[{"external_id":{"isi":["000490183000068"],"pmid":["31575745"]},"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"doi":"10.1073/pnas.1911892116","date_published":"2019-10-15T00:00:00Z","isi":1,"month":"10","type":"journal_article","page":"21274-21284","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","abstract":[{"text":"Plasmodesmata (PD) are plant-specific membrane-lined channels that create cytoplasmic and membrane continuities between adjacent cells, thereby facilitating cell–cell communication and virus movement. Plant cells have evolved diverse mechanisms to regulate PD plasticity in response to numerous environmental stimuli. In particular, during defense against plant pathogens, the defense hormone, salicylic acid (SA), plays a crucial role in the regulation of PD permeability in a callose-dependent manner. Here, we uncover a mechanism by which plants restrict the spreading of virus and PD cargoes using SA signaling by increasing lipid order and closure of PD. We showed that exogenous SA application triggered the compartmentalization of lipid raft nanodomains through a modulation of the lipid raft-regulatory protein, Remorin (REM). Genetic studies, superresolution imaging, and transmission electron microscopy observation together demonstrated that Arabidopsis REM1.2 and REM1.3 are crucial for plasma membrane nanodomain assembly to control PD aperture and functionality. In addition, we also found that a 14-3-3 epsilon protein modulates REM clustering and membrane nanodomain compartmentalization through its direct interaction with REM proteins. This study unveils a molecular mechanism by which the key plant defense hormone, SA, triggers membrane lipid nanodomain reorganization, thereby regulating PD closure to impede virus spreading.","lang":"eng"}],"year":"2019","status":"public","title":"Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization","has_accepted_license":"1","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"file":[{"file_id":"7012","file_name":"2019_PNAS_Huang.pdf","checksum":"258c666bc6253eab81961f61169eefae","relation":"main_file","date_created":"2019-11-13T08:22:28Z","access_level":"open_access","creator":"dernst","content_type":"application/pdf","date_updated":"2020-07-14T12:47:46Z","file_size":3287466}],"_id":"6999","citation":{"apa":"Huang, D., Sun, Y., Ma, Z., Ke, M., Cui, Y., Chen, Z., … Chen, X. (2019). Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1911892116\">https://doi.org/10.1073/pnas.1911892116</a>","ama":"Huang D, Sun Y, Ma Z, et al. Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2019;116(42):21274-21284. doi:<a href=\"https://doi.org/10.1073/pnas.1911892116\">10.1073/pnas.1911892116</a>","ieee":"D. Huang <i>et al.</i>, “Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 116, no. 42. National Academy of Sciences, pp. 21274–21284, 2019.","short":"D. Huang, Y. Sun, Z. Ma, M. Ke, Y. Cui, Z. Chen, C. Chen, C. Ji, T. Tran, L. Yang, S. Lam, Y. Han, G. Shu, J. Friml, Y. Miao, L. Jiang, X. Chen, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 21274–21284.","ista":"Huang D, Sun Y, Ma Z, Ke M, Cui Y, Chen Z, Chen C, Ji C, Tran T, Yang L, Lam S, Han Y, Shu G, Friml J, Miao Y, Jiang L, Chen X. 2019. Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of the National Academy of Sciences of the United States of America. 116(42), 21274–21284.","chicago":"Huang, D, Y Sun, Z Ma, M Ke, Y Cui, Z Chen, C Chen, et al. “Salicylic Acid-Mediated Plasmodesmal Closure via Remorin-Dependent Lipid Organization.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2019. <a href=\"https://doi.org/10.1073/pnas.1911892116\">https://doi.org/10.1073/pnas.1911892116</a>.","mla":"Huang, D., et al. “Salicylic Acid-Mediated Plasmodesmal Closure via Remorin-Dependent Lipid Organization.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 116, no. 42, National Academy of Sciences, 2019, pp. 21274–84, doi:<a href=\"https://doi.org/10.1073/pnas.1911892116\">10.1073/pnas.1911892116</a>."},"day":"15","quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","oa":1,"scopus_import":"1","article_processing_charge":"No","department":[{"_id":"JiFr"}],"author":[{"first_name":"D","last_name":"Huang","full_name":"Huang, D"},{"last_name":"Sun","full_name":"Sun, Y","first_name":"Y"},{"last_name":"Ma","full_name":"Ma, Z","first_name":"Z"},{"first_name":"M","last_name":"Ke","full_name":"Ke, M"},{"first_name":"Y","full_name":"Cui, Y","last_name":"Cui"},{"last_name":"Chen","full_name":"Chen, Z","first_name":"Z"},{"last_name":"Chen","full_name":"Chen, C","first_name":"C"},{"last_name":"Ji","full_name":"Ji, C","first_name":"C"},{"first_name":"TM","full_name":"Tran, TM","last_name":"Tran"},{"first_name":"L","full_name":"Yang, L","last_name":"Yang"},{"last_name":"Lam","full_name":"Lam, SM","first_name":"SM"},{"full_name":"Han, Y","last_name":"Han","first_name":"Y"},{"last_name":"Shu","full_name":"Shu, G","first_name":"G"},{"last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"full_name":"Miao, Y","last_name":"Miao","first_name":"Y"},{"last_name":"Jiang","full_name":"Jiang, L","first_name":"L"},{"first_name":"X","full_name":"Chen, X","last_name":"Chen"}],"language":[{"iso":"eng"}],"issue":"42","intvolume":"       116","fulldoi":"https://doi.org/10.1073/pnas.1911892116","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1073/pnas.2004738117"}]},"date_updated":"2025-05-14T10:56:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-11-12T11:42:05Z","oa_version":"Published Version","article_type":"original","pmid":1,"publisher":"National Academy of