[{"_id":"9646","citation":{"ama":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. Quantitative analysis of assertion violations in probabilistic programs. In: <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2021:1171-1186. doi:<a href=\"https://doi.org/10.1145/3453483.3454102\">10.1145/3453483.3454102</a>","chicago":"Wang, Jinyi, Yican Sun, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 1171–86. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3453483.3454102\">https://doi.org/10.1145/3453483.3454102</a>.","apa":"Wang, J., Sun, Y., Fu, H., Chatterjee, K., &#38; Goharshady, A. K. (2021). Quantitative analysis of assertion violations in probabilistic programs. In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 1171–1186). Online: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3453483.3454102\">https://doi.org/10.1145/3453483.3454102</a>","ieee":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Quantitative analysis of assertion violations in probabilistic programs,” in <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Online, 2021, pp. 1171–1186.","mla":"Wang, Jinyi, et al. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2021, pp. 1171–86, doi:<a href=\"https://doi.org/10.1145/3453483.3454102\">10.1145/3453483.3454102</a>.","ista":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. 2021. Quantitative analysis of assertion violations in probabilistic programs. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 1171–1186.","short":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1171–1186."},"oa_version":"Preprint","doi":"10.1145/3453483.3454102","page":"1171-1186","language":[{"iso":"eng"}],"ec_funded":1,"scopus_import":"1","abstract":[{"lang":"eng","text":"We consider the fundamental problem of deriving quantitative bounds on the probability that a given assertion is violated in a probabilistic program. We provide automated algorithms that obtain both lower and upper bounds on the assertion violation probability. The main novelty of our approach is that we prove new and dedicated fixed-point theorems which serve as the theoretical basis of our algorithms and enable us to reason about assertion violation bounds in terms of pre and post fixed-point functions. To synthesize such fixed-points, we devise algorithms that utilize a wide range of mathematical tools, including repulsing ranking supermartingales, Hoeffding's lemma, Minkowski decompositions, Jensen's inequality, and convex optimization. On the theoretical side, we provide (i) the first automated algorithm for lower-bounds on assertion violation probabilities, (ii) the first complete algorithm for upper-bounds of exponential form in affine programs, and (iii) provably and significantly tighter upper-bounds than the previous approaches. On the practical side, we show our algorithms can handle a wide variety of programs from the literature and synthesize bounds that are remarkably tighter than previous results, in some cases by thousands of orders of magnitude."}],"publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","month":"06","date_created":"2021-07-11T22:01:18Z","oa":1,"date_published":"2021-06-01T00:00:00Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","arxiv":1,"publication_identifier":{"isbn":["9781450383912"]},"type":"conference","publication_status":"published","department":[{"_id":"KrCh"}],"title":"Quantitative analysis of assertion violations in probabilistic programs","article_processing_charge":"No","date_updated":"2025-04-15T07:55:05Z","main_file_link":[{"url":"https://arxiv.org/abs/2011.14617","open_access":"1"}],"quality_controlled":"1","author":[{"first_name":"Jinyi","full_name":"Wang, Jinyi","last_name":"Wang"},{"full_name":"Sun, Yican","first_name":"Yican","last_name":"Sun"},{"full_name":"Fu, Hongfei","first_name":"Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","last_name":"Fu"},{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Association for Computing Machinery","conference":{"location":"Online","start_date":"2021-06-20","name":"PLDI: Programming Language Design and Implementation","end_date":"2021-06-26"},"project":[{"call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies"}],"external_id":{"arxiv":["2011.14617"],"isi":["000723661700076"]},"year":"2021","day":"01","isi":1,"acknowledgement":"We are very thankful to the anonymous reviewers for the helpful and valuable comments. The work was partially supported by the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the ERC CoG 863818 (ForM-SMArt), the Facebook PhD Fellowship Program and DOC Fellowship #24956 of the Austrian Academy of Sciences (ÖAW)."},{"file_date_updated":"2022-05-12T12:13:27Z","project":[{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211"}],"external_id":{"isi":["000710180500002"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","article_type":"original","day":"04","volume":893,"year":"2021","acknowledgement":"Tatjana Petrov’s research was supported in part by SNSF Advanced Postdoctoral Mobility Fellowship grant number P300P2 161067, the Ministry of Science, Research and the Arts of the state of Baden-Wurttemberg, and the DFG Centre of Excellence 2117 ‘Centre for the Advanced Study of Collective Behaviour’ (ID: 422037984). Claudia Igler is the recipient of a DOC Fellowship of the Austrian Academy of Sciences. Thomas A. Henzinger’s research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","isi":1,"file":[{"date_updated":"2022-05-12T12:13:27Z","checksum":"d3aef34cfb13e53bba4cf44d01680793","access_level":"open_access","file_id":"11364","date_created":"2022-05-12T12:13:27Z","success":1,"file_size":2566504,"file_name":"2021_TheoreticalComputerScience_Petrov.pdf","creator":"dernst","content_type":"application/pdf","relation":"main_file"}],"type":"journal_article","publication_status":"published","has_accepted_license":"1","date_updated":"2025-04-15T06:25:56Z","title":"Long lived transients in gene regulation","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"article_processing_charge":"No","quality_controlled":"1","author":[{"first_name":"Tatjana","full_name":"Petrov, Tatjana","last_name":"Petrov"},{"first_name":"Claudia","full_name":"Igler, Claudia","last_name":"Igler","id":"46613666-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ali","full_name":"Sezgin, Ali","last_name":"Sezgin","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2985-7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C"}],"ddc":["004"],"publisher":"Elsevier","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-06-04T00:00:00Z","tmp":{"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)","image":"/images/cc_by_nc_nd.png"},"publication_identifier":{"issn":["0304-3975"]},"citation":{"mla":"Petrov, Tatjana, et al. “Long Lived Transients in Gene Regulation.” <i>Theoretical Computer Science</i>, vol. 893, Elsevier, 2021, pp. 1–16, doi:<a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">10.1016/j.tcs.2021.05.023</a>.","ista":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. 2021. Long lived transients in gene regulation. Theoretical Computer Science. 893, 1–16.","short":"T. Petrov, C. Igler, A. Sezgin, T.A. Henzinger, C.C. Guet, Theoretical Computer Science 893 (2021) 1–16.","ama":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. Long lived transients in gene regulation. <i>Theoretical Computer Science</i>. 2021;893:1-16. doi:<a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">10.1016/j.tcs.2021.05.023</a>","chicago":"Petrov, Tatjana, Claudia Igler, Ali Sezgin, Thomas A Henzinger, and Calin C Guet. “Long Lived Transients in Gene Regulation.” <i>Theoretical Computer Science</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">https://doi.org/10.1016/j.tcs.2021.05.023</a>.","ieee":"T. Petrov, C. Igler, A. Sezgin, T. A. Henzinger, and C. C. Guet, “Long lived transients in gene regulation,” <i>Theoretical Computer Science</i>, vol. 893. Elsevier, pp. 1–16, 2021.","apa":"Petrov, T., Igler, C., Sezgin, A., Henzinger, T. A., &#38; Guet, C. C. (2021). Long lived transients in gene regulation. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">https://doi.org/10.1016/j.tcs.2021.05.023</a>"},"oa_version":"Published Version","doi":"10.1016/j.tcs.2021.05.023","intvolume":"       893","_id":"9647","corr_author":"1","language":[{"iso":"eng"}],"page":"1-16","abstract":[{"text":"Gene expression is regulated by the set of transcription factors (TFs) that bind to the promoter. The ensuing regulating function is often represented as a combinational logic circuit, where output (gene expression) is determined by current input values (promoter bound TFs) only. However, the simultaneous arrival of TFs is a strong assumption, since transcription and translation of genes introduce intrinsic time delays and there is no global synchronisation among the arrival times of different molecular species at their targets. We present an experimentally implementable genetic circuit with two inputs and one output, which in the presence of small delays in input arrival, exhibits qualitatively distinct population-level phenotypes, over timescales that are longer than typical cell doubling times. From a dynamical systems point of view, these phenotypes represent long-lived transients: although they converge to the same value eventually, they do so after a very long time span. The key feature of this toy model genetic circuit is that, despite having only two inputs and one output, it is regulated by twenty-three distinct DNA-TF configurations, two of which are more stable than others (DNA looped states), one promoting and another blocking the expression of the output gene. Small delays in input arrival time result in a majority of cells in the population quickly reaching the stable state associated with the first input, while exiting of this stable state occurs at a slow timescale. In order to mechanistically model the behaviour of this genetic circuit, we used a rule-based modelling language, and implemented a grid-search to find parameter combinations giving rise to long-lived transients. Our analysis shows that in the absence of feedback, there exist path-dependent gene regulatory mechanisms based on the long timescale of transients. The behaviour of this toy model circuit suggests that gene regulatory networks can exploit event timing to create phenotypes, and it opens the possibility that they could use event timing to memorise events, without regulatory feedback. The model reveals the importance of (i) mechanistically modelling the transitions between the different DNA-TF states, and (ii) employing transient analysis thereof.","lang":"eng"}],"scopus_import":"1","oa":1,"date_created":"2021-07-11T22:01:18Z","month":"06","publication":"Theoretical Computer Science"},{"isi":1,"acknowledgement":"We are grateful to Lukas Fiedler, Alexandra Mally (IST Austria) and Dr. Bartel Vanholme (VIB, Ghent) for their critical comments on the manuscript. We apologize to those researchers whose great work was not cited. This work is supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship, 201506870018) and a starting grant from Jiangxi Agriculture University (9232308314).","volume":232,"year":"2021","day":"01","article_type":"original","license":"https://creativecommons.org/licenses/by/4.0/","project":[{"grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF"}],"external_id":{"pmid":["34254313"],"isi":["000680587100001"]},"file_date_updated":"2021-10-07T13:42:47Z","ddc":["580"],"publisher":"Wiley","quality_controlled":"1","author":[{"first_name":"Huibin","full_name":"Han, Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Adamowski, Maciek","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","last_name":"Adamowski"},{"id":"44B04502-A9ED-11E9-B6FC-583AE6697425","orcid":"0000-0001-5187-8401","last_name":"Qi","full_name":"Qi, Linlin","first_name":"Linlin"},{"first_name":"SS","full_name":"Alotaibi, SS","last_name":"Alotaibi"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří"}],"title":"PIN-mediated polar auxin transport regulations in plant tropic responses","department":[{"_id":"JiFr"}],"article_processing_charge":"Yes (via OA deal)","issue":"2","has_accepted_license":"1","date_updated":"2025-04-14T07:45:00Z","type":"journal_article","publication_status":"published","file":[{"file_name":"2021_NewPhytologist_Han.pdf","content_type":"application/pdf","creator":"kschuh","relation":"main_file","file_id":"10105","date_created":"2021-10-07T13:42:47Z","file_size":1939800,"success":1,"checksum":"6422a6eb329b52d96279daaee0fcf189","access_level":"open_access","date_updated":"2021-10-07T13:42:47Z"}],"publication_identifier":{"issn":["0028-646x"],"eissn":["1469-8137"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_published":"2021-10-01T00:00:00Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2021-07-14T15:29:14Z","publication":"New Phytologist","month":"10","pmid":1,"oa":1,"scopus_import":"1","ec_funded":1,"abstract":[{"text":"Tropisms, growth responses to environmental stimuli such as light or gravity, are spectacular examples of adaptive plant development. The plant hormone auxin serves as a major coordinative signal. The PIN auxin exporters, through their dynamic polar subcellular localizations, redirect auxin fluxes in response to environmental stimuli and the resulting auxin gradients across organs underly differential cell elongation and bending. In this review, we discuss recent advances concerning regulations of PIN polarity during tropisms, focusing on PIN phosphorylation and trafficking. We also cover how environmental cues regulate PIN actions during tropisms, and a crucial role of auxin feedback on PIN polarity during bending termination. Finally, the interactions between different tropisms are reviewed to understand plant adaptive growth in the natural environment.","lang":"eng"}],"page":"510-522","language":[{"iso":"eng"}],"intvolume":"       232","corr_author":"1","_id":"9656","citation":{"apa":"Han, H., Adamowski, M., Qi, L., Alotaibi, S., &#38; Friml, J. (2021). PIN-mediated polar auxin transport regulations in plant tropic responses. