[{"file_date_updated":"2023-02-27T07:17:42Z","page":"358-374","issue":"5","doi":"10.1002/evl3.295","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We thank A. Wright and four anonymous reviewers for valuable comments on an earlier draft of this manuscript and all members of the Littorina group for helpful discussions. This work was supported by a European Research Council grant to RKB and by a Natural Environment Research Council studentship to KEH through the ACCE doctoral training program. KJ acknowledges support from the Swedish Science Research Council VR (Vetenskaprådet) (2017-03798). RF was supported by an FCT CEEC (Fundação para a Ciênca e a Tecnologia, Concurso Estímulo ao Emprego Científico) contract (2020.00275.CEECIND).","isi":1,"day":"01","citation":{"short":"K.E. Hearn, E.L. Koch, S. Stankowski, R.K. Butlin, R. Faria, K. Johannesson, A.M. Westram, Evolution Letters 6 (2022) 358–374.","ieee":"K. E. Hearn <i>et al.</i>, “Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis,” <i>Evolution Letters</i>, vol. 6, no. 5. Oxford University Press, pp. 358–374, 2022.","chicago":"Hearn, Katherine E., Eva L. Koch, Sean Stankowski, Roger K. Butlin, Rui Faria, Kerstin Johannesson, and Anja M Westram. “Differing Associations between Sex Determination and Sex-Linked Inversions in Two Ecotypes of Littorina Saxatilis.” <i>Evolution Letters</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1002/evl3.295\">https://doi.org/10.1002/evl3.295</a>.","ista":"Hearn KE, Koch EL, Stankowski S, Butlin RK, Faria R, Johannesson K, Westram AM. 2022. Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. Evolution Letters. 6(5), 358–374.","ama":"Hearn KE, Koch EL, Stankowski S, et al. Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. <i>Evolution Letters</i>. 2022;6(5):358-374. doi:<a href=\"https://doi.org/10.1002/evl3.295\">10.1002/evl3.295</a>","apa":"Hearn, K. E., Koch, E. L., Stankowski, S., Butlin, R. K., Faria, R., Johannesson, K., &#38; Westram, A. M. (2022). Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. <i>Evolution Letters</i>. Oxford University Press. <a href=\"https://doi.org/10.1002/evl3.295\">https://doi.org/10.1002/evl3.295</a>","mla":"Hearn, Katherine E., et al. “Differing Associations between Sex Determination and Sex-Linked Inversions in Two Ecotypes of Littorina Saxatilis.” <i>Evolution Letters</i>, vol. 6, no. 5, Oxford University Press, 2022, pp. 358–74, doi:<a href=\"https://doi.org/10.1002/evl3.295\">10.1002/evl3.295</a>."},"file":[{"checksum":"2dcd06186a11b7d1be4cddc6b189f8fb","creator":"dernst","access_level":"open_access","file_name":"2022_EvolutionLetters_Hearn.pdf","date_updated":"2023-02-27T07:17:42Z","date_created":"2023-02-27T07:17:42Z","relation":"main_file","content_type":"application/pdf","file_size":2368965,"file_id":"12686","success":1}],"department":[{"_id":"NiBa"}],"quality_controlled":"1","publication_status":"published","type":"journal_article","ddc":["570"],"publication":"Evolution Letters","has_accepted_license":"1","publisher":"Oxford University Press","article_processing_charge":"Yes","article_type":"original","language":[{"iso":"eng"}],"status":"public","scopus_import":"1","month":"10","title":"Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis","date_published":"2022-10-01T00:00:00Z","year":"2022","_id":"12001","intvolume":"         6","date_updated":"2025-06-12T06:22:56Z","publication_identifier":{"eissn":["2056-3744"]},"date_created":"2022-08-28T22:02:02Z","author":[{"first_name":"Katherine E.","last_name":"Hearn","full_name":"Hearn, Katherine E."},{"last_name":"Koch","first_name":"Eva L.","full_name":"Koch, Eva L."},{"full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Sexual antagonism is a common hypothesis for driving the evolution of sex chromosomes, whereby recombination suppression is favored between sexually antagonistic loci and the sex-determining locus to maintain beneficial combinations of alleles. This results in the formation of a sex-determining region. Chromosomal inversions may contribute to recombination suppression but their precise role in sex chromosome evolution remains unclear. Because local adaptation is frequently facilitated through the suppression of recombination between adaptive loci by chromosomal inversions, there is potential for inversions that cover sex-determining regions to be involved in local adaptation as well, particularly if habitat variation creates environment-dependent sexual antagonism. With these processes in mind, we investigated sex determination in a well-studied example of local adaptation within a species: the intertidal snail, Littorina saxatilis. Using SNP data from a Swedish hybrid zone, we find novel evidence for a female-heterogametic sex determination system that is restricted to one ecotype. Our results suggest that four putative chromosomal inversions, two previously described and two newly discovered, span the putative sex chromosome pair. We determine their differing associations with sex, which suggest distinct strata of differing ages. The same inversions are found in the second ecotype but do not show any sex association. The striking disparity in inversion-sex associations between ecotypes that are connected by gene flow across a habitat transition that is just a few meters wide indicates a difference in selective regime that has produced a distinct barrier to the spread of the newly discovered sex-determining region between ecotypes. Such sex chromosome-environment interactions have not previously been uncovered in L. saxatilis and are known in few other organisms. A combination of both sex-specific selection and divergent natural selection is required to explain these highly unusual patterns."}],"volume":6,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"external_id":{"pmid":["36254259"],"isi":["000839621100001"]}},{"volume":173,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","abstract":[{"text":"The Tibetan plateau (TP) plays an important role in the Asian summer monsoon (ASM) dynamics as a heat source during the pre-monsoon and monsoon seasons. A significant contribution to the pre-monsoon TP heating comes from the sensible heat flux (SHF), which depend on the surface properties. A glaciated surface would have a different SHF compared to a non-glaciated surface. Therefore, the TP glaciers potentially can also impact the hydrological cycle in the Asian continent by impacting the ASM rainfall via its contribution to the total plateau heating. However, there is no assessment of this putative link available. Here, we attempt to qualitatively study the role of TP glaciers on ASM by analyzing the sensitivity of an atmospheric model to the absence of TP glaciers. We find that the absence of the glaciers is most felt in climatologically less snowy regions (which are mostly located at the south-central boundary of the TP during the pre-monsoon season), which leads to positive SHF anomalies. The resulting positive diabatic heating leads to rising air in the eastern TP and sinking air in the western TP. This altered circulation in turn leads to a positive SHF memory in the western TP, which persists until the end of the monsoon season. The impact of SHF anomalies on diabatic heating results in a large-scale subsidence over the ASM domain. The net result is a reduced seasonal ASM rainfall. Given the relentless warming and the vulnerability of glaciers to warming, this is another flag in the ASM variability and change that needs further attention.","lang":"eng"}],"author":[{"id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","last_name":"GOSWAMI","first_name":"BIDYUT B","full_name":"GOSWAMI, BIDYUT B"},{"full_name":"An, Soon-Il","first_name":"Soon-Il","last_name":"An"},{"first_name":"Raghu","last_name":"Murtugudde","full_name":"Murtugudde, Raghu"}],"date_created":"2022-09-03T07:24:13Z","date_updated":"2022-09-05T08:33:33Z","publication_identifier":{"issn":["0165-0009","1573-1480"]},"_id":"12007","year":"2022","intvolume":"       173","title":"Role of the Tibetan plateau glaciers in the Asian summer monsoon","extern":"1","scopus_import":"1","month":"08","date_published":"2022-08-30T00:00:00Z","status":"public","article_type":"original","article_processing_charge":"No","language":[{"iso":"eng"}],"has_accepted_license":"1","publisher":"Springer Nature","publication":"Climatic Change","ddc":["550"],"quality_controlled":"1","type":"journal_article","publication_status":"published","file":[{"file_name":"2022_ClimateChange_Goswami.pdf","date_updated":"2022-09-05T08:29:27Z","creator":"dernst","checksum":"38071d5c142bb76f8c8665dc374838a8","access_level":"open_access","relation":"main_file","date_created":"2022-09-05T08:29:27Z","file_size":1350575,"content_type":"application/pdf","success":1,"file_id":"12021"}],"citation":{"chicago":"GOSWAMI, BIDYUT B, Soon-Il An, and Raghu Murtugudde. “Role of the Tibetan Plateau Glaciers in the Asian Summer Monsoon.” <i>Climatic Change</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s10584-022-03426-8\">https://doi.org/10.1007/s10584-022-03426-8</a>.","ista":"GOSWAMI BB, An S-I, Murtugudde R. 2022. Role of the Tibetan plateau glaciers in the Asian summer monsoon. Climatic Change. 173(3–4), 29.","ama":"GOSWAMI BB, An S-I, Murtugudde R. Role of the Tibetan plateau glaciers in the Asian summer monsoon. <i>Climatic Change</i>. 2022;173(3-4). doi:<a href=\"https://doi.org/10.1007/s10584-022-03426-8\">10.1007/s10584-022-03426-8</a>","apa":"GOSWAMI, B. B., An, S.-I., &#38; Murtugudde, R. (2022). Role of the Tibetan plateau glaciers in the Asian summer monsoon. <i>Climatic Change</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10584-022-03426-8\">https://doi.org/10.1007/s10584-022-03426-8</a>","mla":"GOSWAMI, BIDYUT B., et al. “Role of the Tibetan Plateau Glaciers in the Asian Summer Monsoon.” <i>Climatic Change</i>, vol. 173, no. 3–4, 29, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s10584-022-03426-8\">10.1007/s10584-022-03426-8</a>.","short":"B.B. GOSWAMI, S.-I. An, R. Murtugudde, Climatic Change 173 (2022).","ieee":"B. B. GOSWAMI, S.-I. An, and R. Murtugudde, “Role of the Tibetan plateau glaciers in the Asian summer monsoon,” <i>Climatic Change</i>, vol. 173, no. 3–4. Springer Nature, 2022."},"day":"30","acknowledgement":"This research is funded by the IRCC research funding.","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"3-4","doi":"10.1007/s10584-022-03426-8","article_number":"29","file_date_updated":"2022-09-05T08:29:27Z","keyword":["Atmospheric Science","Global and Planetary Change"]},{"article_number":"873","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We would like to thank the Vogels Lab for feedback on an earlier version of this manuscript. D.W.J. was supported by a Marshall Scholarship and a Clarendon Scholarship. R.P.C. and T.P.V. were supported by a Wellcome Trust and Royal Society Sir Henry Dale Fellowship (WT 100000), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z), and an ERC Consolidator Grant (SYNAPSEEK).","doi":"10.1038/s42003-022-03801-2","citation":{"apa":"Jia, D. W., Vogels, T. P., &#38; Costa, R. P. (2022). Developmental depression-to-facilitation shift controls excitation-inhibition balance. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-022-03801-2\">https://doi.org/10.1038/s42003-022-03801-2</a>","ama":"Jia DW, Vogels TP, Costa RP. Developmental depression-to-facilitation shift controls excitation-inhibition balance. <i>Communications biology</i>. 2022;5. doi:<a href=\"https://doi.org/10.1038/s42003-022-03801-2\">10.1038/s42003-022-03801-2</a>","ista":"Jia DW, Vogels TP, Costa RP. 2022. Developmental depression-to-facilitation shift controls excitation-inhibition balance. Communications biology. 5, 873.","chicago":"Jia, David W., Tim P Vogels, and Rui Ponte Costa. “Developmental Depression-to-Facilitation Shift Controls Excitation-Inhibition Balance.” <i>Communications Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s42003-022-03801-2\">https://doi.org/10.1038/s42003-022-03801-2</a>.","mla":"Jia, David W., et al. “Developmental Depression-to-Facilitation Shift Controls Excitation-Inhibition Balance.” <i>Communications Biology</i>, vol. 5, 873, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s42003-022-03801-2\">10.1038/s42003-022-03801-2</a>.","ieee":"D. W. Jia, T. P. Vogels, and R. P. Costa, “Developmental depression-to-facilitation shift controls excitation-inhibition balance,” <i>Communications biology</i>, vol. 5. Springer Nature, 2022.","short":"D.W. Jia, T.P. Vogels, R.P. Costa, Communications Biology 5 (2022)."