Sciences","ddc":["580"],"file_date_updated":"2020-07-14T12:47:46Z","volume":116},{"doi":"10.1007/s40314-019-0955-9","date_published":"2019-12-01T00:00:00Z","arxiv":1,"external_id":{"isi":["000488973100005"],"arxiv":["2101.09081"]},"publication_identifier":{"eissn":["1807-0302"],"issn":["2238-3603"]},"main_file_link":[{"url":"https://doi.org/10.1007/s40314-019-0955-9","open_access":"1"}],"type":"journal_article","ec_funded":1,"isi":1,"month":"12","abstract":[{"text":"The main contributions of this paper are the proposition and the convergence analysis of a class of inertial projection-type algorithm for solving variational inequality problems in real Hilbert spaces where the underline operator is monotone and uniformly continuous. We carry out a unified analysis of the proposed method under very mild assumptions. In particular, weak convergence of the generated sequence is established and nonasymptotic O(1 / n) rate of convergence is established, where n denotes the iteration counter. We also present some experimental results to illustrate the profits gained by introducing the inertial extrapolation steps.","lang":"eng"}],"year":"2019","status":"public","title":"Convergence analysis of projection method for variational inequalities","corr_author":"1","_id":"7000","day":"01","citation":{"ama":"Shehu Y, Iyiola OS, Li X-H, Dong Q-L. Convergence analysis of projection method for variational inequalities. <i>Computational and Applied Mathematics</i>. 2019;38(4). doi:<a href=\"https://doi.org/10.1007/s40314-019-0955-9\">10.1007/s40314-019-0955-9</a>","ieee":"Y. Shehu, O. S. Iyiola, X.-H. Li, and Q.-L. Dong, “Convergence analysis of projection method for variational inequalities,” <i>Computational and Applied Mathematics</i>, vol. 38, no. 4. Springer Nature, 2019.","apa":"Shehu, Y., Iyiola, O. S., Li, X.-H., &#38; Dong, Q.-L. (2019). Convergence analysis of projection method for variational inequalities. <i>Computational and Applied Mathematics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40314-019-0955-9\">https://doi.org/10.1007/s40314-019-0955-9</a>","chicago":"Shehu, Yekini, Olaniyi S. Iyiola, Xiao-Huan Li, and Qiao-Li Dong. “Convergence Analysis of Projection Method for Variational Inequalities.” <i>Computational and Applied Mathematics</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/s40314-019-0955-9\">https://doi.org/10.1007/s40314-019-0955-9</a>.","mla":"Shehu, Yekini, et al. “Convergence Analysis of Projection Method for Variational Inequalities.” <i>Computational and Applied Mathematics</i>, vol. 38, no. 4, 161, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1007/s40314-019-0955-9\">10.1007/s40314-019-0955-9</a>.","short":"Y. Shehu, O.S. Iyiola, X.-H. Li, Q.-L. Dong, Computational and Applied Mathematics 38 (2019).","ista":"Shehu Y, Iyiola OS, Li X-H, Dong Q-L. 2019. Convergence analysis of projection method for variational inequalities. Computational and Applied Mathematics. 38(4), 161."},"publication":"Computational and Applied Mathematics","quality_controlled":"1","publication_status":"published","has_accepted_license":"1","oa":1,"scopus_import":"1","article_processing_charge":"No","author":[{"orcid":"0000-0001-9224-7139","first_name":"Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","full_name":"Shehu, Yekini","last_name":"Shehu"},{"first_name":"Olaniyi S.","last_name":"Iyiola","full_name":"Iyiola, Olaniyi S."},{"first_name":"Xiao-Huan","last_name":"Li","full_name":"Li, Xiao-Huan"},{"first_name":"Qiao-Li","full_name":"Dong, Qiao-Li","last_name":"Dong"}],"department":[{"_id":"VlKo"}],"article_number":"161","intvolume":"        38","issue":"4","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"}],"fulldoi":"https://doi.org/10.1007/s40314-019-0955-9","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-11-12T12:41:44Z","date_updated":"2024-11-04T13:52:44Z","ddc":["510","515","518"],"volume":38,"oa_version":"Published Version","article_type":"original","publisher":"Springer Nature"},{"month":"07","isi":1,"ec_funded":1,"type":"journal_article","publication_identifier":{"issn":["0730-0301"]},"external_id":{"isi":["000475740600011"]},"date_published":"2019-07-01T00:00:00Z","doi":"10.1145/3306346.3323009","publication_status":"published","publication":"ACM Transactions on Graphics","quality_controlled":"1","citation":{"apa":"Kondapaneni, I., Vevoda, P., Grittmann, P., Skrivan, T., Slusallek, P., &#38; Křivánek, J. (2019). Optimal multiple importance sampling. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3306346.3323009\">https://doi.org/10.1145/3306346.3323009</a>","ama":"Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J. Optimal multiple importance sampling. <i>ACM Transactions on Graphics</i>. 2019;38(4). doi:<a href=\"https://doi.org/10.1145/3306346.3323009\">10.1145/3306346.3323009</a>","ieee":"I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, and J. Křivánek, “Optimal multiple importance sampling,” <i>ACM Transactions on Graphics</i>, vol. 38, no. 4. ACM, 2019.","short":"I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, J. Křivánek, ACM Transactions on Graphics 38 (2019).","ista":"Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J. 2019. Optimal multiple importance sampling. ACM Transactions on Graphics. 38(4), 37.","mla":"Kondapaneni, Ivo, et al. “Optimal Multiple Importance Sampling.” <i>ACM Transactions on Graphics</i>, vol. 38, no. 4, 37, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3306346.3323009\">10.1145/3306346.3323009</a>.","chicago":"Kondapaneni, Ivo, Petr Vevoda, Pascal Grittmann, Tomas Skrivan, Philipp Slusallek, and Jaroslav Křivánek. “Optimal Multiple Importance Sampling.” <i>ACM Transactions on Graphics</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3306346.3323009\">https://doi.org/10.1145/3306346.3323009</a>."