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.17617\">https://doi.org/10.1111/nph.17617</a>","chicago":"Han, Huibin, Maciek Adamowski, Linlin Qi, SS Alotaibi, and Jiří Friml. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” <i>New Phytologist</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/nph.17617\">https://doi.org/10.1111/nph.17617</a>.","ieee":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, and J. Friml, “PIN-mediated polar auxin transport regulations in plant tropic responses,” <i>New Phytologist</i>, vol. 232, no. 2. Wiley, pp. 510–522, 2021.","ama":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. PIN-mediated polar auxin transport regulations in plant tropic responses. <i>New Phytologist</i>. 2021;232(2):510-522. doi:<a href=\"https://doi.org/10.1111/nph.17617\">10.1111/nph.17617</a>","mla":"Han, Huibin, et al. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” <i>New Phytologist</i>, vol. 232, no. 2, Wiley, 2021, pp. 510–22, doi:<a href=\"https://doi.org/10.1111/nph.17617\">10.1111/nph.17617</a>.","ista":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. 2021. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. 232(2), 510–522.","short":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, J. Friml, New Phytologist 232 (2021) 510–522."},"doi":"10.1111/nph.17617","oa_version":"Published Version"},{"file_date_updated":"2021-07-19T12:13:34Z","external_id":{"isi":["000702165300012"],"pmid":["34240197"]},"article_type":"original","day":"07","year":"2021","volume":33,"isi":1,"file":[{"checksum":"6715712ec306c321f0204c817b7f8ae7","access_level":"open_access","date_updated":"2021-07-19T12:13:34Z","file_name":"2021_PlantCell_Gao.pdf","content_type":"application/pdf","creator":"cziletti","relation":"main_file","file_id":"9691","date_created":"2021-07-19T12:13:34Z","file_size":10566921,"success":1}],"publication_status":"published","type":"journal_article","date_updated":"2024-10-21T06:02:03Z","issue":"9","has_accepted_license":"1","article_processing_charge":"No","department":[{"_id":"JiFr"}],"title":"GmPIN-dependent polar auxin transport is involved in soybean nodule development","author":[{"full_name":"Gao, Z","first_name":"Z","last_name":"Gao"},{"last_name":"Chen","first_name":"Z","full_name":"Chen, Z"},{"last_name":"Cui","full_name":"Cui, Y","first_name":"Y"},{"first_name":"M","full_name":"Ke, M","last_name":"Ke"},{"last_name":"Xu","full_name":"Xu, H","first_name":"H"},{"last_name":"Xu","full_name":"Xu, Q","first_name":"Q"},{"full_name":"Chen, J","first_name":"J","last_name":"Chen"},{"full_name":"Li, Y","first_name":"Y","last_name":"Li"},{"last_name":"Huang","full_name":"Huang, L","first_name":"L"},{"last_name":"Zhao","first_name":"H","full_name":"Zhao, H"},{"last_name":"Huang","first_name":"D","full_name":"Huang, D"},{"full_name":"Mai, S","first_name":"S","last_name":"Mai"},{"last_name":"Xu","first_name":"T","full_name":"Xu, T"},{"last_name":"Liu","first_name":"X","full_name":"Liu, X"},{"last_name":"Li","full_name":"Li, S","first_name":"S"},{"full_name":"Guan, Y","first_name":"Y","last_name":"Guan"},{"full_name":"Yang, W","first_name":"W","last_name":"Yang"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří"},{"first_name":"J","full_name":"Petrášek, J","last_name":"Petrášek"},{"last_name":"Zhang","full_name":"Zhang, J","first_name":"J"},{"last_name":"Chen","full_name":"Chen, X","first_name":"X"}],"quality_controlled":"1","publisher":"American Society of Plant Biologists","ddc":["580"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","date_published":"2021-07-07T00:00:00Z","tmp":{"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)","image":"/images/cc_by_nc_nd.png"},"publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"oa_version":"Published Version","doi":"10.1093/plcell/koab183","citation":{"ieee":"Z. Gao <i>et al.</i>, “GmPIN-dependent polar auxin transport is involved in soybean nodule development,” <i>Plant Cell</i>, vol. 33, no. 9. American Society of Plant Biologists, pp. 2981–3003, 2021.","apa":"Gao, Z., Chen, Z., Cui, Y., Ke, M., Xu, H., Xu, Q., … Chen, X. (2021). GmPIN-dependent polar auxin transport is involved in soybean nodule development. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1093/plcell/koab183\">https://doi.org/10.1093/plcell/koab183</a>","chicago":"Gao, Z, Z Chen, Y Cui, M Ke, H Xu, Q Xu, J Chen, et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” <i>Plant Cell</i>. American Society of Plant Biologists, 2021. <a href=\"https://doi.org/10.1093/plcell/koab183\">https://doi.org/10.1093/plcell/koab183</a>.","ama":"Gao Z, Chen Z, Cui Y, et al. GmPIN-dependent polar auxin transport is involved in soybean nodule development. <i>Plant Cell</i>. 2021;33(9):2981–3003. doi:<a href=\"https://doi.org/10.1093/plcell/koab183\">10.1093/plcell/koab183</a>","short":"Z. Gao, Z. Chen, Y. Cui, M. Ke, H. Xu, Q. Xu, J. Chen, Y. Li, L. Huang, H. Zhao, D. Huang, S. Mai, T. Xu, X. Liu, S. Li, Y. Guan, W. Yang, J. Friml, J. Petrášek, J. Zhang, X. Chen, Plant Cell 33 (2021) 2981–3003.","ista":"Gao Z, Chen Z, Cui Y, Ke M, Xu H, Xu Q, Chen J, Li Y, Huang L, Zhao H, Huang D, Mai S, Xu T, Liu X, Li S, Guan Y, Yang W, Friml J, Petrášek J, Zhang J, Chen X. 2021. GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. 33(9), 2981–3003.","mla":"Gao, Z., et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” <i>Plant Cell</i>, vol. 33, no. 9, American Society of Plant Biologists, 2021, pp. 2981–3003, doi:<a href=\"https://doi.org/10.1093/plcell/koab183\">10.1093/plcell/koab183</a>."},"_id":"9657","intvolume":"        33","language":[{"iso":"eng"}],"page":"2981–3003","abstract":[{"lang":"eng","text":"To overcome nitrogen deficiency, legume roots establish symbiotic interactions with nitrogen-fixing rhizobia that is fostered in specialized organs (nodules). Similar to other organs, nodule formation is determined by a local maximum of the phytohormone auxin at the primordium site. However, how auxin regulates nodule development remains poorly understood. Here, we found that in soybean, (Glycine max), dynamic auxin transport driven by PIN-FORMED (PIN) transporter GmPIN1 is involved in nodule primordium formation. GmPIN1 was specifically expressed in nodule primordium cells and GmPIN1 was polarly localized in these cells. Two nodulation regulators, (iso)flavonoids trigger expanded distribution of GmPIN1b to root cortical cells, and cytokinin rearranges GmPIN1b polarity. Gmpin1abc triple mutants generated with CRISPR-Cas9 showed impaired establishment of auxin maxima in nodule meristems and aberrant divisions in the nodule primordium cells. Moreover, overexpression of GmPIN1 suppressed nodule primordium initiation. GmPIN9d, an ortholog of Arabidopsis thaliana PIN2, acts together with GmPIN1 later in nodule development to acropetally transport auxin in vascular bundles, fine-tuning the auxin supply for nodule enlargement. Our findings reveal how PIN-dependent auxin transport modulates different aspects of soybean nodule development and suggest that establishment of auxin gradient is a prerequisite for the proper interaction between legumes and rhizobia."}],"scopus_import":"1","oa":1,"pmid":1,"month":"07","date_created":"2021-07-14T15:32:43Z","publication":"Plant Cell"},{"has_accepted_license":"1","issue":"1","date_updated":"2023-02-23T14:04:20Z","title":"Quantum-mechanical exploration of the phase diagram of water","article_processing_charge":"No","file":[{"relation":"main_file","content_type":"application/pdf","creator":"asandaue","file_name":"2021_NatureCommunications_Reinhardt.pdf","file_size":1180227,"success":1,"date_created":"2021-07-15T13:55:46Z","file_id":"9670","access_level":"open_access","checksum":"8b5e1fbe2f1ab936047008043150e894","date_updated":"2021-07-15T13:55:46Z"}],"extern":"1","type":"journal_article","publication_status":"published","ddc":["530","540"],"publisher":"Springer Nature","quality_controlled":"1","author":[{"first_name":"Aleks","full_name":"Reinhardt, Aleks","last_name":"Reinhardt"},{"first_name":"Bingqing","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"external_id":{"pmid":["33500405"],"arxiv":["2010.13729"]},"article_type":"original","file_date_updated":"2021-07-15T13:55:46Z","day":"26","volume":12,"year":"2021","language":[{"iso":"eng"}],"citation":{"short":"A. Reinhardt, B. Cheng, Nature Communications 12 (2021).","ista":"Reinhardt A, Cheng B. 2021. Quantum-mechanical exploration of the phase diagram of water. Nature Communications. 12(1), 588.","mla":"Reinhardt, Aleks, and Bingqing Cheng. “Quantum-Mechanical Exploration of the Phase Diagram of Water.” <i>Nature Communications</i>, vol. 12, no. 1, 588, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-020-20821-w\">10.1038/s41467-020-20821-w</a>.","ama":"Reinhardt A, Cheng B. Quantum-mechanical exploration of the phase diagram of water. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-020-20821-w\">10.1038/s41467-020-20821-w</a>","apa":"Reinhardt, A., &#38; Cheng, B. (2021). Quantum-mechanical exploration of the phase diagram of water. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-20821-w\">https://doi.org/10.1038/s41467-020-20821-w</a>","ieee":"A. Reinhardt and B. Cheng, “Quantum-mechanical exploration of the phase diagram of water,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","chicago":"Reinhardt, Aleks, and Bingqing Cheng. “Quantum-Mechanical Exploration of the Phase Diagram of Water.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-020-20821-w\">https://doi.org/10.1038/s41467-020-20821-w</a>."