i>. Springer Nature, 2021."},"publication_identifier":{"issn":["2199-675X"],"eissn":["2199-6768"]},"department":[{"_id":"HeEd"}],"title":"Coarse infinite-dimensionality of hyperspaces of finite subsets","publication":"European Journal of Mathematics","publisher":"Springer Nature","oa_version":"Published Version","date_created":"2022-01-09T23:01:27Z","abstract":[{"lang":"eng","text":"We consider infinite-dimensional properties in coarse geometry for hyperspaces consisting of finite subsets of metric spaces with the Hausdorff metric. We see that several infinite-dimensional properties are preserved by taking the hyperspace of subsets with at most n points. On the other hand, we prove that, if a metric space contains a sequence of long intervals coarsely, then its hyperspace of finite subsets is not coarsely embeddable into any uniformly convex Banach space. As a corollary, the hyperspace of finite subsets of the real line is not coarsely embeddable into any uniformly convex Banach space. It is also shown that every (not necessarily bounded geometry) metric space with straight finite decomposition complexity has metric sparsification property."}],"publication_status":"published","file":[{"file_name":"2021_EuJournalMath_Weighill.pdf","checksum":"c435dcfa1ad3aadc5cdd7366bc7f4e98","file_size":384908,"date_updated":"2022-01-10T08:33:22Z","file_id":"10610","success":1,"date_created":"2022-01-10T08:33:22Z","content_type":"application/pdf","access_level":"open_access","creator":"cchlebak","relation":"main_file"}],"day":"30","ddc":["500"],"language":[{"iso":"eng"}],"month":"12","file_date_updated":"2022-01-10T08:33:22Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2021-12-30T00:00:00Z","author":[{"last_name":"Weighill","first_name":"Thomas","full_name":"Weighill, Thomas"},{"full_name":"Yamauchi, Takamitsu","last_name":"Yamauchi","first_name":"Takamitsu"},{"last_name":"Zava","first_name":"Nicolò","id":"c8b3499c-7a77-11eb-b046-aa368cbbf2ad","full_name":"Zava, Nicolò"}],"doi":"10.1007/s40879-021-00515-3","date_updated":"2022-01-10T08:36:55Z","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","quality_controlled":"1"},{"year":"2021","_id":"10609","type":"conference","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"335-364","volume":13091,"publication_identifier":{"isbn":["978-3-030-92074-6"],"issn":["0302-9743"],"eisbn":["978-3-030-92075-3"],"eissn":["1611-3349"]},"citation":{"ieee":"S. Chakraborty, C. Ganesh, M. Pancholi, and P. Sarkar, “Reverse firewalls for adaptively secure MPC without setup,” in <i>27th International Conference on the Theory and Application of Cryptology and Information Security</i>, Virtual, Singapore, 2021, vol. 13091, pp. 335–364.","chicago":"Chakraborty, Suvradip, Chaya Ganesh, Mahak Pancholi, and Pratik Sarkar. “Reverse Firewalls for Adaptively Secure MPC without Setup.” In <i>27th International Conference on the Theory and Application of Cryptology and Information Security</i>, 13091:335–64. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-92075-3_12\">https://doi.org/10.1007/978-3-030-92075-3_12</a>.","apa":"Chakraborty, S., Ganesh, C., Pancholi, M., &#38; Sarkar, P. (2021). Reverse firewalls for adaptively secure MPC without setup. In <i>27th International Conference on the Theory and Application of Cryptology and Information Security</i> (Vol. 13091, pp. 335–364). Virtual, Singapore: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-92075-3_12\">https://doi.org/10.1007/978-3-030-92075-3_12</a>","ama":"Chakraborty S, Ganesh C, Pancholi M, Sarkar P. Reverse firewalls for adaptively secure MPC without setup. In: <i>27th International Conference on the Theory and Application of Cryptology and Information Security</i>. Vol 13091. Springer Nature; 2021:335-364. doi:<a href=\"https://doi.org/10.1007/978-3-030-92075-3_12\">10.1007/978-3-030-92075-3_12</a>","ista":"Chakraborty S, Ganesh C, Pancholi M, Sarkar P. 2021. Reverse firewalls for adaptively secure MPC without setup. 27th International Conference on the Theory and Application of Cryptology and Information Security. ASIACRYPT: International Conference on Cryptology in Asia, LNCS, vol. 13091, 335–364.","mla":"Chakraborty, Suvradip, et al. “Reverse Firewalls for Adaptively Secure MPC without Setup.” <i>27th International Conference on the Theory and Application of Cryptology and Information Security</i>, vol. 13091, Springer Nature, 2021, pp. 335–64, doi:<a href=\"https://doi.org/10.1007/978-3-030-92075-3_12\">10.1007/978-3-030-92075-3_12</a>.","short":"S. Chakraborty, C. Ganesh, M. Pancholi, P. Sarkar, in:, 27th International Conference on the Theory and Application of Cryptology and Information Security, Springer Nature, 2021, pp. 335–364."},"external_id":{"isi":["000927876200012"]},"oa":1,"status":"public","oa_version":"Preprint","date_created":"2022-01-09T23:01:27Z","ec_funded":1,"publisher":"Springer Nature","title":"Reverse firewalls for adaptively secure MPC without setup","department":[{"_id":"KrPi"}],"publication":"27th International Conference on the Theory and Application of Cryptology and Information Security","abstract":[{"lang":"eng","text":"We study Multi-party computation (MPC) in the setting of subversion, where the adversary tampers with the machines of honest parties. Our goal is to construct actively secure MPC protocols where parties are corrupted adaptively by an adversary (as in the standard adaptive security setting), and in addition, honest parties’ machines are compromised.\r\nThe idea of reverse firewalls (RF) was introduced at EUROCRYPT’15 by Mironov and Stephens-Davidowitz as an approach to protecting protocols against corruption of honest parties’ devices. Intuitively, an RF for a party   P  is an external entity that sits between   P  and the outside world and whose scope is to sanitize   P ’s incoming and outgoing messages in the face of subversion of their computer. Mironov and Stephens-Davidowitz constructed a protocol for passively-secure two-party computation. At CRYPTO’20, Chakraborty, Dziembowski and Nielsen constructed a protocol for secure computation with firewalls that improved on this result, both by extending it to multi-party computation protocol, and considering active security in the presence of static corruptions. In this paper, we initiate the study of RF for MPC in the adaptive setting. We put forward a definition for adaptively secure MPC in the reverse firewall setting, explore relationships among the security notions, and then construct reverse firewalls for MPC in this stronger setting of adaptive security. We also resolve the open question of Chakraborty, Dziembowski and Nielsen by removing the need for a trusted setup in constructing RF for MPC. Towards this end, we construct reverse firewalls for adaptively secure augmented coin tossing and adaptively secure zero-knowledge protocols and obtain a constant round adaptively secure MPC protocol in the reverse firewall setting without setup. Along the way, we propose a new multi-party adaptively secure coin tossing protocol in the plain model, that is of independent interest."}],"publication_status":"published","main_file_link":[{"url":"https://eprint.iacr.org/2021/1262","open_access":"1"}],"intvolume":"     13091","project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"month":"12","isi":1,"day":"01","conference":{"start_date":"2021-12-06","location":"Virtual, Singapore","end_date":"2021-12-10","name":"ASIACRYPT: International Conference on Cryptology in Asia"},"quality_controlled":"1","scopus_import":"1","alternative_title":["LNCS"],"doi":"10.1007/978-3-030-92075-3_12","date_updated":"2023-08-17T06:34:41Z","article_processing_charge":"No","date_published":"2021-12-01T00:00:00Z","author":[{"id":"B9CD0494-D033-11E9-B219-A439E6697425","full_name":"Chakraborty, Suvradip","last_name":"Chakraborty","first_name":"Suvradip"},{"last_name":"Ganesh","first_name":"Chaya","full_name":"Ganesh, Chaya"},{"full_name":"Pancholi, Mahak","first_name":"Mahak","last_name":"Pancholi"},{"full_name":"Sarkar, Pratik","first_name":"Pratik","last_name":"Sarkar"}]},{"acknowledgement":"F.S. would like to thank Mario Ayala and Frank Redig for useful discussions. J.P.C. acknowledges partial financial support from the US National Science Foundation (DMS-1855604). F.S. was financially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411.\r\n","oa":1,"status":"public","issue":"3","external_id":{"arxiv":["2008.13403"]},"article_type":"original","citation":{"ieee":"J. P. Chen and F. Sau, “Higher-order hydrodynamics and equilibrium fluctuations of interacting particle systems,” <i>Markov Processes And Related Fields</i>, vol. 27, no. 3. Polymat Publishing, pp. 339–380, 2021.","chicago":"Chen, Joe P., and Federico Sau. “Higher-Order Hydrodynamics and Equilibrium Fluctuations of Interacting Particle Systems.” <i>Markov Processes And Related Fields</i>. Polymat Publishing, 2021.","apa":"Chen, J. P., &#38; Sau, F. (2021). Higher-order hydrodynamics and equilibrium fluctuations of interacting particle systems. <i>Markov Processes And Related Fields</i>. Polymat Publishing.","ama":"Chen JP, Sau F. Higher-order hydrodynamics and equilibrium fluctuations of interacting particle systems. <i>Markov Processes And Related Fields</i>. 