},"day":"01","_id":"7002","status":"public","title":"Optimal multiple importance sampling","abstract":[{"text":"Multiple Importance Sampling (MIS) is a key technique for achieving robustness of Monte Carlo estimators in computer graphics and other fields. We derive optimal weighting functions for MIS that provably minimize the variance of an MIS estimator, given a set of sampling techniques. We show that the resulting variance reduction over the balance heuristic can be higher than predicted by the variance bounds derived by Veach and Guibas, who assumed only non-negative weights in their proof. We theoretically analyze the variance of the optimal MIS weights and show the relation to the variance of the balance heuristic. Furthermore, we establish a connection between the new weighting functions and control variates as previously applied to mixture sampling. We apply the new optimal weights to integration problems in light transport and show that they allow for new design considerations when choosing the appropriate sampling techniques for a given integration problem.","lang":"eng"}],"year":"2019","language":[{"iso":"eng"}],"project":[{"grant_number":"642841","name":"Distributed 3D Object Design","call_identifier":"H2020","_id":"2508E324-B435-11E9-9278-68D0E5697425"}],"fulldoi":"https://doi.org/10.1145/3306346.3323009","intvolume":"        38","issue":"4","article_number":"37","department":[{"_id":"ChWo"}],"author":[{"full_name":"Kondapaneni, Ivo","last_name":"Kondapaneni","first_name":"Ivo"},{"first_name":"Petr","full_name":"Vevoda, Petr","last_name":"Vevoda"},{"first_name":"Pascal","last_name":"Grittmann","full_name":"Grittmann, Pascal"},{"id":"486A5A46-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","last_name":"Skrivan","full_name":"Skrivan, Tomas"},{"first_name":"Philipp","last_name":"Slusallek","full_name":"Slusallek, Philipp"},{"last_name":"Křivánek","full_name":"Křivánek, Jaroslav","first_name":"Jaroslav"}],"article_processing_charge":"No","scopus_import":"1","publisher":"ACM","article_type":"original","oa_version":"None","volume":38,"date_updated":"2025-03-31T15:58:17Z","date_created":"2019-11-12T13:05:40Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"ddc":["570"],"file_date_updated":"2020-07-14T12:47:47Z","volume":151,"article_type":"original","oa_version":"Published Version","publisher":"Wiley","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-11-12T14:37:08Z","date_updated":"2023-08-30T07:21:50Z","intvolume":"       151","issue":"5","fulldoi":"https://doi.org/10.1111/jnc.14862","language":[{"iso":"eng"}],"oa":1,"scopus_import":"1","department":[{"_id":"SiHi"}],"article_processing_charge":"No","author":[{"orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T","last_name":"Cheung","full_name":"Cheung, Giselle T"},{"full_name":"Cousin, Michael A.","last_name":"Cousin","first_name":"Michael A."}],"_id":"7005","quality_controlled":"1","publication":"Journal of Neurochemistry","citation":{"short":"G.T. Cheung, M.A. Cousin, Journal of Neurochemistry 151 (2019) 570–583.","ista":"Cheung GT, Cousin MA. 2019. Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. Journal of Neurochemistry. 151(5), 570–583.","mla":"Cheung, Giselle T., and Michael A. Cousin. “Synaptic Vesicle Generation from Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent Dynamin–Syndapin Interaction.” <i>Journal of Neurochemistry</i>, vol. 151, no. 5, Wiley, 2019, pp. 570–83, doi:<a href=\"https://doi.org/10.1111/jnc.14862\">10.1111/jnc.14862</a>.","chicago":"Cheung, Giselle T, and Michael A. Cousin. “Synaptic Vesicle Generation from Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent Dynamin–Syndapin Interaction.” <i>Journal of Neurochemistry</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/jnc.14862\">https://doi.org/10.1111/jnc.14862</a>.","apa":"Cheung, G. T., &#38; Cousin, M. A. (2019). Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. <i>Journal of Neurochemistry</i>. Wiley. <a href=\"https://doi.org/10.1111/jnc.14862\">https://doi.org/10.1111/jnc.14862</a>","ama":"Cheung GT, Cousin MA. Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. <i>Journal of Neurochemistry</i>. 2019;151(5):570-583. doi:<a href=\"https://doi.org/10.1111/jnc.14862\">10.1111/jnc.14862</a>","ieee":"G. T. Cheung and M. A. Cousin, “Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction,” <i>Journal of Neurochemistry</i>, vol. 151, no. 5. Wiley, pp. 570–583, 2019."},"day":"01","has_accepted_license":"1","publication_status":"published","file":[{"file_size":4334962,"date_updated":"2020-07-14T12:47:47Z","access_level":"open_access","date_created":"2020-02-05T10:30:02Z","creator":"dernst","content_type":"application/pdf","relation":"main_file","checksum":"ec1fb2aebb874009bc309adaada6e1d7","file_id":"7452","file_name":"2019_JournNeurochemistry_Cheung.pdf"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"license":"https://creativecommons.org/licenses/by/4.0/","year":"2019","abstract":[{"text":"Activity-dependent bulk endocytosis generates synaptic vesicles (SVs) during intense neuronal activity via a two-step process. First, bulk endosomes are formed direct from the plasma membrane from which SVs are then generated. SV generation from bulk endosomes requires the efflux of previously accumulated calcium and activation of the protein phosphatase calcineurin. However, it is still unknown how calcineurin mediates SV generation. We addressed this question using a series of acute interventions that decoupled the generation of SVs from bulk endosomes in rat primary neuronal culture. This was achieved by either disruption of protein–protein interactions via delivery of competitive peptides, or inhibition of enzyme activity by known inhibitors. SV generation was monitored using either a morphological horseradish peroxidase assay or an optical assay that monitors the replenishment of the reserve SV pool. We found that SV generation