},"isi":1,"day":"25","file_date_updated":"2022-09-05T08:55:11Z","ddc":["570"],"publication":"Communications biology","publisher":"Springer Nature","has_accepted_license":"1","department":[{"_id":"TiVo"}],"file":[{"content_type":"application/pdf","file_size":2491191,"file_id":"12022","success":1,"file_name":"2022_CommBiology_Jia.pdf","date_updated":"2022-09-05T08:55:11Z","access_level":"open_access","creator":"dernst","checksum":"3ec724c4f6d3440028c217305e32915f","relation":"main_file","date_created":"2022-09-05T08:55:11Z"}],"type":"journal_article","publication_status":"published","quality_controlled":"1","date_published":"2022-08-25T00:00:00Z","title":"Developmental depression-to-facilitation shift controls excitation-inhibition balance","month":"08","scopus_import":"1","intvolume":"         5","year":"2022","_id":"12009","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","ec_funded":1,"status":"public","abstract":[{"lang":"eng","text":"Changes in the short-term dynamics of excitatory synapses over development have been observed throughout cortex, but their purpose and consequences remain unclear. Here, we propose that developmental changes in synaptic dynamics buffer the effect of slow inhibitory long-term plasticity, allowing for continuously stable neural activity. Using computational modeling we demonstrate that early in development excitatory short-term depression quickly stabilises neural activity, even in the face of strong, unbalanced excitation. We introduce a model of the commonly observed developmental shift from depression to facilitation and show that neural activity remains stable throughout development, while inhibitory synaptic plasticity slowly balances excitation, consistent with experimental observations. Our model predicts changes in the input responses from phasic to phasic-and-tonic and more precise spike timings. We also observe a gradual emergence of short-lasting memory traces governed by short-term plasticity development. We conclude that the developmental depression-to-facilitation shift may control excitation-inhibition balance throughout development with important functional consequences."}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000844814800007"]},"oa":1,"volume":5,"publication_identifier":{"eissn":["2399-3642"]},"date_updated":"2025-04-14T09:44:14Z","project":[{"_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks.","grant_number":"214316/Z/18/Z"},{"_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","call_identifier":"H2020","grant_number":"819603","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning."}],"author":[{"full_name":"Jia, David W.","last_name":"Jia","first_name":"David W."},{"orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","first_name":"Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"},{"full_name":"Costa, Rui Ponte","first_name":"Rui Ponte","last_name":"Costa"}],"date_created":"2022-09-04T22:02:02Z"},{"isi":1,"day":"12","citation":{"mla":"Brunnbauer, Axel, et al. “Latent Imagination Facilitates Zero-Shot Transfer in Autonomous Racing.” <i>2022 International Conference on Robotics and Automation</i>, IEEE, 2022, pp. 7513–20, doi:<a href=\"https://doi.org/10.1109/ICRA46639.2022.9811650\">10.1109/ICRA46639.2022.9811650</a>.","ista":"Brunnbauer A, Berducci L, Brandstatter A, Lechner M, Hasani R, Rus D, Grosu R. 2022. Latent imagination facilitates zero-shot transfer in autonomous racing. 2022 International Conference on Robotics and Automation. ICRA: International Conference on Robotics and Automation, 7513–7520.","chicago":"Brunnbauer, Axel, Luigi Berducci, Andreas Brandstatter, Mathias Lechner, Ramin Hasani, Daniela Rus, and Radu Grosu. “Latent Imagination Facilitates Zero-Shot Transfer in Autonomous Racing.” In <i>2022 International Conference on Robotics and Automation</i>, 7513–20. IEEE, 2022. <a href=\"https://doi.org/10.1109/ICRA46639.2022.9811650\">https://doi.org/10.1109/ICRA46639.2022.9811650</a>.","ama":"Brunnbauer A, Berducci L, Brandstatter A, et al. Latent imagination facilitates zero-shot transfer in autonomous racing. In: <i>2022 International Conference on Robotics and Automation</i>. IEEE; 2022:7513-7520. doi:<a href=\"https://doi.org/10.1109/ICRA46639.2022.9811650\">10.1109/ICRA46639.2022.9811650</a>","apa":"Brunnbauer, A., Berducci, L., Brandstatter, A., Lechner, M., Hasani, R., Rus, D., &#38; Grosu, R. (2022). Latent imagination facilitates zero-shot transfer in autonomous racing. In <i>2022 International Conference on Robotics and Automation</i> (pp. 7513–7520). Philadelphia, PA, United States: IEEE. <a href=\"https://doi.org/10.1109/ICRA46639.2022.9811650\">https://doi.org/10.1109/ICRA46639.2022.9811650</a>","short":"A. Brunnbauer, L. Berducci, A. Brandstatter, M. Lechner, R. Hasani, D. Rus, R. Grosu, in:, 2022 International Conference on Robotics and Automation, IEEE, 2022, pp. 7513–7520.","ieee":"A. Brunnbauer <i>et al.</i>, “Latent imagination facilitates zero-shot transfer in autonomous racing,” in <i>2022 International Conference on Robotics and Automation</i>, Philadelphia, PA, United States, 2022, pp. 7513–7520."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2103.04909"}],"doi":"10.1109/ICRA46639.2022.9811650","acknowledgement":"L.B. was supported by the Doctoral College Resilient Embedded Systems. M.L. was supported in part by the ERC2020-AdG 101020093 and the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). R.H. and D.R. were supported by The Boeing Company and the Office of Naval Research (ONR) Grant N00014-18-1-2830. R.G. was partially supported by the Horizon-2020 ECSEL Project grant No. 783163 (iDev40) and A.B. by FFG Project ADEX.","conference":{"end_date":"2022-05-27","name":"ICRA: International Conference on Robotics and Automation","location":"Philadelphia, PA, United States","start_date":"2022-05-23"},"page":"7513-7520","publisher":"IEEE","publication":"2022 International Conference on Robotics and Automation","publication_status":"published","type":"conference","quality_controlled":"1","department":[{"_id":"ToHe"}],"year":"2022","_id":"12010","date_published":"2022-07-12T00:00:00Z","scopus_import":"1","month":"07","title":"Latent imagination facilitates zero-shot transfer in autonomous racing","status":"public","ec_funded":1,"language":[{"iso":"eng"}],"article_processing_charge":"No","external_id":{"isi":["000941277600124"],"arxiv":["2103.04909"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"abstract":[{"text":"World models learn behaviors in a latent imagination space to enhance the sample-efficiency of deep reinforcement learning (RL) algorithms. While learning world models for high-dimensional observations (e.g., pixel inputs) has become practicable on standard RL benchmarks and some games, their effectiveness in real-world robotics applications has not been explored. In this paper, we investigate how such agents generalize to real-world autonomous vehicle control tasks, where advanced model-free deep RL algorithms fail. In particular, we set up a series of time-lap tasks for an F1TENTH racing robot, equipped with a high-dimensional LiDAR sensor, on a set of test tracks with a gradual increase in their complexity. In this continuous-control setting, we show that model-based agents capable of learning in imagination substantially outperform model-free agents with respect to performance, sample efficiency, successful task completion, and generalization. Moreover, we show that the generalization ability of model-based agents strongly depends on the choice of their observation model. We provide extensive empirical evidence for the effectiveness of world models provided with long enough memory horizons in sim2real tasks.","lang":"eng"}],"oa_version":"Preprint","arxiv":1,"project":[{"call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"},{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"date_created":"2022-09-04T22:02:02Z","author":[{"last_name":"Brunnbauer","first_name":"Axel","full_name":"Brunnbauer, Axel"},{"first_name":"Luigi","last_name":"Berducci","full_name":"Berducci, Luigi"},{"first_name":"Andreas","last_name":"Brandstatter","full_name":"Brandstatter, Andreas"},{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner","full_name":"Lechner, Mathias"},{"last_name":"Hasani","first_name":"Ramin","full_name":"Hasani, Ramin"},{"last_name":"Rus","first_name":"Daniela","full_name":"Rus, Daniela"},{"full_name":"Grosu, Radu","first_name":"Radu","last_name":"Grosu"}],"publication_identifier":{"isbn":["9781728196817"],"issn":["1050-4729"]},"date_updated":"2025-09-10T09:39:53Z"},{"department":[{"_id":"MaMo"}],"quality_controlled":"1","publication_status":"published","type":"conference","publication":"2022 IEEE International Symposium on Information Theory","publisher":"IEEE","page":"2523-2528","conference":{"start_date":"2022-06-26","location":"Espoo, Finland","name":"ISIT: International Symposium on Information Theory","end_date":"2022-07-01"},"doi":"10.1109/ISIT50566.2022.9834709","acknowledgement":"The work of ADS and ML was supported in part by the US National Science Foundation under awards CCF-1909468 and CCF-1909451.","day":"03","isi":1,"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2205.06708","open_access":"1"}],"citation":{"short":"Y. Zhang, S. Jaggi, M. Langberg, A.D. Sarwate, in:, 2022 IEEE International Symposium on Information Theory, IEEE, 2022, pp. 2523–2528.","ieee":"Y. Zhang, S. Jaggi, M. Langberg, and A. D. Sarwate, “The capacity of causal adversarial channels,” in <i>2022 IEEE International Symposium on Information Theory</i>, Espoo, Finland, 2022, vol. 2022, pp. 2523–2528.","chicago":"Zhang, Yihan, Sidharth Jaggi, Michael Langberg, and Anand D. Sarwate. “The Capacity of Causal Adversarial Channels.” In <i>2022 IEEE International Symposium on Information Theory</i>, 2022:2523–28. IEEE, 2022. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834709\">https://doi.org/10.1109/ISIT50566.2022.9834709</a>.","ista":"Zhang Y, Jaggi S, Langberg M, Sarwate AD. 2022. The capacity of causal adversarial channels. 2022 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory vol. 2022, 2523–2528.","apa":"Zhang, Y., Jaggi, S., Langberg, M., &#38; Sarwate, A. D. (2022). The capacity of causal adversarial channels. In <i>2022 IEEE International Symposium on Information Theory</i> (Vol. 2022, pp. 2523–2528). Espoo, Finland: IEEE. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834709\">https://doi.org/10.1109/ISIT50566.2022.9834709</a>","ama":"Zhang Y, Jaggi S, Langberg M, Sarwate AD. The capacity of causal adversarial channels. In: <i>2022 IEEE International Symposium on Information Theory</i>. Vol 2022. IEEE; 2022:2523-2528. doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834709\">10.1109/ISIT50566.2022.9834709</a>","mla":"Zhang, Yihan, et al. “The Capacity of Causal Adversarial Channels.” <i>2022 IEEE International Symposium on Information Theory</i>, vol. 2022, IEEE, 2022, pp. 2523–28, doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834709\">10.1109/ISIT50566.2022.9834709</a>."},"date_updated":"2025-09-10T09:40:42Z","publication_identifier":{"issn":["2157-8095"],"isbn":["9781665421591"]},"date_created":"2022-09-04T22:02:03Z","author":[{"last_name":"Zhang","first_name":"Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","full_name":"Zhang, Yihan","orcid":"0000-0002-6465-6258"},{"full_name":"Jaggi, Sidharth","last_name":"Jaggi","first_name":"Sidharth"},{"full_name":"Langberg, Michael","last_name":"Langberg","first_name":"Michael"},{"full_name":"Sarwate, Anand D.","first_name":"Anand D.","last_name":"Sarwate"}],"arxiv":1,"oa_version":"Preprint","abstract":[{"text":"We characterize the capacity for the discrete-time arbitrarily varying channel with discrete inputs, outputs, and states when (a) the encoder and decoder do not share common randomness, (b) the input and state are subject to cost constraints, (c) the transition matrix of the channel is deterministic given the state, and (d) at each time step the adversary can only observe the current and past channel inputs when choosing the state at that time. The achievable strategy involves stochastic encoding together with list decoding and a disambiguation step. The converse uses a two-phase \"babble-and-push\" strategy where the adversary chooses the state randomly in the first phase, list decodes the output, and then chooses state inputs to symmetrize the channel in the second phase. These results generalize prior work on specific channels models (additive, erasure) to general discrete alphabets and models.","lang":"eng"}],"oa":1,"volume":2022,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["001254261902114"],"arxiv":["2205.06708"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","scopus_import":"1","month":"08","title":"The capacity of causal adversarial channels","date_published":"2022-08-03T00:00:00Z","_id":"12011","year":"2022","intvolume":"      2022"},{"intvolume":"      2022","_id":"12012","year":"2022","date_published":"2022-08-03T00:00:00Z","title":"Heterogeneous differential privacy via graphs","scopus_import":"1","month":"08","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","external_id":{"arxiv":["2203.15429"],"isi":["001254261901131"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":2022,"oa":1,"abstract":[{"lang":"eng","text":"This paper is eligible for the Jack Keil Wolf ISIT Student Paper Award. We generalize a previous framework for designing utility-optimal differentially private (DP) mechanisms via graphs, where datasets are vertices in the graph and edges represent dataset neighborhood. The boundary set contains datasets where an individual’s response changes the binary-valued query compared to its neighbors. Previous work was limited to the homogeneous case where the privacy parameter ε across all datasets was the same and the mechanism at boundary datasets was identical. In our work, the mechanism can take different distributions at the boundary and the privacy parameter ε is a function of neighboring datasets, which recovers an earlier definition of personalized DP as special case. The problem is how to extend the mechanism, which is only defined at the boundary set, to other datasets in the graph in a computationally efficient and utility optimal manner. Using the concept of strongest induced DP condition we solve this problem efficiently in polynomial time (in the size of the graph)."