},"oa_version":"Published Version","doi":"10.1038/s41467-020-20821-w","intvolume":"        12","_id":"9669","oa":1,"publication":"Nature Communications","date_created":"2021-07-15T13:48:13Z","month":"01","pmid":1,"abstract":[{"text":"The set of known stable phases of water may not be complete, and some of the phase boundaries between them are fuzzy. Starting from liquid water and a comprehensive set of 50 ice structures, we compute the phase diagram at three hybrid density-functional-theory levels of approximation, accounting for thermal and nuclear fluctuations as well as proton disorder. Such calculations are only made tractable because we combine machine-learning methods and advanced free-energy techniques. The computed phase diagram is in qualitative agreement with experiment, particularly at pressures ≲ 8000 bar, and the discrepancy in chemical potential is comparable with the subtle uncertainties introduced by proton disorder and the spread between the three hybrid functionals. None of the hypothetical ice phases considered is thermodynamically stable in our calculations, suggesting the completeness of the experimental water phase diagram in the region considered. Our work demonstrates the feasibility of predicting the phase diagram of a polymorphic system from first principles and provides a thermodynamic way of testing the limits of quantum-mechanical calculations.","lang":"eng"}],"scopus_import":"1","article_number":"588","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_published":"2021-01-26T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"arxiv":1,"publication_identifier":{"eissn":["2041-1723"]}},{"arxiv":1,"publication_identifier":{"isbn":["9781450380706"]},"status":"public","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"15074"}]},"date_published":"2021-07-06T00:00:00Z","scopus_import":"1","abstract":[{"lang":"eng","text":"We introduce a new graph problem, the token dropping game, and we show how to solve it efficiently in a distributed setting. We use the token dropping game as a tool to design an efficient distributed algorithm for stable orientations and more generally for locally optimal semi-matchings. The prior work by Czygrinow et al. (DISC 2012) finds a stable orientation in O(Δ^5) rounds in graphs of maximum degree Δ, while we improve it to O(Δ^4) and also prove a lower bound of Ω(Δ). For the more general problem of locally optimal semi-matchings, the prior upper bound is O(S^5) and our new algorithm runs in O(C · S^4) rounds, which is an improvement for C = o(S); here C and S are the maximum degrees of customers and servers, respectively."}],"ec_funded":1,"oa":1,"date_created":"2021-07-18T22:01:22Z","publication":"Annual ACM Symposium on Parallelism in Algorithms and Architectures","month":"07","citation":{"ama":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. Efficient load-balancing through distributed token dropping. In: <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>. ; 2021:129-139. doi:<a href=\"https://doi.org/10.1145/3409964.3461785\">10.1145/3409964.3461785</a>","ieee":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, and J. Uitto, “Efficient load-balancing through distributed token dropping,” in <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>,  Virtual Event, United States, 2021, pp. 129–139.","chicago":"Brandt, Sebastian, Barbara Keller, Joel Rybicki, Jukka Suomela, and Jara Uitto. “Efficient Load-Balancing through Distributed Token Dropping.” In <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>, 129–39, 2021. <a href=\"https://doi.org/10.1145/3409964.3461785\">https://doi.org/10.1145/3409964.3461785</a>.","apa":"Brandt, S., Keller, B., Rybicki, J., Suomela, J., &#38; Uitto, J. (2021). Efficient load-balancing through distributed token dropping. In <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i> (pp. 129–139).  Virtual Event, United States. <a href=\"https://doi.org/10.1145/3409964.3461785\">https://doi.org/10.1145/3409964.3461785</a>","mla":"Brandt, Sebastian, et al. “Efficient Load-Balancing through Distributed Token Dropping.” <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>, 2021, pp. 129–39, doi:<a href=\"https://doi.org/10.1145/3409964.3461785\">10.1145/3409964.3461785</a>.","ista":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. 2021. Efficient load-balancing through distributed token dropping. Annual ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures , 129–139.","short":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, J. Uitto, in:, Annual ACM Symposium on Parallelism in Algorithms and Architectures, 2021, pp. 129–139."},"oa_version":"Preprint","doi":"10.1145/3409964.3461785","_id":"9678","language":[{"iso":"eng"}],"page":"129-139","day":"06","year":"2021","acknowledgement":"We thank Orr Fischer, Juho Hirvonen, and Tuomo Lempiäinen for valuable discussions. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 840605.","project":[{"grant_number":"840605","call_identifier":"H2020","name":"Coordination in constrained and natural distributed systems","_id":"26A5D39A-B435-11E9-9278-68D0E5697425"}],"external_id":{"arxiv":["2005.07761"]},"conference":{"start_date":"2021-07-06","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures ","end_date":"2021-07-08","location":" Virtual Event, United States"},"main_file_link":[{"url":"https://arxiv.org/abs/2005.07761","open_access":"1"}],"quality_controlled":"1","author":[{"full_name":"Brandt, Sebastian","first_name":"Sebastian","last_name":"Brandt"},{"last_name":"Keller","first_name":"Barbara","full_name":"Keller, Barbara"},{"last_name":"Rybicki","orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel","full_name":"Rybicki, Joel"},{"first_name":"Jukka","full_name":"Suomela, Jukka","last_name":"Suomela"},{"full_name":"Uitto, Jara","first_name":"Jara","last_name":"Uitto"}],"type":"conference","publication_status":"published","date_updated":"2025-04-14T07:50:55Z","title":"Efficient load-balancing through distributed token dropping","department":[{"_id":"DaAl"}],"article_processing_charge":"No"},{"oa":1,"date_created":"2021-07-20T06:42:29Z","publication":"arXiv","month":"03","author":[{"full_name":"Cheng, Bingqing","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","last_name":"Cheng"},{"full_name":"Bethkenhagen, Mandy","first_name":"Mandy","last_name":"Bethkenhagen"},{"last_name":"Pickard","full_name":"Pickard, Chris J.","first_name":"Chris J."},{"first_name":"Sebastien","full_name":"Hamel, Sebastien","last_name":"Hamel"}],"abstract":[{"lang":"eng","text":"Most water in the universe may be superionic, and its thermodynamic and transport properties are crucial for planetary science but difficult to probe experimentally or theoretically. We use machine learning and free energy methods to overcome the limitations of quantum mechanical simulations, and characterize hydrogen diffusion, superionic transitions, and phase behaviors of water at extreme conditions. We predict that a close-packed superionic phase with mixed stacking is stable over a wide temperature and pressure range, while a body-centered cubic phase is only thermodynamically stable in a small window but is kinetically favored. Our phase boundaries, which are consistent with the existing-albeit scarce-experimental observations, help resolve the fractions of insulating ice, different superionic phases, and liquid water inside of ice giants."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.09035"}],"language":[{"iso":"eng"}],"date_updated":"2025-06-26T11:49:07Z","article_processing_charge":"No","title":"Predicting the phase behaviors of superionic water at planetary conditions","oa_version":"Preprint","doi":"10.48550/arXiv.2103.09035","extern":"1","citation":{"mla":"Cheng, Bingqing, et al. “Predicting the Phase Behaviors of Superionic Water at Planetary Conditions.” <i>ArXiv</i>, 2103.09035, doi:<a href=\"https://doi.org/10.48550/arXiv.2103.09035\">10.48550/arXiv.2103.09035</a>.","ista":"Cheng B, Bethkenhagen M, Pickard CJ, Hamel S. Predicting the phase behaviors of superionic water at planetary conditions. arXiv, 2103.09035.","short":"B. Cheng, M. Bethkenhagen, C.J. Pickard, S. Hamel, ArXiv (n.d.).","chicago":"Cheng, Bingqing, Mandy Bethkenhagen, Chris J. Pickard, and Sebastien Hamel. “Predicting the Phase Behaviors of Superionic Water at Planetary Conditions.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2103.09035\">https://doi.org/10.48550/arXiv.2103.09035</a>.","apa":"Cheng, B., Bethkenhagen, M., Pickard, C. J., &#38; Hamel, S. (n.d.). Predicting the phase behaviors of superionic water at planetary conditions. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2103.09035\">https://doi.org/10.48550/arXiv.2103.09035</a>","ieee":"B. Cheng, M. Bethkenhagen, C. J. Pickard, and S. Hamel, “Predicting the phase behaviors of superionic water at planetary conditions,” <i>arXiv</i>. .","ama":"Cheng B, Bethkenhagen M, Pickard CJ, Hamel S. Predicting the phase behaviors of superionic water at planetary conditions. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2103.09035\">10.48550/arXiv.2103.09035</a>"},"publication_status":"submitted","_id":"9696","type":"preprint","day":"16","year":"2021","arxiv":1,"external_id":{"arxiv":["2103.09035"]},"article_number":"2103.09035","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","related_material":{"record":[{"id":"19909","status":"public","relation":"later_version"}]},"date_published":"2021-03-16T00:00:00Z"},{"type":"journal_article","publication_status":"published","extern":"1","title":"Combining machine learning and computational chemistry for predictive insights into chemical systems","article_processing_charge":"No","issue":"16","date_updated":"2023-05-08T11:31:03Z","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1021/acs.chemrev.1c00107","open_access":"1"}],"author":[{"first_name":"John A.","full_name":"Keith, John A.","last_name":"Keith"},{"first_name":"Valentin","full_name":"Valentin Vassilev-Galindo, Valentin","last_name":"Valentin Vassilev-Galindo"},{"last_name":"Cheng","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","full_name":"Cheng, Bingqing"},{"last_name":"Chmiela","full_name":"Chmiela, Stefan","first_name":"Stefan"},{"last_name":"Gastegger","first_name":"Michael","full_name":"Gastegger, Michael"},{"last_name":"Müller","full_name":"Müller, Klaus-Robert","first_name":"Klaus-Robert"},{"last_name":"Tkatchenko","full_name":"Tkatchenko, Alexandre","first_name":"Alexandre"}],"publisher":"American Chemical Society","article_type":"review","external_id":{"arxiv":["2102.06321"]},"volume":121,"year":"2021","day":"07","intvolume":"       121","_id":"9698","citation":{"ama":"Keith JA, Valentin Vassilev-Galindo V, Cheng B, et al. Combining machine learning and computational chemistry for predictive insights into chemical systems. <i>Chemical Reviews</i>. 2021;121(16):9816-9872. doi:<a href=\"https://doi.org/10.1021/acs.chemrev.1c00107\">10.1021/acs.chemrev.1c00107</a>","apa":"Keith, J. A., Valentin Vassilev-Galindo, V., Cheng, B., Chmiela, S., Gastegger, M., Müller, K.-R., &#38; Tkatchenko, A. (2021). Combining machine learning and computational chemistry for predictive insights into chemical systems. <i>Chemical Reviews</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.chemrev.1c00107\">https://doi.org/10.1021/acs.chemrev.1c00107</a>","ieee":"J. A. Keith <i>et al.</i>, “Combining machine learning and computational chemistry for predictive insights into chemical systems,” <i>Chemical Reviews</i>, vol. 121, no. 16. American Chemical Society, pp. 9816–9872, 2021.","chicago":"Keith, John A., Valentin Valentin Vassilev-Galindo, Bingqing Cheng, Stefan Chmiela, Michael Gastegger, Klaus-Robert Müller, and Alexandre Tkatchenko. “Combining Machine Learning and Computational Chemistry for Predictive Insights into Chemical Systems.” <i>Chemical Reviews</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acs.chemrev.1c00107\">https://doi.org/10.1021/acs.chemrev.1c00107</a>.","mla":"Keith, John A., et al. “Combining Machine Learning and Computational Chemistry for Predictive Insights into Chemical Systems.” <i>Chemical Reviews</i>, vol. 121, no. 16, American Chemical Society, 2021, pp. 9816–72, doi:<a href=\"https://doi.org/10.1021/acs.chemrev.1c00107\">10.1021/acs.chemrev.1c00107</a>.","ista":"Keith JA, Valentin Vassilev-Galindo V, Cheng B, Chmiela S, Gastegger M, Müller K-R, Tkatchenko A. 2021. Combining machine learning and computational chemistry for predictive insights into chemical systems. Chemical Reviews. 121(16), 9816–9872.","short":"J.A. Keith, V. Valentin Vassilev-Galindo, B. Cheng, S. Chmiela, M. Gastegger, K.-R. Müller, A. Tkatchenko, Chemical Reviews 121 (2021) 9816–9872."