2021;27(3):339-380.","short":"J.P. Chen, F. Sau, Markov Processes And Related Fields 27 (2021) 339–380.","mla":"Chen, Joe P., and Federico Sau. “Higher-Order Hydrodynamics and Equilibrium Fluctuations of Interacting Particle Systems.” <i>Markov Processes And Related Fields</i>, vol. 27, no. 3, Polymat Publishing, 2021, pp. 339–80.","ista":"Chen JP, Sau F. 2021. Higher-order hydrodynamics and equilibrium fluctuations of interacting particle systems. Markov Processes And Related Fields. 27(3), 339–380."},"publication_identifier":{"issn":["1024-2953"]},"volume":27,"page":"339-380","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","_id":"10613","year":"2021","arxiv":1,"abstract":[{"text":"Motivated by the recent preprint [\\emph{arXiv:2004.08412}] by Ayala, Carinci, and Redig, we first provide a general framework for the study of scaling limits of higher-order fields. Then, by considering the same class of infinite interacting particle systems as in [\\emph{arXiv:2004.08412}], namely symmetric simple exclusion and inclusion processes in the d-dimensional Euclidean lattice, we prove the hydrodynamic limit, and convergence for the equilibrium fluctuations, of higher-order fields. In particular, the limit fields exhibit a tensor structure. Our fluctuation result differs from that in [\\emph{arXiv:2004.08412}], since we considered-dimensional Euclidean lattice, we prove the hydrodynamic limit, and convergence for the equilibrium fluctuations, of higher-order fields. In particular, the limit fields exhibit a tensor structure. Our fluctuation result differs from that in [\\emph{arXiv:2004.08412}], since we consider a different notion of higher-order fluctuation fields.","lang":"eng"}],"publication":"Markov Processes And Related Fields","title":"Higher-order hydrodynamics and equilibrium fluctuations of interacting particle systems","department":[{"_id":"JaMa"}],"publisher":"Polymat Publishing","ec_funded":1,"date_created":"2022-01-10T14:02:31Z","oa_version":"Preprint","day":"16","month":"03","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/2008.13403","open_access":"1"}],"intvolume":"        27","publication_status":"published","author":[{"full_name":"Chen, Joe P.","last_name":"Chen","first_name":"Joe P."},{"first_name":"Federico","last_name":"Sau","full_name":"Sau, Federico","id":"E1836206-9F16-11E9-8814-AEFDE5697425"}],"date_published":"2021-03-16T00:00:00Z","article_processing_charge":"No","related_material":{"link":[{"description":"Link to Abstract on publisher's website","relation":"other","url":"http://math-mprf.org/journal/articles/id1614/"},{"url":"https://arxiv.org/abs/2004.08412","description":"Referred to in Abstract","relation":"used_for_analysis_in"}]},"date_updated":"2022-01-10T15:29:08Z","keyword":["interacting particle systems","higher-order fields","hydrodynamic limit","equilibrium fluctuations","duality"],"quality_controlled":"1"},{"file":[{"file_size":2533102,"file_name":"2021_NewJourPhys_Ghazaryan.pdf","checksum":"0c3cb6816242fa8afd1cc87a5fe77821","date_updated":"2022-01-17T10:01:58Z","file_id":"10632","content_type":"application/pdf","success":1,"date_created":"2022-01-17T10:01:58Z","relation":"main_file","access_level":"open_access","creator":"cchlebak"}],"publication_status":"published","intvolume":"        23","isi":1,"month":"12","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"ddc":["530"],"day":"23","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"123042","file_date_updated":"2022-01-17T10:01:58Z","quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","date_updated":"2023-08-17T06:54:54Z","doi":"10.1088/1367-2630/ac4124","author":[{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","first_name":"Areg"},{"full_name":"Nica, Emilian M.","last_name":"Nica","first_name":"Emilian M."},{"full_name":"Erten, Onur","first_name":"Onur","last_name":"Erten"},{"first_name":"Pouyan","last_name":"Ghaemi","full_name":"Ghaemi, Pouyan"}],"date_published":"2021-12-23T00:00:00Z","has_accepted_license":"1","year":"2021","_id":"10628","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":23,"publication_identifier":{"issn":["1367-2630"]},"citation":{"chicago":"Ghazaryan, Areg, Emilian M. Nica, Onur Erten, and Pouyan Ghaemi. “Shadow Surface States in Topological Kondo Insulators.” <i>New Journal of Physics</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1367-2630/ac4124\">https://doi.org/10.1088/1367-2630/ac4124</a>.","ieee":"A. Ghazaryan, E. M. Nica, O. Erten, and P. Ghaemi, “Shadow surface states in topological Kondo insulators,” <i>New Journal of Physics</i>, vol. 23, no. 12. IOP Publishing, 2021.","apa":"Ghazaryan, A., Nica, E. M., Erten, O., &#38; Ghaemi, P. (2021). Shadow surface states in topological Kondo insulators. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ac4124\">https://doi.org/10.1088/1367-2630/ac4124</a>","ama":"Ghazaryan A, Nica EM, Erten O, Ghaemi P. Shadow surface states in topological Kondo insulators. <i>New Journal of Physics</i>. 2021;23(12). doi:<a href=\"https://doi.org/10.1088/1367-2630/ac4124\">10.1088/1367-2630/ac4124</a>","mla":"Ghazaryan, Areg, et al. “Shadow Surface States in Topological Kondo Insulators.” <i>New Journal of Physics</i>, vol. 23, no. 12, 123042, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1367-2630/ac4124\">10.1088/1367-2630/ac4124</a>.","ista":"Ghazaryan A, Nica EM, Erten O, Ghaemi P. 2021. Shadow surface states in topological Kondo insulators. New Journal of Physics. 23(12), 123042.","short":"A. Ghazaryan, E.M. Nica, O. Erten, P. Ghaemi, New Journal of Physics 23 (2021)."},"issue":"12","article_type":"original","external_id":{"isi":["000734063700001"],"arxiv":["2012.11625"]},"acknowledgement":"PG acknowledges support from National Science Foundation Awards No. DMR-1824265 for this work. AG acknowledges support from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. EMN is supported by ASU startup grant. OE is in part supported by NSF-DMR-1904716.","status":"public","oa":1,"date_created":"2022-01-16T23:01:28Z","ec_funded":1,"oa_version":"Published Version","publisher":"IOP Publishing","publication":"New Journal of Physics","title":"Shadow surface states in topological Kondo insulators","department":[{"_id":"MiLe"}],"abstract":[{"lang":"eng","text":"The surface states of 3D topological insulators in general have negligible quantum oscillations (QOs) when the chemical potential is tuned to the Dirac points. In contrast, we find that topological Kondo insulators (TKIs) can support surface states with an arbitrarily large Fermi surface (FS) when the chemical potential is pinned to the Dirac point. We illustrate that these FSs give rise to finite-frequency QOs, which can become comparable to the extremal area of the unhybridized bulk bands. We show that this occurs when the crystal symmetry is lowered from cubic to tetragonal in a minimal two-orbital model. We label such surface modes as 'shadow surface states'. Moreover, we show that the sufficient next-nearest neighbor out-of-plane hybridization leading to shadow surface states can be self-consistently stabilized for tetragonal TKIs. Consequently, shadow surface states provide an important example of high-frequency QOs beyond the context of cubic TKIs."}],"arxiv":1},{"has_accepted_license":"1","year":"2021","_id":"10629","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"conference","volume":213,"publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-9597-7215-0"]},"citation":{"ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Quantitative verification on product graphs of small treewidth. In: <i>41st IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>. Vol 213. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2021.42\">10.4230/LIPIcs.FSTTCS.2021.42</a>","mla":"Chatterjee, Krishnendu, et al. “Quantitative Verification on Product Graphs of Small Treewidth.” <i>41st IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, vol. 213, 42, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2021.42\">10.4230/LIPIcs.FSTTCS.2021.42</a>.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, 41st IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2021. Quantitative verification on product graphs of small treewidth. 41st IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 213, 42.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Quantitative verification on product graphs of small treewidth,” in <i>41st IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, Virtual, 2021, vol. 213.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Quantitative Verification on Product Graphs of Small Treewidth.” In <i>41st IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, Vol. 213. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2021.42\">https://doi.org/10.4230/LIPIcs.FSTTCS.2021.42</a>.","apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2021). Quantitative verification on product graphs of small treewidth. In <i>41st IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i> (Vol. 213). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2021.42\">https://doi.org/10.4230/LIPIcs.FSTTCS.2021.42</a>"},"oa":1,"status":"public","date_created":"2022-01-16T23:01:28Z","oa_version":"Published Version","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication":"41st IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science","title":"Quantitative verification on product graphs of small treewidth","department":[{"_id":"KrCh"}],"abstract":[{"text":"Product graphs arise naturally in formal verification and program analysis. For example, the analysis of two concurrent threads requires the product of two component control-flow graphs, and for language inclusion of deterministic automata the product of two automata is constructed. In many cases, the component graphs have constant treewidth, e.g., when the input contains control-flow graphs of programs. We consider the algorithmic analysis of products of two constant-treewidth graphs with respect to three classic specification languages, namely, (a) algebraic properties, (b) mean-payoff properties, and (c) initial credit for energy properties.\r\nOur main contributions are as follows. Consider a graph G that is the product of two constant-treewidth graphs of size n each. First, given an idempotent semiring, we present an algorithm that computes the semiring transitive closure of G in time Õ(n⁴). Since the output has size Θ(n⁴), our algorithm is optimal (up to polylog factors). Second, given a mean-payoff objective, we present an O(n³)-time algorithm for deciding whether the value of a starting state is non-negative, improving the previously known O(n⁴) bound. Third, given an initial credit for energy objective, we present an O(n⁵)-time algorithm for computing the minimum initial credit for all nodes of G, improving the previously known O(n⁸) bound. At the heart of our approach lies an algorithm for the efficient construction of strongly-balanced tree decompositions of constant-treewidth graphs. Given a constant-treewidth graph G' of n nodes and a positive integer λ, our algorithm constructs a binary tree decomposition of G' of width O(λ) with the property that the size of each subtree decreases geometrically with rate (1/2 + 2^{-λ}).","lang":"eng"}],"file":[{"date_updated":"2022-01-17T10:36:08Z","file_id":"10633","file_size":891566,"checksum":"71141acdeffa9056f24d6dbef952d254","file_name":"2021_LIPIcs_Chatterjee.pdf","relation":"main_file","creator":"cchlebak","access_level":"open_access","content_type":"application/pdf","date_created":"2022-01-17T10:36:08Z","success":1}],"publication_status":"published","intvolume":"       213","month":"11","language":[{"iso":"eng"}],"ddc":["000"],"day":"29","conference":{"start_date":"2021-12-15","location":"Virtual","end_date":"2021-12-17","name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science"},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"42","file_date_updated":"2022-01-17T10:36:08Z","quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","alternative_title":["LIPIcs"],"date_updated":"2022-01-17T10:39:40Z","doi":"10.4230/LIPIcs.FSTTCS.2021.42","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389"},{"first_name":"Andreas","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2021-11-29T00:00:00Z"},{"volume":213,"type":"conference","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10630","year":"2021","has_accepted_license":"1","oa":1,"acknowledgement":"We like to thank Lukas Fleischer and Michael Wehar for our discussions. This work started at the Schloss Dagstuhl Event 20483 Moderne Aspekte der Komplexitätstheorie in der Automatentheorie https://www.dagstuhl.de/20483.\r\n","status":"public","external_id":{"arxiv":["2110.01279"]},"citation":{"ista":"Arrighi E, Fernau H, Hoffmann S, Holzer M, Jecker IR, De Oliveira Oliveira M, Wolf P. 2021. On the complexity of intersection non-emptiness for star-free language classes. 41st IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 213, 34.","mla":"Arrighi, Emmanuel, et al. “On the Complexity of Intersection Non-Emptiness for Star-Free Language Classes.” <i>41st IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, vol. 213, 34, Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2021.34\">10.4230/LIPIcs.FSTTCS.2021.34</a>.","short":"E. Arrighi, H. Fernau, S. Hoffmann, M. Holzer, I.R. Jecker, M. De Oliveira Oliveira, P. Wolf, in:, 41st IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science, Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021.","ama":"Arrighi E, Fernau H, Hoffmann S, et al. On the complexity of intersection non-emptiness for star-free language classes. In: <i>41st IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>. Vol 213. Schloss Dagstuhl - Leibniz Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2021.34\">10.4230/LIPIcs.FSTTCS.2021.34</a>","apa":"Arrighi, E., Fernau, H., Hoffmann, S., Holzer, M., Jecker, I. R., De Oliveira Oliveira, M., &#38; Wolf, P. (2021). On the complexity of intersection non-emptiness for star-free language classes. In <i>41st IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i> (Vol. 213). Virtual: Schloss Dagstuhl - Leibniz Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2021.34\">https://doi.org/10.4230/LIPIcs.FSTTCS.2021.34</a>","ieee":"E. Arrighi <i>et al.</i>, “On the complexity of intersection non-emptiness for star-free language classes,” in <i>41st IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, Virtual, 2021, vol. 213.","chicago":"Arrighi, Emmanuel, Henning Fernau, Stefan Hoffmann, Markus Holzer, Ismael R Jecker, Mateus De Oliveira Oliveira, and Petra Wolf. “On the Complexity of Intersection Non-Emptiness for Star-Free Language Classes.” In <i>41st IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, Vol. 213. Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2021.34\">https://doi.org/10.4230/LIPIcs.FSTTCS.2021.34</a>."},"publication_identifier":{"isbn":["978-3-9597-7215-0"],"issn":["1868-8969"]},"department":[{"_id":"KrCh"}],"title":"On the complexity of intersection non-emptiness for star-free language classes","publication":"41st IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science","publisher":"Schloss Dagstuhl - Leibniz Zentrum für Informatik","oa_version":"Published Version","ec_funded":1,"date_created":"2022-01-16T23:01:29Z","arxiv":1,"abstract":[{"lang":"eng","text":"In the Intersection Non-emptiness problem, we are given a list of finite automata A_1, A_2,… , A_m over a common alphabet Σ as input, and the goal is to determine whether some string w ∈ Σ^* lies in the intersection of the languages accepted by the automata in the list. We analyze the complexity of the Intersection Non-emptiness problem under the promise that all input automata accept a language in some level of the dot-depth hierarchy, or some level of the Straubing-Thérien hierarchy. Automata accepting languages from the lowest levels of these hierarchies arise naturally in the context of model checking. We identify a dichotomy in the dot-depth hierarchy by showing that the problem is already NP-complete when all input automata accept languages of the levels B_0 or B_{1/2} and already PSPACE-hard when all automata accept a language from the level B_1. Conversely, we identify a tetrachotomy in the Straubing-Thérien hierarchy. More precisely, we show that the problem is in AC^0 when restricted to level L_0; complete for L or NL, depending on the input representation, when restricted to languages in the level L_{1/2}; NP-complete when the input is given as DFAs accepting a language in L_1 or L_{3/2}; and finally, PSPACE-complete when the input automata accept languages in level L_2 or higher. Moreover, we show that the proof technique used to show containment in NP for DFAs accepting languages in L_1 or L_{3/2} does not generalize to the context of NFAs. To prove this, we identify a family of languages that provide an exponential separation between the state complexity of general NFAs and that of partially ordered NFAs. To the best of our knowledge, this is the first superpolynomial separation between these two models of computation."}],"intvolume":"       213","publication_status":"published","file":[{"creator":"cchlebak","access_level":"open_access","relation":"main_file","date_created":"2022-01-17T10:49:03Z","success":1,"content_type":"application/pdf","file_id":"10634","date_updated":"2022-01-17T10:49:03Z","checksum":"d5a82ba893c3bc5da5914edbb3efb92b","file_name":"2021_LIPIcs_Arrighi.pdf","file_size":844224}],"day":"29","ddc":["000"],"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"month":"11","file_date_updated":"2022-01-17T10:49:03Z","article_number":"34","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"conference":{"end_date":"2021-12-17","name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science","start_date":"2021-12-15","location":"Virtual"},"date_published":"2021-11-29T00:00:00Z","author":[{"full_name":"Arrighi, Emmanuel","first_name":"Emmanuel","last_name":"Arrighi"},{"first_name":"Henning","last_name":"Fernau","full_name":"Fernau, Henning"},{"full_name":"Hoffmann, Stefan","last_name":"Hoffmann","first_name":"Stefan"},{"full_name":"Holzer, Markus","last_name":"Holzer","first_name":"Markus"},{"full_name":"Jecker, Ismael R","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","first_name":"Ismael R","last_name":"Jecker"},{"full_name":"De Oliveira Oliveira, Mateus","first_name":"Mateus","last_name":"De Oliveira Oliveira"},{"full_name":"Wolf, Petra","first_name":"Petra","last_name":"Wolf"}],"date_updated":"2022-01-17T10:56:19Z","alternative_title":["LIPIcs"],"doi":"10.4230/LIPIcs.FSTTCS.2021.34","article_processing_charge":"No","scopus_import":"1","quality_controlled":"1"},{"publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"citation":{"ama":"Cherepanov I, Bighin G, Schouder CA, et al. Excited rotational states of molecules in a superfluid. <i>Physical Review A</i>. 