}],"arxiv":1,"oa_version":"Preprint","author":[{"full_name":"Torkamani, Sahel","id":"0503e7f8-2d05-11ed-aa17-db0640c720fc","last_name":"Torkamani","first_name":"Sahel"},{"full_name":"Ebrahimi, Javad B.","first_name":"Javad B.","last_name":"Ebrahimi"},{"last_name":"Sadeghi","first_name":"Parastoo","full_name":"Sadeghi, Parastoo"},{"first_name":"Rafael G.L.","last_name":"D'Oliveira","full_name":"D'Oliveira, Rafael G.L."},{"first_name":"Muriel","last_name":"Médard","full_name":"Médard, Muriel"}],"date_created":"2022-09-04T22:02:04Z","publication_identifier":{"issn":["2157-8095"],"isbn":["9781665421591"]},"date_updated":"2025-09-10T09:42:41Z","citation":{"ieee":"S. Torkamani, J. B. Ebrahimi, P. Sadeghi, R. G. L. D’Oliveira, and M. Médard, “Heterogeneous differential privacy via graphs,” in <i>2022 IEEE International Symposium on Information Theory</i>, Espoo, Finland, 2022, vol. 2022, pp. 1623–1628.","short":"S. Torkamani, J.B. Ebrahimi, P. Sadeghi, R.G.L. D’Oliveira, M. Médard, in:, 2022 IEEE International Symposium on Information Theory, IEEE, 2022, pp. 1623–1628.","ama":"Torkamani S, Ebrahimi JB, Sadeghi P, D’Oliveira RGL, Médard M. Heterogeneous differential privacy via graphs. In: <i>2022 IEEE International Symposium on Information Theory</i>. Vol 2022. IEEE; 2022:1623-1628. doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834711\">10.1109/ISIT50566.2022.9834711</a>","apa":"Torkamani, S., Ebrahimi, J. B., Sadeghi, P., D’Oliveira, R. G. L., &#38; Médard, M. (2022). Heterogeneous differential privacy via graphs. In <i>2022 IEEE International Symposium on Information Theory</i> (Vol. 2022, pp. 1623–1628). Espoo, Finland: IEEE. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834711\">https://doi.org/10.1109/ISIT50566.2022.9834711</a>","ista":"Torkamani S, Ebrahimi JB, Sadeghi P, D’Oliveira RGL, Médard M. 2022. Heterogeneous differential privacy via graphs. 2022 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory vol. 2022, 1623–1628.","chicago":"Torkamani, Sahel, Javad B. Ebrahimi, Parastoo Sadeghi, Rafael G.L. D’Oliveira, and Muriel Médard. “Heterogeneous Differential Privacy via Graphs.” In <i>2022 IEEE International Symposium on Information Theory</i>, 2022:1623–28. IEEE, 2022. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834711\">https://doi.org/10.1109/ISIT50566.2022.9834711</a>.","mla":"Torkamani, Sahel, et al. “Heterogeneous Differential Privacy via Graphs.” <i>2022 IEEE International Symposium on Information Theory</i>, vol. 2022, IEEE, 2022, pp. 1623–28, doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834711\">10.1109/ISIT50566.2022.9834711</a>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2203.15429"}],"isi":1,"day":"03","doi":"10.1109/ISIT50566.2022.9834711","page":"1623-1628","conference":{"start_date":"2022-06-26","end_date":"2022-07-01","name":"ISIT: International Symposium on Information Theory","location":"Espoo, Finland"},"publisher":"IEEE","publication":"2022 IEEE International Symposium on Information Theory","type":"conference","publication_status":"published","quality_controlled":"1","department":[{"_id":"MaMo"}]},{"page":"504-509","conference":{"start_date":"2022-06-26","name":"ISIT: International Symposium on Information Theory","end_date":"2022-07-01","location":"Espoo, Finland"},"day":"03","isi":1,"citation":{"ieee":"P. Joshi, A. Purkayastha, Y. Zhang, A. J. Budkuley, and S. Jaggi, “On the capacity of additive AVCs with feedback,” in <i>2022 IEEE International Symposium on Information Theory</i>, Espoo, Finland, 2022, vol. 2022, pp. 504–509.","short":"P. Joshi, A. Purkayastha, Y. Zhang, A.J. Budkuley, S. Jaggi, in:, 2022 IEEE International Symposium on Information Theory, IEEE, 2022, pp. 504–509.","apa":"Joshi, P., Purkayastha, A., Zhang, Y., Budkuley, A. J., &#38; Jaggi, S. (2022). On the capacity of additive AVCs with feedback. In <i>2022 IEEE International Symposium on Information Theory</i> (Vol. 2022, pp. 504–509). Espoo, Finland: IEEE. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834850\">https://doi.org/10.1109/ISIT50566.2022.9834850</a>","ama":"Joshi P, Purkayastha A, Zhang Y, Budkuley AJ, Jaggi S. On the capacity of additive AVCs with feedback. In: <i>2022 IEEE International Symposium on Information Theory</i>. Vol 2022. IEEE; 2022:504-509. doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834850\">10.1109/ISIT50566.2022.9834850</a>","ista":"Joshi P, Purkayastha A, Zhang Y, Budkuley AJ, Jaggi S. 2022. On the capacity of additive AVCs with feedback. 2022 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory vol. 2022, 504–509.","chicago":"Joshi, Pranav, Amritakshya Purkayastha, Yihan Zhang, Amitalok J. Budkuley, and Sidharth Jaggi. “On the Capacity of Additive AVCs with Feedback.” In <i>2022 IEEE International Symposium on Information Theory</i>, 2022:504–9. IEEE, 2022. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834850\">https://doi.org/10.1109/ISIT50566.2022.9834850</a>.","mla":"Joshi, Pranav, et al. “On the Capacity of Additive AVCs with Feedback.” <i>2022 IEEE International Symposium on Information Theory</i>, vol. 2022, IEEE, 2022, pp. 504–09, doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834850\">10.1109/ISIT50566.2022.9834850</a>."},"doi":"10.1109/ISIT50566.2022.9834850","quality_controlled":"1","publication_status":"published","type":"conference","department":[{"_id":"MaMo"}],"publisher":"IEEE","publication":"2022 IEEE International Symposium on Information Theory","status":"public","article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"12013","year":"2022","intvolume":"      2022","scopus_import":"1","month":"08","title":"On the capacity of additive AVCs with feedback","date_published":"2022-08-03T00:00:00Z","date_created":"2022-09-04T22:02:04Z","author":[{"full_name":"Joshi, Pranav","last_name":"Joshi","first_name":"Pranav"},{"last_name":"Purkayastha","first_name":"Amritakshya","full_name":"Purkayastha, Amritakshya"},{"orcid":"0000-0002-6465-6258","full_name":"Zhang, Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","first_name":"Yihan","last_name":"Zhang"},{"full_name":"Budkuley, Amitalok J.","first_name":"Amitalok J.","last_name":"Budkuley"},{"last_name":"Jaggi","first_name":"Sidharth","full_name":"Jaggi, Sidharth"}],"date_updated":"2025-09-10T09:42:04Z","publication_identifier":{"issn":["2157-8095"],"isbn":["9781665421591"]},"volume":2022,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["001254261900085"]},"oa_version":"None","abstract":[{"text":"We consider the problem of communication over adversarial channels with feedback. Two parties comprising sender Alice and receiver Bob seek to communicate reliably. An adversary James observes Alice's channel transmission entirely and chooses, maliciously, its additive channel input or jamming state thereby corrupting Bob's observation. Bob can communicate over a one-way reverse link with Alice; we assume that transmissions over this feedback link cannot be corrupted by James. Our goal in this work is to study the optimum throughput or capacity over such channels with feedback. We first present results for the quadratically-constrained additive channel where communication is known to be impossible when the noise-to-signal (power) ratio (NSR) is at least 1. We present a novel achievability scheme to establish that positive rate communication is possible even when the NSR is as high as 8/9. We also present new converse upper bounds on the capacity of this channel under potentially stochastic encoders and decoders. We also study feedback communication over the more widely studied q-ary alphabet channel under additive noise. For the q -ary channel, where q > 2, it is well known that capacity is positive under full feedback if and only if the adversary can corrupt strictly less than half the transmitted symbols. We generalize this result and show that the same threshold holds for positive rate communication when the noiseless feedback may only be partial; our scheme employs a stochastic decoder. We extend this characterization, albeit partially, to fully deterministic schemes under partial noiseless feedback. We also present new converse upper bounds for q-ary channels under full feedback, where the encoder and/or decoder may privately randomize. Our converse results bring to the fore an interesting alternate expression for the well known converse bound for the q—ary channel under full feedback which, when specialized to the binary channel, also equals its known capacity.","lang":"eng"}]},{"doi":"10.1109/ISIT50566.2022.9834512","citation":{"short":"Y. Zhang, S. Vatedka, in:, 2022 IEEE International Symposium on Information Theory, IEEE, 2022, pp. 2559–2564.","ieee":"Y. Zhang and S. Vatedka, “List-decodability of Poisson Point Processes,” in <i>2022 IEEE International Symposium on Information Theory</i>, Espoo, Finland, 2022, vol. 2022, pp. 2559–2564.","mla":"Zhang, Yihan, and Shashank Vatedka. “List-Decodability of Poisson Point Processes.” <i>2022 IEEE International Symposium on Information Theory</i>, vol. 2022, IEEE, 2022, pp. 2559–64, doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834512\">10.1109/ISIT50566.2022.9834512</a>.","ista":"Zhang Y, Vatedka S. 2022. List-decodability of Poisson Point Processes. 2022 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory vol. 2022, 2559–2564.","chicago":"Zhang, Yihan, and Shashank Vatedka. “List-Decodability of Poisson Point Processes.” In <i>2022 IEEE International Symposium on Information Theory</i>, 2022:2559–64. IEEE, 2022. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834512\">https://doi.org/10.1109/ISIT50566.2022.9834512</a>.","ama":"Zhang Y, Vatedka S. List-decodability of Poisson Point Processes. In: <i>2022 IEEE International Symposium on Information Theory</i>. Vol 2022. IEEE; 2022:2559-2564. doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834512\">10.1109/ISIT50566.2022.9834512</a>","apa":"Zhang, Y., &#38; Vatedka, S. (2022). List-decodability of Poisson Point Processes. In <i>2022 IEEE International Symposium on Information Theory</i> (Vol. 2022, pp. 2559–2564). Espoo, Finland: IEEE. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834512\">https://doi.org/10.1109/ISIT50566.2022.9834512</a>"},"day":"03","isi":1,"page":"2559-2564","conference":{"name":"ISIT: International Symposium on Information Theory","end_date":"2022-07-01","location":"Espoo, Finland","start_date":"2022-06-26"},"publication":"2022 IEEE International Symposium on Information Theory","publisher":"IEEE","department":[{"_id":"MaMo"}],"type":"conference","publication_status":"published","quality_controlled":"1","date_published":"2022-08-03T00:00:00Z","title":"List-decodability of Poisson Point Processes","month":"08","scopus_import":"1","intvolume":"      2022","year":"2022","_id":"12014","language":[{"iso":"eng"}],"article_processing_charge":"No","status":"public","abstract":[{"lang":"eng","text":"We study the problem of high-dimensional multiple packing in Euclidean space. Multiple packing is a natural generalization of sphere packing and is defined as follows. Let N > 0 and L∈Z≥2. A multiple packing is a set C of points in Rn such that any point in Rn lies in the intersection of at most L – 1 balls of radius nN−−−√ around points in C. Given a well-known connection with coding theory, multiple packings can be viewed as the Euclidean analog of list-decodable codes, which are well-studied for finite fields. In this paper, we exactly pin down the asymptotic density of (expurgated) Poisson Point Processes under a stronger notion called average-radius multiple packing. To this end, we apply tools from high-dimensional geometry and large deviation theory. This gives rise to the best known lower bound on the largest multiple packing density. Our result corrects a mistake in a previous paper by Blinovsky [Bli05]."