was inhibited by, (i) peptides that disrupt calcineurin interactions, (ii) an inhibitor of dynamin I GTPase activity and (iii) peptides that disrupt the phosphorylation-dependent dynamin I–syndapin I interaction. Peptides that disrupted syndapin I interactions with eps15 homology domain-containing proteins had no effect. This revealed that (i) calcineurin must be localized at bulk endosomes to mediate its effect, (ii) dynamin I GTPase activity is essential for SV fission and (iii) the calcineurin-dependent interaction between dynamin I and syndapin I is essential for SV generation. We therefore propose that a calcineurin-dependent dephosphorylation cascade that requires both dynamin I GTPase and syndapin I lipid-deforming activity is essential for SV generation from bulk endosomes.","lang":"eng"}],"title":"Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction","status":"public","type":"journal_article","page":"570-583","month":"12","isi":1,"doi":"10.1111/jnc.14862","date_published":"2019-12-01T00:00:00Z","external_id":{"pmid":["31479508"],"isi":["000490703100001"]},"publication_identifier":{"eissn":["1471-4159"],"issn":["0022-3042"]}},{"corr_author":"1","title":"A new coding paradigm for the primitive relay channel","status":"public","abstract":[{"lang":"eng","text":"We consider the primitive relay channel, where the source sends a message to the relay and to the destination, and the relay helps the communication by transmitting an additional message to the destination via a separate channel. Two well-known coding techniques have been introduced for this setting: decode-and-forward and compress-and-forward. In decode-and-forward, the relay completely decodes the message and sends some information to the destination; in compress-and-forward, the relay does not decode, and it sends a compressed version of the received signal to the destination using Wyner–Ziv coding. In this paper, we present a novel coding paradigm that provides an improved achievable rate for the primitive relay channel. The idea is to combine compress-and-forward and decode-and-forward via a chaining construction. We transmit over pairs of blocks: in the first block, we use compress-and-forward; and, in the second block, we use decode-and-forward. More specifically, in the first block, the relay does not decode, it compresses the received signal via Wyner–Ziv, and it sends only part of the compression to the destination. In the second block, the relay completely decodes the message, it sends some information to the destination, and it also sends the remaining part of the compression coming from the first block. By doing so, we are able to strictly outperform both compress-and-forward and decode-and-forward. Note that the proposed coding scheme can be implemented with polar codes. As such, it has the typical attractive properties of polar coding schemes, namely, quasi-linear encoding and decoding complexity, and error probability that decays at super-polynomial speed. As a running example, we take into account the special case of the erasure relay channel, and we provide a comparison between the rates achievable by our proposed scheme and the existing upper and lower bounds."}],"year":"2019","file":[{"file_name":"2019_Algorithms_Mondelli.pdf","file_id":"7008","relation":"main_file","checksum":"267756d8f9db572f496cd1663c89d59a","creator":"dernst","content_type":"application/pdf","access_level":"open_access","date_created":"2019-11-12T14:48:45Z","file_size":696791,"date_updated":"2020-07-14T12:47:47Z"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published","has_accepted_license":"1","quality_controlled":"1","publication":"Algorithms","citation":{"ista":"Mondelli M, Hassani SH, Urbanke R. 2019. A new coding paradigm for the primitive relay channel. Algorithms. 12(10), 218.","short":"M. Mondelli, S.H. Hassani, R. Urbanke, Algorithms 12 (2019).","chicago":"Mondelli, Marco, S. Hamed Hassani, and Rüdiger Urbanke. “A New Coding Paradigm for the Primitive Relay Channel.” <i>Algorithms</i>. MDPI, 2019. <a href=\"https://doi.org/10.3390/a12100218\">https://doi.org/10.3390/a12100218</a>.","mla":"Mondelli, Marco, et al. “A New Coding Paradigm for the Primitive Relay Channel.” <i>Algorithms</i>, vol. 12, no. 10, 218, MDPI, 2019, doi:<a href=\"https://doi.org/10.3390/a12100218\">10.3390/a12100218</a>.","apa":"Mondelli, M., Hassani, S. H., &#38; Urbanke, R. (2019). A new coding paradigm for the primitive relay channel. <i>Algorithms</i>. MDPI. <a href=\"https://doi.org/10.3390/a12100218\">https://doi.org/10.3390/a12100218</a>","ieee":"M. Mondelli, S. H. Hassani, and R. Urbanke, “A new coding paradigm for the primitive relay channel,” <i>Algorithms</i>, vol. 12, no. 10. MDPI, 2019.","ama":"Mondelli M, Hassani SH, Urbanke R. A new coding paradigm for the primitive relay channel. <i>Algorithms</i>. 2019;12(10). doi:<a href=\"https://doi.org/10.3390/a12100218\">10.3390/a12100218</a>"},"day":"18","_id":"7007","publication_identifier":{"issn":["1999-4893"]},"external_id":{"arxiv":["1801.03153"]},"arxiv":1,"doi":"10.3390/a12100218","date_published":"2019-10-18T00:00:00Z","month":"10","type":"journal_article","date_updated":"2024-10-09T20:59:05Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"6675"}]},"date_created":"2019-11-12T14:46:19Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"MDPI","article_type":"original","oa_version":"Published Version","volume":12,"file_date_updated":"2020-07-14T12:47:47Z","ddc":["510"],"article_number":"218","author":[{"full_name":"Mondelli, Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"full_name":"Hassani, S. Hamed","last_name":"Hassani","first_name":"S. Hamed"},{"last_name":"Urbanke","full_name":"Urbanke, Rüdiger","first_name":"Rüdiger"}],"department":[{"_id":"MaMo"}],"scopus_import":1,"oa":1,"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.3390/a12100218","issue":"10","intvolume":"        12"},{"citation":{"ama":"Yamada K, Sixt MK. Mechanisms of 3D cell migration. <i>Nature Reviews Molecular Cell Biology</i>. 