},"doi":"10.1021/acs.chemrev.1c00107","oa_version":"Published Version","page":"9816-9872","language":[{"iso":"eng"}],"abstract":[{"text":"Machine learning models are poised to make a transformative impact on chemical sciences by dramatically accelerating computational algorithms and amplifying insights available from computational chemistry methods. However, achieving this requires a confluence and coaction of expertise in computer science and physical sciences. This review is written for new and experienced researchers working at the intersection of both fields. We first provide concise tutorials of computational chemistry and machine learning methods, showing how insights involving both can be achieved. We then follow with a critical review of noteworthy applications that demonstrate how computational chemistry and machine learning can be used together to provide insightful (and useful) predictions in molecular and materials modeling, retrosyntheses, catalysis, and drug design.","lang":"eng"}],"scopus_import":"1","month":"07","date_created":"2021-07-20T11:18:37Z","publication":"Chemical Reviews","oa":1,"date_published":"2021-07-07T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"publication_identifier":{"issn":["0009-2665"],"eissn":["1520-6890"]}},{"language":[{"iso":"eng"}],"intvolume":"        10","_id":"9746","citation":{"mla":"Batra, Aditi, et al. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.” <i>ELife</i>, vol. 10, e68876, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.68876\">10.7554/elife.68876</a>.","ista":"Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. 2021. High potency of sequential therapy with only beta-lactam antibiotics. eLife. 10, e68876.","short":"A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, H. Schulenburg, ELife 10 (2021).","ama":"Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. High potency of sequential therapy with only beta-lactam antibiotics. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.68876\">10.7554/elife.68876</a>","ieee":"A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, and H. Schulenburg, “High potency of sequential therapy with only beta-lactam antibiotics,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","chicago":"Batra, Aditi, Roderich Römhild, Emilie Rousseau, Sören Franzenburg, Stefan Niemann, and Hinrich Schulenburg. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.68876\">https://doi.org/10.7554/elife.68876</a>.","apa":"Batra, A., Römhild, R., Rousseau, E., Franzenburg, S., Niemann, S., &#38; Schulenburg, H. (2021). High potency of sequential therapy with only beta-lactam antibiotics. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.68876\">https://doi.org/10.7554/elife.68876</a>"},"doi":"10.7554/elife.68876","oa_version":"Published Version","month":"07","publication":"eLife","date_created":"2021-07-28T13:36:57Z","pmid":1,"oa":1,"abstract":[{"lang":"eng","text":"Evolutionary adaptation is a major source of antibiotic resistance in bacterial pathogens. Evolution-informed therapy aims to constrain resistance by accounting for bacterial evolvability. Sequential treatments with antibiotics that target different bacterial processes were previously shown to limit adaptation through genetic resistance trade-offs and negative hysteresis. Treatment with homogeneous sets of antibiotics is generally viewed to be disadvantageous, as it should rapidly lead to cross-resistance. We here challenged this assumption by determining the evolutionary response of Pseudomonas aeruginosa to experimental sequential treatments involving both heterogenous and homogeneous antibiotic sets. To our surprise, we found that fast switching between only β-lactam antibiotics resulted in increased extinction of bacterial populations. We demonstrate that extinction is favored by low rates of spontaneous resistance emergence and low levels of spontaneous cross-resistance among the antibiotics in sequence. The uncovered principles may help to guide the optimized use of available antibiotics in highly potent, evolution-informed treatment designs."}],"scopus_import":"1","article_number":"e68876","date_published":"2021-07-28T00:00:00Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["2050-084X"]},"title":"High potency of sequential therapy with only beta-lactam antibiotics","department":[{"_id":"CaGu"}],"article_processing_charge":"No","date_updated":"2023-08-11T10:26:29Z","type":"journal_article","publication_status":"published","publisher":"eLife Sciences Publications","main_file_link":[{"open_access":"1","url":"https://doi.org/10.7554/eLife.68876"}],"quality_controlled":"1","author":[{"last_name":"Batra","full_name":"Batra, Aditi","first_name":"Aditi"},{"id":"68E56E44-62B0-11EA-B963-444F3DDC885E","orcid":"0000-0001-9480-5261","last_name":"Römhild","full_name":"Römhild, Roderich","first_name":"Roderich"},{"first_name":"Emilie","full_name":"Rousseau, Emilie","last_name":"Rousseau"},{"last_name":"Franzenburg","first_name":"Sören","full_name":"Franzenburg, Sören"},{"last_name":"Niemann","full_name":"Niemann, Stefan","first_name":"Stefan"},{"full_name":"Schulenburg, Hinrich","first_name":"Hinrich","last_name":"Schulenburg"}],"article_type":"original","external_id":{"pmid":["34318749"],"isi":["000692027800001"]},"isi":1,"acknowledgement":"We would like to thank Leif Tueffers and João Botelho for discussions and suggestions as well as Kira Haas and Julia Bunk for technical support. We acknowledge financial support from the German Science Foundation (grant SCHU 1415/12-2 to HS, and funding under Germany’s Excellence Strategy EXC 2167–390884018 as well as the Research Training Group 2501 TransEvo to HS and SN), the Max Planck Society (IMPRS scholarship to AB; Max-Planck fellowship to HS), and the Leibniz Science Campus Evolutionary Medicine of the Lung (EvoLUNG, to HS and SN). This work was further supported by the German Science Foundation Research Infrastructure NGS_CC (project 407495230) as part of the Next Generation Sequencing Competence Network (project 423957469). NGS analyses were carried out at the Competence Centre for Genomic Analysis Kiel (CCGA Kiel).","volume":10,"year":"2021","day":"28"},{"publication_status":"published","type":"journal_article","file":[{"relation":"main_file","creator":"cchlebak","content_type":"application/pdf","file_name":"2021_PlosCompBio_Bartlett.pdf","file_size":693633,"date_created":"2021-08-05T12:06:49Z","file_id":"9771","access_level":"open_access","checksum":"e56d91f0eeadb36f143a90e2c1b3ab63","date_updated":"2021-08-05T12:06:49Z"}],"article_processing_charge":"Yes","title":"Ten simple rules to improve academic work- life balance","department":[{"_id":"CaHe"}],"date_updated":"2025-07-10T12:02:02Z","has_accepted_license":"1","issue":"7","author":[{"first_name":"Michael John","full_name":"Bartlett, Michael John","last_name":"Bartlett"},{"last_name":"Arslan","orcid":"0000-0001-5809-9566","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","first_name":"Feyza N","full_name":"Arslan, Feyza N"},{"last_name":"Bankston","full_name":"Bankston, Adriana","first_name":"Adriana"},{"last_name":"Sarabipour","full_name":"Sarabipour, Sarvenaz","first_name":"Sarvenaz"}],"ddc":["613"],"publisher":"Public Library of Science","file_date_updated":"2021-08-05T12:06:49Z","article_type":"letter_note","external_id":{"isi":["000677713500008"],"pmid":["34264932"]},"year":"2021","volume":17,"day":"15","isi":1,"acknowledgement":"The authors thank Inez Lam of Johns Hopkins University for valuable comments on an earlier version of the manuscript. We also thank the facilitators of the 2019–2020 eLife Community Ambassador program.","_id":"9759","intvolume":"        17","oa_version":"Published Version","doi":"10.1371/journal.pcbi.1009124","citation":{"mla":"Bartlett, Michael John, et al. “Ten Simple Rules to Improve Academic Work- Life Balance.” <i>PLoS Computational Biology</i>, vol. 17, no. 7, e1009124, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009124\">10.1371/journal.pcbi.1009124</a>.","ista":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. 2021. Ten simple rules to improve academic work- life balance. PLoS Computational Biology. 17(7), e1009124.","short":"M.J. Bartlett, F.N. Arslan, A. Bankston, S. Sarabipour, PLoS Computational Biology 17 (2021).","chicago":"Bartlett, Michael John, Feyza N Arslan, Adriana Bankston, and Sarvenaz Sarabipour. “Ten Simple Rules to Improve Academic Work- Life Balance.” <i>PLoS Computational Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pcbi.1009124\">https://doi.org/10.1371/journal.pcbi.1009124</a>.","ieee":"M. J. Bartlett, F. N. Arslan, A. Bankston, and S. Sarabipour, “Ten simple rules to improve academic work- life balance,” <i>PLoS Computational Biology</i>, vol. 17, no. 7. Public Library of Science, 2021.","apa":"Bartlett, M. J., Arslan, F. N., Bankston, A., &#38; Sarabipour, S. (2021). Ten simple rules to improve academic work- life balance. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1009124\">https://doi.org/10.1371/journal.pcbi.1009124</a>","ama":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. Ten simple rules to improve academic work- life balance. <i>PLoS Computational Biology</i>. 2021;17(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009124\">10.1371/journal.pcbi.1009124</a>"},"language":[{"iso":"eng"}],"scopus_import":"1","pmid":1,"date_created":"2021-08-01T22:01:21Z","month":"07","publication":"PLoS Computational Biology","oa":1,"date_published":"2021-07-15T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","article_number":"e1009124","publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"date_published":"2021-07-13T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","article_number":"008","publication_identifier":{"eissn":["2542-4653"]},"arxiv":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"9769","intvolume":"        11","doi":"10.21468/scipostphys.11.1.008","oa_version":"Published Version","citation":{"short":"F. Brauneis, H.-W. Hammer, M. Lemeshko, A. Volosniev, SciPost Physics 11 (2021).","mla":"Brauneis, Fabian, et al. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” <i>SciPost Physics</i>, vol. 11, no. 1, 008, SciPost Foundation, 2021, doi:<a href=\"https://doi.org/10.21468/scipostphys.11.1.008\">10.21468/scipostphys.11.1.008</a>.","ista":"Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. 2021. Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. 11(1), 008.","ama":"Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. Impurities in a one-dimensional Bose gas: The flow equation approach. <i>SciPost Physics</i>. 2021;11(1). doi:<a href=\"https://doi.org/10.21468/scipostphys.11.1.008\">10.21468/scipostphys.11.1.008</a>","apa":"Brauneis, F., Hammer, H.-W., Lemeshko, M., &#38; Volosniev, A. (2021). Impurities in a one-dimensional Bose gas: The flow equation approach. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.11.1.008\">https://doi.org/10.21468/scipostphys.11.1.008</a>","ieee":"F. Brauneis, H.-W. Hammer, M. Lemeshko, and A. Volosniev, “Impurities in a one-dimensional Bose gas: The flow equation approach,” <i>SciPost Physics</i>, vol. 11, no. 1. SciPost Foundation, 2021.","chicago":"Brauneis, Fabian, Hans-Werner Hammer, Mikhail Lemeshko, and Artem Volosniev. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” <i>SciPost Physics</i>. SciPost Foundation, 2021. <a href=\"https://doi.org/10.21468/scipostphys.11.1.008\">https://doi.org/10.21468/scipostphys.11.1.008</a>."},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"A few years ago, flow equations were introduced as a technique for calculating the ground-state energies of cold Bose gases with and without impurities. In this paper, we extend this approach to compute observables other than the energy. As an example, we calculate the densities, and phase fluctuations of one-dimensional Bose gases with one and two impurities. For a single mobile impurity, we use flow equations to validate the mean-field results obtained upon the Lee-Low-Pines transformation. We show that the mean-field approximation is accurate for all values of the boson-impurity interaction strength as long as the phase coherence length is much larger than the healing length of the condensate. For two static impurities, we calculate impurity-impurity interactions induced by the Bose gas. We find that leading order perturbation theory fails when boson-impurity interactions are stronger than boson-boson interactions. The mean-field approximation reproduces the flow equation results for all values of the boson-impurity interaction strength as long as boson-boson interactions are weak."