}],"oa_version":"None","external_id":{"isi":["001254261902120"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":2022,"publication_identifier":{"isbn":["9781665421591"],"issn":["2157-8095"]},"date_updated":"2025-09-10T09:41:24Z","author":[{"orcid":"0000-0002-6465-6258","full_name":"Zhang, Yihan","first_name":"Yihan","last_name":"Zhang","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c"},{"first_name":"Shashank","last_name":"Vatedka","full_name":"Vatedka, Shashank"}],"date_created":"2022-09-04T22:02:04Z"},{"status":"public","article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"12015","year":"2022","intvolume":"      2022","month":"08","scopus_import":"1","title":"Lower bounds for multiple packing","date_published":"2022-08-03T00:00:00Z","date_created":"2022-09-04T22:02:05Z","author":[{"first_name":"Yihan","last_name":"Zhang","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","orcid":"0000-0002-6465-6258","full_name":"Zhang, Yihan"},{"first_name":"Shashank","last_name":"Vatedka","full_name":"Vatedka, Shashank"}],"date_updated":"2025-09-10T09:44:24Z","publication_identifier":{"isbn":["9781665421591"],"issn":["2157-8095"]},"volume":2022,"external_id":{"isi":["001254261903042"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"None","abstract":[{"text":"We study the problem of high-dimensional multiple packing in Euclidean space. Multiple packing is a natural generalization of sphere packing and is defined as follows. Let P, N > 0 and L∈Z≥2. A multiple packing is a set C of points in Bn(0–,nP−−−√) such that any point in ℝ n lies in the intersection of at most L – 1 balls of radius nN−−−√ around points in C. 1 In this paper, we derive two lower bounds on the largest possible density of a multiple packing. These bounds are obtained through a stronger notion called average-radius multiple packing. Specifically, we exactly pin down the asymptotics of (expurgated) Gaussian codes and (expurgated) spherical codes under average-radius multiple packing. To this end, we apply tools from high-dimensional geometry and large deviation theory. The bound for spherical codes matches the previous best known bound which was obtained for the standard (weaker) notion of multiple packing through a curious connection with error exponents [Bli99], [ZV21]. The bound for Gaussian codes suggests that they are strictly inferior to spherical codes.","lang":"eng"}],"conference":{"start_date":"2022-06-26","location":"Espoo, Finland","end_date":"2022-07-01","name":"ISIT: International Symposium on Information Theory"},"page":"3085-3090","day":"03","isi":1,"citation":{"mla":"Zhang, Yihan, and Shashank Vatedka. “Lower Bounds for Multiple Packing.” <i>2022 IEEE International Symposium on Information Theory</i>, vol. 2022, IEEE, 2022, pp. 3085–90, doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834443\">10.1109/ISIT50566.2022.9834443</a>.","ista":"Zhang Y, Vatedka S. 2022. Lower bounds for multiple packing. 2022 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory vol. 2022, 3085–3090.","chicago":"Zhang, Yihan, and Shashank Vatedka. “Lower Bounds for Multiple Packing.” In <i>2022 IEEE International Symposium on Information Theory</i>, 2022:3085–90. IEEE, 2022. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834443\">https://doi.org/10.1109/ISIT50566.2022.9834443</a>.","ama":"Zhang Y, Vatedka S. Lower bounds for multiple packing. In: <i>2022 IEEE International Symposium on Information Theory</i>. Vol 2022. IEEE; 2022:3085-3090. doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834443\">10.1109/ISIT50566.2022.9834443</a>","apa":"Zhang, Y., &#38; Vatedka, S. (2022). Lower bounds for multiple packing. In <i>2022 IEEE International Symposium on Information Theory</i> (Vol. 2022, pp. 3085–3090). Espoo, Finland: IEEE. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834443\">https://doi.org/10.1109/ISIT50566.2022.9834443</a>","short":"Y. Zhang, S. Vatedka, in:, 2022 IEEE International Symposium on Information Theory, IEEE, 2022, pp. 3085–3090.","ieee":"Y. Zhang and S. Vatedka, “Lower bounds for multiple packing,” in <i>2022 IEEE International Symposium on Information Theory</i>, Espoo, Finland, 2022, vol. 2022, pp. 3085–3090."},"doi":"10.1109/ISIT50566.2022.9834443","quality_controlled":"1","publication_status":"published","type":"conference","department":[{"_id":"MaMo"}],"publisher":"IEEE","publication":"2022 IEEE International Symposium on Information Theory"},{"page":"2154-2159","conference":{"location":"Espoo, Finland","end_date":"2022-07-01","name":"ISIT: International Symposium on Information Theory","start_date":"2022-06-26"},"isi":1,"day":"03","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2201.10082","open_access":"1"}],"citation":{"short":"D. Fathollahi, M. Mondelli, in:, 2022 IEEE International Symposium on Information Theory, IEEE, 2022, pp. 2154–2159.","ieee":"D. Fathollahi and M. Mondelli, “Polar coded computing: The role of the scaling exponent,” in <i>2022 IEEE International Symposium on Information Theory</i>, Espoo, Finland, 2022, vol. 2022, pp. 2154–2159.","ista":"Fathollahi D, Mondelli M. 2022. Polar coded computing: The role of the scaling exponent. 2022 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory vol. 2022, 2154–2159.","chicago":"Fathollahi, Dorsa, and Marco Mondelli. “Polar Coded Computing: The Role of the Scaling Exponent.” In <i>2022 IEEE International Symposium on Information Theory</i>, 2022:2154–59. IEEE, 2022. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834712\">https://doi.org/10.1109/ISIT50566.2022.9834712</a>.","apa":"Fathollahi, D., &#38; Mondelli, M. (2022). Polar coded computing: The role of the scaling exponent. In <i>2022 IEEE International Symposium on Information Theory</i> (Vol. 2022, pp. 2154–2159). Espoo, Finland: IEEE. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834712\">https://doi.org/10.1109/ISIT50566.2022.9834712</a>","ama":"Fathollahi D, Mondelli M. Polar coded computing: The role of the scaling exponent. In: <i>2022 IEEE International Symposium on Information Theory</i>. Vol 2022. IEEE; 2022:2154-2159. doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834712\">10.1109/ISIT50566.2022.9834712</a>","mla":"Fathollahi, Dorsa, and Marco Mondelli. “Polar Coded Computing: The Role of the Scaling Exponent.” <i>2022 IEEE International Symposium on Information Theory</i>, vol. 2022, IEEE, 2022, pp. 2154–59, doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834712\">10.1109/ISIT50566.2022.9834712</a>."},"doi":"10.1109/ISIT50566.2022.9834712","acknowledgement":"D. Fathollahi and M. Mondelli were partially supported by the 2019 Lopez-Loreta Prize. The authors thank Hamed Hassani and Hessam Mahdavifar for helpful discussions.","publication_status":"published","type":"conference","quality_controlled":"1","department":[{"_id":"MaMo"}],"publisher":"IEEE","publication":"2022 IEEE International Symposium on Information Theory","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","intvolume":"      2022","year":"2022","_id":"12016","date_published":"2022-08-03T00:00:00Z","month":"08","scopus_import":"1","title":"Polar coded computing: The role of the scaling exponent","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"date_created":"2022-09-04T22:02:05Z","author":[{"full_name":"Fathollahi, Dorsa","last_name":"Fathollahi","first_name":"Dorsa"},{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"publication_identifier":{"issn":["2157-8095"],"isbn":["9781665421591"]},"date_updated":"2025-09-10T09:43:32Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"arxiv":["2201.10082"],"isi":["001254261902052"]},"volume":2022,"oa":1,"abstract":[{"lang":"eng","text":"We consider the problem of coded distributed computing using polar codes. The average execution time of a coded computing system is related to the error probability for transmission over the binary erasure channel in recent work by Soleymani, Jamali and Mahdavifar, where the performance of binary linear codes is investigated. In this paper, we focus on polar codes and unveil a connection between the average execution time and the scaling exponent μ of the family of codes. In the finite-length characterization of polar codes, the scaling exponent is a key object capturing the speed of convergence to capacity. In particular, we show that (i) the gap between the normalized average execution time of polar codes and that of optimal MDS codes is O(n –1/μ ), and (ii) this upper bound can be improved to roughly O(n –1/2 ) by considering polar codes with large kernels. We conjecture that these bounds could be improved to O(n –2/μ ) and O(n –1 ), respectively, and provide a heuristic argument as well as numerical evidence supporting this view."}],"oa_version":"Preprint","arxiv":1},{"status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","intvolume":"      2022","_id":"12017","year":"2022","date_published":"2022-08-03T00:00:00Z","title":"New results on AVCs with omniscient and myopic adversaries","month":"08","scopus_import":"1","author":[{"last_name":"Yadav","first_name":"Anuj Kumar","full_name":"Yadav, Anuj Kumar"},{"full_name":"Alimohammadi, Mohammadreza","last_name":"Alimohammadi","first_name":"Mohammadreza"},{"id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","first_name":"Yihan","last_name":"Zhang","orcid":"0000-0002-6465-6258","full_name":"Zhang, Yihan"},{"full_name":"Budkuley, Amitalok J.","first_name":"Amitalok J.","last_name":"Budkuley"},{"last_name":"Jaggi","first_name":"Sidharth","full_name":"Jaggi, Sidharth"}],"date_created":"2022-09-04T22:02:06Z","publication_identifier":{"issn":["2157-8095"],"isbn":["9781665421591"]},"date_updated":"2025-09-10T09:45:03Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["001254261902116"]},"volume":2022,"abstract":[{"lang":"eng","text":"In the classic adversarial communication problem, two parties communicate over a noisy channel in the presence of a malicious jamming adversary. The arbitrarily varying channels (AVCs) offer an elegant framework to study a wide range of interesting adversary models. The optimal throughput or capacity over such AVCs is intimately tied to the underlying adversary model; in some cases, capacity is unknown and the problem is known to be notoriously hard. The omniscient adversary, one which knows the sender’s entire channel transmission a priori, is one of such classic models of interest; the capacity under such an adversary remains an exciting open problem. The myopic adversary is a generalization of that model where the adversary’s observation may be corrupted over a noisy discrete memoryless channel. Through the adversary’s myopicity, one can unify the slew of different adversary models, ranging from the omniscient adversary to one that is completely blind to the transmission (the latter is the well known oblivious model where the capacity is fully characterized).In this work, we present new results on the capacity under both the omniscient and myopic adversary models. We completely characterize the positive capacity threshold over general AVCs with omniscient adversaries. The characterization is in terms of two key combinatorial objects: the set of completely positive distributions and the CP-confusability set. For omniscient AVCs with positive capacity, we present non-trivial lower and upper bounds on the capacity; unlike some of the previous bounds, our bounds hold under fairly general input and jamming constraints. Our lower bound improves upon the generalized Gilbert-Varshamov bound for general AVCs while the upper bound generalizes the well known Elias-Bassalygo bound (known for binary and q-ary alphabets). For the myopic AVCs, we build on prior results known for the so-called sufficiently myopic model, and present new results on the positive rate communication threshold over the so-called insufficiently myopic regime (a completely insufficient myopic adversary specializes to an omniscient adversary). We present interesting examples for the widely studied models of adversarial bit-flip and bit-erasure channels. In fact, for the bit-flip AVC with additive adversarial noise as well as random noise, we completely characterize the omniscient model capacity when the random noise is sufficiently large vis-a-vis the adversary’s budget."