2019;20(12):738–752. doi:<a href=\"https://doi.org/10.1038/s41580-019-0172-9\">10.1038/s41580-019-0172-9</a>","ieee":"K. Yamada and M. K. Sixt, “Mechanisms of 3D cell migration,” <i>Nature Reviews Molecular Cell Biology</i>, vol. 20, no. 12. Springer Nature, pp. 738–752, 2019.","apa":"Yamada, K., &#38; Sixt, M. K. (2019). Mechanisms of 3D cell migration. <i>Nature Reviews Molecular Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41580-019-0172-9\">https://doi.org/10.1038/s41580-019-0172-9</a>","mla":"Yamada, KM, and Michael K. Sixt. “Mechanisms of 3D Cell Migration.” <i>Nature Reviews Molecular Cell Biology</i>, vol. 20, no. 12, Springer Nature, 2019, pp. 738–752, doi:<a href=\"https://doi.org/10.1038/s41580-019-0172-9\">10.1038/s41580-019-0172-9</a>.","chicago":"Yamada, KM, and Michael K Sixt. “Mechanisms of 3D Cell Migration.” <i>Nature Reviews Molecular Cell Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41580-019-0172-9\">https://doi.org/10.1038/s41580-019-0172-9</a>.","ista":"Yamada K, Sixt MK. 2019. Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. 20(12), 738–752.","short":"K. Yamada, M.K. Sixt, Nature Reviews Molecular Cell Biology 20 (2019) 738–752."},"day":"01","publication":"Nature Reviews Molecular Cell Biology","quality_controlled":"1","_id":"7009","publication_status":"published","title":"Mechanisms of 3D cell migration","status":"public","year":"2019","abstract":[{"lang":"eng","text":"Cell migration is essential for physiological processes as diverse as development, immune defence and wound healing. It is also a hallmark of cancer malignancy. Thousands of publications have elucidated detailed molecular and biophysical mechanisms of cultured cells migrating on flat, 2D substrates of glass and plastic. However, much less is known about how cells successfully navigate the complex 3D environments of living tissues. In these more complex, native environments, cells use multiple modes of migration, including mesenchymal, amoeboid, lobopodial and collective, and these are governed by the local extracellular microenvironment, specific modalities of Rho GTPase signalling and non- muscle myosin contractility. Migration through 3D environments is challenging because it requires the cell to squeeze through complex or dense extracellular structures. Doing so requires specific cellular adaptations to mechanical features of the extracellular matrix (ECM) or its remodelling. In addition, besides navigating through diverse ECM environments and overcoming extracellular barriers, cells often interact with neighbouring cells and tissues through physical and signalling interactions. Accordingly, cells need to call on an impressively wide diversity of mechanisms to meet these challenges. This Review examines how cells use both classical and novel mechanisms of locomotion as they traverse challenging 3D matrices and cellular environments. It focuses on principles rather than details of migratory mechanisms and draws comparisons between 1D, 2D and 3D migration."}],"page":"738–752","type":"journal_article","isi":1,"month":"12","date_published":"2019-12-01T00:00:00Z","doi":"10.1038/s41580-019-0172-9","publication_identifier":{"issn":["1471-0072"],"eissn":["1471-0080"]},"external_id":{"isi":["000497966900007"],"pmid":["31582855"]},"volume":20,"pmid":1,"publisher":"Springer Nature","oa_version":"None","article_type":"review","date_created":"2019-11-12T14:54:42Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-30T07:22:20Z","fulldoi":"https://doi.org/10.1038/s41580-019-0172-9","issue":"12","intvolume":"        20","language":[{"iso":"eng"}],"author":[{"full_name":"Yamada, KM","last_name":"Yamada","first_name":"KM"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"department":[{"_id":"MiSi"}],"article_processing_charge":"No","scopus_import":"1"},{"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1117/12.2527058","intvolume":"     11076","article_number":"110760V","article_processing_charge":"No","department":[{"_id":"MaLo"}],"author":[{"full_name":"Davies, Heather S.","last_name":"Davies","first_name":"Heather S."},{"last_name":"Baranova","full_name":"Baranova, Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","first_name":"Natalia S.","orcid":"0000-0002-3086-9124"},{"first_name":"Nouha","full_name":"El Amri, Nouha","last_name":"El Amri"},{"first_name":"Liliane","full_name":"Coche-Guérente, Liliane","last_name":"Coche-Guérente"},{"last_name":"Verdier","full_name":"Verdier, Claude","first_name":"Claude"},{"full_name":"Bureau, Lionel","last_name":"Bureau","first_name":"Lionel"},{"first_name":"Ralf P.","last_name":"Richter","full_name":"Richter, Ralf P."},{"first_name":"Delphine","last_name":"Débarre","full_name":"Débarre, Delphine"}],"scopus_import":"1","oa":1,"publisher":"SPIE","oa_version":"Published Version","volume":11076,"ddc":["570"],"date_updated":"2026-06-18T19:16:05Z","date_created":"2019-11-12T15:10:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"month":"07","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-02368135/file/110760V.pdf","open_access":"1"}],"type":"conference","publication_identifier":{"isbn":["9781510628458"],"issn":["1605-7422"]},"external_id":{"isi":["000535353000023"]},"doi":"10.1117/12.2527058","date_published":"2019-07-22T00:00:00Z","publication_status":"published","day":"22","citation":{"ama":"Davies HS, Baranova NS, El Amri N, et al. Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. In: <i>Advances in Microscopic Imaging II</i>. Vol 11076. SPIE; 2019. doi:<a href=\"https://doi.org/10.1117/12.2527058\">10.1117/12.2527058</a>","ieee":"H. S. Davies <i>et al.