}],"scopus_import":"1","ec_funded":1,"publication":"SciPost Physics","date_created":"2021-08-04T15:00:55Z","month":"07","oa":1,"file_date_updated":"2021-08-10T11:44:59Z","article_type":"original","external_id":{"arxiv":["2101.10958"],"isi":["000680039500013"]},"project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","grant_number":"801770"}],"year":"2021","volume":11,"day":"13","isi":1,"acknowledgement":"We thank Matthias Heinz and Volker Karle for helpful comments on the manuscript; Zoran Ristivojevic for useful correspondence regarding mean-field calculations of induced impurity-impurity interactions; Fabian Grusdt for sharing with us the data for the densities presented in Ref. [14]. This work has received funding from the DFG Project No. 413495248 [VO 2437/1-1] (F. B., H.-W. H., A. G. V.) and European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A. G. V.). M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). H.-W.H. thanks the ECT* for hospitality during the workshop “Universal physics in Many-Body Quantum Systems – From Atoms to Quarks\". This infrastructure is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824093. H.-W.H. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 279384907 - SFB 1245.","publication_status":"published","type":"journal_article","file":[{"relation":"main_file","creator":"asandaue","content_type":"application/pdf","file_name":"2021_SciPostPhysics_Brauneis.pdf","file_size":1085300,"success":1,"date_created":"2021-08-10T11:44:59Z","file_id":"9875","access_level":"open_access","checksum":"eaa847346b1a023d97bbb291779610ed","date_updated":"2021-08-10T11:44:59Z"}],"article_processing_charge":"Yes","department":[{"_id":"MiLe"}],"title":"Impurities in a one-dimensional Bose gas: The flow equation approach","date_updated":"2025-05-14T10:51:56Z","issue":"1","has_accepted_license":"1","author":[{"last_name":"Brauneis","full_name":"Brauneis, Fabian","first_name":"Fabian"},{"full_name":"Hammer, Hans-Werner","first_name":"Hans-Werner","last_name":"Hammer"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","first_name":"Mikhail"},{"first_name":"Artem","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","ddc":["530"],"publisher":"SciPost Foundation"},{"isi":1,"acknowledgement":"We thank Rafael Barfknecht for useful discussions. This work has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.\r\nand A.G.V.). M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). Y.P. and O.M. acknowledge funding from the Nidersachsen Ministry of Science and Culture, and from the\r\nAcademia Sinica Research Program. O.M. is thankful for support through the Harry de Jur Chair in Applied Science.","volume":104,"year":"2021","day":"01","article_type":"original","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle"}],"external_id":{"arxiv":["2101.05173"],"isi":["000678780800003"]},"publisher":"American Physical Society","main_file_link":[{"url":"https://arxiv.org/abs/2101.05173","open_access":"1"}],"quality_controlled":"1","author":[{"first_name":"Artem","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hen","full_name":"Alpern, Hen","last_name":"Alpern"},{"full_name":"Paltiel, Yossi","first_name":"Yossi","last_name":"Paltiel"},{"full_name":"Millo, Oded","first_name":"Oded","last_name":"Millo"},{"first_name":"Mikhail","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg","full_name":"Ghazaryan, Areg"}],"title":"Interplay between friction and spin-orbit coupling as a source of spin polarization","department":[{"_id":"MiLe"}],"article_processing_charge":"No","issue":"2","date_updated":"2025-04-14T07:43:49Z","type":"journal_article","publication_status":"published","arxiv":1,"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"article_number":"024430","date_published":"2021-07-01T00:00:00Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"07","date_created":"2021-08-04T15:05:32Z","publication":"Physical Review B","oa":1,"abstract":[{"lang":"eng","text":"We study an effective one-dimensional quantum model that includes friction and spin-orbit coupling (SOC), and show that the model exhibits spin polarization when both terms are finite. Most important, strong spin polarization can be observed even for moderate SOC, provided that the friction is strong. Our findings might help to explain the pronounced effect of chirality on spin distribution and transport in chiral molecules. In particular, our model implies static magnetic properties of a chiral molecule, which lead to Shiba-like states when a molecule is placed on a superconductor, in accordance with recent experimental data."}],"scopus_import":"1","ec_funded":1,"language":[{"iso":"eng"}],"intvolume":"       104","_id":"9770","citation":{"ieee":"A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, and A. Ghazaryan, “Interplay between friction and spin-orbit coupling as a source of spin polarization,” <i>Physical Review B</i>, vol. 104, no. 2. American Physical Society, 2021.","chicago":"Volosniev, Artem, Hen Alpern, Yossi Paltiel, Oded Millo, Mikhail Lemeshko, and Areg Ghazaryan. “Interplay between Friction and Spin-Orbit Coupling as a Source of Spin Polarization.” <i>Physical Review B</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevb.104.024430\">https://doi.org/10.1103/physrevb.104.024430</a>.","apa":"Volosniev, A., Alpern, H., Paltiel, Y., Millo, O., Lemeshko, M., &#38; Ghazaryan, A. (2021). Interplay between friction and spin-orbit coupling as a source of spin polarization. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.104.024430\">https://doi.org/10.1103/physrevb.104.024430</a>","ama":"Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. Interplay between friction and spin-orbit coupling as a source of spin polarization. <i>Physical Review B</i>. 2021;104(2). doi:<a href=\"https://doi.org/10.1103/physrevb.104.024430\">10.1103/physrevb.104.024430</a>","mla":"Volosniev, Artem, et al. “Interplay between Friction and Spin-Orbit Coupling as a Source of Spin Polarization.” <i>Physical Review B</i>, vol. 104, no. 2, 024430, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevb.104.024430\">10.1103/physrevb.104.024430</a>.","ista":"Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. 2021. Interplay between friction and spin-orbit coupling as a source of spin polarization. Physical Review B. 104(2), 024430.","short":"A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, A. Ghazaryan, Physical Review B 104 (2021)."},"oa_version":"Preprint","doi":"10.1103/physrevb.104.024430"},{"author":[{"id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","last_name":"Vandael","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","first_name":"David H"},{"full_name":"Okamoto, Yuji","first_name":"Yuji","id":"3337E116-F248-11E8-B48F-1D18A9856A87","last_name":"Okamoto","orcid":"0000-0003-0408-6094"},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M"}],"quality_controlled":"1","publisher":"Springer","ddc":["570"],"file":[{"date_updated":"2021-12-17T11:34:50Z","access_level":"open_access","checksum":"6036a8cdae95e1707c2a04d54e325ff4","success":1,"file_size":3108845,"file_id":"10563","date_created":"2021-12-17T11:34:50Z","relation":"main_file","file_name":"2021_NatureCommunications_Vandael.pdf","creator":"kschuh","content_type":"application/pdf"}],"publication_status":"published","type":"journal_article","date_updated":"2025-06-12T06:28:45Z","issue":"1","has_accepted_license":"1","article_processing_charge":"Yes","title":"Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses","department":[{"_id":"PeJo"}],"day":"18","year":"2021","volume":12,"acknowledgement":"We thank Drs. Carolina Borges-Merjane and Jose Guzman for critically reading the manuscript, and Pablo Castillo for discussions. We are grateful to Alois Schlögl for help with analysis, Florian Marr for excellent technical assistance and cell reconstruction, Christina Altmutter for technical help, Eleftheria Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for support. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award), both to P.J.","isi":1,"file_date_updated":"2021-12-17T11:34:50Z","external_id":{"isi":["000655481800014"],"pmid":["34006874"]},"keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692","call_identifier":"H2020"},{"name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","call_identifier":"FWF"}],"article_type":"original","abstract":[{"text":"The hippocampal mossy fiber synapse is a key synapse of the trisynaptic circuit. Post-tetanic potentiation (PTP) is the most powerful form of plasticity at this synaptic connection. It is widely believed that mossy fiber PTP is an entirely presynaptic phenomenon, implying that PTP induction is input-specific, and requires neither activity of multiple inputs nor stimulation of postsynaptic neurons. To directly test cooperativity and associativity, we made paired recordings between single mossy fiber terminals and postsynaptic CA3 pyramidal neurons in rat brain slices. By stimulating non-overlapping mossy fiber inputs converging onto single CA3 neurons, we confirm that PTP is input-specific and non-cooperative. Unexpectedly, mossy fiber PTP exhibits anti-associative induction properties. EPSCs show only minimal PTP after combined pre- and postsynaptic high-frequency stimulation with intact postsynaptic Ca2+ signaling, but marked PTP in the absence of postsynaptic spiking and after suppression of postsynaptic Ca2+ signaling (10 mM EGTA). PTP is largely recovered by inhibitors of voltage-gated R- and L-type Ca2+ channels, group II mGluRs, and vacuolar-type H+-ATPase, suggesting the involvement of retrograde vesicular glutamate signaling. Transsynaptic regulation of PTP extends the repertoire of synaptic computations, implementing a brake on mossy fiber detonation and a “smart teacher” function of hippocampal mossy fiber synapses.","lang":"eng"}],"scopus_import":"1","ec_funded":1,"OA_place":"publisher","oa":1,"pmid":1,"date_created":"2021-08-06T07:22:55Z","month":"05","publication":"Nature Communications","oa_version":"Published Version","doi":"10.1038/s41467-021-23153-5","citation":{"ama":"Vandael DH, Okamoto Y, Jonas PM. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23153-5\">10.1038/s41467-021-23153-5</a>","apa":"Vandael, D. H., Okamoto, Y., &#38; Jonas, P. M. (2021). Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. <i>Nature Communications</i>. Springer. <a href=\"https://doi.org/10.1038/s41467-021-23153-5\">https://doi.org/10.1038/s41467-021-23153-5</a>","ieee":"D. H. Vandael, Y. Okamoto, and P. M. Jonas, “Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses,” <i>Nature Communications</i>, vol. 12, no. 1. Springer, 2021.","chicago":"Vandael, David H, Yuji Okamoto, and Peter M Jonas. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” <i>Nature Communications</i>. Springer, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23153-5\">https://doi.org/10.1038/s41467-021-23153-5</a>.","mla":"Vandael, David H., et al. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” <i>Nature Communications</i>, vol. 12, no. 1, 2912, Springer, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23153-5\">10.1038/s41467-021-23153-5</a>.","ista":"Vandael DH, Okamoto Y, Jonas PM. 2021. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. 12(1), 2912.","short":"D.H. Vandael, Y. Okamoto, P.M. Jonas, Nature Communications 12 (2021)."