}],"oa_version":"None","page":"2535-2540","conference":{"start_date":"2022-06-26","name":"ISIT: Internation Symposium on Information Theory","end_date":"2022-07-01","location":"Espoo, Finland"},"citation":{"ama":"Yadav AK, Alimohammadi M, Zhang Y, Budkuley AJ, Jaggi S. New results on AVCs with omniscient and myopic adversaries. In: <i>2022 IEEE International Symposium on Information Theory</i>. Vol 2022. Institute of Electrical and Electronics Engineers; 2022:2535-2540. doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834632\">10.1109/ISIT50566.2022.9834632</a>","apa":"Yadav, A. K., Alimohammadi, M., Zhang, Y., Budkuley, A. J., &#38; Jaggi, S. (2022). New results on AVCs with omniscient and myopic adversaries. In <i>2022 IEEE International Symposium on Information Theory</i> (Vol. 2022, pp. 2535–2540). Espoo, Finland: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834632\">https://doi.org/10.1109/ISIT50566.2022.9834632</a>","chicago":"Yadav, Anuj Kumar, Mohammadreza Alimohammadi, Yihan Zhang, Amitalok J. Budkuley, and Sidharth Jaggi. “New Results on AVCs with Omniscient and Myopic Adversaries.” In <i>2022 IEEE International Symposium on Information Theory</i>, 2022:2535–40. Institute of Electrical and Electronics Engineers, 2022. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834632\">https://doi.org/10.1109/ISIT50566.2022.9834632</a>.","ista":"Yadav AK, Alimohammadi M, Zhang Y, Budkuley AJ, Jaggi S. 2022. New results on AVCs with omniscient and myopic adversaries. 2022 IEEE International Symposium on Information Theory. ISIT: Internation Symposium on Information Theory vol. 2022, 2535–2540.","mla":"Yadav, Anuj Kumar, et al. “New Results on AVCs with Omniscient and Myopic Adversaries.” <i>2022 IEEE International Symposium on Information Theory</i>, vol. 2022, Institute of Electrical and Electronics Engineers, 2022, pp. 2535–40, doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834632\">10.1109/ISIT50566.2022.9834632</a>.","ieee":"A. K. Yadav, M. Alimohammadi, Y. Zhang, A. J. Budkuley, and S. Jaggi, “New results on AVCs with omniscient and myopic adversaries,” in <i>2022 IEEE International Symposium on Information Theory</i>, Espoo, Finland, 2022, vol. 2022, pp. 2535–2540.","short":"A.K. Yadav, M. Alimohammadi, Y. Zhang, A.J. Budkuley, S. Jaggi, in:, 2022 IEEE International Symposium on Information Theory, Institute of Electrical and Electronics Engineers, 2022, pp. 2535–2540."},"isi":1,"day":"03","doi":"10.1109/ISIT50566.2022.9834632","type":"conference","publication_status":"published","quality_controlled":"1","department":[{"_id":"MaMo"}],"publisher":"Institute of Electrical and Electronics Engineers","publication":"2022 IEEE International Symposium on Information Theory"},{"author":[{"id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","first_name":"Yihan","last_name":"Zhang","orcid":"0000-0002-6465-6258","full_name":"Zhang, Yihan"},{"last_name":"Vatedka","first_name":"Shashank","full_name":"Vatedka, Shashank"}],"date_created":"2022-09-04T22:02:06Z","publication_identifier":{"issn":["2157-8095"],"isbn":["9781665421591"]},"date_updated":"2025-09-10T09:45:40Z","external_id":{"isi":["001254261901080"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":2022,"abstract":[{"text":"We study the problem of characterizing the maximal rates of list decoding in Euclidean spaces for finite list sizes. For any positive integer L ≥ 2 and real N > 0, we say that a subset C⊂Rn is an (N,L – 1)-multiple packing or an (N,L– 1)-list decodable code if every Euclidean ball of radius nN−−−√ in ℝ n contains no more than L − 1 points of C. We study this problem with and without ℓ 2 norm constraints on C, and derive the best-known lower bounds on the maximal rate for (N,L−1) multiple packing. Our bounds are obtained via error exponents for list decoding over Additive White Gaussian Noise (AWGN) channels. We establish a curious inequality which relates the error exponent, a quantity of average-case nature, to the list-decoding radius, a quantity of worst-case nature. We derive various bounds on the error exponent for list decoding in both bounded and unbounded settings which could be of independent interest beyond multiple packing.","lang":"eng"}],"oa_version":"None","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","intvolume":"      2022","_id":"12018","year":"2022","date_published":"2022-08-03T00:00:00Z","title":"Lower bounds on list decoding capacity using error exponents","scopus_import":"1","month":"08","type":"conference","publication_status":"published","quality_controlled":"1","department":[{"_id":"MaMo"}],"publisher":"Institute of Electrical and Electronics Engineers","publication":"2022 IEEE International Symposium on Information Theory","page":"1324-1329","conference":{"start_date":"2022-06-26","location":"Espoo, Finland","name":"ISIT: International Symposium on Information Theory","end_date":"2022-07-01"},"citation":{"short":"Y. Zhang, S. Vatedka, in:, 2022 IEEE International Symposium on Information Theory, Institute of Electrical and Electronics Engineers, 2022, pp. 1324–1329.","ieee":"Y. Zhang and S. Vatedka, “Lower bounds on list decoding capacity using error exponents,” in <i>2022 IEEE International Symposium on Information Theory</i>, Espoo, Finland, 2022, vol. 2022, pp. 1324–1329.","mla":"Zhang, Yihan, and Shashank Vatedka. “Lower Bounds on List Decoding Capacity Using Error Exponents.” <i>2022 IEEE International Symposium on Information Theory</i>, vol. 2022, Institute of Electrical and Electronics Engineers, 2022, pp. 1324–29, doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834815\">10.1109/ISIT50566.2022.9834815</a>.","ista":"Zhang Y, Vatedka S. 2022. Lower bounds on list decoding capacity using error exponents. 2022 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory vol. 2022, 1324–1329.","chicago":"Zhang, Yihan, and Shashank Vatedka. “Lower Bounds on List Decoding Capacity Using Error Exponents.” In <i>2022 IEEE International Symposium on Information Theory</i>, 2022:1324–29. Institute of Electrical and Electronics Engineers, 2022. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834815\">https://doi.org/10.1109/ISIT50566.2022.9834815</a>.","apa":"Zhang, Y., &#38; Vatedka, S. (2022). Lower bounds on list decoding capacity using error exponents. In <i>2022 IEEE International Symposium on Information Theory</i> (Vol. 2022, pp. 1324–1329). Espoo, Finland: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834815\">https://doi.org/10.1109/ISIT50566.2022.9834815</a>","ama":"Zhang Y, Vatedka S. Lower bounds on list decoding capacity using error exponents. In: <i>2022 IEEE International Symposium on Information Theory</i>. Vol 2022. Institute of Electrical and Electronics Engineers; 2022:1324-1329. doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834815\">10.1109/ISIT50566.2022.9834815</a>"},"isi":1,"day":"03","doi":"10.1109/ISIT50566.2022.9834815"},{"volume":2022,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["001254261902119"]},"oa_version":"None","abstract":[{"lang":"eng","text":"This paper studies combinatorial properties of codes for the Z-channel. A Z-channel with error fraction τ takes as input a length-n binary codeword and injects in an adversarial manner up to nτ asymmetric errors, i.e., errors that only zero out bits but do not flip 0’s to 1’s. It is known that the largest (L − 1)-list-decodable code for the Z-channel with error fraction τ has exponential (in n) size if τ is less than a critical value that we call the Plotkin point and has constant size if τ is larger than the threshold. The (L−1)-list-decoding Plotkin point is known to be L−1L−1−L−LL−1. In this paper, we show that the largest (L−1)-list-decodable code ε-above the Plotkin point has size Θ L (ε −3/2 ) for any L − 1 ≥ 1."}],"author":[{"first_name":"Nikita","last_name":"Polyanskii","full_name":"Polyanskii, Nikita"},{"orcid":"0000-0002-6465-6258","full_name":"Zhang, Yihan","first_name":"Yihan","last_name":"Zhang","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c"}],"date_created":"2022-09-04T22:02:07Z","date_updated":"2025-09-10T09:46:15Z","publication_identifier":{"issn":["2157-8095"],"isbn":["9781665421591"]},"year":"2022","_id":"12019","intvolume":"      2022","title":"List-decodable zero-rate codes for the Z-channel","scopus_import":"1","month":"08","date_published":"2022-08-03T00:00:00Z","status":"public","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Institute of Electrical and Electronics Engineers","publication":"2022 IEEE International Symposium on Information Theory","quality_controlled":"1","type":"conference","publication_status":"published","department":[{"_id":"MaMo"}],"citation":{"ama":"Polyanskii N, Zhang Y. List-decodable zero-rate codes for the Z-channel. In: <i>2022 IEEE International Symposium on Information Theory</i>. Vol 2022. Institute of Electrical and Electronics Engineers; 2022:2553-2558. doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834829\">10.1109/ISIT50566.2022.9834829</a>","apa":"Polyanskii, N., &#38; Zhang, Y. (2022). List-decodable zero-rate codes for the Z-channel. In <i>2022 IEEE International Symposium on Information Theory</i> (Vol. 2022, pp. 2553–2558). Espoo, Finland: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834829\">https://doi.org/10.1109/ISIT50566.2022.9834829</a>","chicago":"Polyanskii, Nikita, and Yihan Zhang. “List-Decodable Zero-Rate Codes for the Z-Channel.” In <i>2022 IEEE International Symposium on Information Theory</i>, 2022:2553–58. Institute of Electrical and Electronics Engineers, 2022. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834829\">https://doi.org/10.1109/ISIT50566.2022.9834829</a>.","ista":"Polyanskii N, Zhang Y. 2022. List-decodable zero-rate codes for the Z-channel. 2022 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory vol. 2022, 2553–2558.","mla":"Polyanskii, Nikita, and Yihan Zhang. “List-Decodable Zero-Rate Codes for the Z-Channel.” <i>2022 IEEE International Symposium on Information Theory</i>, vol. 2022, Institute of Electrical and Electronics Engineers, 2022, pp. 2553–58, doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834829\">10.1109/ISIT50566.2022.9834829</a>.","ieee":"N. Polyanskii and Y. Zhang, “List-decodable zero-rate codes for the Z-channel,” in <i>2022 IEEE International Symposium on Information Theory</i>, Espoo, Finland, 2022, vol. 2022, pp. 2553–2558.","short":"N. Polyanskii, Y. Zhang, in:, 2022 IEEE International Symposium on Information Theory, Institute of Electrical and Electronics Engineers, 2022, pp. 2553–2558."},"isi":1,"day":"03","doi":"10.1109/ISIT50566.2022.9834829","conference":{"start_date":"2022-06-26","location":"Espoo, Finland","end_date":"2022-07-01","name":"ISIT: International Symposium on Information Theory"},"page":"2553-2558"},{"oa_version":"Published Version","abstract":[{"text":"Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is a major determinant of cellular growth, and dysregulation is observed in many cancer types. Here, we present the purification of human Pol I from cells carrying a genomic GFP fusion on the largest subunit allowing the structural and functional analysis of the enzyme across species. In contrast to yeast, human Pol I carries a single-subunit stalk, and in vitro transcription indicates a reduced proofreading activity. Determination of the human Pol I cryo-EM reconstruction in a close-to-native state rationalizes the effects of disease-associated mutations and uncovers an additional domain that is built into the sequence of Pol I subunit RPA1. This “dock II” domain resembles a truncated HMG box incapable of DNA binding which may serve as a downstream transcription factor–binding platform in metazoans. Biochemical analysis, in situ modelling, and ChIP data indicate that Topoisomerase 2a can be recruited to Pol I via the domain and cooperates with the HMG box domain–containing factor UBF. These adaptations of the metazoan Pol I transcription system may allow efficient release of positive DNA supercoils accumulating downstream of the transcription bubble.","lang":"eng"}],"oa":1,"volume":5,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000972702600001"]},"date_updated":"2024-10-21T06:01:48Z","publication_identifier":{"issn":["2575-1077"]},"date_created":"2022-09-06T18:45:23Z","author":[{"full_name":"Daiß, Julia L","last_name":"Daiß","first_name":"Julia L"},{"full_name":"Pilsl, Michael","first_name":"Michael","last_name":"Pilsl"},{"first_name":"Kristina","last_name":"Straub","full_name":"Straub, Kristina"},{"last_name":"Bleckmann","first_name":"Andrea","full_name":"Bleckmann, Andrea"},{"full_name":"Höcherl, Mona","last_name":"Höcherl","first_name":"Mona"},{"last_name":"Heiss","first_name":"Florian