[{"year":"2022","publication_identifier":{"eissn":["2056-3744"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","oa_version":"Published Version","author":[{"full_name":"Hearn, Katherine E.","last_name":"Hearn","first_name":"Katherine E."},{"first_name":"Eva L.","full_name":"Koch, Eva L.","last_name":"Koch"},{"full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram"}],"page":"358-374","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes","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."}],"external_id":{"isi":["000839621100001"]},"file_date_updated":"2023-02-27T07:17:42Z","language":[{"iso":"eng"}],"oa":1,"ddc":["570"],"_id":"12001","issue":"5","doi":"10.1002/evl3.295","file":[{"content_type":"application/pdf","file_id":"12686","checksum":"2dcd06186a11b7d1be4cddc6b189f8fb","access_level":"open_access","date_created":"2023-02-27T07:17:42Z","date_updated":"2023-02-27T07:17:42Z","relation":"main_file","success":1,"file_name":"2022_EvolutionLetters_Hearn.pdf","file_size":2368965,"creator":"dernst"}],"volume":6,"intvolume":"         6","department":[{"_id":"NiBa"}],"date_created":"2022-08-28T22:02:02Z","date_updated":"2023-08-03T13:18:17Z","citation":{"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.","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 Academic. <a href=\"https://doi.org/10.1002/evl3.295\">https://doi.org/10.1002/evl3.295</a>","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>","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 Academic, pp. 358–374, 2022.","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.","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 Academic, 2022, pp. 358–74, doi:<a href=\"https://doi.org/10.1002/evl3.295\">10.1002/evl3.295</a>.","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 Academic, 2022. <a href=\"https://doi.org/10.1002/evl3.295\">https://doi.org/10.1002/evl3.295</a>."},"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).","article_type":"original","month":"10","publisher":"Oxford Academic","scopus_import":"1","type":"journal_article","publication_status":"published","quality_controlled":"1","has_accepted_license":"1","publication":"Evolution Letters","isi":1,"day":"01","title":"Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis","date_published":"2022-10-01T00:00:00Z"},{"title":"Role of the Tibetan plateau glaciers in the Asian summer monsoon","date_published":"2022-08-30T00:00:00Z","keyword":["Atmospheric Science","Global and Planetary Change"],"day":"30","publication":"Climatic Change","has_accepted_license":"1","quality_controlled":"1","type":"journal_article","publication_status":"published","scopus_import":"1","publisher":"Springer Nature","article_type":"original","month":"08","acknowledgement":"This research is funded by the IRCC research funding.","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>.","short":"B.B. GOSWAMI, S.-I. An, R. Murtugudde, Climatic Change 173 (2022).","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>.","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.","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>","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."},"date_created":"2022-09-03T07:24:13Z","date_updated":"2022-09-05T08:33:33Z","intvolume":"       173","volume":173,"file":[{"file_size":1350575,"file_name":"2022_ClimateChange_Goswami.pdf","creator":"dernst","content_type":"application/pdf","checksum":"38071d5c142bb76f8c8665dc374838a8","file_id":"12021","date_created":"2022-09-05T08:29:27Z","date_updated":"2022-09-05T08:29:27Z","access_level":"open_access","relation":"main_file","success":1}],"doi":"10.1007/s10584-022-03426-8","issue":"3-4","_id":"12007","extern":"1","ddc":["550"],"oa":1,"language":[{"iso":"eng"}],"article_number":"29","file_date_updated":"2022-09-05T08:29:27Z","article_processing_charge":"No","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"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"BIDYUT B","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","last_name":"GOSWAMI","full_name":"GOSWAMI, BIDYUT B"},{"last_name":"An","full_name":"An, Soon-Il","first_name":"Soon-Il"},{"last_name":"Murtugudde","full_name":"Murtugudde, Raghu","first_name":"Raghu"}],"oa_version":"Published Version","status":"public","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["0165-0009","1573-1480"]},"year":"2022"},{"status":"public","oa_version":"Published Version","author":[{"last_name":"Jia","full_name":"Jia, David W.","first_name":"David W."},{"orcid":"0000-0003-3295-6181","last_name":"Vogels","full_name":"Vogels, Tim P","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"},{"full_name":"Costa, Rui Ponte","last_name":"Costa","first_name":"Rui Ponte"}],"year":"2022","publication_identifier":{"eissn":["2399-3642"]},"ec_funded":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"oa":1,"ddc":["570"],"article_processing_charge":"No","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."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000844814800007"]},"file_date_updated":"2022-09-05T08:55:11Z","article_number":"873","intvolume":"         5","date_updated":"2023-08-03T13:22:42Z","date_created":"2022-09-04T22:02:02Z","department":[{"_id":"TiVo"}],"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).","citation":{"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>.","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.","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>.","short":"D.W. Jia, T.P. Vogels, R.P. Costa, Communications Biology 5 (2022).","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."},"month":"08","article_type":"original","_id":"12009","project":[{"_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","grant_number":"214316/Z/18/Z","name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks."},{"grant_number":"819603","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","call_identifier":"H2020","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234"}],"doi":"10.1038/s42003-022-03801-2","volume":5,"file":[{"success":1,"checksum":"3ec724c4f6d3440028c217305e32915f","file_id":"12022","date_created":"2022-09-05T08:55:11Z","date_updated":"2022-09-05T08:55:11Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","creator":"dernst","file_size":2491191,"file_name":"2022_CommBiology_Jia.pdf"}],"isi":1,"publication":"Communications biology","date_published":"2022-08-25T00:00:00Z","title":"Developmental depression-to-facilitation shift controls excitation-inhibition balance","day":"25","publisher":"Springer Nature","publication_status":"published","quality_controlled":"1","type":"journal_article","scopus_import":"1","has_accepted_license":"1"},{"day":"12","date_published":"2022-07-12T00:00:00Z","title":"Latent imagination facilitates zero-shot transfer in autonomous racing","publication":"2022 International Conference on Robotics and Automation","arxiv":1,"scopus_import":"1","publication_status":"published","type":"conference","quality_controlled":"1","publisher":"IEEE","month":"07","citation":{"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>.","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.","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>.","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.","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>","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>","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."