},"_id":"9778","corr_author":"1","intvolume":"        12","OA_type":"gold","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_identifier":{"issn":["2041-1723"]},"acknowledged_ssus":[{"_id":"SSU"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/synaptic-transmission-not-a-one-way-street/"}]},"date_published":"2021-05-18T00:00:00Z","article_number":"2912"},{"abstract":[{"text":"Astrocytes extensively infiltrate the neuropil to regulate critical aspects of synaptic development and function. This process is regulated by transcellular interactions between astrocytes and neurons via cell adhesion molecules. How astrocytes coordinate developmental processes among one another to parse out the synaptic neuropil and form non-overlapping territories is unknown. Here we identify a molecular mechanism regulating astrocyte-astrocyte interactions during development to coordinate astrocyte morphogenesis and gap junction coupling. We show that hepaCAM, a disease-linked, astrocyte-enriched cell adhesion molecule, regulates astrocyte competition for territory and morphological complexity in the developing mouse cortex. Furthermore, conditional deletion of Hepacam from developing astrocytes significantly impairs gap junction coupling between astrocytes and disrupts the balance between synaptic excitation and inhibition. Mutations in HEPACAM cause megalencephalic leukoencephalopathy with subcortical cysts in humans. Therefore, our findings suggest that disruption of astrocyte self-organization mechanisms could be an underlying cause of neural pathology.","lang":"eng"}],"scopus_import":"1","ec_funded":1,"oa":1,"pmid":1,"month":"08","date_created":"2021-08-06T09:08:25Z","publication":"Neuron","doi":"10.1016/j.neuron.2021.05.025","oa_version":"Published Version","citation":{"chicago":"Baldwin, Katherine T., Christabel X. Tan, Samuel T. Strader, Changyu Jiang, Justin T. Savage, Xabier Elorza-Vidal, Ximena Contreras, et al. “HepaCAM Controls Astrocyte Self-Organization and Coupling.” <i>Neuron</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.neuron.2021.05.025\">https://doi.org/10.1016/j.neuron.2021.05.025</a>.","apa":"Baldwin, K. T., Tan, C. X., Strader, S. T., Jiang, C., Savage, J. T., Elorza-Vidal, X., … Eroglu, C. (2021). HepaCAM controls astrocyte self-organization and coupling. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2021.05.025\">https://doi.org/10.1016/j.neuron.2021.05.025</a>","ieee":"K. T. Baldwin <i>et al.</i>, “HepaCAM controls astrocyte self-organization and coupling,” <i>Neuron</i>, vol. 109, no. 15. Elsevier, p. 2427–2442.e10, 2021.","ama":"Baldwin KT, Tan CX, Strader ST, et al. HepaCAM controls astrocyte self-organization and coupling. <i>Neuron</i>. 2021;109(15):2427-2442.e10. doi:<a href=\"https://doi.org/10.1016/j.neuron.2021.05.025\">10.1016/j.neuron.2021.05.025</a>","mla":"Baldwin, Katherine T., et al. “HepaCAM Controls Astrocyte Self-Organization and Coupling.” <i>Neuron</i>, vol. 109, no. 15, Elsevier, 2021, p. 2427–2442.e10, doi:<a href=\"https://doi.org/10.1016/j.neuron.2021.05.025\">10.1016/j.neuron.2021.05.025</a>.","ista":"Baldwin KT, Tan CX, Strader ST, Jiang C, Savage JT, Elorza-Vidal X, Contreras X, Rülicke T, Hippenmeyer S, Estévez R, Ji R-R, Eroglu C. 2021. HepaCAM controls astrocyte self-organization and coupling. Neuron. 109(15), 2427–2442.e10.","short":"K.T. Baldwin, C.X. Tan, S.T. Strader, C. Jiang, J.T. Savage, X. Elorza-Vidal, X. Contreras, T. Rülicke, S. Hippenmeyer, R. Estévez, R.-R. Ji, C. Eroglu, Neuron 109 (2021) 2427–2442.e10."},"_id":"9793","intvolume":"       109","language":[{"iso":"eng"}],"page":"2427-2442.e10","publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2021-08-04T00:00:00Z","author":[{"last_name":"Baldwin","first_name":"Katherine T.","full_name":"Baldwin, Katherine T."},{"first_name":"Christabel X.","full_name":"Tan, Christabel X.","last_name":"Tan"},{"first_name":"Samuel T.","full_name":"Strader, Samuel T.","last_name":"Strader"},{"full_name":"Jiang, Changyu","first_name":"Changyu","last_name":"Jiang"},{"first_name":"Justin T.","full_name":"Savage, Justin T.","last_name":"Savage"},{"full_name":"Elorza-Vidal, Xabier","first_name":"Xabier","last_name":"Elorza-Vidal"},{"last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","full_name":"Contreras, Ximena"},{"last_name":"Rülicke","first_name":"Thomas","full_name":"Rülicke, Thomas"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"},{"last_name":"Estévez","full_name":"Estévez, Raúl","first_name":"Raúl"},{"last_name":"Ji","first_name":"Ru-Rong","full_name":"Ji, Ru-Rong"},{"full_name":"Eroglu, Cagla","first_name":"Cagla","last_name":"Eroglu"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2021.05.025"}],"publisher":"Elsevier","publication_status":"published","type":"journal_article","date_updated":"2025-04-14T07:43:03Z","issue":"15","article_processing_charge":"No","title":"HepaCAM controls astrocyte self-organization and coupling","department":[{"_id":"SiHi"}],"day":"04","year":"2021","volume":109,"acknowledgement":"This work was supported by the National Institutes of Health (R01 DA047258 and R01 NS102237 to C.E., F32 NS100392 to K.T.B.) and the Holland-Trice Brain Research Award (to C.E.). K.T.B. was supported by postdoctoral fellowships from the Foerster-Bernstein Family and The Hartwell Foundation. The Hippenmeyer lab was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovations program (725780 LinPro) to S.H. R.E. was supported by Ministerio de Ciencia y Tecnología (RTI2018-093493-B-I00). We thank the Duke Light Microscopy Core Facility, the Duke Transgenic Mouse Facility, Dr. U. Schulte for assistance with proteomic experiments, and Dr. D. Silver for critical review of the manuscript. Cartoon elements of figure panels were created using BioRender.com.","isi":1,"external_id":{"isi":["000692851900010"],"pmid":["34171291"]},"project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"725780"}],"article_type":"original"},{"abstract":[{"lang":"eng","text":"The quantum bits (qubits) on which superconducting quantum computers are based have energy scales corresponding to photons with GHz frequencies. The energy of photons in the gigahertz domain is too low to allow transmission through the noisy room-temperature environment, where the signal would be lost in thermal noise. Optical photons, on the other hand, have much higher energies, and signals can be detected using highly efficient single-photon detectors. Transduction from microwave to optical frequencies is therefore a potential enabling technology for quantum devices. However, in such a device the optical pump can be a source of thermal noise and thus degrade the fidelity; the similarity of input microwave state to the output optical state. In order to investigate the magnitude of this effect we model the sub-Kelvin thermal behavior of an electro-optic transducer based on a lithium niobate whispering gallery mode resonator. We find that there is an optimum power level for a continuous pump, whilst pulsed operation of the pump increases the fidelity of the conversion."}],"scopus_import":"1","month":"07","publication":"Quantum Science and Technology","date_created":"2021-08-08T22:01:25Z","oa":1,"_id":"9815","intvolume":"         6","oa_version":"Published Version","doi":"10.1088/2058-9565/ac0f36","citation":{"ieee":"S. Mobassem, N. J. Lambert, A. R. Rueda Sanchez, J. M. Fink, G. Leuchs, and H. G. L. Schwefel, “Thermal noise in electro-optic devices at cryogenic temperatures,” <i>Quantum Science and Technology</i>, vol. 6, no. 4. IOP Publishing, 2021.","chicago":"Mobassem, Sonia, Nicholas J. Lambert, Alfredo R Rueda Sanchez, Johannes M Fink, Gerd Leuchs, and Harald G.L. Schwefel. “Thermal Noise in Electro-Optic Devices at Cryogenic Temperatures.” <i>Quantum Science and Technology</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/2058-9565/ac0f36\">https://doi.org/10.1088/2058-9565/ac0f36</a>.","apa":"Mobassem, S., Lambert, N. J., Rueda Sanchez, A. R., Fink, J. M., Leuchs, G., &#38; Schwefel, H. G. L. (2021). Thermal noise in electro-optic devices at cryogenic temperatures. <i>Quantum Science and Technology</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/2058-9565/ac0f36\">https://doi.org/10.1088/2058-9565/ac0f36</a>","ama":"Mobassem S, Lambert NJ, Rueda Sanchez AR, Fink JM, Leuchs G, Schwefel HGL. Thermal noise in electro-optic devices at cryogenic temperatures. <i>Quantum Science and Technology</i>. 2021;6(4). doi:<a href=\"https://doi.org/10.1088/2058-9565/ac0f36\">10.1088/2058-9565/ac0f36</a>","short":"S. Mobassem, N.J. Lambert, A.R. Rueda Sanchez, J.M. Fink, G. Leuchs, H.G.L. Schwefel, Quantum Science and Technology 6 (2021).","mla":"Mobassem, Sonia, et al. “Thermal Noise in Electro-Optic Devices at Cryogenic Temperatures.” <i>Quantum Science and Technology</i>, vol. 6, no. 4, 045005, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/2058-9565/ac0f36\">10.1088/2058-9565/ac0f36</a>.","ista":"Mobassem S, Lambert NJ, Rueda Sanchez AR, Fink JM, Leuchs G, Schwefel HGL. 2021. Thermal noise in electro-optic devices at cryogenic temperatures. Quantum Science and Technology. 6(4), 045005."},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2058-9565"]},"arxiv":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_published":"2021-07-15T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","article_number":"045005","author":[{"full_name":"Mobassem, Sonia","first_name":"Sonia","last_name":"Mobassem"},{"last_name":"Lambert","full_name":"Lambert, Nicholas J.","first_name":"Nicholas J."},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","last_name":"Rueda Sanchez","full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R"},{"first_name":"Johannes M","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gerd","full_name":"Leuchs, Gerd","last_name":"Leuchs"},{"last_name":"Schwefel","first_name":"Harald G.L.","full_name":"Schwefel, Harald G.L."}],"quality_controlled":"1","ddc":["530"],"publisher":"IOP Publishing","publication_status":"published","type":"journal_article","file":[{"relation":"main_file","creator":"cchlebak","content_type":"application/pdf","file_name":"2021_QuantumScienceTechnology_Mobassem.pdf","file_size":2366118,"date_created":"2021-08-09T12:23:13Z","file_id":"9836","access_level":"open_access","checksum":"b15c2c228487a75002c3b52d56f23d5c","date_updated":"2021-08-09T12:23:13Z"}],"article_processing_charge":"Yes","department":[{"_id":"JoFi"}],"title":"Thermal noise in electro-optic devices at cryogenic temperatures","date_updated":"2023-10-17T12:54:54Z","issue":"4","has_accepted_license":"1","year":"2021","volume":6,"day":"15","isi":1,"acknowledgement":"NJL is supported by the MBIE Endeavour Fund (UOOX1805) and GL is by the Julius von Haast Fellowship of New Zealand. SM acknowledges stimulating discussions with T M Jensen.","file_date_updated":"2021-08-09T12:23:13Z","article_type":"original","external_id":{"arxiv":["2008.08764"],"isi":["000673081500001"]}},{"_id":"9816","intvolume":"        16","doi":"10.1371/journal.pone.0255267","oa_version":"Published Version","citation":{"ista":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 16(7), e0255267.","mla":"Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” <i>PLoS ONE</i>, vol. 16, no. 7, e0255267, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pone.0255267\">10.1371/journal.pone.0255267</a>.","short":"M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch, PLoS ONE 16 (2021).","ama":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. <i>PLoS ONE</i>. 2021;16(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0255267\">10.1371/journal.pone.0255267</a>","ieee":"M. Hledik, J. Polechova, M. Beiglböck, A. N. Herdina, R. Strassl, and M. Posch, “Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program,” <i>PLoS ONE</i>, vol. 16, no. 7. Public Library of Science, 2021.","apa":"Hledik, M., Polechova, J., Beiglböck, M., Herdina, A. N., Strassl, R., &#38; Posch, M. (2021). Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0255267\">https://doi.org/10.1371/journal.pone.0255267</a>","chicago":"Hledik, Michal, Jitka Polechova, Mathias Beiglböck, Anna Nele Herdina, Robert Strassl, and Martin Posch. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” <i>PLoS ONE</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pone.0255267\">https://doi.org/10.1371/journal.pone.0255267</a>."},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Aims: Mass antigen testing programs have been challenged because of an alleged insufficient specificity, leading to a large number of false positives. The objective of this study is to derive a lower bound of the specificity of the SD Biosensor Standard Q Ag-Test in large scale practical use.\r\nMethods: Based on county data from the nationwide tests for SARS-CoV-2 in Slovakia between 31.10.–1.11. 2020 we calculate a lower confidence bound for the specificity. As positive test results were not systematically verified by PCR tests, we base the lower bound on a worst case assumption, assuming all positives to be false positives.\r\nResults: 3,625,332 persons from 79 counties were tested. The lowest positivity rate was observed in the county of Rožňava where 100 out of 34307 (0.29%) tests were positive. This implies a test specificity of at least 99.6% (97.5% one-sided lower confidence bound, adjusted for multiplicity).