2021;104(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.104.L061303\">10.1103/PhysRevA.104.L061303</a>","mla":"Cherepanov, Igor, et al. “Excited Rotational States of Molecules in a Superfluid.” <i>Physical Review A</i>, vol. 104, no. 6, L061303, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/PhysRevA.104.L061303\">10.1103/PhysRevA.104.L061303</a>.","ista":"Cherepanov I, Bighin G, Schouder CA, Chatterley AS, Albrechtsen SH, Muñoz AV, Christiansen L, Stapelfeldt H, Lemeshko M. 2021. Excited rotational states of molecules in a superfluid. Physical Review A. 104(6), L061303.","short":"I. Cherepanov, G. Bighin, C.A. Schouder, A.S. Chatterley, S.H. Albrechtsen, A.V. Muñoz, L. Christiansen, H. Stapelfeldt, M. Lemeshko, Physical Review A 104 (2021).","chicago":"Cherepanov, Igor, Giacomo Bighin, Constant A. Schouder, Adam S. Chatterley, Simon H. Albrechtsen, Alberto Viñas Muñoz, Lars Christiansen, Henrik Stapelfeldt, and Mikhail Lemeshko. “Excited Rotational States of Molecules in a Superfluid.” <i>Physical Review A</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PhysRevA.104.L061303\">https://doi.org/10.1103/PhysRevA.104.L061303</a>.","ieee":"I. Cherepanov <i>et al.</i>, “Excited rotational states of molecules in a superfluid,” <i>Physical Review A</i>, vol. 104, no. 6. American Physical Society, 2021.","apa":"Cherepanov, I., Bighin, G., Schouder, C. A., Chatterley, A. S., Albrechtsen, S. H., Muñoz, A. V., … Lemeshko, M. (2021). Excited rotational states of molecules in a superfluid. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.104.L061303\">https://doi.org/10.1103/PhysRevA.104.L061303</a>"},"issue":"6","external_id":{"isi":["000739618300001"],"arxiv":["2107.00468"]},"article_type":"original","oa":1,"acknowledgement":"I.C. acknowledges the support by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665385. G.B. acknowledges support from the Austrian Science Fund (FWF), under project No. M2461-N27. M.L. acknowledges support by the Austrian Science Fund (FWF), under project No. P29902-N27, and by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). H.S acknowledges support from the European Research Council-AdG (Project No. 320459, DropletControl) and from The Villum Foundation through a Villum Investigator grant no. 25886.","status":"public","year":"2021","_id":"10631","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":104,"abstract":[{"text":"We combine experimental and theoretical approaches to explore excited rotational states of molecules embedded in helium nanodroplets using CS2 and I2 as examples. Laser-induced nonadiabatic molecular alignment is employed to measure spectral lines for rotational states extending beyond those initially populated at the 0.37 K droplet temperature. We construct a simple quantum-mechanical model, based on a linear rotor coupled to a single-mode bosonic bath, to determine the rotational energy structure in its entirety. The calculated and measured spectral lines are in good agreement. We show that the effect of the surrounding superfluid on molecular rotation can be rationalized by a single quantity, the angular momentum, transferred from the molecule to the droplet.","lang":"eng"}],"arxiv":1,"ec_funded":1,"date_created":"2022-01-16T23:01:29Z","oa_version":"Preprint","publisher":"American Physical Society","publication":"Physical Review A","department":[{"_id":"MiLe"}],"title":"Excited rotational states of molecules in a superfluid","isi":1,"month":"12","language":[{"iso":"eng"}],"project":[{"call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment"},{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"M02641","name":"A path-integral approach to composite impurities","_id":"26986C82-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"day":"30","publication_status":"published","intvolume":"       104","main_file_link":[{"open_access":"1","url":"http://128.84.4.18/abs/2107.00468"}],"quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","date_updated":"2024-08-07T07:16:52Z","doi":"10.1103/PhysRevA.104.L061303","date_published":"2021-12-30T00:00:00Z","author":[{"id":"339C7E5A-F248-11E8-B48F-1D18A9856A87","full_name":"Cherepanov, Igor","last_name":"Cherepanov","first_name":"Igor"},{"full_name":"Bighin, Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo","orcid":"0000-0001-8823-9777","last_name":"Bighin"},{"full_name":"Schouder, Constant A.","last_name":"Schouder","first_name":"Constant A."},{"full_name":"Chatterley, Adam S.","last_name":"Chatterley","first_name":"Adam S."},{"full_name":"Albrechtsen, Simon H.","first_name":"Simon H.","last_name":"Albrechtsen"},{"last_name":"Muñoz","first_name":"Alberto Viñas","full_name":"Muñoz, Alberto Viñas"},{"last_name":"Christiansen","first_name":"Lars","full_name":"Christiansen, Lars"},{"full_name":"Stapelfeldt, Henrik","first_name":"Henrik","last_name":"Stapelfeldt"},{"first_name":"Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"article_number":"L061303"},{"day":"15","ddc":["519"],"project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"month":"12","publication_status":"published","file":[{"checksum":"cd9af6b331918608f2e3d1c7940cbf4f","file_name":"10_24072_pcjournal_69.pdf","file_size":3311494,"file_id":"10636","date_updated":"2022-01-17T11:15:26Z","date_created":"2022-01-17T11:15:26Z","success":1,"content_type":"application/pdf","creator":"mnardin","access_level":"open_access","relation":"main_file"}],"intvolume":"         1","date_updated":"2022-01-17T13:30:01Z","doi":"10.24072/pcjournal.69","article_processing_charge":"No","date_published":"2021-12-15T00:00:00Z","author":[{"full_name":"Nardin, Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","first_name":"Michele","last_name":"Nardin","orcid":"0000-0001-8849-6570"},{"full_name":"Phillips, James W.","last_name":"Phillips","first_name":"James W."},{"full_name":"Podlaski, William F.","first_name":"William F.","last_name":"Podlaski"},{"full_name":"Keemink, Sander W.","first_name":"Sander W.","last_name":"Keemink"}],"quality_controlled":"1","article_number":"e68","file_date_updated":"2022-01-17T11:15:26Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"arxiv":["2009.03857"]},"article_type":"original","acknowledgement":"A preprint version of this article has been peer-reviewed and recommended by Peer Community In Neuroscience (DOI link to the recommendation: https://doi.org/10.24072/pci.cneuro.100003).\r\nWe thank Christian Machens and Nuno Calaim for useful discussions on the project. This report\r\ncame out of a collaboration started at the CAJAL Advanced Neuroscience Training Programme in\r\nComputational Neuroscience in Lisbon, Portugal, during the 2019 summer. The authors would\r\nlike to thank the participants, TAs, lecturers, and organizers of the summer school. SWK was\r\nsupported by the Simons Collaboration on the Global Brain (543009). WFP was supported by\r\nFCT (032077). MN was supported by European Union Horizon 2020 (665385).\r\n","status":"public","oa":1,"publication_identifier":{"eissn":["2804-3871"]},"citation":{"mla":"Nardin, Michele, et al. “Nonlinear Computations in Spiking Neural Networks through Multiplicative Synapses.” <i>Peer Community Journal</i>, vol. 1, e68, Centre Mersenne ; Peer Community In, 2021, doi:<a href=\"https://doi.org/10.24072/pcjournal.69\">10.24072/pcjournal.69</a>.","short":"M. Nardin, J.W. Phillips, W.F. Podlaski, S.W. Keemink, Peer Community Journal 1 (2021).","ista":"Nardin M, Phillips JW, Podlaski WF, Keemink SW. 2021. Nonlinear computations in spiking neural networks through multiplicative synapses. Peer Community Journal. 1, e68.","ama":"Nardin M, Phillips JW, Podlaski WF, Keemink SW. Nonlinear computations in spiking neural networks through multiplicative synapses. <i>Peer Community Journal</i>. 2021;1. doi:<a href=\"https://doi.org/10.24072/pcjournal.69\">10.24072/pcjournal.69</a>","apa":"Nardin, M., Phillips, J. W., Podlaski, W. F., &#38; Keemink, S. W. (2021). Nonlinear computations in spiking neural networks through multiplicative synapses. <i>Peer Community Journal</i>. Centre Mersenne ; Peer Community In. <a href=\"https://doi.org/10.24072/pcjournal.69\">https://doi.org/10.24072/pcjournal.69</a>","ieee":"M. Nardin, J. W. Phillips, W. F. Podlaski, and S. W. Keemink, “Nonlinear computations in spiking neural networks through multiplicative synapses,” <i>Peer Community Journal</i>, vol. 1. Centre Mersenne ; Peer Community In, 2021.","chicago":"Nardin, Michele, James W. Phillips, William F. Podlaski, and Sander W. Keemink. “Nonlinear Computations in Spiking Neural Networks through Multiplicative Synapses.” <i>Peer Community Journal</i>. Centre Mersenne ; Peer Community In, 2021. <a href=\"https://doi.org/10.24072/pcjournal.69\">https://doi.org/10.24072/pcjournal.69</a>."