},"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.","department":[{"_id":"ToHe"}],"date_updated":"2022-09-05T08:46:12Z","date_created":"2022-09-04T22:02:02Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2103.04909"}],"doi":"10.1109/ICRA46639.2022.9811650","project":[{"name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"conference":{"name":"ICRA: International Conference on Robotics and Automation","end_date":"2022-05-27","location":"Philadelphia, PA, United States","start_date":"2022-05-23"},"_id":"12010","oa":1,"language":[{"iso":"eng"}],"external_id":{"arxiv":["2103.04909"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","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"}],"author":[{"first_name":"Axel","full_name":"Brunnbauer, Axel","last_name":"Brunnbauer"},{"full_name":"Berducci, Luigi","last_name":"Berducci","first_name":"Luigi"},{"first_name":"Andreas","full_name":"Brandstatter, Andreas","last_name":"Brandstatter"},{"first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias","last_name":"Lechner"},{"last_name":"Hasani","full_name":"Hasani, Ramin","first_name":"Ramin"},{"first_name":"Daniela","last_name":"Rus","full_name":"Rus, Daniela"},{"first_name":"Radu","last_name":"Grosu","full_name":"Grosu, Radu"}],"page":"7513-7520","oa_version":"Preprint","status":"public","ec_funded":1,"publication_identifier":{"issn":["1050-4729"],"isbn":["9781728196817"]},"year":"2022"},{"year":"2022","publication_identifier":{"isbn":["9781665421591"],"issn":["2157-8095"]},"status":"public","oa_version":"Preprint","author":[{"last_name":"Zhang","full_name":"Zhang, Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","first_name":"Yihan"},{"first_name":"Sidharth","full_name":"Jaggi, Sidharth","last_name":"Jaggi"},{"first_name":"Michael","last_name":"Langberg","full_name":"Langberg, Michael"},{"first_name":"Anand D.","last_name":"Sarwate","full_name":"Sarwate, Anand D."}],"page":"2523-2528","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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"}],"article_processing_charge":"No","external_id":{"arxiv":["2205.06708"]},"language":[{"iso":"eng"}],"oa":1,"conference":{"location":"Espoo, Finland","start_date":"2022-06-26","name":"ISIT: Internation Symposium on Information Theory","end_date":"2022-07-01"},"_id":"12011","doi":"10.1109/ISIT50566.2022.9834709","volume":2022,"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2205.06708","open_access":"1"}],"intvolume":"      2022","department":[{"_id":"MaMo"}],"date_updated":"2022-09-05T09:09:15Z","date_created":"2022-09-04T22:02:03Z","citation":{"ista":"Zhang Y, Jaggi S, Langberg M, Sarwate AD. 2022. The capacity of causal adversarial channels. 2022 IEEE International Symposium on Information Theory. ISIT: Internation 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>","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.","short":"Y. Zhang, S. Jaggi, M. Langberg, A.D. Sarwate, in:, 2022 IEEE International Symposium on Information Theory, IEEE, 2022, pp. 2523–2528.","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>.","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>."},"acknowledgement":"The work of ADS and ML was supported in part by the US National Science Foundation under awards CCF-1909468 and CCF-1909451.","month":"08","publisher":"IEEE","publication_status":"published","type":"conference","scopus_import":"1","quality_controlled":"1","arxiv":1,"publication":"2022 IEEE International Symposium on Information Theory","day":"03","title":"The capacity of causal adversarial channels","date_published":"2022-08-03T00:00:00Z"},{"date_published":"2022-08-03T00:00:00Z","title":"Heterogeneous differential privacy via graphs","day":"03","publication":"2022 IEEE International Symposium on Information Theory","publication_status":"published","scopus_import":"1","type":"conference","quality_controlled":"1","publisher":"IEEE","arxiv":1,"date_updated":"2022-09-05T10:28:35Z","date_created":"2022-09-04T22:02:04Z","department":[{"_id":"MaMo"}],"intvolume":"      2022","month":"08","citation":{"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>.","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.","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.","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: Internation Symposium on Information Theory vol. 2022, 1623–1628."},"_id":"12012","conference":{"name":"ISIT: Internation Symposium on Information Theory","end_date":"2022-07-01","start_date":"2022-06-26","location":"Espoo, Finland"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2203.15429"}],"volume":2022,"doi":"10.1109/ISIT50566.2022.9834711","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["2203.15429"]},"article_processing_charge":"No","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)."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","status":"public","page":"1623-1628","author":[{"full_name":"Torkamani, Sahel","last_name":"Torkamani","id":"0503e7f8-2d05-11ed-aa17-db0640c720fc","first_name":"Sahel"},{"last_name":"Ebrahimi","full_name":"Ebrahimi, Javad B.","first_name":"Javad B."},{"last_name":"Sadeghi","full_name":"Sadeghi, Parastoo","first_name":"Parastoo"},{"first_name":"Rafael G.L.","full_name":"D'Oliveira, Rafael G.L.","last_name":"D'Oliveira"},{"last_name":"Médard","full_name":"Médard, Muriel","first_name":"Muriel"}],"year":"2022","publication_identifier":{"isbn":["9781665421591"],"issn":["2157-8095"]}},{"arxiv":1,"scopus_import":"1","type":"conference","publication_status":"published","quality_controlled":"1","publisher":"IEEE","day":"03","title":"Polar coded computing: The role of the scaling exponent","date_published":"2022-08-03T00:00:00Z","publication":"2022 IEEE International Symposium on Information Theory","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2201.10082"}],"volume":2022,"doi":"10.1109/ISIT50566.2022.9834712","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"conference":{"end_date":"2022-07-01","name":"ISIT: Internation Symposium on Information Theory","location":"Espoo, Finland","start_date":"2022-06-26"},"_id":"12016","month":"08","citation":{"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>.","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.","short":"D. Fathollahi, M. Mondelli, in:, 2022 IEEE International Symposium on Information Theory, IEEE, 2022, pp. 2154–2159.","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>.","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>","ista":"Fathollahi D, Mondelli M. 2022. Polar coded computing: The role of the scaling exponent. 2022 IEEE International Symposium on Information Theory. ISIT: Internation Symposium on Information Theory vol. 2022, 2154–2159."},"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.","department":[{"_id":"MaMo"}],"date_created":"2022-09-04T22:02:05Z","date_updated":"2024-09-10T13:03:17Z","intvolume":"      2022","external_id":{"arxiv":["2201.10082"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","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":1,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781665421591"],"issn":["2157-8095"]},"year":"2022","author":[{"last_name":"Fathollahi","full_name":"Fathollahi, Dorsa","first_name":"Dorsa"},{"orcid":"0000-0002-3242-7020","last_name":"Mondelli","full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco"}],"page":"2154-2159","oa_version":"Preprint","status":"public"},{"oa_version":"Published Version","status":"public","author":[{"full_name":"Daiß, Julia L","last_name":"Daiß","first_name":"Julia L"},{"first_name":"Michael","full_name":"Pilsl, Michael","last_name":"Pilsl"},{"first_name":"Kristina","last_name":"Straub","full_name":"Straub, Kristina"},{"full_name":"Bleckmann, Andrea","last_name":"Bleckmann","first_name":"Andrea"},{"first_name":"Mona","last_name":"Höcherl","full_name":"Höcherl, Mona"},{"last_name":"Heiss","full_name":"Heiss, Florian B","first_name":"Florian B"},{"last_name":"Abascal-Palacios","full_name":"Abascal-Palacios, Guillermo","first_name":"Guillermo"},{"last_name":"Ramsay","full_name":"Ramsay, Ewan P","first_name":"Ewan