\r\nConclusion: The obtained lower bound suggests a higher specificity compared to earlier studies in spite of the underlying worst case assumption and the application in a mass testing setting. The actual specificity is expected to exceed 99.6% if the prevalence in the respective regions was non-negligible at the time of testing. To our knowledge, this estimate constitutes the first bound obtained from large scale practical use of an antigen test."}],"scopus_import":"1","pmid":1,"month":"07","publication":"PLoS ONE","date_created":"2021-08-08T22:01:26Z","oa":1,"date_published":"2021-07-29T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","article_number":"e0255267","publication_identifier":{"eissn":["1932-6203"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_status":"published","type":"journal_article","file":[{"success":1,"file_size":773921,"file_id":"9835","date_created":"2021-08-09T11:52:14Z","relation":"main_file","file_name":"2021_PLoSONE_Hledík.pdf","creator":"asandaue","content_type":"application/pdf","date_updated":"2021-08-09T11:52:14Z","access_level":"open_access","checksum":"ae4df60eb62f4491278588548d0c1f93"}],"article_processing_charge":"Yes","department":[{"_id":"NiBa"}],"title":"Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program","date_updated":"2023-08-10T14:26:32Z","issue":"7","has_accepted_license":"1","author":[{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik","full_name":"Hledik, Michal","first_name":"Michal"},{"first_name":"Jitka","full_name":"Polechova, Jitka","last_name":"Polechova","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Beiglböck","full_name":"Beiglböck, Mathias","first_name":"Mathias"},{"last_name":"Herdina","full_name":"Herdina, Anna Nele","first_name":"Anna Nele"},{"last_name":"Strassl","first_name":"Robert","full_name":"Strassl, Robert"},{"full_name":"Posch, Martin","first_name":"Martin","last_name":"Posch"}],"quality_controlled":"1","publisher":"Public Library of Science","ddc":["610"],"file_date_updated":"2021-08-09T11:52:14Z","article_type":"original","external_id":{"isi":["000685248200095"],"pmid":["34324553"]},"year":"2021","volume":16,"day":"29","isi":1,"acknowledgement":"We would like to thank Alfred Uhl, Richard Kollár and Katarína Bod’ová for very helpful comments. We also thank Matej Mišík for discussion and information regarding the Slovak testing data and Ag-Test used."},{"external_id":{"isi":["000594805800001"],"arxiv":["1910.10435"]},"article_type":"original","day":"01","year":"2021","volume":53,"isi":1,"publication_status":"published","type":"journal_article","date_updated":"2024-10-09T20:59:03Z","issue":"2","article_processing_charge":"No","title":"The positivity of local equivariant Hirzebruch class for toric varieties","department":[{"_id":"TaHa"}],"author":[{"full_name":"Rychlewicz, Kamil P","first_name":"Kamil P","id":"85A07246-A8BF-11E9-B4FA-D9E3E5697425","last_name":"Rychlewicz"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1910.10435","open_access":"1"}],"publisher":"Wiley","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","date_published":"2021-04-01T00:00:00Z","publication_identifier":{"issn":["0024-6093"],"eissn":["1469-2120"]},"arxiv":1,"oa_version":"Preprint","doi":"10.1112/blms.12442","citation":{"chicago":"Rychlewicz, Kamil P. “The Positivity of Local Equivariant Hirzebruch Class for Toric Varieties.” <i>Bulletin of the London Mathematical Society</i>. Wiley, 2021. <a href=\"https://doi.org/10.1112/blms.12442\">https://doi.org/10.1112/blms.12442</a>.","apa":"Rychlewicz, K. P. (2021). The positivity of local equivariant Hirzebruch class for toric varieties. <i>Bulletin of the London Mathematical Society</i>. Wiley. <a href=\"https://doi.org/10.1112/blms.12442\">https://doi.org/10.1112/blms.12442</a>","ieee":"K. P. Rychlewicz, “The positivity of local equivariant Hirzebruch class for toric varieties,” <i>Bulletin of the London Mathematical Society</i>, vol. 53, no. 2. Wiley, pp. 560–574, 2021.","ama":"Rychlewicz KP. The positivity of local equivariant Hirzebruch class for toric varieties. <i>Bulletin of the London Mathematical Society</i>. 2021;53(2):560-574. doi:<a href=\"https://doi.org/10.1112/blms.12442\">10.1112/blms.12442</a>","short":"K.P. Rychlewicz, Bulletin of the London Mathematical Society 53 (2021) 560–574.","mla":"Rychlewicz, Kamil P. “The Positivity of Local Equivariant Hirzebruch Class for Toric Varieties.” <i>Bulletin of the London Mathematical Society</i>, vol. 53, no. 2, Wiley, 2021, pp. 560–74, doi:<a href=\"https://doi.org/10.1112/blms.12442\">10.1112/blms.12442</a>.","ista":"Rychlewicz KP. 2021. The positivity of local equivariant Hirzebruch class for toric varieties. Bulletin of the London Mathematical Society. 53(2), 560–574."},"corr_author":"1","_id":"6965","intvolume":"        53","language":[{"iso":"eng"}],"page":"560-574","abstract":[{"lang":"eng","text":"The central object of investigation of this paper is the Hirzebruch class, a deformation of the Todd class, given by Hirzebruch (for smooth varieties). The generalization for singular varieties is due to Brasselet–Schürmann–Yokura. Following the work of Weber, we investigate its equivariant version for (possibly singular) toric varieties. The local decomposition of the Hirzebruch class to the fixed points of the torus action and a formula for the local class in terms of the defining fan are recalled. After this review part, we prove the positivity of local Hirzebruch classes for all toric varieties, thus proving false the alleged counterexample given by Weber."}],"scopus_import":"1","oa":1,"date_created":"2019-10-24T08:04:09Z","publication":"Bulletin of the London Mathematical Society","month":"04"},{"publication_status":"published","type":"journal_article","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"title":"Identification of neural oscillations and epileptiform changes in human brain organoids","date_updated":"2025-07-09T09:00:12Z","author":[{"first_name":"Ranmal A.","full_name":"Samarasinghe, Ranmal A.","last_name":"Samarasinghe"},{"full_name":"Miranda, Osvaldo","first_name":"Osvaldo","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","orcid":"0000-0001-6618-6889","last_name":"Miranda"},{"last_name":"Buth","full_name":"Buth, Jessie E.","first_name":"Jessie E."},{"last_name":"Mitchell","first_name":"Simon","full_name":"Mitchell, Simon"},{"full_name":"Ferando, Isabella","first_name":"Isabella","last_name":"Ferando"},{"last_name":"Watanabe","first_name":"Momoko","full_name":"Watanabe, Momoko"},{"full_name":"Kurdian, Arinnae","first_name":"Arinnae","last_name":"Kurdian"},{"last_name":"Golshani","full_name":"Golshani, Peyman","first_name":"Peyman"},{"last_name":"Plath","first_name":"Kathrin","full_name":"Plath, Kathrin"},{"last_name":"Lowry","first_name":"William E.","full_name":"Lowry, William E."},{"full_name":"Parent, Jack M.","first_name":"Jack M.","last_name":"Parent"},{"full_name":"Mody, Istvan","first_name":"Istvan","last_name":"Mody"},{"full_name":"Novitch, Bennett G.","first_name":"Bennett G.","last_name":"Novitch"}],"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1101/820183","open_access":"1"}],"publisher":"Springer Nature","article_type":"review","external_id":{"isi":["000687516300001"],"pmid":["34426698 "]},"year":"2021","volume":24,"day":"23","isi":1,"acknowledgement":"We thank S. Butler, T. Carmichael and members of the laboratory of B.G.N. for helpful discussions and comments on the manuscript; N. Vishlaghi and F. Turcios-Hernandez for technical assistance, and J. Lee, S.-K. Lee, H. Shinagawa and K. Yoshikawa for valuable reagents. We also thank the UCLA Eli and Edythe Broad Stem Cell Research Center (BSCRC) and Intellectual and Developmental Disabilities Research Center microscopy cores for access to imaging facilities. This work was supported by grants from the California Institute for Regenerative Medicine (CIRM) (DISC1-08819 to B.G.N.), the National Institute of Health (R01NS089817, R01DA051897 and P50HD103557 to B.G.N.; K08NS119747 to R.A.S.; K99HD096105 to M.W.; R01MH123922, R01MH121521 and P50HD103557 to M.J.G.; R01GM099134 to K.P.; R01NS103788 to W.E.L.; R01NS088571 to J.M.P.; R01NS030549 and R01AG050474 to I.M.), and research awards from the UCLA Jonsson Comprehensive Cancer Center and BSCRC Ablon Scholars Program (to B.G.N.), the BSCRC Innovation Program (to B.G.N., K.P. and W.E.L.), the UCLA BSCRC Steffy Brain Aging Research Fund (to B.G.N. and W.E.L.) and the UCLA Clinical and Translational Science Institute (to B.G.N.), Paul Allen Family Foundation Frontiers Group (to K.P. and W.E.L.), the March of Dimes Foundation (to W.E.L.) and the Simons Foundation Autism Research Initiative Bridge to Independence Program (to R.A.S. and M.J.G.). R.A.S. was also supported by the UCLA/NINDS Translational Neuroscience Training Grant (R25NS065723), a Research and Training Fellowship from the American Epilepsy Society, a Taking Flight Award from CURE Epilepsy and a Clinician Scientist training award from the UCLA BSCRC. J.E.B. was supported by the UCLA BSCRC Rose Hills Foundation Graduate Scholarship Training Program. M.W. was supported by postdoctoral training awards provided by the UCLA BSCRC and the Uehara Memorial Foundation. O.A.M. and A.K. were supported in part by the UCLA-California State University Northridge CIRM-Bridges training program (EDUC2-08411). We also acknowledge the support of the IDDRC Cells, Circuits and Systems Analysis, Microscopy and Genetics and Genomics Cores of the Semel Institute of Neuroscience at UCLA, which are supported by the NICHD (U54HD087101 and P50HD10355701). We lastly acknowledge support from a Quantitative and Computational Biosciences Collaboratory Postdoctoral Fellowship to S.M. and the Quantitative and Computational Biosciences Collaboratory community, directed by M. Pellegrini.","_id":"6995","OA_type":"green","intvolume":"        24","oa_version":"Preprint","doi":"10.1038/s41593-021-00906-5","citation":{"apa":"Samarasinghe, R. A., Miranda, O., Buth, J. E., Mitchell, S., Ferando, I., Watanabe, M., … Novitch, B. G. (2021). Identification of neural oscillations and epileptiform changes in human brain organoids. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41593-021-00906-5\">https://doi.org/10.1038/s41593-021-00906-5</a>","chicago":"Samarasinghe, Ranmal A., Osvaldo Miranda, Jessie E. Buth, Simon Mitchell, Isabella Ferando, Momoko Watanabe, Arinnae Kurdian, et al. “Identification of Neural Oscillations and Epileptiform Changes in Human Brain Organoids.” <i>Nature Neuroscience</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41593-021-00906-5\">https://doi.org/10.1038/s41593-021-00906-5</a>.","ieee":"R. A. Samarasinghe <i>et al.</i>, “Identification of neural oscillations and epileptiform changes in human brain organoids,” <i>Nature Neuroscience</i>, vol. 24. Springer Nature, p. 32, 2021.","ama":"Samarasinghe RA, Miranda O, Buth JE, et al. Identification of neural oscillations and epileptiform changes in human brain organoids. <i>Nature Neuroscience</i>. 2021;24:32. doi:<a href=\"https://doi.org/10.1038/s41593-021-00906-5\">10.1038/s41593-021-00906-5</a>","short":"R.A. Samarasinghe, O. Miranda, J.E. Buth, S. Mitchell, I. Ferando, M. Watanabe, A. Kurdian, P. Golshani, K. Plath, W.E. Lowry, J.M. Parent, I. Mody, B.G. Novitch, Nature Neuroscience 24 (2021) 32.","mla":"Samarasinghe, Ranmal A., et al. “Identification of Neural Oscillations and Epileptiform Changes in Human Brain Organoids.” <i>Nature Neuroscience</i>, vol. 24, Springer Nature, 2021, p. 32, doi:<a href=\"https://doi.org/10.1038/s41593-021-00906-5\">10.1038/s41593-021-00906-5</a>.","ista":"Samarasinghe RA, Miranda O, Buth JE, Mitchell S, Ferando I, Watanabe M, Kurdian A, Golshani P, Plath K, Lowry WE, Parent JM, Mody I, Novitch BG. 2021. Identification of neural oscillations and epileptiform changes in human brain organoids. Nature Neuroscience. 24, 32."