B","full_name":"Heiss, Florian B"},{"full_name":"Abascal-Palacios, Guillermo","last_name":"Abascal-Palacios","first_name":"Guillermo"},{"first_name":"Ewan P","last_name":"Ramsay","full_name":"Ramsay, Ewan P"},{"full_name":"Tluckova, Katarina","last_name":"Tluckova","first_name":"Katarina","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jean-Clement","last_name":"Mars","full_name":"Mars, Jean-Clement"},{"first_name":"Torben","last_name":"Fürtges","full_name":"Fürtges, Torben"},{"full_name":"Bruckmann, Astrid","last_name":"Bruckmann","first_name":"Astrid"},{"full_name":"Rudack, Till","last_name":"Rudack","first_name":"Till"},{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky","first_name":"Carrie A","full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036"},{"first_name":"Valérie","last_name":"Lamour","full_name":"Lamour, Valérie"},{"first_name":"Konstantin","last_name":"Panov","full_name":"Panov, Konstantin"},{"last_name":"Vannini","first_name":"Alessandro","full_name":"Vannini, Alessandro"},{"first_name":"Tom","last_name":"Moss","full_name":"Moss, Tom"},{"first_name":"Christoph","last_name":"Engel","full_name":"Engel, Christoph"}],"month":"09","scopus_import":"1","title":"The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans","date_published":"2022-09-01T00:00:00Z","_id":"12051","year":"2022","intvolume":"         5","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"status":"public","publication":"Life Science Alliance","ddc":["570"],"has_accepted_license":"1","publisher":"Life Science Alliance","file":[{"creator":"dernst","access_level":"open_access","checksum":"4201d876a3e5e8b65e319d03300014ad","file_name":"2022_LifeScienceAlliance_Daiss.pdf","date_updated":"2022-09-08T06:41:14Z","date_created":"2022-09-08T06:41:14Z","relation":"main_file","content_type":"application/pdf","file_size":3183129,"file_id":"12062","success":1}],"department":[{"_id":"CaBe"}],"quality_controlled":"1","publication_status":"published","type":"journal_article","issue":"11","doi":"10.26508/lsa.202201568","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"The authors especially thank Philip Gunkel for his contribution. We thank all\r\npast and present members of the Engel lab, Achim Griesenbeck, Colyn Crane-\r\nRobinson, Christophe Lotz, Marlene Vayssieres, Klaus Grasser, Herbert Tschochner, and Philipp Milkereit for help and discussion; Gerhard Lehmann and Nobert Eichner for IT support; Joost Zomerdijk for UBF-constructs, Volker Cordes for the Hela P2 cell line; Remco Sprangers for shared cell culture; Dina Grohmann and the Archaea Center for fermentation; and Thomas\r\nDresselhaus for access to fluorescence microscopes. This work was in part supported by the Emmy-Noether Programm (DFG grant no. EN 1204/1-1 to C Engel) of the German Research Council and Collaborative Research Center 960 (TP-A8 to C Engel).","article_number":"e202201568","day":"01","isi":1,"citation":{"apa":"Daiß, J. L., Pilsl, M., Straub, K., Bleckmann, A., Höcherl, M., Heiss, F. B., … Engel, C. (2022). The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. <i>Life Science Alliance</i>. Life Science Alliance. <a href=\"https://doi.org/10.26508/lsa.202201568\">https://doi.org/10.26508/lsa.202201568</a>","ama":"Daiß JL, Pilsl M, Straub K, et al. The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. <i>Life Science Alliance</i>. 2022;5(11). doi:<a href=\"https://doi.org/10.26508/lsa.202201568\">10.26508/lsa.202201568</a>","chicago":"Daiß, Julia L, Michael Pilsl, Kristina Straub, Andrea Bleckmann, Mona Höcherl, Florian B Heiss, Guillermo Abascal-Palacios, et al. “The Human RNA Polymerase I Structure Reveals an HMG-like Docking Domain Specific to Metazoans.” <i>Life Science Alliance</i>. Life Science Alliance, 2022. <a href=\"https://doi.org/10.26508/lsa.202201568\">https://doi.org/10.26508/lsa.202201568</a>.","ista":"Daiß JL, Pilsl M, Straub K, Bleckmann A, Höcherl M, Heiss FB, Abascal-Palacios G, Ramsay EP, Tluckova K, Mars J-C, Fürtges T, Bruckmann A, Rudack T, Bernecky C, Lamour V, Panov K, Vannini A, Moss T, Engel C. 2022. The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. Life Science Alliance. 5(11), e202201568.","mla":"Daiß, Julia L., et al. “The Human RNA Polymerase I Structure Reveals an HMG-like Docking Domain Specific to Metazoans.” <i>Life Science Alliance</i>, vol. 5, no. 11, e202201568, Life Science Alliance, 2022, doi:<a href=\"https://doi.org/10.26508/lsa.202201568\">10.26508/lsa.202201568</a>.","ieee":"J. L. Daiß <i>et al.</i>, “The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans,” <i>Life Science Alliance</i>, vol. 5, no. 11. Life Science Alliance, 2022.","short":"J.L. Daiß, M. Pilsl, K. Straub, A. Bleckmann, M. Höcherl, F.B. Heiss, G. Abascal-Palacios, E.P. Ramsay, K. Tluckova, J.-C. Mars, T. Fürtges, A. Bruckmann, T. Rudack, C. Bernecky, V. Lamour, K. Panov, A. Vannini, T. Moss, C. Engel, Life Science Alliance 5 (2022)."},"keyword":["Health","Toxicology and Mutagenesis","Plant Science","Biochemistry","Genetics and Molecular Biology (miscellaneous)","Ecology"],"file_date_updated":"2022-09-08T06:41:14Z"},{"date_updated":"2025-04-15T07:32:09Z","publication_identifier":{"issn":["2041-1723"]},"date_created":"2022-09-07T14:19:26Z","author":[{"full_name":"Konstantinova, N","last_name":"Konstantinova","first_name":"N"},{"orcid":"0000-0001-8295-2926","full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas","last_name":"Hörmayer"},{"full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","last_name":"Glanc","first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"full_name":"Keshkeih, R","last_name":"Keshkeih","first_name":"R"},{"first_name":"Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang"},{"last_name":"Di Donato","first_name":"M","full_name":"Di Donato, M"},{"full_name":"Retzer, K","last_name":"Retzer","first_name":"K"},{"full_name":"Moulinier-Anzola, J","first_name":"J","last_name":"Moulinier-Anzola"},{"full_name":"Schwihla, M","last_name":"Schwihla","first_name":"M"},{"first_name":"B","last_name":"Korbei","full_name":"Korbei, B"},{"last_name":"Geisler","first_name":"M","full_name":"Geisler, M"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"C","last_name":"Luschnig","full_name":"Luschnig, C"}],"project":[{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"oa_version":"Published Version","abstract":[{"text":"Directionality in the intercellular transport of the plant hormone auxin is determined by polar plasma membrane localization of PIN-FORMED (PIN) auxin transport proteins. However, apart from PIN phosphorylation at conserved motifs, no further determinants explicitly controlling polar PIN sorting decisions have been identified. Here we present Arabidopsis WAVY GROWTH 3 (WAV3) and closely related RING-finger E3 ubiquitin ligases, whose loss-of-function mutants show a striking apical-to-basal polarity switch in PIN2 localization in root meristem cells. WAV3 E3 ligases function as essential determinants for PIN polarity, acting independently from PINOID/WAG-dependent PIN phosphorylation. They antagonize ectopic deposition of de novo synthesized PIN proteins already immediately following completion of cell division, presumably via preventing PIN sorting into basal, ARF GEF-mediated trafficking. Our findings reveal an involvement of E3 ligases in the selective targeting of apically localized PINs in higher plants.","lang":"eng"}],"oa":1,"volume":13,"pmid":1,"external_id":{"pmid":["36050482"],"isi":["000848744900004"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"status":"public","scopus_import":"1","month":"09","title":"WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions","date_published":"2022-09-01T00:00:00Z","_id":"12052","year":"2022","intvolume":"        13","file":[{"date_created":"2022-09-08T07:46:16Z","relation":"main_file","checksum":"43336758c89cd6c045839089af070afe","access_level":"open_access","creator":"dernst","date_updated":"2022-09-08T07:46:16Z","file_name":"2022_NatureCommunications_Konstantinova.pdf","file_id":"12063","success":1,"file_size":6678579,"content_type":"application/pdf"}],"department":[{"_id":"JiFr"}],"quality_controlled":"1","publication_status":"published","type":"journal_article","ddc":["580"],"publication":"Nature Communications","has_accepted_license":"1","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-33198-9","relation":"erratum"}]},"publisher":"Springer Nature","file_date_updated":"2022-09-08T07:46:16Z","doi":"10.1038/s41467-022-32888-8","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We would like to thank Tatsuo Sakai, Marcus Heisler, Toru Fujiwara, Lucia Strader, Christian Hardtke, Malcolm Bennett, Claus Schwechheimer, Gerd Jürgens and Remko Offringa for sharing published materials and Alba Grau Gimeno for support. We are greatly indebted to Bert de Rybel for supporting N.K. and M.G. to work on the final stages of manuscript preparation as postdocs in his laboratory. A full-length SOR1 cDNA clone (J090099M14) was obtained from the National Agriculture and Food Research Organization (NARO, Japan). Support by the Multiscale Imaging Core Facility at the BOKU is greatly acknowledged. This work has been supported by grants from the Austrian Science Fund (FWF P25931-B16; P31493-B25 to Christian Luschnig; I3630-B25 to Jiří Friml; P30850-B32 to Barbara Korbei) and from the Swiss National Funds (31003A-165877/1 to Markus Geisler) and the European Union’s Horizon 2020 research and innovation program (Marie Skłodowska-Curie grant agreement No 885979 to Matouš Glanc).","article_number":"5147","isi":1,"day":"01","citation":{"short":"N. Konstantinova, L. Hörmayer, M. Glanc, R. Keshkeih, S. Tan, M. Di Donato, K. Retzer, J. Moulinier-Anzola, M. Schwihla, B. Korbei, M. Geisler, J. Friml, C. Luschnig, Nature Communications 13 (2022).","ieee":"N. Konstantinova <i>et al.</i>, “WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","chicago":"Konstantinova, N, Lukas Hörmayer, Matous Glanc, R Keshkeih, Shutang Tan, M Di Donato, K Retzer, et al. “WAVY GROWTH Arabidopsis E3 Ubiquitin Ligases Affect Apical PIN Sorting Decisions.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-32888-8\">https://doi.org/10.1038/s41467-022-32888-8</a>.","ista":"Konstantinova N, Hörmayer L, Glanc M, Keshkeih R, Tan S, Di Donato M, Retzer K, Moulinier-Anzola J, Schwihla M, Korbei B, Geisler M, Friml J, Luschnig C. 2022. WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions. Nature Communications. 13, 5147.","apa":"Konstantinova, N., Hörmayer, L., Glanc, M., Keshkeih, R., Tan, S., Di Donato, M., … Luschnig, C. (2022). WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-32888-8\">https://doi.org/10.1038/s41467-022-32888-8</a>","ama":"Konstantinova N, Hörmayer L, Glanc M, et al. WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-32888-8\">10.1038/s41467-022-32888-8</a>","mla":"Konstantinova, N., et al. “WAVY GROWTH Arabidopsis E3 Ubiquitin Ligases Affect Apical PIN Sorting Decisions.” <i>Nature Communications</i>, vol. 13, 5147, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-32888-8\">10.1038/s41467-022-32888-8</a>."}},{"department":[{"_id":"JiFr"}],"file":[{"relation":"main_file","date_created":"2023-01-20T08:29:12Z","date_updated":"2023-01-20T08:29:12Z","file_name":"2022_PlantCell_Tian.pdf","checksum":"1c606d9545f29dfca15235f69ad27b58","access_level":"open_access","creator":"dernst","file_id":"12318","success":1,"file_size":3282540,"content_type":"application/pdf"}],"type":"journal_article","publication_status":"published","quality_controlled":"1","publication":"The Plant Cell","ddc":["580"],"publisher":"Oxford University Press","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1093/plcell/koac342"}]},"has_accepted_license":"1","file_date_updated":"2023-01-20T08:29:12Z","page":"4816-4839","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","acknowledgement":"This work was supported by the National Natural Science Foundation of China (32070549), Shaanxi Youth Entrusted Talent Program (20190205), Fundamental Research Funds for the Central Universities (GK202002005 and GK202201017), Young Elite Scientists Sponsorship Program by China Association for Science and Technology (CAST) (2019-2021QNRC001), State Key Laboratory of Cotton Biology Open Fund (CB2020A12 and CB2021A21) and FWF Stand-alone Project (P29988).","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"doi":"10.1093/plcell/koac270","issue":"12","citation":{"short":"Z. Tian, Y. Zhang, L. Zhu, B. Jiang, H. Wang, R. Gao, J. Friml, G. Xiao, The Plant Cell 34 (2022) 4816–4839.","ieee":"Z. Tian <i>et al.