P"},{"last_name":"Tluckova","full_name":"Tluckova, Katarina","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina"},{"first_name":"Jean-Clement","full_name":"Mars, Jean-Clement","last_name":"Mars"},{"first_name":"Torben","full_name":"Fürtges, Torben","last_name":"Fürtges"},{"first_name":"Astrid","last_name":"Bruckmann","full_name":"Bruckmann, Astrid"},{"first_name":"Till","last_name":"Rudack","full_name":"Rudack, Till"},{"first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A","last_name":"Bernecky","orcid":"0000-0003-0893-7036"},{"last_name":"Lamour","full_name":"Lamour, Valérie","first_name":"Valérie"},{"full_name":"Panov, Konstantin","last_name":"Panov","first_name":"Konstantin"},{"last_name":"Vannini","full_name":"Vannini, Alessandro","first_name":"Alessandro"},{"full_name":"Moss, Tom","last_name":"Moss","first_name":"Tom"},{"full_name":"Engel, Christoph","last_name":"Engel","first_name":"Christoph"}],"year":"2022","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["2575-1077"]},"language":[{"iso":"eng"}],"ddc":["570"],"oa":1,"external_id":{"isi":["000972702600001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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"}],"article_processing_charge":"No","article_number":"e202201568","file_date_updated":"2022-09-08T06:41:14Z","department":[{"_id":"CaBe"}],"date_updated":"2023-08-03T13:39:36Z","date_created":"2022-09-06T18:45:23Z","intvolume":"         5","month":"09","article_type":"original","citation":{"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>","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>","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.","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>.","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>.","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).","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."},"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).","issue":"11","_id":"12051","file":[{"date_created":"2022-09-08T06:41:14Z","date_updated":"2022-09-08T06:41:14Z","access_level":"open_access","relation":"main_file","checksum":"4201d876a3e5e8b65e319d03300014ad","file_id":"12062","success":1,"content_type":"application/pdf","creator":"dernst","file_size":3183129,"file_name":"2022_LifeScienceAlliance_Daiss.pdf"}],"volume":5,"doi":"10.26508/lsa.202201568","day":"01","keyword":["Health","Toxicology and Mutagenesis","Plant Science","Biochemistry","Genetics and Molecular Biology (miscellaneous)","Ecology"],"title":"The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans","date_published":"2022-09-01T00:00:00Z","publication":"Life Science Alliance","isi":1,"publication_status":"published","quality_controlled":"1","type":"journal_article","publisher":"Life Science Alliance","has_accepted_license":"1"},{"publication_identifier":{"issn":["2041-1723"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2022","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-022-33198-9"}]},"author":[{"first_name":"N","last_name":"Konstantinova","full_name":"Konstantinova, N"},{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas","last_name":"Hörmayer","full_name":"Hörmayer, Lukas"},{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","full_name":"Glanc, Matous","last_name":"Glanc","orcid":"0000-0003-0619-7783"},{"full_name":"Keshkeih, R","last_name":"Keshkeih","first_name":"R"},{"full_name":"Tan, Shutang","last_name":"Tan","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang"},{"full_name":"Di Donato, M","last_name":"Di Donato","first_name":"M"},{"last_name":"Retzer","full_name":"Retzer, K","first_name":"K"},{"last_name":"Moulinier-Anzola","full_name":"Moulinier-Anzola, J","first_name":"J"},{"first_name":"M","last_name":"Schwihla","full_name":"Schwihla, M"},{"last_name":"Korbei","full_name":"Korbei, B","first_name":"B"},{"first_name":"M","full_name":"Geisler, M","last_name":"Geisler"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"last_name":"Luschnig","full_name":"Luschnig, C","first_name":"C"}],"status":"public","oa_version":"Published Version","file_date_updated":"2022-09-08T07:46:16Z","article_number":"5147","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","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"}],"external_id":{"isi":["000848744900004"],"pmid":["36050482"]},"oa":1,"ddc":["580"],"language":[{"iso":"eng"}],"pmid":1,"doi":"10.1038/s41467-022-32888-8","project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF"}],"file":[{"file_name":"2022_NatureCommunications_Konstantinova.pdf","file_size":6678579,"creator":"dernst","content_type":"application/pdf","date_created":"2022-09-08T07:46:16Z","relation":"main_file","access_level":"open_access","date_updated":"2022-09-08T07:46:16Z","file_id":"12063","checksum":"43336758c89cd6c045839089af070afe","success":1}],"volume":13,"_id":"12052","citation":{"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>","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>","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.","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>.","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>.","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."},"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_type":"original","month":"09","intvolume":"        13","department":[{"_id":"JiFr"}],"date_updated":"2023-08-03T13:40:32Z","date_created":"2022-09-07T14:19:26Z","has_accepted_license":"1","publisher":"Springer Nature","type":"journal_article","quality_controlled":"1","publication_status":"published","publication":"Nature Communications","isi":1,"day":"01","date_published":"2022-09-01T00:00:00Z","title":"WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions"},{"isi":1,"publication":"The Plant Cell","title":"Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum)","date_published":"2022-12-01T00:00:00Z","day":"01","has_accepted_license":"1","publisher":"Oxford University Press","quality_controlled":"1","scopus_import":"1","type":"journal_article","publication_status":"published","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).","citation":{"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.","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>","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>","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>.","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>."},"article_type":"original","month":"12","intvolume":"        34","date_updated":"2023-08-03T13:41:06Z","date_created":"2022-09-07T14:19:39Z","department":[{"_id":"JiFr"}],"project":[{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development","grant_number":"P29988"}],"doi":"10.1093/plcell/koac270","volume":34,"file":[{"file_name":"2022_PlantCell_Tian.pdf","file_size":3282540,"creator":"dernst","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-01-20T08:29:12Z","date_updated":"2023-01-20T08:29:12Z","file_id":"12318","checksum":"1c606d9545f29dfca15235f69ad27b58","success":1}],"_id":"12053","issue":"12","oa":1,"ddc":["580"],"language":[{"iso":"eng"}],"pmid":1,"file_date_updated":"2023-01-20T08:29:12Z","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."