},"page":"32","language":[{"iso":"eng"}],"OA_place":"publisher","abstract":[{"lang":"eng","text":"Human brain organoids represent a powerful tool for the study of human neurological diseases particularly those that impact brain growth and structure. However, many neurological diseases lack obvious anatomical abnormalities, yet significantly impact neural network functions, raising the question of whether organoids possess sufficient neural network architecture and complexity to model these conditions. Here, we explore the network level functions of brain organoids using calcium sensor imaging and extracellular recording approaches that together reveal the existence of complex oscillatory network behaviors reminiscent of intact brain preparations. We further demonstrate strikingly abnormal epileptiform network activity in organoids derived from a Rett Syndrome patient despite only modest anatomical differences from isogenically matched controls, and rescue with an unconventional neuromodulatory drug Pifithrin-α. Together, these findings provide an essential foundation for the utilization of human brain organoids to study intact and disordered human brain network formation and illustrate their utility in therapeutic discovery."}],"scopus_import":"1","pmid":1,"publication":"Nature Neuroscience","date_created":"2019-11-10T11:23:58Z","month":"08","oa":1,"date_published":"2021-08-23T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]}},{"isi":1,"acknowledgement":"LdA would like to acknowledge the financial support from MIUR-PRIN2017 WZFTZP and VALERE:VAnviteLli pEr la RicErca 2019. FL acknowledges support from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 754411. HJH would like to thank the Agencies CAPES and FUNCAP for financial support.","year":"2021","volume":461,"day":"13","article_type":"original","external_id":{"isi":["000704086300015"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"publisher":"Elsevier","author":[{"full_name":"Lombardi, Fabrizio","first_name":"Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","last_name":"Lombardi","orcid":"0000-0003-2623-5249"},{"first_name":"Oren","full_name":"Shriki, Oren","last_name":"Shriki"},{"last_name":"Herrmann","first_name":"Hans J","full_name":"Herrmann, Hans J"},{"first_name":"Lucilla","full_name":"de Arcangelis, Lucilla","last_name":"de Arcangelis"}],"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1101/2020.02.03.930966","open_access":"1"}],"article_processing_charge":"No","department":[{"_id":"GaTk"}],"title":"Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches","date_updated":"2025-04-14T07:44:02Z","publication_status":"published","type":"journal_article","publication_identifier":{"eissn":["1872-8286"],"issn":["0925-2312"]},"date_published":"2021-05-13T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","date_created":"2020-02-06T16:09:14Z","month":"05","publication":"Neurocomputing","oa":1,"ec_funded":1,"abstract":[{"lang":"eng","text":"Resting-state brain activity is characterized by the presence of neuronal avalanches showing absence of characteristic size. Such evidence has been interpreted in the context of criticality and associated with the normal functioning of the brain. A distinctive attribute of systems at criticality is the presence of long-range correlations. Thus, to verify the hypothesis that the brain operates close to a critical point and consequently assess deviations from criticality for diagnostic purposes, it is of primary importance to robustly and reliably characterize correlations in resting-state brain activity. Recent works focused on the analysis of narrow-band electroencephalography (EEG) and magnetoencephalography (MEG) signal amplitude envelope, showing evidence of long-range temporal correlations (LRTC) in neural oscillations. However, brain activity is a broadband phenomenon, and a significant piece of information useful to precisely discriminate between normal (critical) and pathological behavior (non-critical), may be encoded in the broadband spatio-temporal cortical dynamics. Here we propose to characterize the temporal correlations in the broadband brain activity through the lens of neuronal avalanches. To this end, we consider resting-state EEG and long-term MEG recordings, extract the corresponding neuronal avalanche sequences, and study their temporal correlations. We demonstrate that the broadband resting-state brain activity consistently exhibits long-range power-law correlations in both EEG and MEG recordings, with similar values of the scaling exponents. Importantly, although we observe that the avalanche size distribution depends on scale parameters, scaling exponents characterizing long-range correlations are quite robust. In particular, they are independent of the temporal binning (scale of analysis), indicating that our analysis captures intrinsic characteristics of the underlying dynamics. Because neuronal avalanches constitute a fundamental feature of neural systems with universal characteristics, the proposed approach may serve as a general, systems- and experiment-independent procedure to infer the existence of underlying long-range correlations in extended neural systems, and identify pathological behaviors in the complex spatio-temporal interplay of cortical rhythms."}],"scopus_import":"1","page":"657-666","language":[{"iso":"eng"}],"_id":"7463","intvolume":"       461","oa_version":"Preprint","doi":"10.1016/j.neucom.2020.05.126","citation":{"ama":"Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. <i>Neurocomputing</i>. 2021;461:657-666. doi:<a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">10.1016/j.neucom.2020.05.126</a>","chicago":"Lombardi, Fabrizio, Oren Shriki, Hans J Herrmann, and Lucilla de Arcangelis. “Long-Range Temporal Correlations in the Broadband Resting State Activity of the Human Brain Revealed by Neuronal Avalanches.” <i>Neurocomputing</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">https://doi.org/10.1016/j.neucom.2020.05.126</a>.","ieee":"F. Lombardi, O. Shriki, H. J. Herrmann, and L. de Arcangelis, “Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches,” <i>Neurocomputing</i>, vol. 461. Elsevier, pp. 657–666, 2021.","apa":"Lombardi, F., Shriki, O., Herrmann, H. J., &#38; de Arcangelis, L. (2021). Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. <i>Neurocomputing</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">https://doi.org/10.1016/j.neucom.2020.05.126</a>","mla":"Lombardi, Fabrizio, et al. “Long-Range Temporal Correlations in the Broadband Resting State Activity of the Human Brain Revealed by Neuronal Avalanches.” <i>Neurocomputing</i>, vol. 461, Elsevier, 2021, pp. 657–66, doi:<a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">10.1016/j.neucom.2020.05.126</a>.","ista":"Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. 2021. Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. Neurocomputing. 461, 657–666.","short":"F. Lombardi, O. Shriki, H.J. Herrmann, L. de Arcangelis, Neurocomputing 461 (2021) 657–666."}},{"page":"P25-38.E5","language":[{"iso":"eng"}],"intvolume":"        31","_id":"7551","citation":{"mla":"Fredes Tolorza, Felipe A., et al. “Ventro-Dorsal Hippocampal Pathway Gates Novelty-Induced Contextual Memory Formation.” <i>Current Biology</i>, vol. 31, no. 1, Elsevier, 2021, p. P25–38.E5, doi:<a href=\"https://doi.org/10.1016/j.cub.2020.09.074\">10.1016/j.cub.2020.09.074</a>.","ista":"Fredes Tolorza FA, Silva Sifuentes MA, Koppensteiner P, Kobayashi K, Jösch MA, Shigemoto R. 2021. Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation. Current Biology. 31(1), P25–38.E5.","short":"F.A. Fredes Tolorza, M.A. Silva Sifuentes, P. Koppensteiner, K. Kobayashi, M.A. Jösch, R. Shigemoto, Current Biology 31 (2021) P25–38.E5.","apa":"Fredes Tolorza, F. A., Silva Sifuentes, M. A., Koppensteiner, P., Kobayashi, K., Jösch, M. A., &#38; Shigemoto, R. (2021). Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2020.09.074\">https://doi.org/10.1016/j.cub.2020.09.074</a>","chicago":"Fredes Tolorza, Felipe A, Maria A Silva Sifuentes, Peter Koppensteiner, Kenta Kobayashi, Maximilian A Jösch, and Ryuichi Shigemoto. “Ventro-Dorsal Hippocampal Pathway Gates Novelty-Induced Contextual Memory Formation.” <i>Current Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cub.2020.09.074\">https://doi.org/10.1016/j.cub.2020.09.074</a>.","ieee":"F. A. Fredes Tolorza, M. A. Silva Sifuentes, P. Koppensteiner, K. Kobayashi, M. A. Jösch, and R. Shigemoto, “Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation,” <i>Current Biology</i>, vol. 31, no. 1. Elsevier, p. P25–38.E5, 2021.","ama":"Fredes Tolorza FA, Silva Sifuentes MA, Koppensteiner P, Kobayashi K, Jösch MA, Shigemoto R. Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation. <i>Current Biology</i>. 2021;31(1):P25-38.E5. doi:<a href=\"https://doi.org/10.1016/j.cub.2020.09.074\">10.1016/j.cub.2020.09.074</a>"},"oa_version":"Published Version","doi":"10.1016/j.cub.2020.09.074","date_created":"2020-02-28T10:56:18Z","publication":"Current Biology","month":"01","pmid":1,"oa":1,"ec_funded":1,"abstract":[{"lang":"eng","text":"Novelty facilitates formation of memories. The detection of novelty and storage of contextual memories are both mediated by the hippocampus, yet the mechanisms that link these two functions remain to be defined. Dentate granule cells (GCs) of the dorsal hippocampus fire upon novelty exposure forming engrams of contextual memory. However, their key excitatory inputs from the entorhinal cortex are not responsive to novelty and are insufficient to make dorsal GCs fire reliably. Here we uncover a powerful glutamatergic pathway to dorsal GCs from ventral hippocampal mossy cells (MCs) that relays novelty, and is necessary and sufficient for driving dorsal GCs activation. Furthermore, manipulation of ventral MCs activity bidirectionally regulates novelty-induced contextual memory acquisition. Our results show that ventral MCs activity controls memory formation through an intra-hippocampal interaction mechanism gated by novelty."}],"scopus_import":"1","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/remembering-novelty/"}]},"date_published":"2021-01-11T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"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)","image":"/images/cc_by_nc_nd.png"},"department":[{"_id":"MaJö"},{"_id":"RySh"}],"title":"Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation","article_processing_charge":"No","has_accepted_license":"1","issue":"1","date_updated":"2025-06-12T06:54:22Z","type":"journal_article","publication_status":"published","file":[{"checksum":"b7b9c8bc84a08befce365c675229a7d1","access_level":"open_access","date_updated":"2020-10-19T13:31:28Z","file_name":"2021_CurrentBiology_Fredes.pdf","content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8678","date_created":"2020-10-19T13:31:28Z","file_size":4915964,"success":1}],"ddc":["570"],"publisher":"Elsevier","quality_controlled":"1","author":[{"full_name":"Fredes Tolorza, Felipe A","first_name":"Felipe A","id":"384825DA-F248-11E8-B48F-1D18A9856A87","last_name":"Fredes Tolorza"},{"full_name":"Silva Sifuentes, Maria A","first_name":"Maria A","id":"371B3D6E-F248-11E8-B48F-1D18A9856A87","last_name":"Silva Sifuentes"},{"full_name":"Koppensteiner, Peter","first_name":"Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948","last_name":"Koppensteiner"},{"full_name":"Kobayashi, Kenta","first_name":"Kenta","last_name":"Kobayashi"},{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","last_name":"Jösch","full_name":"Jösch, Maximilian A","first_name":"Maximilian A"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444"}],"article_type":"original","project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020","grant_number":"694539"}],"external_id":{"isi":["000614361000020"],"pmid":["33065009"]},"file_date_updated":"2020-10-19T13:31:28Z","isi":1,"acknowledgement":"We thank Peter Jonas and Peter Somogyi for critically reading the manuscript, Satoshi Kida for helpful discussion, Taijia Makinen for providing the Prox1-creERT2 mouse line, and Hiromu Yawo for the VAMP2-Venus construct. We also thank Vivek Jayaraman, Ph.D.; Rex A. Kerr, Ph.D.; Douglas S. Kim, Ph.D.; Loren L. Looger, Ph.D.; and Karel Svoboda, Ph.D. from the GENIE Project, Janelia Farm Research Campus, Howard Hughes Medical Institute for the viral constructs used for GCaMP6s expression. We also thank Jacqueline Montanaro, Vanessa Zheden, David Kleindienst, and Laura Burnett for technical assistance, as well as Robert Beattie for imaging assistance. This work was supported by a European Research Council Advanced Grant 694539 to R.S.","volume":31,"year":"2021","day":"11"}]