</i>, “Blood cell-vessel wall interactions probed by reflection interference contrast microscopy,” in <i>Advances in Microscopic Imaging II</i>, Munich, Germany, 2019, vol. 11076.","apa":"Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C., Bureau, L., … Débarre, D. (2019). Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. In <i>Advances in Microscopic Imaging II</i> (Vol. 11076). Munich, Germany: SPIE. <a href=\"https://doi.org/10.1117/12.2527058\">https://doi.org/10.1117/12.2527058</a>","mla":"Davies, Heather S., et al. “Blood Cell-Vessel Wall Interactions Probed by Reflection Interference Contrast Microscopy.” <i>Advances in Microscopic Imaging II</i>, vol. 11076, 110760V, SPIE, 2019, doi:<a href=\"https://doi.org/10.1117/12.2527058\">10.1117/12.2527058</a>.","chicago":"Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente, Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “Blood Cell-Vessel Wall Interactions Probed by Reflection Interference Contrast Microscopy.” In <i>Advances in Microscopic Imaging II</i>, Vol. 11076. SPIE, 2019. <a href=\"https://doi.org/10.1117/12.2527058\">https://doi.org/10.1117/12.2527058</a>.","short":"H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L. Bureau, R.P. Richter, D. Débarre, in:, Advances in Microscopic Imaging II, SPIE, 2019.","ista":"Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L, Richter RP, Débarre D. 2019. Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. Advances in Microscopic Imaging II. European Conferences on Biomedical Optics vol. 11076, 110760V."},"publication":"Advances in Microscopic Imaging II","quality_controlled":"1","_id":"7010","conference":{"start_date":"2019-06-26","location":"Munich, Germany","name":"European Conferences on Biomedical Optics","end_date":"2019-06-27"},"status":"public","title":"Blood cell-vessel wall interactions probed by reflection interference contrast microscopy","abstract":[{"text":"Numerous biophysical questions require the quantification of short-range interactions between (functionalized) surfaces and synthetic or biological objects such as cells. Here, we present an original, custom built setup for reflection interference contrast microscopy that can assess distances between a substrate and a flowing object at high speed with nanometric accuracy. We demonstrate its use to decipher the complex biochemical and mechanical interplay regulating blood cell homing at the vessel wall in the microcirculation using an in vitro approach. We show that in the absence of specific biochemical interactions, flowing cells are repelled from the soft layer lining the vessel wall, contributing to red blood cell repulsion in vivo. In contrast, this so-called glycocalyx stabilizes rolling of cells under flow in the presence of a specific receptor naturally present on activated leucocytes and a number of cancer cell lines.","lang":"eng"}],"year":"2019"},{"intvolume":"       100","issue":"13","fulldoi":"https://doi.org/10.1103/physrevb.100.134504","language":[{"iso":"eng"}],"oa":1,"scopus_import":"1","author":[{"first_name":"Tuure","full_name":"Orell, Tuure","last_name":"Orell"},{"full_name":"Michailidis, Alexios","last_name":"Michailidis","orcid":"0000-0002-8443-1064","first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2399-5827","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","last_name":"Serbyn"},{"last_name":"Silveri","full_name":"Silveri, Matti","first_name":"Matti"}],"article_processing_charge":"No","department":[{"_id":"MaSe"}],"article_number":"134504","volume":100,"article_type":"original","oa_version":"Preprint","publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-11-13T08:25:48Z","date_updated":"2024-02-28T13:13:13Z","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.04043"}],"month":"10","isi":1,"date_published":"2019-10-01T00:00:00Z","doi":"10.1103/physrevb.100.134504","arxiv":1,"external_id":{"arxiv":["1907.04043"],"isi":["000489036500004"]},"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"_id":"7013","quality_controlled":"1","publication":"Physical Review B","citation":{"short":"T. Orell, A. Michailidis, M. Serbyn, M. Silveri, Physical Review B 100 (2019).","ista":"Orell T, Michailidis A, Serbyn M, Silveri M. 2019. Probing the many-body localization phase transition with superconducting circuits. Physical Review B. 100(13), 134504.","mla":"Orell, Tuure, et al. “Probing the Many-Body Localization Phase Transition with Superconducting Circuits.” <i>Physical Review B</i>, vol. 100, no. 13, 134504, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/physrevb.100.134504\">10.1103/physrevb.100.134504</a>.","chicago":"Orell, Tuure, Alexios Michailidis, Maksym Serbyn, and Matti Silveri. “Probing the Many-Body Localization Phase Transition with Superconducting Circuits.” <i>Physical Review B</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/physrevb.100.134504\">https://doi.org/10.1103/physrevb.100.134504</a>.","apa":"Orell, T., Michailidis, A., Serbyn, M., &#38; Silveri, M. (2019). Probing the many-body localization phase transition with superconducting circuits. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.100.134504\">https://doi.org/10.1103/physrevb.100.134504</a>","ama":"Orell T, Michailidis A, Serbyn M, Silveri M. Probing the many-body localization phase transition with superconducting circuits. <i>Physical Review B</i>. 2019;100(13). doi:<a href=\"https://doi.org/10.1103/physrevb.100.134504\">10.1103/physrevb.100.134504</a>","ieee":"T. Orell, A. Michailidis, M. Serbyn, and M. Silveri, “Probing the many-body localization phase transition with superconducting circuits,” <i>Physical Review B</i>, vol. 100, no. 13. American Physical Society, 2019."