}],"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000852753000001"],"pmid":["36040191"]},"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1093/plcell/koac342"}]},"page":"4816-4839","author":[{"first_name":"Z","last_name":"Tian","full_name":"Tian, Z"},{"full_name":"Zhang, Yuzhou","last_name":"Zhang","orcid":"0000-0003-2627-6956","first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"L","last_name":"Zhu","full_name":"Zhu, L"},{"first_name":"B","last_name":"Jiang","full_name":"Jiang, B"},{"full_name":"Wang, H","last_name":"Wang","first_name":"H"},{"first_name":"R","last_name":"Gao","full_name":"Gao, R"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"last_name":"Xiao","full_name":"Xiao, G","first_name":"G"}],"status":"public","oa_version":"Published Version","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"year":"2022"},{"page":"611-615","author":[{"last_name":"Yang","full_name":"Yang, Z","first_name":"Z"},{"full_name":"Xia, J","last_name":"Xia","first_name":"J"},{"full_name":"Hong, J","last_name":"Hong","first_name":"J"},{"last_name":"Zhang","full_name":"Zhang, C","first_name":"C"},{"last_name":"Wei","full_name":"Wei, H","first_name":"H"},{"last_name":"Ying","full_name":"Ying, W","first_name":"W"},{"last_name":"Sun","full_name":"Sun, C","first_name":"C"},{"first_name":"L","full_name":"Sun, L","last_name":"Sun"},{"last_name":"Mao","full_name":"Mao, Y","first_name":"Y"},{"full_name":"Gao, Y","last_name":"Gao","first_name":"Y"},{"full_name":"Tan, S","last_name":"Tan","first_name":"S"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří"},{"first_name":"D","last_name":"Li","full_name":"Li, D"},{"last_name":"Liu","full_name":"Liu, X","first_name":"X"},{"first_name":"L","last_name":"Sun","full_name":"Sun, L"}],"status":"public","oa_version":"Published Version","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2022","oa":1,"ddc":["580"],"language":[{"iso":"eng"}],"pmid":1,"file_date_updated":"2022-09-08T08:02:54Z","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"}],"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["35917925"],"isi":["000848082900002"]},"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.","citation":{"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.","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>","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.","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.","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>.","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>."},"month":"08","article_type":"original","intvolume":"       609","date_updated":"2023-08-03T13:41:44Z","date_created":"2022-09-07T14:19:52Z","department":[{"_id":"JiFr"}],"doi":"10.1038/s41586-022-05143-9","volume":609,"file":[{"creator":"dernst","file_size":32344580,"file_name":"2022_Nature_Yang.pdf","success":1,"date_updated":"2022-09-08T08:02:54Z","date_created":"2022-09-08T08:02:54Z","relation":"main_file","access_level":"open_access","file_id":"12064","checksum":"3136a585f8e1c7e73b5e1418b3d01898","content_type":"application/pdf"}],"_id":"12054","issue":"7927","isi":1,"publication":"Nature","date_published":"2022-08-02T00:00:00Z","title":"Structural insights into auxin recognition and efflux by Arabidopsis PIN1","day":"02","has_accepted_license":"1","publisher":"Springer Nature","publication_status":"published","type":"journal_article","quality_controlled":"1","scopus_import":"1"},{"publication":"ACS Energy Letters","isi":1,"day":"29","date_published":"2022-08-29T00:00:00Z","title":"Exclusive solution discharge in Li-O₂ batteries?","publisher":"American Chemical Society","publication_status":"published","quality_controlled":"1","scopus_import":"1","type":"journal_article","has_accepted_license":"1","intvolume":"         7","department":[{"_id":"StFr"},{"_id":"EM-Fac"}],"date_updated":"2023-08-03T13:47:56Z","date_created":"2022-09-08T09:51:09Z","citation":{"ama":"Prehal C, Mondal S, Lovicar L, Freunberger SA. Exclusive solution discharge in Li-O₂ batteries? <i>ACS Energy Letters</i>. 2022;7(9):3112-3119. doi:<a href=\"https://doi.org/10.1021/acsenergylett.2c01711\">10.1021/acsenergylett.2c01711</a>","apa":"Prehal, C., Mondal, S., Lovicar, L., &#38; Freunberger, S. A. (2022). Exclusive solution discharge in Li-O₂ batteries? <i>ACS Energy Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsenergylett.2c01711\">https://doi.org/10.1021/acsenergylett.2c01711</a>","ista":"Prehal C, Mondal S, Lovicar L, Freunberger SA. 2022. Exclusive solution discharge in Li-O₂ batteries? ACS Energy Letters. 7(9), 3112–3119.","chicago":"Prehal, Christian, Soumyadip Mondal, Ludek Lovicar, and Stefan Alexander Freunberger. “Exclusive Solution Discharge in Li-O₂ Batteries?” <i>ACS Energy Letters</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acsenergylett.2c01711\">https://doi.org/10.1021/acsenergylett.2c01711</a>.","mla":"Prehal, Christian, et al. “Exclusive Solution Discharge in Li-O₂ Batteries?” <i>ACS Energy Letters</i>, vol. 7, no. 9, American Chemical Society, 2022, pp. 3112–19, doi:<a href=\"https://doi.org/10.1021/acsenergylett.2c01711\">10.1021/acsenergylett.2c01711</a>.","short":"C. Prehal, S. Mondal, L. Lovicar, S.A. Freunberger, ACS Energy Letters 7 (2022) 3112–3119.","ieee":"C. Prehal, S. Mondal, L. Lovicar, and S. A. Freunberger, “Exclusive solution discharge in Li-O₂ batteries?,” <i>ACS Energy Letters</i>, vol. 7, no. 9. American Chemical Society, pp. 3112–3119, 2022."},"acknowledgement":"S.A.F. and C.P. are indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 636069). This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant NanoEvolution, Grant Agreement No. 894042. S.A.F. and S.M. are indebted to Institute of Science and Technology Austria (ISTA) for support. This research was supported by the Scientific Service Units of ISTA through resources provided by the Electron Microscopy Facility and the Miba Machine Shop. C.P. thanks Vanessa Wood (ETH Zürich) for her continuing support.","month":"08","article_type":"original","_id":"12065","issue":"9","doi":"10.1021/acsenergylett.2c01711","file":[{"file_size":3827583,"file_name":"2022_ACSEnergyLetters_Prehal.pdf","creator":"dernst","content_type":"application/pdf","date_created":"2023-01-20T08:43:51Z","relation":"main_file","access_level":"open_access","date_updated":"2023-01-20T08:43:51Z","file_id":"12319","checksum":"cf0bed3a2535c11d27244cd029dbc1d0","success":1}],"volume":7,"language":[{"iso":"eng"}],"oa":1,"ddc":["540"],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"M-Shop"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Capacity, rate performance, and cycle life of aprotic Li–O2 batteries critically depend on reversible electrodeposition of Li2O2. Current understanding states surface-adsorbed versus solvated LiO2 controls Li2O2 growth as surface film or as large particles. Herein, we show that Li2O2 forms across a wide range of electrolytes, carbons, and current densities as particles via solution-mediated LiO2 disproportionation, bringing into question the prevalence of any surface growth under practical conditions. We describe a unified O2 reduction mechanism, which can explain all found capacity relations and Li2O2 morphologies with exclusive solution discharge. Determining particle morphology and achievable capacities are species mobilities, true areal rate, and the degree of LiO2 association in solution. Capacity is conclusively limited by mass transport through the tortuous Li2O2 rather than electron transport through a passivating Li2O2 film. Provided that species mobilities and surface growth are high, high capacities are also achieved with weakly solvating electrolytes, which were previously considered prototypical for low capacity via surface growth."