</i>, “Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum),” <i>The Plant Cell</i>, vol. 34, no. 12. Oxford University Press, pp. 4816–4839, 2022.","chicago":"Tian, Z, Yuzhou Zhang, L Zhu, B Jiang, H Wang, R Gao, Jiří Friml, and G Xiao. “Strigolactones Act Downstream of Gibberellins to Regulate Fiber Cell Elongation and Cell Wall Thickness in Cotton (Gossypium Hirsutum).” <i>The Plant Cell</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/plcell/koac270\">https://doi.org/10.1093/plcell/koac270</a>.","ista":"Tian Z, Zhang Y, Zhu L, Jiang B, Wang H, Gao R, Friml J, Xiao G. 2022. Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum). The Plant Cell. 34(12), 4816–4839.","apa":"Tian, Z., Zhang, Y., Zhu, L., Jiang, B., Wang, H., Gao, R., … Xiao, G. (2022). Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum). <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koac270\">https://doi.org/10.1093/plcell/koac270</a>","ama":"Tian Z, Zhang Y, Zhu L, et al. Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum). <i>The Plant Cell</i>. 2022;34(12):4816-4839. doi:<a href=\"https://doi.org/10.1093/plcell/koac270\">10.1093/plcell/koac270</a>","mla":"Tian, Z., et al. “Strigolactones Act Downstream of Gibberellins to Regulate Fiber Cell Elongation and Cell Wall Thickness in Cotton (Gossypium Hirsutum).” <i>The Plant Cell</i>, vol. 34, no. 12, Oxford University Press, 2022, pp. 4816–39, doi:<a href=\"https://doi.org/10.1093/plcell/koac270\">10.1093/plcell/koac270</a>."},"isi":1,"day":"01","publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"date_updated":"2025-04-15T08:12:07Z","project":[{"name":"RNA-directed DNA methylation in plant development","grant_number":"P29988","call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Tian","first_name":"Z","full_name":"Tian, Z"},{"id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou","last_name":"Zhang","orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou"},{"full_name":"Zhu, L","last_name":"Zhu","first_name":"L"},{"full_name":"Jiang, B","last_name":"Jiang","first_name":"B"},{"last_name":"Wang","first_name":"H","full_name":"Wang, H"},{"last_name":"Gao","first_name":"R","full_name":"Gao, R"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Xiao, G","last_name":"Xiao","first_name":"G"}],"date_created":"2022-09-07T14:19:39Z","abstract":[{"lang":"eng","text":"Strigolactones (SLs) are a class of phytohormones that regulate plant shoot branching and adventitious root development. However, little is known regarding the role of SLs in controlling the behavior of the smallest unit of the organism, the single cell. Here, taking advantage of a classic single-cell model offered by the cotton (Gossypium hirsutum) fiber cell, we show that SLs, whose biosynthesis is fine-tuned by gibberellins (GAs), positively regulate cell elongation and cell wall thickness by promoting the biosynthesis of very-long-chain fatty acids (VLCFAs) and cellulose, respectively. Furthermore, we identified two layers of transcription factors (TFs) involved in the hierarchical regulation of this GA-SL crosstalk. The top-layer TF GROWTH-REGULATING FACTOR 4 (GhGRF4) directly activates expression of the SL biosynthetic gene DWARF27 (D27) to increase SL accumulation in fiber cells and GAs induce GhGRF4 expression. SLs induce the expression of four second-layer TF genes (GhNAC100-2, GhBLH51, GhGT2, and GhB9SHZ1), which transmit SL signals downstream to two ketoacyl-CoA synthase genes (KCS) and three cellulose synthase (CesA) genes by directly activating their transcription. Finally, the KCS and CesA enzymes catalyze the biosynthesis of very long chain fatty acids and cellulose, respectively, to regulate development of high-grade cotton fibers. In addition to providing a theoretical basis for cotton fiber improvement, our results shed light on SL signaling in plant development at the single-cell level."}],"oa_version":"Published Version","external_id":{"pmid":["36040191"],"isi":["000852753000001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"volume":34,"oa":1,"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","status":"public","date_published":"2022-12-01T00:00:00Z","title":"Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum)","scopus_import":"1","month":"12","intvolume":"        34","year":"2022","_id":"12053"},{"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We thank the Cryo-EM Center of the University of Science and Technology of China (USTC) and the Center for Biological Imaging (CBI), Institute of Biophysics, Chinese Academy of Science, for the EM facility support; we thank B. Zhu, X. Huang and all the other staff members for their technical support on cryo-EM data collection. We thank J. Ren for his technical support with the transport assays and M. Seeger for providing the sybody libraries. This work was supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDB 37020204 to D.L. and XDB37020103 to Linfeng Sun), National Natural Science Foundation of China (82151215 and 31870726 to D.L., 31900885 to X.L., and 31870732 to Linfeng Sun), Natural Science Foundation of Anhui Province (2008085MC90 to X.L. and 2008085J15 to Linfeng Sun), the Fundamental Research Funds for the Central Universities (WK9100000031 to Linfeng Sun), and the USTC Research Funds of the Double First-Class Initiative (YD9100002004 to Linfeng Sun). Linfeng Sun is supported by an Outstanding Young Scholar Award from the Qiu Shi Science and Technologies Foundation, and a Young Scholar Award from the Cyrus Tang Foundation.","issue":"7927","doi":"10.1038/s41586-022-05143-9","citation":{"short":"Z. Yang, J. Xia, J. Hong, C. Zhang, H. Wei, W. Ying, C. Sun, L. Sun, Y. Mao, Y. Gao, S. Tan, J. Friml, D. Li, X. Liu, L. Sun, Nature 609 (2022) 611–615.","ieee":"Z. Yang <i>et al.</i>, “Structural insights into auxin recognition and efflux by Arabidopsis PIN1,” <i>Nature</i>, vol. 609, no. 7927. Springer Nature, pp. 611–615, 2022.","mla":"Yang, Z., et al. “Structural Insights into Auxin Recognition and Efflux by Arabidopsis PIN1.” <i>Nature</i>, vol. 609, no. 7927, Springer Nature, 2022, pp. 611–15, doi:<a href=\"https://doi.org/10.1038/s41586-022-05143-9\">10.1038/s41586-022-05143-9</a>.","ista":"Yang Z, Xia J, Hong J, Zhang C, Wei H, Ying W, Sun C, Sun L, Mao Y, Gao Y, Tan S, Friml J, Li D, Liu X, Sun L. 2022. Structural insights into auxin recognition and efflux by Arabidopsis PIN1. Nature. 609(7927), 611–615.","chicago":"Yang, Z, J Xia, J Hong, C Zhang, H Wei, W Ying, C Sun, et al. “Structural Insights into Auxin Recognition and Efflux by Arabidopsis PIN1.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05143-9\">https://doi.org/10.1038/s41586-022-05143-9</a>.","apa":"Yang, Z., Xia, J., Hong, J., Zhang, C., Wei, H., Ying, W., … Sun, L. (2022). Structural insights into auxin recognition and efflux by Arabidopsis PIN1. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05143-9\">https://doi.org/10.1038/s41586-022-05143-9</a>","ama":"Yang Z, Xia J, Hong J, et al. Structural insights into auxin recognition and efflux by Arabidopsis PIN1. <i>Nature</i>. 2022;609(7927):611-615. doi:<a href=\"https://doi.org/10.1038/s41586-022-05143-9\">10.1038/s41586-022-05143-9</a>"},"isi":1,"day":"02","file_date_updated":"2022-09-08T08:02:54Z","page":"611-615","publication":"Nature","ddc":["580"],"publisher":"Springer Nature","has_accepted_license":"1","department":[{"_id":"JiFr"}],"file":[{"date_created":"2022-09-08T08:02:54Z","relation":"main_file","creator":"dernst","access_level":"open_access","checksum":"3136a585f8e1c7e73b5e1418b3d01898","date_updated":"2022-09-08T08:02:54Z","file_name":"2022_Nature_Yang.pdf","file_id":"12064","success":1,"file_size":32344580,"content_type":"application/pdf"}],"type":"journal_article","publication_status":"published","quality_controlled":"1","date_published":"2022-08-02T00:00:00Z","title":"Structural insights into auxin recognition and efflux by Arabidopsis PIN1","scopus_import":"1","month":"08","intvolume":"       609","year":"2022","_id":"12054","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","status":"public","abstract":[{"text":"Polar auxin transport is unique to plants and coordinates their growth and development1,2. The PIN-FORMED (PIN) auxin transporters exhibit highly asymmetrical localizations at the plasma membrane and drive polar auxin transport3,4; however, their structures and transport mechanisms remain largely unknown. Here, we report three inward-facing conformation structures of Arabidopsis thaliana PIN1: the apo state, bound to the natural auxin indole-3-acetic acid (IAA), and in complex with the polar auxin transport inhibitor N-1-naphthylphthalamic acid (NPA). The transmembrane domain of PIN1 shares a conserved NhaA fold5. In the substrate-bound structure, IAA is coordinated by both hydrophobic stacking and hydrogen bonding. NPA competes with IAA for the same site at the intracellular pocket, but with a much higher affinity. These findings inform our understanding of the substrate recognition and transport mechanisms of PINs and set up a framework for future research on directional auxin transport, one of the most crucial processes underlying plant development.","lang":"eng"}],"oa_version":"Published Version","external_id":{"pmid":["35917925"],"isi":["000848082900002"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"volume":609,"oa":1,"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"date_updated":"2023-08-03T13:41:44Z","author":[{"first_name":"Z","last_name":"Yang","full_name":"Yang, Z"},{"last_name":"Xia","first_name":"J","full_name":"Xia, J"},{"last_name":"Hong","first_name":"J","full_name":"Hong, J"},{"last_name":"Zhang","first_name":"C","full_name":"Zhang, C"},{"full_name":"Wei, H","last_name":"Wei","first_name":"H"},{"full_name":"Ying, W","last_name":"Ying","first_name":"W"},{"last_name":"Sun","first_name":"C","full_name":"Sun, C"},{"first_name":"L","last_name":"Sun","full_name":"Sun, L"},{"first_name":"Y","last_name":"Mao","full_name":"Mao, Y"},{"first_name":"Y","last_name":"Gao","full_name":"Gao, Y"},{"last_name":"Tan","first_name":"S","full_name":"Tan, S"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"full_name":"Li, D","first_name":"D","last_name":"Li"},{"first_name":"X","last_name":"Liu","full_name":"Liu, X"},{"first_name":"L","last_name":"Sun","full_name":"Sun, L"}],"date_created":"2022-09-07T14:19:52Z"},{"language":[{"iso":"eng"}],"article_processing_charge":"No","article_type":"original","status":"public","date_published":"2022-07-17T00:00:00Z","month":"07","scopus_import":"1","extern":"1","title":"Benzylic fluorination induced by a charge-transfer complex with a solvent-dependent selectivity switch","intvolume":"        24","_id":"12067","year":"2022","publication_identifier":{"eissn":["1523-7052"],"issn":["1523-7060"]},"date_updated":"2024-10-14T12:04:54Z","date_created":"2022-09-08T11:34:30Z","author":[{"first_name":"Amiera","last_name":"Madani","full_name":"Madani, Amiera"},{"last_name":"Anghileri","first_name":"Lucia","full_name":"Anghileri, Lucia"},{"first_name":"Matthias","last_name":"Heydenreich","full_name":"Heydenreich, Matthias"},{"last_name":"Möller","first_name":"Heiko M.","full_name":"Möller, Heiko M."},{"id":"93e5e5b2-0da6-11ed-8a41-af589a024726","first_name":"Bartholomäus","last_name":"Pieber","orcid":"0000-0001-8689-388X","full_name":"Pieber, Bartholomäus"}],"abstract":[{"text":"We present a divergent strategy for the fluorination of phenylacetic acid derivatives that is induced by a charge-transfer complex between Selectfluor and 4-(dimethylamino)pyridine. A comprehensive investigation of the conditions revealed a critical role of the solvent on the reaction outcome. In the presence of water, decarboxylative fluorination through a single-electron oxidation is dominant. Non-aqueous conditions result in the clean formation of α-fluoro-α-arylcarboxylic acids.","lang":"eng"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"volume":24,"page":"5376–5380","issue":"29","doi":"10.1021/acs.orglett.2c02050","day":"17","citation":{"mla":"Madani, Amiera, et al. “Benzylic Fluorination Induced by a Charge-Transfer Complex with a Solvent-Dependent Selectivity Switch.” <i>Organic Letters</i>, vol. 24, no. 29, American Chemical Society, 2022, pp. 5376–5380, doi:<a href=\"https://doi.org/10.1021/acs.orglett.2c02050\">10.1021/acs.orglett.2c02050</a>.","ama":"Madani A, Anghileri L, Heydenreich M, Möller HM, Pieber B. Benzylic fluorination induced by a charge-transfer complex with a solvent-dependent selectivity switch. <i>Organic Letters</i>. 