},"day":"01","publication_status":"published","abstract":[{"text":"Chains of superconducting circuit devices provide a natural platform for studies of synthetic bosonic quantum matter. Motivated by the recent experimental progress in realizing disordered and interacting chains of superconducting transmon devices, we study the bosonic many-body localization phase transition using the methods of exact diagonalization as well as matrix product state dynamics. We estimate the location of transition separating the ergodic and the many-body localized phases as a function of the disorder strength and the many-body on-site interaction strength. The main difference between the bosonic model realized by superconducting circuits and similar fermionic model is that the effect of the on-site interaction is stronger due to the possibility of multiple excitations occupying the same site. The phase transition is found to be robust upon including longer-range hopping and interaction terms present in the experiments. Furthermore, we calculate experimentally relevant local observables and show that their temporal fluctuations can be used to distinguish between the dynamics of Anderson insulator, many-body localization, and delocalized phases. While we consider unitary dynamics, neglecting the effects of dissipation, decoherence, and measurement back action, the timescales on which the dynamics is unitary are sufficient for observation of characteristic dynamics in the many-body localized phase. Moreover, the experimentally available disorder strength and interactions allow for tuning the many-body localization phase transition, thus making the arrays of superconducting circuit devices a promising platform for exploring localization physics and phase transition.","lang":"eng"}],"year":"2019","status":"public","title":"Probing the many-body localization phase transition with superconducting circuits"},{"language":[{"iso":"eng"}],"issue":"3","intvolume":"       100","project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"fulldoi":"https://doi.org/10.1103/physrevb.100.035127","article_number":"035127","scopus_import":"1","oa":1,"article_processing_charge":"No","author":[{"last_name":"Lewin","full_name":"Lewin, Mathieu","first_name":"Mathieu"},{"first_name":"Elliott H.","last_name":"Lieb","full_name":"Lieb, Elliott H."},{"last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"department":[{"_id":"RoSe"}],"article_type":"original","oa_version":"Preprint","publisher":"American Physical Society","volume":100,"date_updated":"2025-04-14T07:27:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-11-13T08:41:48Z","month":"07","isi":1,"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.09138"}],"ec_funded":1,"external_id":{"isi":["000477888200001"],"arxiv":["1905.09138"]},"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"doi":"10.1103/physrevb.100.035127","date_published":"2019-07-25T00:00:00Z","arxiv":1,"publication_status":"published","_id":"7015","publication":"Physical Review B","quality_controlled":"1","citation":{"apa":"Lewin, M., Lieb, E. H., &#38; Seiringer, R. (2019). Floating Wigner crystal with no boundary charge fluctuations. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.100.035127\">https://doi.org/10.1103/physrevb.100.035127</a>","ama":"Lewin M, Lieb EH, Seiringer R. Floating Wigner crystal with no boundary charge fluctuations. <i>Physical Review B</i>. 2019;100(3). doi:<a href=\"https://doi.org/10.1103/physrevb.100.035127\">10.1103/physrevb.100.035127</a>","ieee":"M. Lewin, E. H. Lieb, and R. Seiringer, “Floating Wigner crystal with no boundary charge fluctuations,” <i>Physical Review B</i>, vol. 100, no. 3. American Physical Society, 2019.","short":"M. Lewin, E.H. Lieb, R. Seiringer, Physical Review B 100 (2019).","ista":"Lewin M, Lieb EH, Seiringer R. 2019. Floating Wigner crystal with no boundary charge fluctuations. Physical Review B. 100(3), 035127.","chicago":"Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “Floating Wigner Crystal with No Boundary Charge Fluctuations.” <i>Physical Review B</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/physrevb.100.035127\">https://doi.org/10.1103/physrevb.100.035127</a>.","mla":"Lewin, Mathieu, et al. “Floating Wigner Crystal with No Boundary Charge Fluctuations.” <i>Physical Review B</i>, vol. 100, no. 3, 035127, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/physrevb.100.035127\">10.1103/physrevb.100.035127</a>."},"day":"25","abstract":[{"lang":"eng","text":"We modify the \"floating crystal\" trial state for the classical homogeneous electron gas (also known as jellium), in order to suppress the boundary charge fluctuations that are known to lead to a macroscopic increase of the energy. The argument is to melt a thin layer of the crystal close to the boundary and consequently replace it by an incompressible fluid. With the aid of this trial state we show that three different definitions of the ground-state energy of jellium coincide. In the first point of view the electrons are placed in a neutralizing uniform background. In the second definition there is no background but the electrons are submitted to the constraint that their density is constant, as is appropriate in density functional theory. Finally, in the third system each electron interacts with a periodic image of itself; that is, periodic boundary conditions are imposed on the interaction potential."