}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000860787000001"]},"file_date_updated":"2023-01-20T08:43:51Z","status":"public","oa_version":"Published Version","author":[{"first_name":"Christian","last_name":"Prehal","full_name":"Prehal, Christian"},{"id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","first_name":"Soumyadip","last_name":"Mondal","full_name":"Mondal, Soumyadip"},{"id":"36DB3A20-F248-11E8-B48F-1D18A9856A87","first_name":"Ludek","full_name":"Lovicar, Ludek","last_name":"Lovicar"},{"first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander"}],"page":"3112-3119","year":"2022","publication_identifier":{"eissn":["2380-8195"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"status":"public","oa_version":"Published Version","page":"5376–5380","author":[{"full_name":"Madani, Amiera","last_name":"Madani","first_name":"Amiera"},{"first_name":"Lucia","last_name":"Anghileri","full_name":"Anghileri, Lucia"},{"first_name":"Matthias","full_name":"Heydenreich, Matthias","last_name":"Heydenreich"},{"first_name":"Heiko M.","full_name":"Möller, Heiko M.","last_name":"Möller"},{"first_name":"Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","last_name":"Pieber","full_name":"Pieber, Bartholomäus","orcid":"0000-0001-8689-388X"}],"year":"2022","publication_identifier":{"issn":["1523-7060"],"eissn":["1523-7052"]},"language":[{"iso":"eng"}],"oa":1,"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"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        24","date_updated":"2023-05-08T08:39:34Z","date_created":"2022-09-08T11:34:30Z","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>.","short":"A. Madani, L. Anghileri, M. Heydenreich, H.M. Möller, B. Pieber, Organic Letters 24 (2022) 5376–5380.","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.","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>.","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.","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>"},"article_type":"original","month":"07","_id":"12067","extern":"1","issue":"29","doi":"10.1021/acs.orglett.2c02050","main_file_link":[{"url":"https://doi.org/10.26434/chemrxiv-2022-mstv5","open_access":"1"}],"volume":24,"publication":"Organic Letters","date_published":"2022-07-17T00:00:00Z","title":"Benzylic fluorination induced by a charge-transfer complex with a solvent-dependent selectivity switch","day":"17","publisher":"American Chemical Society","scopus_import":"1","type":"journal_article","quality_controlled":"1","publication_status":"published"},{"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-023-7"]},"ec_funded":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"year":"2022","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"12076"},{"relation":"part_of_dissertation","status":"public","id":"12077"}]},"author":[{"id":"440EB050-F248-11E8-B48F-1D18A9856A87","first_name":"Alec L","orcid":"0000-0002-1812-2810","last_name":"Shute","full_name":"Shute, Alec L"}],"page":"208","status":"public","oa_version":"Published Version","file_date_updated":"2022-09-12T11:24:21Z","degree_awarded":"PhD","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","abstract":[{"lang":"eng","text":"In this thesis, we study two of the most important questions in Arithmetic geometry: that of the existence and density of solutions to Diophantine equations. In order for a Diophantine equation to have any solutions over the rational numbers, it must have solutions everywhere locally, i.e., over R and over Qp for every prime p. The converse, called the Hasse principle, is known to fail in general. However, it is still a central question in Arithmetic geometry to determine for which varieties the Hasse principle does hold. In this work, we establish the Hasse principle for a wide new family of varieties of the form f(t) = NK/Q(x) ̸= 0, where f is a polynomial with integer coefficients and NK/Q denotes the norm\r\nform associated to a number field K. Our results cover products of arbitrarily many linear, quadratic or cubic factors, and generalise an argument of Irving [69], which makes use of the beta sieve of Rosser and Iwaniec. We also demonstrate how our main sieve results can be applied to treat new cases of a conjecture of Harpaz and Wittenberg on locally split values of polynomials over number fields, and discuss consequences for rational points in fibrations.\r\nIn the second question, about the density of solutions, one defines a height function and seeks to estimate asymptotically the number of points of height bounded by B as B → ∞. Traditionally, one either counts rational points, or\r\nintegral points with respect to a suitable model. However, in this thesis, we study an emerging area of interest in Arithmetic geometry known as Campana points, which in some sense interpolate between rational and integral points.\r\nMore precisely, we count the number of nonzero integers z1, z2, z3 such that gcd(z1, z2, z3) = 1, and z1, z2, z3, z1 + z2 + z3 are all squareful and bounded by B. Using the circle method, we obtain an asymptotic formula which agrees in\r\nthe power of B and log B with a bold new generalisation of Manin’s conjecture to the setting of Campana points, recently formulated by Pieropan, Smeets, Tanimoto and Várilly-Alvarado [96]. However, in this thesis we also provide the first known counterexamples to leading constant predicted by their conjecture. "}],"oa":1,"ddc":["512"],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12072","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"}],"supervisor":[{"orcid":"0000-0002-8314-0177","last_name":"Browning","full_name":"Browning, Timothy D","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87"}],"file":[{"creator":"ashute","file_name":"Thesis_final_draft.pdf","file_size":1907386,"success":1,"relation":"main_file","date_created":"2022-09-08T21:50:34Z","date_updated":"2022-09-08T21:50:34Z","access_level":"open_access","file_id":"12073","checksum":"bf073344320e05d92c224786cec2e92d","content_type":"application/pdf"},{"date_updated":"2022-09-12T11:24:21Z","date_created":"2022-09-08T21:50:42Z","access_level":"closed","relation":"source_file","checksum":"b054ac6baa09f70e8235403a4abbed80","file_id":"12074","content_type":"application/octet-stream","creator":"ashute","file_name":"athesis.tex","file_size":495393},{"relation":"source_file","access_level":"closed","date_created":"2022-09-09T12:05:00Z","date_updated":"2022-09-12T11:24:21Z","file_id":"12078","checksum":"0a31e905f1cff5eb8110978cc90e1e79","content_type":"application/x-zip-compressed","creator":"ashute","file_size":944534,"file_name":"qfcjsfmtvtbfrjjvhdzrnqxfvgjvxtbf.zip"}],"_id":"12072","citation":{"ama":"Shute AL. Existence and density problems in Diophantine geometry: From norm forms to Campana points. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12072\">10.15479/at:ista:12072</a>","apa":"Shute, A. L. (2022). <i>Existence and density problems in Diophantine geometry: From norm forms to Campana points</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12072\">https://doi.org/10.15479/at:ista:12072</a>","ista":"Shute AL. 2022. Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria.","chicago":"Shute, Alec L. “Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12072\">https://doi.org/10.15479/at:ista:12072</a>.","mla":"Shute, Alec L. <i>Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12072\">10.15479/at:ista:12072</a>.","short":"A.L. Shute, Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points, Institute of Science and Technology Austria, 2022.","ieee":"A. L. Shute, “Existence and density problems in Diophantine geometry: From norm forms to Campana points,” Institute of Science and Technology Austria, 2022."},"acknowledgement":"I acknowledge the received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska Curie Grant Agreement No. 665385.","month":"09","department":[{"_id":"GradSch"},{"_id":"TiBr"}],"date_created":"2022-09-08T21:53:03Z","date_updated":"2023-02-21T16:37:35Z","has_accepted_license":"1","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","publication_status":"published","type":"dissertation","day":"08","date_published":"2022-09-08T00:00:00Z","title":"Existence and density problems in Diophantine geometry: From norm forms to Campana points"},{"oa_version":"Published Version","status":"public","author":[{"first_name":"Sebastian","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","full_name":"Hensel, Sebastian","last_name":"Hensel","orcid":"0000-0001-7252-8072"},{"full_name":"Moser, Maximilian","last_name":"Moser","first_name":"Maximilian","id":"a60047a9-da77-11eb-85b4-c4dc385ebb8c"}],"year":"2022","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"publication_identifier":{"issn":["0944-2669"],"eissn":["1432-0835"]},"language":[{"iso":"eng"}],"ddc":["510"],"oa":1,"external_id":{"isi":["000844247300008"]},"article_processing_charge":"No","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)."