},"type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":1,"has_accepted_license":"1","year":"2021","_id":"10635","arxiv":1,"abstract":[{"lang":"eng","text":"The brain efficiently performs nonlinear computations through its intricate networks of spiking neurons, but how this is done remains elusive. While nonlinear computations can be implemented successfully in spiking neural networks, this requires supervised training and the resulting connectivity can be hard to interpret. In contrast, the required connectivity for any computation in the form of a linear dynamical system can be directly derived and understood with the spike coding network (SCN) framework. These networks also have biologically realistic activity patterns and are highly robust to cell death. Here we extend the SCN framework to directly implement any polynomial dynamical system, without the need for training. This results in networks requiring a mix of synapse types (fast, slow, and multiplicative), which we term multiplicative spike coding networks (mSCNs). Using mSCNs, we demonstrate how to directly derive the required connectivity for several nonlinear dynamical systems. We also show how to carry out higher-order polynomials with coupled networks that use only pair-wise multiplicative synapses, and provide expected numbers of connections for each synapse type. Overall, our work demonstrates a novel method for implementing nonlinear computations in spiking neural networks, while keeping the attractive features of standard SCNs (robustness, realistic activity patterns, and interpretable connectivity). Finally, we discuss the biological plausibility of our approach, and how the high accuracy and robustness of the approach may be of interest for neuromorphic computing."}],"publisher":"Centre Mersenne ; Peer Community In","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"title":"Nonlinear computations in spiking neural networks through multiplicative synapses","publication":"Peer Community Journal","oa_version":"Published Version","ec_funded":1,"date_created":"2022-01-17T11:12:40Z"},{"author":[{"first_name":"Russell","last_name":"Lake","full_name":"Lake, Russell"},{"first_name":"Slawomir","last_name":"Simbierowicz","full_name":"Simbierowicz, Slawomir"},{"full_name":"Krantz, Philip","last_name":"Krantz","first_name":"Philip"},{"full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","first_name":"Farid","last_name":"Hassani"},{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X"}],"date_published":"2021-04-20T00:00:00Z","date_updated":"2022-01-19T09:11:33Z","alternative_title":["Bluefors Blog"],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"The purpose of this application note is to demonstrate a working example of a superconducting qubit measurement in a Bluefors cryostat using the Keysight quantum control hardware. Our motivation is twofold. First, we provide pre-qualification data that the Bluefors cryostat, including filtering and wiring, can support long-lived qubits. Second, we demonstrate that the Keysight system (controlled using Labber) provides a straightforward solution to perform these characterization measurements. This document is intended as a brief guide for starting an experimental platform for testing superconducting qubits. The setup described here is an immediate jumping off point for a suite of applications including testing quantum logical gates, quantum optics with microwaves, or even using the qubit itself as a sensitive probe of local electromagnetic fields. Qubit measurements rely on high performance of both the physical sample environment and the measurement electronics. An overview of the cryogenic system is shown in Figure 1, and an overview of the integration between the electronics and cryostat (including wiring details) is shown in Figure 2."}],"keyword":["Application note"],"quality_controlled":"1","title":"The Bluefors dilution refrigerator as an integrated quantum measurement system","department":[{"_id":"JoFi"}],"publisher":"Bluefors Oy","oa_version":"Published Version","date_created":"2022-01-19T08:29:57Z","oa":1,"status":"public","day":"20","citation":{"ama":"Lake R, Simbierowicz S, Krantz P, Hassani F, Fink JM. <i>The Bluefors Dilution Refrigerator as an Integrated Quantum Measurement System</i>. Helsinki, Finland: Bluefors Oy; 2021.","short":"R. Lake, S. Simbierowicz, P. Krantz, F. Hassani, J.M. Fink, The Bluefors Dilution Refrigerator as an Integrated Quantum Measurement System, Bluefors Oy, Helsinki, Finland, 2021.","ista":"Lake R, Simbierowicz S, Krantz P, Hassani F, Fink JM. 2021. The Bluefors dilution refrigerator as an integrated quantum measurement system, Helsinki, Finland: Bluefors Oy, 9p.","mla":"Lake, Russell, et al. <i>The Bluefors Dilution Refrigerator as an Integrated Quantum Measurement System</i>. Bluefors Oy, 2021.","ieee":"R. Lake, S. Simbierowicz, P. Krantz, F. Hassani, and J. M. Fink, <i>The Bluefors dilution refrigerator as an integrated quantum measurement system</i>. Helsinki, Finland: Bluefors Oy, 2021.","chicago":"Lake, Russell, Slawomir Simbierowicz, Philip Krantz, Farid Hassani, and Johannes M Fink. <i>The Bluefors Dilution Refrigerator as an Integrated Quantum Measurement System</i>. Helsinki, Finland: Bluefors Oy, 2021.","apa":"Lake, R., Simbierowicz, S., Krantz, P., Hassani, F., &#38; Fink, J. M. (2021). <i>The Bluefors dilution refrigerator as an integrated quantum measurement system</i>. Helsinki, Finland: Bluefors Oy."},"language":[{"iso":"eng"}],"month":"04","page":"9","type":"other_academic_publication","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10644","main_file_link":[{"open_access":"1","url":"https://bluefors.com/blog/integrated-quantum-measurement-system/"}],"place":"Helsinki, Finland","publication_status":"published","year":"2021"},{"day":"03","status":"public","oa":1,"language":[{"iso":"eng"}],"month":"06","citation":{"ama":"Simbierowicz S, Shi C, Collodo M, et al. <i>Qubit Energy-Relaxation Statistics in the Bluefors Quantum Measurement System</i>. Helsinki, Finland: Bluefors Oy; 2021.","ista":"Simbierowicz S, Shi C, Collodo M, Kirste M, Hassani F, Fink JM, Bylander J, Perez Lozano D, Lake R. 2021. Qubit energy-relaxation statistics in the Bluefors quantum measurement system, Helsinki, Finland: Bluefors Oy, 8p.","short":"S. Simbierowicz, C. Shi, M. Collodo, M. Kirste, F. Hassani, J.M. Fink, J. Bylander, D. Perez Lozano, R. Lake, Qubit Energy-Relaxation Statistics in the Bluefors Quantum Measurement System, Bluefors Oy, Helsinki, Finland, 2021.","mla":"Simbierowicz, Slawomir, et al. <i>Qubit Energy-Relaxation Statistics in the Bluefors Quantum Measurement System</i>. Bluefors Oy, 2021.","chicago":"Simbierowicz, Slawomir, Chunyan Shi, Michele Collodo, Moritz Kirste, Farid Hassani, Johannes M Fink, Jonas Bylander, Daniel Perez Lozano, and Russell Lake. <i>Qubit Energy-Relaxation Statistics in the Bluefors Quantum Measurement System</i>. Helsinki, Finland: Bluefors Oy, 2021.","ieee":"S. Simbierowicz <i>et al.</i>, <i>Qubit energy-relaxation statistics in the Bluefors quantum measurement system</i>. Helsinki, Finland: Bluefors Oy, 2021.","apa":"Simbierowicz, S., Shi, C., Collodo, M., Kirste, M., Hassani, F., Fink, J. M., … Lake, R. (2021). <i>Qubit energy-relaxation statistics in the Bluefors quantum measurement system</i>. Helsinki, Finland: Bluefors Oy."},"type":"other_academic_publication","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"8","publication_status":"published","year":"2021","_id":"10645","main_file_link":[{"open_access":"1","url":"https://bluefors.com/blog/application-note-qubit-energy-relaxation-statistics-bluefors-quantum-measurement-system/"}],"place":"Helsinki, Finland","alternative_title":["Bluefors Blog"],"date_updated":"2022-01-19T09:11:39Z","article_processing_charge":"No","date_published":"2021-06-03T00:00:00Z","author":[{"first_name":"Slawomir","last_name":"Simbierowicz","full_name":"Simbierowicz, Slawomir"},{"first_name":"Chunyan","last_name":"Shi","full_name":"Shi, Chunyan"},{"full_name":"Collodo, Michele","last_name":"Collodo","first_name":"Michele"},{"full_name":"Kirste, Moritz","first_name":"Moritz","last_name":"Kirste"},{"full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","first_name":"Farid","last_name":"Hassani"},{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink"},{"first_name":"Jonas","last_name":"Bylander","full_name":"Bylander, Jonas"},{"last_name":"Perez Lozano","first_name":"Daniel","full_name":"Perez Lozano, Daniel"},{"full_name":"Lake, Russell","first_name":"Russell","last_name":"Lake"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"Superconducting qubits have emerged as a highly versatile and useful platform for quantum technological applications [1]. Bluefors and Zurich Instruments have supported the growth of this field from the 2010s onwards by providing well-engineered and reliable measurement infrastructure [2]– [6]. Having a long and stable qubit lifetime is a critical system property. Therefore, considerable effort has already gone into measuring qubit energy-relaxation timescales and their fluctuations, see Refs. [7]–[10] among others. Accurately extracting the statistics of a quantum device requires users to perform time consuming measurements. One measurement challenge is that the detection of the state-dependent\r\nresponse of a superconducting resonator due to a dispersively-coupled qubit requires an inherently low signal level. Consequently, measurements must be performed using a microwave probe that contains only a few microwave photons. Improving the signal-to-noise ratio (SNR) by using near-quantum limited parametric amplifiers as well as the use of optimized signal processing enabled by efficient room temperature instrumentation help to reduce measurement time. An empirical observation for fixed frequency transmons from recent literature is that as the energy-relaxation time 𝑇𝑇1 increases, so do its natural temporal fluctuations [7], [10]. This necessitates many repeated measurements to understand the statistics (see for example, Ref. [10]). In addition, as state-of-the-art qubits increase in lifetime, longer\r\nmeasurement times are expected to obtain accurate statistics. As described below, the scaling of the widths of the qubit energy-relaxation distributions also reveal clues about the origin of the energy-relaxation."