2022;24(29):5376–5380. doi:<a href=\"https://doi.org/10.1021/acs.orglett.2c02050\">10.1021/acs.orglett.2c02050</a>","apa":"Madani, A., Anghileri, L., Heydenreich, M., Möller, H. M., &#38; Pieber, B. (2022). Benzylic fluorination induced by a charge-transfer complex with a solvent-dependent selectivity switch. <i>Organic Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.orglett.2c02050\">https://doi.org/10.1021/acs.orglett.2c02050</a>","ista":"Madani A, Anghileri L, Heydenreich M, Möller HM, Pieber B. 2022. Benzylic fluorination induced by a charge-transfer complex with a solvent-dependent selectivity switch. Organic Letters. 24(29), 5376–5380.","chicago":"Madani, Amiera, Lucia Anghileri, Matthias Heydenreich, Heiko M. Möller, and Bartholomäus Pieber. “Benzylic Fluorination Induced by a Charge-Transfer Complex with a Solvent-Dependent Selectivity Switch.” <i>Organic Letters</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acs.orglett.2c02050\">https://doi.org/10.1021/acs.orglett.2c02050</a>.","ieee":"A. Madani, L. Anghileri, M. Heydenreich, H. M. Möller, and B. Pieber, “Benzylic fluorination induced by a charge-transfer complex with a solvent-dependent selectivity switch,” <i>Organic Letters</i>, vol. 24, no. 29. American Chemical Society, pp. 5376–5380, 2022.","short":"A. Madani, L. Anghileri, M. Heydenreich, H.M. Möller, B. Pieber, Organic Letters 24 (2022) 5376–5380."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.26434/chemrxiv-2022-mstv5"}],"publication_status":"published","type":"journal_article","quality_controlled":"1","publication":"Organic Letters","publisher":"American Chemical Society"},{"date_created":"2022-09-11T22:01:54Z","author":[{"orcid":"0000-0001-7252-8072","full_name":"Hensel, Sebastian","first_name":"Sebastian","last_name":"Hensel","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Moser, Maximilian","last_name":"Moser","first_name":"Maximilian","id":"a60047a9-da77-11eb-85b4-c4dc385ebb8c"}],"project":[{"grant_number":"948819","name":"Bridging Scales in Random Materials","call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"date_updated":"2025-04-14T07:53:59Z","publication_identifier":{"issn":["0944-2669"],"eissn":["1432-0835"]},"volume":61,"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000844247300008"]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We extend the recent rigorous convergence result of Abels and Moser (SIAM J Math Anal 54(1):114–172, 2022. https://doi.org/10.1137/21M1424925) concerning convergence rates for solutions of the Allen–Cahn equation with a nonlinear Robin boundary condition towards evolution by mean curvature flow with constant contact angle. More precisely, in the present work we manage to remove the perturbative assumption on the contact angle being close to 90∘. We establish under usual double-well type assumptions on the potential and for a certain class of boundary energy densities the sub-optimal convergence rate of order ε12 for general contact angles α∈(0,π). For a very specific form of the boundary energy density, we even obtain from our methods a sharp convergence rate of order ε; again for general contact angles α∈(0,π). Our proof deviates from the popular strategy based on rigorous asymptotic expansions and stability estimates for the linearized Allen–Cahn operator. Instead, we follow the recent approach by Fischer et al. (SIAM J Math Anal 52(6):6222–6233, 2020. https://doi.org/10.1137/20M1322182), thus relying on a relative entropy technique. We develop a careful adaptation of their approach in order to encode the constant contact angle condition. In fact, we perform this task at the level of the notion of gradient flow calibrations. This concept was recently introduced in the context of weak-strong uniqueness for multiphase mean curvature flow by Fischer et al. (arXiv:2003.05478v2)."}],"status":"public","ec_funded":1,"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"year":"2022","_id":"12079","intvolume":"        61","month":"08","scopus_import":"1","title":"Convergence rates for the Allen–Cahn equation with boundary contact energy: The non-perturbative regime","date_published":"2022-08-24T00:00:00Z","quality_controlled":"1","publication_status":"published","type":"journal_article","file":[{"date_created":"2023-01-20T08:56:01Z","relation":"main_file","access_level":"open_access","creator":"dernst","checksum":"b2da020ce50440080feedabeab5b09c4","date_updated":"2023-01-20T08:56:01Z","file_name":"2022_Calculus_Hensel.pdf","success":1,"file_id":"12320","content_type":"application/pdf","file_size":1278493}],"department":[{"_id":"JuFi"}],"has_accepted_license":"1","publisher":"Springer Nature","publication":"Calculus of Variations and Partial Differential Equations","ddc":["510"],"file_date_updated":"2023-01-20T08:56:01Z","day":"24","isi":1,"citation":{"short":"S. Hensel, M. Moser, Calculus of Variations and Partial Differential Equations 61 (2022).","ieee":"S. Hensel and M. Moser, “Convergence rates for the Allen–Cahn equation with boundary contact energy: The non-perturbative regime,” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 61, no. 6. Springer Nature, 2022.","mla":"Hensel, Sebastian, and Maximilian Moser. “Convergence Rates for the Allen–Cahn Equation with Boundary Contact Energy: The Non-Perturbative Regime.” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 61, no. 6, 201, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s00526-022-02307-3\">10.1007/s00526-022-02307-3</a>.","ista":"Hensel S, Moser M. 2022. Convergence rates for the Allen–Cahn equation with boundary contact energy: The non-perturbative regime. Calculus of Variations and Partial Differential Equations. 61(6), 201.","chicago":"Hensel, Sebastian, and Maximilian Moser. “Convergence Rates for the Allen–Cahn Equation with Boundary Contact Energy: The Non-Perturbative Regime.” <i>Calculus of Variations and Partial Differential Equations</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00526-022-02307-3\">https://doi.org/10.1007/s00526-022-02307-3</a>.","apa":"Hensel, S., &#38; Moser, M. (2022). Convergence rates for the Allen–Cahn equation with boundary contact energy: The non-perturbative regime. <i>Calculus of Variations and Partial Differential Equations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00526-022-02307-3\">https://doi.org/10.1007/s00526-022-02307-3</a>","ama":"Hensel S, Moser M. Convergence rates for the Allen–Cahn equation with boundary contact energy: The non-perturbative regime. <i>Calculus of Variations and Partial Differential Equations</i>. 2022;61(6). doi:<a href=\"https://doi.org/10.1007/s00526-022-02307-3\">10.1007/s00526-022-02307-3</a>"},"issue":"6","doi":"10.1007/s00526-022-02307-3","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"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 948819)  , and from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2047/1 - 390685813.\r\nOpen Access funding enabled and organized by Projekt DEAL.","article_number":"201"},{"project":[{"_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","name":"Molecular mechanisms of neural circuit function","grant_number":"209504/A/17/Z"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Artan, Murat","orcid":"0000-0001-8945-6992","id":"C407B586-6052-11E9-B3AE-7006E6697425","last_name":"Artan","first_name":"Murat"},{"last_name":"Hartl","first_name":"Markus","full_name":"Hartl, Markus"},{"first_name":"Weiqiang","last_name":"Chen","full_name":"Chen, Weiqiang"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"De Bono","first_name":"Mario","full_name":"De Bono, Mario","orcid":"0000-0001-8347-0443"}],"date_created":"2022-09-11T22:01:55Z","publication_identifier":{"eissn":["1083-351X"],"issn":["0021-9258"]},"date_updated":"2025-04-14T07:44:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["35933017"],"isi":["000884241800011"]},"pmid":1,"oa":1,"volume":298,"abstract":[{"lang":"eng","text":"Proximity-dependent protein labeling provides a powerful in vivo strategy to characterize the interactomes of specific proteins. We previously optimized a proximity labeling protocol for Caenorhabditis elegans using the highly active biotin ligase TurboID. A significant constraint on the sensitivity of TurboID is the presence of abundant endogenously biotinylated proteins that take up bandwidth in the mass spectrometer, notably carboxylases that use biotin as a cofactor. In C. elegans, these comprise POD-2/acetyl-CoA carboxylase alpha, PCCA-1/propionyl-CoA carboxylase alpha, PYC-1/pyruvate carboxylase, and MCCC-1/methylcrotonyl-CoA carboxylase alpha. Here, we developed ways to remove these carboxylases prior to streptavidin purification and mass spectrometry by engineering their corresponding genes to add a C-terminal His10 tag. This allows us to deplete them from C. elegans lysates using immobilized metal affinity chromatography. To demonstrate the method's efficacy, we use it to expand the interactome map of the presynaptic active zone protein ELKS-1. We identify many known active zone proteins, including UNC-10/RIM, SYD-2/liprin-alpha, SAD-1/BRSK1, CLA-1/CLArinet, C16E9.2/Sentryn, as well as previously uncharacterized potentially synaptic proteins such as the ortholog of human angiomotin, F59C12.3 and the uncharacterized protein R148.3. Our approach provides a quick and inexpensive solution to a common contaminant problem in biotin-dependent proximity labeling. The approach may be applicable to other model organisms and will enable deeper and more complete analysis of interactors for proteins of interest."}],"oa_version":"Published Version","ec_funded":1,"status":"public","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","intvolume":"       298","year":"2022","_id":"12082","date_published":"2022-09-01T00:00:00Z","title":"Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans","scopus_import":"1","month":"09","type":"journal_article","publication_status":"published","quality_controlled":"1","department":[{"_id":"MaDe"}],"corr_author":"1","file":[{"relation":"main_file","date_created":"2022-09-12T08:14:50Z","file_name":"2022_JBC_Artan.pdf","date_updated":"2022-09-12T08:14:50Z","creator":"dernst","checksum":"e726c7b9315230e6710e0b1f1d1677e9","access_level":"open_access","success":1,"file_id":"12092","content_type":"application/pdf","file_size":2101656}],"publisher":"Elsevier","has_accepted_license":"1","ddc":["570"],"publication":"Journal of Biological Chemistry","file_date_updated":"2022-09-12T08:14:50Z","citation":{"short":"M. Artan, M. Hartl, W. Chen, M. de Bono, Journal of Biological Chemistry 298 (2022).","ieee":"M. Artan, M. Hartl, W. Chen, and M. de Bono, “Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans,” <i>Journal of Biological Chemistry</i>, vol. 298, no. 9. Elsevier, 2022.","mla":"Artan, Murat, et al. “Depletion of Endogenously Biotinylated Carboxylases Enhances the Sensitivity of TurboID-Mediated Proximity Labeling in Caenorhabditis Elegans.” <i>Journal of Biological Chemistry</i>, vol. 298, no. 9, 102343, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jbc.2022.102343\">10.1016/j.jbc.2022.102343</a>.","ista":"Artan M, Hartl M, Chen W, de Bono M. 2022. Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans. Journal of Biological Chemistry. 298(9), 102343.","chicago":"Artan, Murat, Markus Hartl, Weiqiang Chen, and Mario de Bono. “Depletion of Endogenously Biotinylated Carboxylases Enhances the Sensitivity of TurboID-Mediated Proximity Labeling in Caenorhabditis Elegans.” <i>Journal of Biological Chemistry</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jbc.2022.102343\">https://doi.org/10.1016/j.jbc.2022.102343</a>.","apa":"Artan, M., Hartl, M., Chen, W., &#38; de Bono, M. (2022). Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans. <i>Journal of Biological Chemistry</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jbc.2022.102343\">https://doi.org/10.1016/j.jbc.2022.102343</a>","ama":"Artan M, Hartl M, Chen W, de Bono M. Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans. <i>Journal of Biological Chemistry</i>. 2022;298(9). doi:<a href=\"https://doi.org/10.1016/j.jbc.2022.102343\">10.1016/j.jbc.2022.102343</a>"},"isi":1,"day":"01","article_number":"102343","acknowledgement":"We thank de Bono laboratory members for helpful comments on the article and the Mass Spec Facilities at IST Austria and Max Perutz Labs for invaluable discussions and comments on how to optimize mass spec analyses of worm samples. We are grateful to Ekaterina Lashmanova for designing the degron knock-in constructs and preparing the injection mixes for CRISPR/Cas9-mediated genome editing. All LC–MS/MS analyses were performed on instruments of the Vienna BioCenter Core Facilities instrument pool.\r\nThis work was supported by a Wellcome Investigator Award (grant no.: 209504/Z/17/Z ) to M.d.B. and an ISTplus Fellowship to M.A. (Marie Sklodowska-Curie agreement no.: 754411).","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"9","acknowledged_ssus":[{"_id":"Bio"}],"doi":"10.1016/j.jbc.2022.102343"}]