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"201","file_date_updated":"2023-01-20T08:56:01Z","date_created":"2022-09-11T22:01:54Z","date_updated":"2023-08-03T13:48:30Z","department":[{"_id":"JuFi"}],"intvolume":"        61","month":"08","article_type":"original","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.","citation":{"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>.","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>.","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.","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>","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>","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."},"issue":"6","_id":"12079","volume":61,"file":[{"date_created":"2023-01-20T08:56:01Z","date_updated":"2023-01-20T08:56:01Z","access_level":"open_access","relation":"main_file","checksum":"b2da020ce50440080feedabeab5b09c4","file_id":"12320","success":1,"content_type":"application/pdf","creator":"dernst","file_size":1278493,"file_name":"2022_Calculus_Hensel.pdf"}],"project":[{"_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020","grant_number":"948819","name":"Bridging Scales in Random Materials"}],"doi":"10.1007/s00526-022-02307-3","date_published":"2022-08-24T00:00:00Z","title":"Convergence rates for the Allen–Cahn equation with boundary contact energy: The non-perturbative regime","day":"24","isi":1,"publication":"Calculus of Variations and Partial Differential Equations","scopus_import":"1","publication_status":"published","quality_controlled":"1","type":"journal_article","publisher":"Springer Nature","has_accepted_license":"1"},{"article_number":"e202112138","file_date_updated":"2023-02-21T23:30:39Z","external_id":{"pmid":["35984332"],"isi":["000932770500001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Endocytosis is a multistep process involving the sequential recruitment and action of numerous proteins. This process can be divided into two phases: an early phase, in which sites of endocytosis are formed, and a late phase in which clathrin-coated vesicles are formed and internalized into the cytosol, but how these phases link to each other remains unclear. In this study, we demonstrate that anchoring the yeast Eps15-like protein Pan1p to the peroxisome triggers most of the events occurring during the late phase at the peroxisome. At this ectopic location, Pan1p recruits most proteins that function in the late phases—including actin nucleation promoting factors—and then initiates actin polymerization. Pan1p also recruited Prk1 kinase and actin depolymerizing factors, thereby triggering disassembly immediately after actin assembly and inducing dissociation of endocytic proteins from the peroxisome. These observations suggest that Pan1p is a key regulator for initiating, processing, and completing the late phase of endocytosis."}],"ddc":["570"],"oa":1,"pmid":1,"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"year":"2022","author":[{"last_name":"Enshoji","full_name":"Enshoji, Mariko","first_name":"Mariko"},{"full_name":"Miyano, Yoshiko","last_name":"Miyano","first_name":"Yoshiko"},{"full_name":"Yoshida, Nao","last_name":"Yoshida","first_name":"Nao"},{"first_name":"Makoto","full_name":"Nagano, Makoto","last_name":"Nagano"},{"first_name":"Minami","full_name":"Watanabe, Minami","last_name":"Watanabe"},{"last_name":"Kunihiro","full_name":"Kunihiro, Mayumi","first_name":"Mayumi"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353"},{"first_name":"Junko Y.","full_name":"Toshima, Junko Y.","last_name":"Toshima"},{"first_name":"Jiro","full_name":"Toshima, Jiro","last_name":"Toshima"}],"oa_version":"Published Version","status":"public","has_accepted_license":"1","quality_controlled":"1","type":"journal_article","scopus_import":"1","publication_status":"published","publisher":"Rockefeller University Press","day":"19","title":"Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway","date_published":"2022-08-19T00:00:00Z","publication":"Journal of Cell Biology","isi":1,"file":[{"content_type":"application/pdf","embargo":"2023-02-20","date_updated":"2023-02-21T23:30:39Z","date_created":"2023-01-20T09:32:53Z","relation":"main_file","access_level":"open_access","file_id":"12321","checksum":"f2e581e66b5cdab9df81b56e850b3eaa","file_size":7816875,"file_name":"2022_JCB_Enshoji.pdf","creator":"dernst"}],"volume":221,"doi":"10.1083/jcb.202112138","issue":"10","_id":"12080","month":"08","article_type":"original","citation":{"ista":"Enshoji M, Miyano Y, Yoshida N, Nagano M, Watanabe M, Kunihiro M, Siekhaus DE, Toshima JY, Toshima J. 2022. Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway. Journal of Cell Biology. 221(10), e202112138.","apa":"Enshoji, M., Miyano, Y., Yoshida, N., Nagano, M., Watanabe, M., Kunihiro, M., … Toshima, J. (2022). Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202112138\">https://doi.org/10.1083/jcb.202112138</a>","ama":"Enshoji M, Miyano Y, Yoshida N, et al. Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway. <i>Journal of Cell Biology</i>. 2022;221(10). doi:<a href=\"https://doi.org/10.1083/jcb.202112138\">10.1083/jcb.202112138</a>","ieee":"M. Enshoji <i>et al.</i>, “Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway,” <i>Journal of Cell Biology</i>, vol. 221, no. 10. Rockefeller University Press, 2022.","short":"M. Enshoji, Y. Miyano, N. Yoshida, M. Nagano, M. Watanabe, M. Kunihiro, D.E. Siekhaus, J.Y. Toshima, J. Toshima, Journal of Cell Biology 221 (2022).","mla":"Enshoji, Mariko, et al. “Eps15/Pan1p Is a Master Regulator of the Late Stages of the Endocytic Pathway.” <i>Journal of Cell Biology</i>, vol. 221, no. 10, e202112138, Rockefeller University Press, 2022, doi:<a href=\"https://doi.org/10.1083/jcb.202112138\">10.1083/jcb.202112138</a>.","chicago":"Enshoji, Mariko, Yoshiko Miyano, Nao Yoshida, Makoto Nagano, Minami Watanabe, Mayumi Kunihiro, Daria E Siekhaus, Junko Y. Toshima, and Jiro Toshima. “Eps15/Pan1p Is a Master Regulator of the Late Stages of the Endocytic Pathway.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2022. <a href=\"https://doi.org/10.1083/jcb.202112138\">https://doi.org/10.1083/jcb.202112138</a>."},"acknowledgement":"This work was supported by JSPS KAKENHI GRANT #18K062291, and the Takeda Science Foundation to J.Y. Toshima, as well as JSPS KAKENHI GRANT #19K065710, the Uehara Memorial Foundation, and Life Science Foundation of JAPAN to J. Toshima.","department":[{"_id":"DaSi"}],"date_created":"2022-09-11T22:01:54Z","date_updated":"2023-08-03T13:49:07Z","intvolume":"       221"},{"author":[{"last_name":"Hledik","full_name":"Hledik, Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","first_name":"Michal"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"1","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"related_material":{"record":[{"id":"15020","status":"public","relation":"dissertation_contains"}]},"oa_version":"Published Version","status":"public","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"year":"2022","ddc":["570"],"oa":1,"pmid":1,"language":[{"iso":"eng"}],"article_number":"e2123152119","file_date_updated":"2022-09-12T08:08:12Z","external_id":{"isi":["000889278400014"],"pmid":["36037343"]},"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Selection accumulates information in the genome—it guides stochastically evolving populations toward states (genotype frequencies) that would be unlikely under neutrality. This can be quantified as the Kullback–Leibler (KL) divergence between the actual distribution of genotype frequencies and the corresponding neutral distribution. First, we show that this population-level information sets an upper bound on the information at the level of genotype and phenotype, limiting how precisely they can be specified by selection. Next, we study how the accumulation and maintenance of information is limited by the cost of selection, measured as the genetic load or the relative fitness variance, both of which we connect to the control-theoretic KL cost of control. The information accumulation rate is upper bounded by the population size times the cost of selection. This bound is very general, and applies across models (Wright–Fisher, Moran, diffusion) and to arbitrary forms of selection, mutation, and recombination. Finally, the cost of maintaining information depends on how it is encoded: Specifying a single allele out of two is expensive, but one bit encoded among many weakly specified loci (as in a polygenic trait) is cheap."