}],"keyword":["Application note"],"publisher":"Bluefors Oy","department":[{"_id":"JoFi"}],"title":"Qubit energy-relaxation statistics in the Bluefors quantum measurement system","oa_version":"Published Version","date_created":"2022-01-19T08:41:14Z"},{"quality_controlled":"1","scopus_import":"1","doi":"10.1016/j.omtm.2021.09.006","date_updated":"2023-11-16T13:12:03Z","article_processing_charge":"Yes","date_published":"2021-12-10T00:00:00Z","author":[{"orcid":"0000-0001-9642-1085","last_name":"Maes","first_name":"Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","full_name":"Maes, Margaret E"},{"first_name":"Gabriele M.","last_name":"Wögenstein","full_name":"Wögenstein, Gabriele M."},{"id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","full_name":"Colombo, Gloria","last_name":"Colombo","orcid":"0000-0001-9434-8902","first_name":"Gloria"},{"orcid":"0000-0001-8293-4568","last_name":"Casado Polanco","first_name":"Raquel","id":"15240fc1-dbcd-11ea-9d1d-ac5a786425fd","full_name":"Casado Polanco, Raquel"},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","first_name":"Sandra"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2022-01-24T07:43:09Z","project":[{"call_identifier":"H2020","_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571","name":"Microglia action towards neuronal circuit formation and function in health and disease"}],"language":[{"iso":"eng"}],"month":"12","isi":1,"day":"10","ddc":["570"],"publication_status":"published","file":[{"content_type":"application/pdf","date_created":"2022-01-24T07:43:09Z","success":1,"relation":"main_file","creator":"cchlebak","access_level":"open_access","file_size":4794147,"checksum":"77dc540e8011c5475031bdf6ccef20a6","file_name":"2021_MolTherMethodsClinDev_Maes.pdf","file_id":"10657","date_updated":"2022-01-24T07:43:09Z"}],"intvolume":"        23","abstract":[{"lang":"eng","text":"Adeno-associated viruses (AAVs) are widely used to deliver genetic material in vivo to distinct cell types such as neurons or glial cells, allowing for targeted manipulation. Transduction of microglia is mostly excluded from this strategy, likely due to the cells’ heterogeneous state upon environmental changes, which makes AAV design challenging. Here, we established the retina as a model system for microglial AAV validation and optimization. First, we show that AAV2/6 transduced microglia in both synaptic layers, where layer preference corresponds to the intravitreal or subretinal delivery method. Surprisingly, we observed significantly enhanced microglial transduction during photoreceptor degeneration. Thus, we modified the AAV6 capsid to reduce heparin binding by introducing four point mutations (K531E, R576Q, K493S, and K459S), resulting in increased microglial transduction in the outer plexiform layer. Finally, to improve microglial-specific transduction, we validated a Cre-dependent transgene delivery cassette for use in combination with the Cx3cr1CreERT2 mouse line. Together, our results provide a foundation for future studies optimizing AAV-mediated microglia transduction and highlight that environmental conditions influence microglial transduction efficiency.\r\n"}],"oa_version":"Published Version","ec_funded":1,"date_created":"2022-01-23T23:01:28Z","publisher":"Elsevier","title":"Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment","department":[{"_id":"SaSi"},{"_id":"SiHi"}],"publication":"Molecular Therapy - Methods and Clinical Development","publication_identifier":{"eissn":["2329-0501"]},"citation":{"ama":"Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. <i>Molecular Therapy - Methods and Clinical Development</i>. 2021;23:210-224. doi:<a href=\"https://doi.org/10.1016/j.omtm.2021.09.006\">10.1016/j.omtm.2021.09.006</a>","short":"M.E. Maes, G.M. Wögenstein, G. Colombo, R. Casado Polanco, S. Siegert, Molecular Therapy - Methods and Clinical Development 23 (2021) 210–224.","mla":"Maes, Margaret E., et al. “Optimizing AAV2/6 Microglial Targeting Identified Enhanced Efficiency in the Photoreceptor Degenerative Environment.” <i>Molecular Therapy - Methods and Clinical Development</i>, vol. 23, Elsevier, 2021, pp. 210–24, doi:<a href=\"https://doi.org/10.1016/j.omtm.2021.09.006\">10.1016/j.omtm.2021.09.006</a>.","ista":"Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. 2021. Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. Molecular Therapy - Methods and Clinical Development. 23, 210–224.","chicago":"Maes, Margaret E, Gabriele M. Wögenstein, Gloria Colombo, Raquel Casado Polanco, and Sandra Siegert. “Optimizing AAV2/6 Microglial Targeting Identified Enhanced Efficiency in the Photoreceptor Degenerative Environment.” <i>Molecular Therapy - Methods and Clinical Development</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.omtm.2021.09.006\">https://doi.org/10.1016/j.omtm.2021.09.006</a>.","ieee":"M. E. Maes, G. M. Wögenstein, G. Colombo, R. Casado Polanco, and S. Siegert, “Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment,” <i>Molecular Therapy - Methods and Clinical Development</i>, vol. 23. Elsevier, pp. 210–224, 2021.","apa":"Maes, M. E., Wögenstein, G. M., Colombo, G., Casado Polanco, R., &#38; Siegert, S. (2021). Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. <i>Molecular Therapy - Methods and Clinical Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.omtm.2021.09.006\">https://doi.org/10.1016/j.omtm.2021.09.006</a>"},"external_id":{"isi":["000748748500019"]},"article_type":"original","status":"public","oa":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 715571). The research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility, the Life Science Facility, and the Pre-Clinical Facility, namely Sonja Haslinger and Michael Schunn for their animal colony management and support. We would also like to thank Chakrabarty Lab for sharing the plasmids for AAV2/6 production. Finally, we would like to thank the Siegert team members for discussion about the manuscript.","has_accepted_license":"1","year":"2021","_id":"10655","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","page":"210-224","volume":23},{"doi":"10.48550/arXiv.2104.06966","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12072"}]},"date_updated":"2023-02-21T16:37:30Z","article_processing_charge":"No","arxiv":1,"author":[{"last_name":"Shute","orcid":"0000-0002-1812-2810","first_name":"Alec L","id":"440EB050-F248-11E8-B48F-1D18A9856A87","full_name":"Shute, Alec L"}],"date_published":"2021-04-15T00:00:00Z","abstract":[{"text":"We find an asymptotic formula for the number of primitive vectors $(z_1,\\ldots,z_4)\\in (\\mathbb{Z}_{\\neq 0})^4$ such that $z_1,\\ldots, z_4$ are all squareful and bounded by $B$, and $z_1+\\cdots + z_4 = 0$. Our result agrees in the power of $B$ and $\\log B$ with the Campana-Manin conjecture of Pieropan, Smeets, Tanimoto and V\\'{a}rilly-Alvarado.","lang":"eng"}],"article_number":"2104.06966","department":[{"_id":"TiBr"}],"title":"Sums of four squareful numbers","publication":"arXiv","oa_version":"Preprint","date_created":"2022-09-09T10:42:51Z","external_id":{"arxiv":["2104.06966"]},"day":"15","status":"public","oa":1,"language":[{"iso":"eng"}],"month":"04","citation":{"ista":"Shute AL. Sums of four squareful numbers. arXiv, 2104.06966.","short":"A.L. Shute, ArXiv (n.d.).","mla":"Shute, Alec L. “Sums of Four Squareful Numbers.” <i>ArXiv</i>, 2104.06966, doi:<a href=\"https://doi.org/10.48550/arXiv.2104.06966\">10.48550/arXiv.2104.06966</a>.","ama":"Shute AL. Sums of four squareful numbers. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2104.06966\">10.48550/arXiv.2104.06966</a>","apa":"Shute, A. L. (n.d.). Sums of four squareful numbers. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2104.06966\">https://doi.org/10.48550/arXiv.2104.06966</a>","ieee":"A. L. Shute, “Sums of four squareful numbers,” <i>arXiv</i>. .","chicago":"Shute, Alec L. “Sums of Four Squareful Numbers.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2104.06966\">https://doi.org/10.48550/arXiv.2104.06966</a>."},"type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"submitted","year":"2021","_id":"12076","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2104.06966"}]},{"status":"public","acknowledgement":"The author would like to thank Damaris Schindler and Florian Wilsch for their helpful comments on the heights and Tamagawa measures used in Section 3, together with Marta Pieropan, Sho Tanimoto and Sam Streeter for providing valuable feedback on an earlier version of this paper, and Tim Browning for many useful comments and discussions during the development of this work. The author is also grateful to the anonymous referee for providing many valuable comments and suggestions that improved the quality of the paper.","oa":1,"external_id":{"arxiv":["2104.14946"]},"day":"30","citation":{"chicago":"Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana Points.