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"08","article_type":"original","acknowledgement":"We thank Ksenia Khudiakova, Wiktor Młynarski, Sean Stankowski, and two anonymous reviewers for discussions and comments on the manuscript. G.T. and M.H. acknowledge funding from the Human Frontier Science Program Grant RGP0032/2018. N.B. acknowledges funding from ERC Grant 250152 “Information and Evolution.”","citation":{"mla":"Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.” <i>Proceedings of the National Academy of Sciences</i>, vol. 119, no. 36, e2123152119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2123152119\">10.1073/pnas.2123152119</a>.","short":"M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of Sciences 119 (2022).","ieee":"M. Hledik, N. H. Barton, and G. Tkačik, “Accumulation and maintenance of information in evolution,” <i>Proceedings of the National Academy of Sciences</i>, vol. 119, no. 36. Proceedings of the National Academy of Sciences, 2022.","chicago":"Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and Maintenance of Information in Evolution.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2123152119\">https://doi.org/10.1073/pnas.2123152119</a>.","ista":"Hledik M, Barton NH, Tkačik G. 2022. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. 119(36), e2123152119.","ama":"Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information in evolution. <i>Proceedings of the National Academy of Sciences</i>. 2022;119(36). doi:<a href=\"https://doi.org/10.1073/pnas.2123152119\">10.1073/pnas.2123152119</a>","apa":"Hledik, M., Barton, N. H., &#38; Tkačik, G. (2022). Accumulation and maintenance of information in evolution. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2123152119\">https://doi.org/10.1073/pnas.2123152119</a>"},"date_updated":"2025-06-30T13:21:05Z","date_created":"2022-09-11T22:01:55Z","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"intvolume":"       119","volume":119,"file":[{"checksum":"6dec51f6567da9039982a571508a8e4d","file_id":"12091","date_created":"2022-09-12T08:08:12Z","date_updated":"2022-09-12T08:08:12Z","relation":"main_file","access_level":"open_access","success":1,"content_type":"application/pdf","creator":"dernst","file_name":"2022_PNAS_Hledik.pdf","file_size":2165752}],"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"}],"doi":"10.1073/pnas.2123152119","issue":"36","_id":"12081","date_published":"2022-08-29T00:00:00Z","title":"Accumulation and maintenance of information in evolution","day":"29","isi":1,"publication":"Proceedings of the National Academy of Sciences","has_accepted_license":"1","scopus_import":"1","quality_controlled":"1","type":"journal_article","publication_status":"published","publisher":"Proceedings of the National Academy of Sciences"},{"external_id":{"isi":["000884241800011"],"pmid":["35933017"]},"article_processing_charge":"No","abstract":[{"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.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledged_ssus":[{"_id":"Bio"}],"article_number":"102343","file_date_updated":"2022-09-12T08:14:50Z","pmid":1,"language":[{"iso":"eng"}],"ddc":["570"],"oa":1,"year":"2022","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"publication_identifier":{"eissn":["1083-351X"],"issn":["0021-9258"]},"oa_version":"Published Version","status":"public","author":[{"full_name":"Artan, Murat","last_name":"Artan","id":"C407B586-6052-11E9-B3AE-7006E6697425","first_name":"Murat"},{"first_name":"Markus","full_name":"Hartl, Markus","last_name":"Hartl"},{"first_name":"Weiqiang","last_name":"Chen","full_name":"Chen, Weiqiang"},{"full_name":"De Bono, Mario","last_name":"De Bono","orcid":"0000-0001-8347-0443","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","publication_status":"published","type":"journal_article","scopus_import":"1","publisher":"Elsevier","has_accepted_license":"1","date_published":"2022-09-01T00:00:00Z","title":"Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans","day":"01","isi":1,"publication":"Journal of Biological Chemistry","issue":"9","_id":"12082","volume":298,"file":[{"content_type":"application/pdf","success":1,"file_id":"12092","checksum":"e726c7b9315230e6710e0b1f1d1677e9","date_created":"2022-09-12T08:14:50Z","date_updated":"2022-09-12T08:14:50Z","access_level":"open_access","relation":"main_file","file_name":"2022_JBC_Artan.pdf","file_size":2101656,"creator":"dernst"}],"project":[{"_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","grant_number":"209504/A/17/Z","name":"Molecular mechanisms of neural circuit function"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"doi":"10.1016/j.jbc.2022.102343","date_created":"2022-09-11T22:01:55Z","date_updated":"2023-08-03T13:56:46Z","department":[{"_id":"MaDe"}],"intvolume":"       298","article_type":"original","month":"09","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).","citation":{"short":"M. Artan, M. Hartl, W. Chen, M. de Bono, Journal of Biological Chemistry 298 (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>.","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.","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>.","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.","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>","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>"}},{"date_updated":"2023-08-03T13:57:19Z","date_created":"2022-09-11T22:01:56Z","department":[{"_id":"RoSe"}],"intvolume":"        63","month":"08","article_type":"original","acknowledgement":"S.R. would like to thank Robert Seiringer and Benedikt Stufler for helpful discussions. Funding from the European Union’s Horizon 2020 Research and Innovation Program under the ERC grant (Grant Agreement No. 694227) and under the Marie Skłodowska-Curie grant (Agreement No. 754411) is acknowledged.","citation":{"ista":"Rademacher SAE. 2022. Dependent random variables in quantum dynamics. Journal of Mathematical Physics. 63(8), 081902.","apa":"Rademacher, S. A. E. (2022). Dependent random variables in quantum dynamics. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0086712\">https://doi.org/10.1063/5.0086712</a>","ama":"Rademacher SAE. Dependent random variables in quantum dynamics. <i>Journal of Mathematical Physics</i>. 2022;63(8). doi:<a href=\"https://doi.org/10.1063/5.0086712\">10.1063/5.0086712</a>","ieee":"S. A. E. Rademacher, “Dependent random variables in quantum dynamics,” <i>Journal of Mathematical Physics</i>, vol. 63, no. 8. AIP Publishing, 2022.","short":"S.A.E. Rademacher, Journal of Mathematical Physics 63 (2022).","mla":"Rademacher, Simone Anna Elvira. “Dependent Random Variables in Quantum Dynamics.” <i>Journal of Mathematical Physics</i>, vol. 63, no. 8, 081902, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0086712\">10.1063/5.0086712</a>.","chicago":"Rademacher, Simone Anna Elvira. “Dependent Random Variables in Quantum Dynamics.