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2104.14946\">https://doi.org/10.48550/arXiv.2104.14946</a>.","ieee":"A. L. Shute, “On the leading constant in the Manin-type conjecture for Campana points,” <i>arXiv</i>. .","apa":"Shute, A. L. (n.d.). On the leading constant in the Manin-type conjecture for Campana points. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2104.14946\">https://doi.org/10.48550/arXiv.2104.14946</a>","ama":"Shute AL. On the leading constant in the Manin-type conjecture for Campana points. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2104.14946\">10.48550/arXiv.2104.14946</a>","mla":"Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana Points.” <i>ArXiv</i>, 2104.14946, doi:<a href=\"https://doi.org/10.48550/arXiv.2104.14946\">10.48550/arXiv.2104.14946</a>.","ista":"Shute AL. On the leading constant in the Manin-type conjecture for Campana points. arXiv, 2104.14946.","short":"A.L. Shute, ArXiv (n.d.)."},"language":[{"iso":"eng"}],"month":"04","type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2104.14946","open_access":"1"}],"_id":"12077","publication_status":"submitted","year":"2021","arxiv":1,"date_published":"2021-04-30T00:00:00Z","author":[{"last_name":"Shute","orcid":"0000-0002-1812-2810","first_name":"Alec L","id":"440EB050-F248-11E8-B48F-1D18A9856A87","full_name":"Shute, Alec L"}],"date_updated":"2023-02-21T16:37:30Z","doi":"10.48550/arXiv.2104.14946","related_material":{"record":[{"id":"12072","relation":"dissertation_contains","status":"public"}]},"article_processing_charge":"No","abstract":[{"text":"We compare the Manin-type conjecture for Campana points recently formulated\r\nby Pieropan, Smeets, Tanimoto and V\\'{a}rilly-Alvarado with an alternative\r\nprediction of Browning and Van Valckenborgh in the special case of the orbifold\r\n$(\\mathbb{P}^1,D)$, where $D =\\frac{1}{2}[0]+\\frac{1}{2}[1]+\\frac{1}{2}[\\infty]$. We find that the two predicted leading constants do not agree, and we discuss whether thin sets\r\ncould explain this discrepancy. Motivated by this, we provide a counterexample\r\nto the Manin-type conjecture for Campana points, by considering orbifolds\r\ncorresponding to squareful values of binary quadratic forms.","lang":"eng"}],"department":[{"_id":"TiBr"}],"title":"On the leading constant in the Manin-type conjecture for Campana points","publication":"arXiv","article_number":"2104.14946","oa_version":"Preprint","date_created":"2022-09-09T10:43:17Z"},{"publisher":"Oxford University Press","publication":"Journal of Experimental Botany","title":"Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors","department":[{"_id":"XiFe"}],"date_created":"2023-01-16T09:14:35Z","oa_version":"None","extern":"1","abstract":[{"text":"Activation of cell-surface and intracellular receptor-mediated immunity results in rapid transcriptional reprogramming that underpins disease resistance. However, the mechanisms by which co-activation of both immune systems lead to transcriptional changes are not clear. Here, we combine RNA-seq and ATAC-seq to define changes in gene expression and chromatin accessibility. Activation of cell-surface or intracellular receptor-mediated immunity, or both, increases chromatin accessibility at induced defence genes. Analysis of ATAC-seq and RNA-seq data combined with publicly available information on transcription factor DNA-binding motifs enabled comparison of individual gene regulatory networks activated by cell-surface or intracellular receptor-mediated immunity, or by both. These results and analyses reveal overlapping and conserved transcriptional regulatory mechanisms between the two immune systems.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":72,"page":"7927-7941","year":"2021","_id":"12186","issue":"22","article_type":"original","external_id":{"pmid":["34387350"]},"status":"public","acknowledgement":"We thank the Gatsby Foundation (UK) for funding to the JDGJ laboratory. PD acknowledges support from the European Union’s Horizon 2020 Research and Innovation Program under Marie Skłodowska Curie Actions (grant agreement: 656243) and a Future Leader Fellowship from the Biotechnology and Biological Sciences Research Council (BBSRC) (grant agreement: BB/R012172/1). TS, RKS, DM, and JDGJ were supported by the Gatsby Foundation funding to the\r\nSainsbury Laboratory. NMP and KV were supported by a BOF grant from Ghent University (grant agreement: BOF24Y2019001901). WG and RZ were supported by the Scottish Government Rural and Environment Science and Analytical Services division (RESAS), and RZ also acknowledges the support from a BBSRC Bioinformatics and Biological Resources Fund (grant agreement: BB/S020160/1).BPMN was supported by the Norwich Research Park (NRP) Biosciences Doctoral Training Partnership (DTP) funded by the BBSRC (grant agreement: BB/M011216/1). SH and XF were supported by a BBSRC Responsive Mode grant (grant agreement: BB/S009620/1) and a European Research Council Starting grant ‘SexMeth’ (grant agreement: 804981). CL was supported by Deutsche Forschungsgemeinschaft (grant agreement: LI 2862/4). ","publication_identifier":{"issn":["0022-0957","1460-2431"]},"citation":{"short":"P. Ding, T. Sakai, R. Krishna Shrestha, N. Manosalva Perez, W. Guo, B.P.M. Ngou, S. He, C. Liu, X. Feng, R. Zhang, K. Vandepoele, D. MacLean, J.D.G. Jones, Journal of Experimental Botany 72 (2021) 7927–7941.","ista":"Ding P, Sakai T, Krishna Shrestha R, Manosalva Perez N, Guo W, Ngou BPM, He S, Liu C, Feng X, Zhang R, Vandepoele K, MacLean D, Jones JDG. 2021. Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. Journal of Experimental Botany. 72(22), 7927–7941.","mla":"Ding, Pingtao, et al. “Chromatin Accessibility Landscapes Activated by Cell-Surface and Intracellular Immune Receptors.” <i>Journal of Experimental Botany</i>, vol. 72, no. 22, Oxford University Press, 2021, pp. 7927–41, doi:<a href=\"https://doi.org/10.1093/jxb/erab373\">10.1093/jxb/erab373</a>.","ama":"Ding P, Sakai T, Krishna Shrestha R, et al. Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. <i>Journal of Experimental Botany</i>. 2021;72(22):7927-7941. doi:<a href=\"https://doi.org/10.1093/jxb/erab373\">10.1093/jxb/erab373</a>","apa":"Ding, P., Sakai, T., Krishna Shrestha, R., Manosalva Perez, N., Guo, W., Ngou, B. P. M., … Jones, J. D. G. (2021). Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/erab373\">https://doi.org/10.1093/jxb/erab373</a>","ieee":"P. Ding <i>et al.</i>, “Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors,” <i>Journal of Experimental Botany</i>, vol. 72, no. 22. Oxford University Press, pp. 7927–7941, 2021.","chicago":"Ding, Pingtao, Toshiyuki Sakai, Ram Krishna Shrestha, Nicolas Manosalva Perez, Wenbin Guo, Bruno Pok Man Ngou, Shengbo He, et al. “Chromatin Accessibility Landscapes Activated by Cell-Surface and Intracellular Immune Receptors.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/jxb/erab373\">https://doi.org/10.1093/jxb/erab373</a>."},"article_processing_charge":"No","doi":"10.1093/jxb/erab373","date_updated":"2023-05-08T11:01:18Z","date_published":"2021-08-13T00:00:00Z","author":[{"first_name":"Pingtao","last_name":"Ding","full_name":"Ding, Pingtao"},{"last_name":"Sakai","first_name":"Toshiyuki","full_name":"Sakai, Toshiyuki"},{"last_name":"Krishna Shrestha","first_name":"Ram","full_name":"Krishna Shrestha, Ram"},{"full_name":"Manosalva Perez, Nicolas","last_name":"Manosalva Perez","first_name":"Nicolas"},{"full_name":"Guo, Wenbin","first_name":"Wenbin","last_name":"Guo"},{"last_name":"Ngou","first_name":"Bruno Pok Man","full_name":"Ngou, Bruno Pok Man"},{"full_name":"He, Shengbo","first_name":"Shengbo","last_name":"He"},{"last_name":"Liu","first_name":"Chang","full_name":"Liu, Chang"},{"first_name":"Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"last_name":"Zhang","first_name":"Runxuan","full_name":"Zhang, Runxuan"},{"full_name":"Vandepoele, Klaas","first_name":"Klaas","last_name":"Vandepoele"},{"last_name":"MacLean","first_name":"Dan","full_name":"MacLean, Dan"},{"last_name":"Jones","first_name":"Jonathan D G","full_name":"Jones, Jonathan D G"}],"quality_controlled":"1","keyword":["Plant Science","Physiology"],"scopus_import":"1","publication_status":"published","intvolume":"        72","day":"13","pmid":1,"month":"08","language":[{"iso":"eng"}]},{"_id":"12187","year":"2021","volume":373,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Long J, Walker J, She W, Aldridge B, Gao H, Deans S, Vickers M, Feng X. 2021. Nurse cell--derived small RNAs define paternal epigenetic inheritance in Arabidopsis. Science. 373(6550).","mla":"Long, Jincheng, et al. “Nurse Cell--Derived Small RNAs Define Paternal Epigenetic Inheritance in Arabidopsis.” <i>Science</i>, vol. 373, no. 6550, American Association for the Advancement of Science (AAAS), 2021, doi:<a href=\"https://doi.org/10.1126/science.abh0556\">10.1126/science.abh0556</a>.","short":"J. Long, J. Walker, W. She, B. Aldridge, H. Gao, S. Deans, M. Vickers, X. Feng, Science 373 (2021).","ama":"Long J, Walker J, She W, et al. Nurse cell--derived small RNAs define paternal epigenetic inheritance in Arabidopsis. <i>Science</i>. 2021;373(6550). doi:<a href=\"https://doi.org/10.1126/science.abh0556\">10.1126/science.abh0556</a>","apa":"Long, J., Walker, J., She, W., Aldridge, B., Gao, H., Deans, S., … Feng, X. (2021). Nurse cell--derived small RNAs define paternal epigenetic inheritance in Arabidopsis. <i>Science</i>. American Association for the Advancement of Science (AAAS). <a href=\"https://doi.org/10.1126/science.abh0556\">https://doi.org/10.1126/science.abh0556</a>","ieee":"J. Long <i>et al.</i>, “Nurse cell--derived small RNAs define paternal epigenetic inheritance in Arabidopsis,” <i>Science</i>, vol. 373, no. 6550. American Association for the Advancement of Science (AAAS), 2021.","chicago":"Long, Jincheng, James Walker, Wenjing She, Billy Aldridge, Hongbo Gao, Samuel Deans, Martin Vickers, and Xiaoqi Feng. “Nurse Cell--Derived Small RNAs Define Paternal Epigenetic Inheritance in Arabidopsis.” <i>Science</i>. American Association for the Advancement of Science (AAAS), 2021. <a href=\"https://doi.org/10.1126/science.abh0556\">https://doi.org/10.1126/science.abh0556</a>."},"publication_identifier":{"issn":["0036-8075","1095-9203"]},"acknowledgement":"We thank the John Innes Centre Bioimaging Facility (S. Lopez, E. Wegel, and K. Findlay) for their assistance with microscopy and the Norwich BioScience Institute Partnership Computing Infrastructure for Science Group for high-performance computing resources. Funding: This work was funded by a European Research Council Starting Grant (“SexMeth” 804981; J.L., J.W., and X.F.), a Sainsbury Charitable Foundation studentship (J.W.), two Biotechnology and Biological Sciences Research Council (BBSRC) grants (BBS0096201 and BBP0135111; W.S., M.V., and X.F.), two John Innes Foundation studentships (B.A. and S.D.), and a BBSRC David Phillips Fellowship (BBL0250431; H.G. and X.F.). Author contributions: J.L., J.W., and X.F. designed the study and wrote the manuscript; J.L., W.S., B.A., H.G., and S.D. performed the experiments; and J.L., J.W., B.A., H.G., S.D., M.V., and X.F. analyzed the data. Competing interests: The authors declare no competing interests. Data and material availability: All sequencing data have been deposited in the Gene Expression Omnibus (GEO) under accession no. GSE161625. Accession nos. of published datasets used in this study are listed in table S6. Published software used in this study include Bowtie v1.2.2 (https://doi.org/10.1002/0471250953.bi1107s32), Bismark v0.22.2 (https://doi.org/10.1093/bioinformatics/btr167), Kallisto v0.43.0 (https://doi.org/10.1038/nbt0816-888d), Shortstack v3.8.5 (https://doi.org/10.1534/g3.116.030452), and Cutadapt v1.15 (https://doi.org/10.1089/cmb.2017.0096). TrimGalore v0.4.1 and MarkDuplicates v1.141 are available from https://github.com/FelixKrueger/TrimGalore and https://github.com/broadinstitute/picard, respectively. All remaining data are in the main paper or the supplementary materials.","status":"public","article_type":"original","external_id":{"pmid":["34210850"]},"issue":"6550","oa_version":"None","date_created":"2023-01-16T09:15:14Z","department":[{"_id":"XiFe"}],"title":"Nurse cell--derived small RNAs define paternal epigenetic inheritance in Arabidopsis","publication":"Science","publisher":"American Association for the Advancement of Science (AAAS)","abstract":[{"text":"Genomes of germ cells present an existential vulnerability to organisms because germ cell mutations will propagate to future generations. Transposable elements are one source of such mutations. In the small flowering plant Arabidopsis, Long et al. found that genome methylation in the male germline is directed by small interfering RNAs (siRNAs) imperfectly transcribed from transposons (see the Perspective by Mosher). These germline siRNAs silence germline transposons and establish inherited methylation patterns in sperm, thus maintaining the integrity of the plant genome across generations.","lang":"eng"}],"extern":"1","intvolume":"       373","publication_status":"published","language":[{"iso":"eng"}],"month":"07","pmid":1,"day":"02","scopus_import":"1","keyword":["Multidisciplinary"],"quality_controlled":"1","author":[{"full_name":"Long, Jincheng","last_name":"Long","first_name":"Jincheng"},{"first_name":"James","last_name":"Walker","full_name":"Walker, James"},{"last_name":"She","first_name":"Wenjing","full_name":"She, Wenjing"},{"full_name":"Aldridge, Billy","last_name":"Aldridge","first_name":"Billy"},{"first_name":"Hongbo","last_name":"Gao","full_name":"Gao, Hongbo"},{"last_name":"Deans","first_name":"Samuel","full_name":"Deans, Samuel"},{"last_name":"Vickers","first_name":"Martin","full_name":"Vickers, Martin"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi"}],"date_published":"2021-07-02T00:00:00Z","doi":"10.1126/science.abh0556","date_updated":"2023-05-08T10:56:39Z","article_processing_charge":"No"},{"citation":{"apa":"Bansal, S., Chatterjee, K., &#38; Vardi, M. Y. (2021). On satisficing in quantitative games. In <i>27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 12651, pp. 20–37). Luxembourg City, Luxembourg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-72016-2\">https://doi.org/10.1007/978-3-030-72016-2</a>","ieee":"S. Bansal, K. Chatterjee, and M. Y. Vardi, “On satisficing in quantitative games,” in <i>27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, Luxembourg City, Luxembourg, 2021, vol. 12651, pp. 20–37.","chicago":"Bansal, Suguman, Krishnendu Chatterjee, and Moshe Y. Vardi. “On Satisficing in Quantitative Games.” In <i>27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, 12651:20–37. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-72016-2\">https://doi.org/10.1007/978-3-030-72016-2</a>.","short":"S. Bansal, K. Chatterjee, M.Y. Vardi, in:, 27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2021, pp. 20–37.","ista":"Bansal S, Chatterjee K, Vardi MY. 2021. On satisficing in quantitative games. 27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 12651, 20–37.","mla":"Bansal, Suguman, et al. “On Satisficing in Quantitative Games.” <i>27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 12651, Springer Nature, 2021, pp. 20–37, doi:<a href=\"https://doi.org/10.1007/978-3-030-72016-2\">10.1007/978-3-030-72016-2</a>.","ama":"Bansal S, Chatterjee K, Vardi MY. On satisficing in quantitative games. In: <i>27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 12651. Springer Nature; 2021:20-37. doi:<a href=\"https://doi.org/10.1007/978-3-030-72016-2\">10.1007/978-3-030-72016-2</a>"},"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783030720155"]},"oa":1,"acknowledgement":"We thank anonymous reviewers for valuable inputs. This work is supported in part by NSF grant 2030859 to the CRA for the CIFellows Project, NSF grants IIS-1527668, CCF-1704883, IIS-1830549, the ERC CoG 863818 (ForM-SMArt), and an award from the Maryland Procurement Office.","status":"public","external_id":{"arxiv":["2101.02594"]},"_id":"12767","year":"2021","has_accepted_license":"1","volume":12651,"page":"20-37","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","abstract":[{"lang":"eng","text":"Several problems in planning and reactive synthesis can be reduced to the analysis of two-player quantitative graph games. Optimization is one form of analysis. We argue that in many cases it may be better to replace the optimization problem with the satisficing problem, where instead of searching for optimal solutions, the goal is to search for solutions that adhere to a given threshold bound.\r\nThis work defines and investigates the satisficing problem on a two-player graph game with the discounted-sum cost model. We show that while the satisficing problem can be solved using numerical methods just like the optimization problem, this approach does not render compelling benefits over optimization. When the discount factor is, however, an integer, we present another approach to satisficing, which is purely based on automata methods. We show that this approach is algorithmically more performant – both theoretically and empirically – and demonstrates the broader applicability of satisficing over optimization."}],"arxiv":1,"date_created":"2023-03-26T22:01:09Z","ec_funded":1,"oa_version":"Published Version","publication":"27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems","department":[{"_id":"KrCh"}],"title":"On satisficing in quantitative games","publisher":"Springer Nature","month":"03","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"ddc":["000"],"day":"21","intvolume":"     12651","file":[{"file_id":"12777","date_updated":"2023-03-28T11:00:33Z","file_size":747418,"file_name":"2021_LNCS_Bansal.pdf","checksum":"b020b78b23587ce7610b1aafb4e63438","relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2023-03-28T11:00:33Z"}],"publication_status":"published","scopus_import":"1","quality_controlled":"1","date_published":"2021-03-21T00:00:00Z","author":[{"last_name":"Bansal","first_name":"Suguman","full_name":"Bansal, Suguman"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Vardi, Moshe Y.","last_name":"Vardi","first_name":"Moshe Y."}],"article_processing_charge":"No","date_updated":"2025-07-14T09:09:51Z","doi":"10.1007/978-3-030-72016-2","alternative_title":["LNCS"],"conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2021-04-01","location":"Luxembourg City, Luxembourg","start_date":"2021-03-27"},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2023-03-28T11:00:33Z"}]