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0086712\">https://doi.org/10.1063/5.0086712</a>."},"issue":"8","_id":"12083","volume":63,"file":[{"file_size":4552261,"file_name":"2022_JourMathPhysics_Rademacher.pdf","creator":"dernst","content_type":"application/pdf","checksum":"e6fb0cf3f0327739c5e69a2cfc4020eb","file_id":"12089","date_created":"2022-09-12T07:35:34Z","date_updated":"2022-09-12T07:35:34Z","relation":"main_file","access_level":"open_access","success":1}],"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"doi":"10.1063/5.0086712","title":"Dependent random variables in quantum dynamics","date_published":"2022-08-25T00:00:00Z","day":"25","isi":1,"publication":"Journal of Mathematical Physics","type":"journal_article","quality_controlled":"1","publication_status":"published","scopus_import":"1","publisher":"AIP Publishing","has_accepted_license":"1","arxiv":1,"oa_version":"Published Version","status":"public","author":[{"orcid":"0000-0001-5059-4466","last_name":"Rademacher","full_name":"Rademacher, Simone Anna Elvira","id":"856966FE-A408-11E9-977E-802DE6697425","first_name":"Simone Anna Elvira"}],"year":"2022","ec_funded":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["0022-2488"]},"language":[{"iso":"eng"}],"ddc":["510"],"oa":1,"external_id":{"isi":["000844402500001"],"arxiv":["2112.04817"]},"abstract":[{"text":"We consider the many-body time evolution of weakly interacting bosons in the mean field regime for initial coherent states. We show that bounded k-particle operators, corresponding to dependent random variables, satisfy both a law of large numbers and a central limit theorem.","lang":"eng"}],"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"081902","file_date_updated":"2022-09-12T07:35:34Z"},{"project":[{"name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks.","grant_number":"214316/Z/18/Z","_id":"c084a126-5a5b-11eb-8a69-d75314a70a87"}],"doi":"10.1371/journal.pcbi.1010365","volume":18,"file":[{"content_type":"application/pdf","success":1,"date_created":"2022-09-12T07:47:55Z","date_updated":"2022-09-12T07:47:55Z","access_level":"open_access","relation":"main_file","checksum":"8a81ab29f837991ee0ea770817c4a50e","file_id":"12090","file_name":"2022_PLoSCompBio_Christodoulou.pdf","file_size":2867337,"creator":"dernst"}],"_id":"12084","issue":"8","acknowledgement":"We thank Friedemann Zenke for his comments, especially on the effect of the self loops on the spectrum. We also thank Ken Miller and Bill Podlaski for helpful comments. This research was funded by a Wellcome Trust and Royal Society Henry Dale Research Fellowship (WT100000; TPV), a Wellcome Senior Research Fellowship (214316/Z/18/Z; GC, EJA, and TPV), and a Research Project Grant by the Leverhulme Trust (RPG-2016-446; EJA and TPV). ","citation":{"ieee":"G. Christodoulou, T. P. Vogels, and E. J. Agnes, “Regimes and mechanisms of transient amplification in abstract and biological neural networks,” <i>PLoS Computational Biology</i>, vol. 18, no. 8. Public Library of Science, 2022.","mla":"Christodoulou, Georgia, et al. “Regimes and Mechanisms of Transient Amplification in Abstract and Biological Neural Networks.” <i>PLoS Computational Biology</i>, vol. 18, no. 8, e1010365, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010365\">10.1371/journal.pcbi.1010365</a>.","short":"G. Christodoulou, T.P. Vogels, E.J. Agnes, PLoS Computational Biology 18 (2022).","chicago":"Christodoulou, Georgia, Tim P Vogels, and Everton J. Agnes. “Regimes and Mechanisms of Transient Amplification in Abstract and Biological Neural Networks.” <i>PLoS Computational Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pcbi.1010365\">https://doi.org/10.1371/journal.pcbi.1010365</a>.","ista":"Christodoulou G, Vogels TP, Agnes EJ. 2022. Regimes and mechanisms of transient amplification in abstract and biological neural networks. PLoS Computational Biology. 18(8), e1010365.","apa":"Christodoulou, G., Vogels, T. P., &#38; Agnes, E. J. (2022). Regimes and mechanisms of transient amplification in abstract and biological neural networks. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1010365\">https://doi.org/10.1371/journal.pcbi.1010365</a>","ama":"Christodoulou G, Vogels TP, Agnes EJ. Regimes and mechanisms of transient amplification in abstract and biological neural networks. <i>PLoS Computational Biology</i>. 2022;18(8). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010365\">10.1371/journal.pcbi.1010365</a>"},"article_type":"original","month":"08","intvolume":"        18","date_updated":"2023-08-03T14:06:29Z","date_created":"2022-09-11T22:01:56Z","department":[{"_id":"TiVo"}],"has_accepted_license":"1","publisher":"Public Library of Science","quality_controlled":"1","publication_status":"published","type":"journal_article","scopus_import":"1","isi":1,"publication":"PLoS Computational Biology","title":"Regimes and mechanisms of transient amplification in abstract and biological neural networks","date_published":"2022-08-15T00:00:00Z","day":"15","publication_identifier":{"eissn":["1553-7358"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2022","author":[{"first_name":"Georgia","full_name":"Christodoulou, Georgia","last_name":"Christodoulou"},{"orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","last_name":"Vogels","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"},{"first_name":"Everton J.","full_name":"Agnes, Everton J.","last_name":"Agnes"}],"status":"public","oa_version":"Published Version","file_date_updated":"2022-09-12T07:47:55Z","article_number":"e1010365","abstract":[{"text":"Neuronal networks encode information through patterns of activity that define the networks’ function. The neurons’ activity relies on specific connectivity structures, yet the link between structure and function is not fully understood. Here, we tackle this structure-function problem with a new conceptual approach. Instead of manipulating the connectivity directly, we focus on upper triangular matrices, which represent the network dynamics in a given orthonormal basis obtained by the Schur decomposition. This abstraction allows us to independently manipulate the eigenspectrum and feedforward structures of a connectivity matrix. Using this method, we describe a diverse repertoire of non-normal transient amplification, and to complement the analysis of the dynamical regimes, we quantify the geometry of output trajectories through the effective rank of both the eigenvector and the dynamics matrices. Counter-intuitively, we find that shrinking the eigenspectrum’s imaginary distribution leads to highly amplifying regimes in linear and long-lasting dynamics in nonlinear networks. We also find a trade-off between amplification and dimensionality of neuronal dynamics, i.e., trajectories in neuronal state-space. Networks that can amplify a large number of orthogonal initial conditions produce neuronal trajectories that lie in the same subspace of the neuronal state-space. Finally, we examine networks of excitatory and inhibitory neurons. We find that the strength of global inhibition is directly linked with the amplitude of amplification, such that weakening inhibitory weights also decreases amplification, and that the eigenspectrum’s imaginary distribution grows with an increase in the ratio between excitatory-to-inhibitory and excitatory-to-excitatory connectivity strengths. Consequently, the strength of global inhibition reveals itself as a strong signature for amplification and a potential control mechanism to switch dynamical regimes. Our results shed a light on how biological networks, i.e., networks constrained by Dale’s law, may be optimised for specific dynamical regimes.","lang":"eng"}],"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000937227700001"]},"oa":1,"ddc":["570"],"language":[{"iso":"eng"}]}]