}],"year":"2019","status":"public","title":"Floating Wigner crystal with no boundary charge fluctuations"},{"date_updated":"2025-06-12T07:34:12Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7652"}]},"date_created":"2019-11-13T09:07:31Z","title":"Data for the paper \"Gene amplification as a form of population-level gene expression regulation\"","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","abstract":[{"text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature.","lang":"eng"}],"file":[{"file_id":"7017","file_name":"D8_S35_R2_001.fastq","checksum":"72441055043eda4cbf1398a422e2c118","relation":"main_file","date_created":"2019-11-13T08:52:21Z","title":"Locus1_amplified","access_level":"open_access","creator":"itomanek","content_type":"application/octet-stream","date_updated":"2020-07-14T12:47:47Z","file_size":2456192500,"description":"Illumina whole genome sequence data for Locus 1 - amplified."},{"file_name":"IT028_S11_R2_001.fastq","file_id":"7018","checksum":"a4ac50bf655d9c751f0305ade5c2ee16","relation":"main_file","content_type":"application/octet-stream","creator":"itomanek","date_created":"2019-11-13T08:52:59Z","access_level":"open_access","title":"Locus1_ancestral","description":"Illumina whole genome sequence data for Locus 1 - ancestral.","date_updated":"2020-07-14T12:47:47Z","file_size":2833452234},{"file_size":2878017264,"date_updated":"2020-07-14T12:47:47Z","description":"Illumina whole genome sequence data for Locus 1 - 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see read_me_FACS","date_created":"2020-01-22T15:44:16Z","access_level":"open_access","title":"FACS data","creator":"itomanek","content_type":"application/zip"},{"file_name":"read_me_FACS.rtf","file_id":"7352","checksum":"a85caf092ae4b17668f70af2d93fad00","relation":"main_file","creator":"itomanek","content_type":"text/rtf","date_created":"2020-01-22T15:44:16Z","access_level":"open_access","date_updated":"2020-07-14T12:47:47Z","file_size":4996},{"date_created":"2020-01-22T15:44:16Z","access_level":"open_access","content_type":"text/rtf","creator":"itomanek","date_updated":"2020-07-14T12:47:47Z","file_size":868,"file_id":"7353","file_name":"read_me_microfluidics.rtf","checksum":"fd8ba5d75d24e47ddf7e70bfdadb40d4","relation":"main_file"},{"creator":"itomanek","content_type":"application/zip","date_created":"2020-01-22T15:44:17Z","title":"microfluidics data","access_level":"open_access","description":"microfluidics time trace data - see read_me_microfluidics","date_updated":"2020-07-14T12:47:47Z","file_size":8141727,"file_name":"microfuidics_data.zip","file_id":"7354","checksum":"69c5dc5ca5c069a138183c934acc1778","relation":"main_file"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","oa_version":"Published Version","citation":{"apa":"Tomanek, I. (2019). Data for the paper “Gene amplification as a form of population-level gene expression regulation.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7016\">https://doi.org/10.15479/AT:ISTA:7016</a>","ama":"Tomanek I. Data for the paper “Gene amplification as a form of population-level gene expression regulation.” 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7016\">10.15479/AT:ISTA:7016</a>","ieee":"I. Tomanek, “Data for the paper ‘Gene amplification as a form of population-level gene expression regulation.’” Institute of Science and Technology Austria, 2019.","short":"I. Tomanek, (2019).","ista":"Tomanek I. 2019. Data for the paper ‘Gene amplification as a form of population-level gene expression regulation’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:7016\">10.15479/AT:ISTA:7016</a>.","mla":"Tomanek, Isabella. <i>Data for the Paper “Gene Amplification as a Form of Population-Level Gene Expression Regulation.”</i> Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7016\">10.15479/AT:ISTA:7016</a>.","chicago":"Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of Population-Level Gene Expression Regulation.’” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:7016\">https://doi.org/10.15479/AT:ISTA:7016</a>."},"day":"13","_id":"7016","file_date_updated":"2020-07-14T12:47:47Z","ddc":["576"],"contributor":[{"last_name":"Guet","contributor_type":"project_leader","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052"}],"keyword":["Escherichia coli","gene amplification","galactose","DOG","experimental evolution","Illumina sequence data","FACS data","microfluidics data"],"author":[{"last_name":"Tomanek","full_name":"Tomanek, Isabella","id":"3981F020-F248-11E8-B48F-1D18A9856A87","first_name":"Isabella","orcid":"0000-0001-6197-363X"}],"article_processing_charge":"No","department":[{"_id":"CaGu"}],"oa":1,"date_published":"2019-11-13T00:00:00Z","doi":"10.15479/AT:ISTA:7016","month":"11","fulldoi":"https://doi.org/10.15479/AT:ISTA:7016","type":"research_data"},{"citation":{"apa":"Lukacisin, M., &#38; Bollenbach, M. T. (2019). Emergent gene expression responses to drug combinations predict higher-order drug interactions. <i>Cell Systems</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cels.2019.10.004\">https://doi.org/10.1016/j.cels.2019.10.004</a>","ama":"Lukacisin M, Bollenbach MT. Emergent gene expression responses to drug combinations predict higher-order drug interactions. <i>Cell Systems</i>. 2019;9(5):423-433.e1-e3. doi:<a href=\"https://doi.org/10.1016/j.cels.2019.10.004\">10.1016/j.cels.2019.10.004</a>","ieee":"M. Lukacisin and M. T. Bollenbach, “Emergent gene expression responses to drug combinations predict higher-order drug interactions,” <i>Cell Systems</i>, vol. 9, no. 5. Cell Press, pp. 423-433.e1-e3, 2019.","short":"M. Lukacisin, M.T. Bollenbach, Cell Systems 9 (2019) 423-433.e1-e3.","ista":"Lukacisin M, Bollenbach MT. 2019. Emergent gene expression responses to drug combinations predict higher-order drug interactions. Cell Systems. 9(5), 423-433.e1-e3.","chicago":"Lukacisin, Martin, and Mark Tobias Bollenbach. “Emergent Gene Expression Responses to Drug Combinations Predict Higher-Order Drug Interactions.” <i>Cell Systems</i>. Cell Press, 2019. <a href=\"https://doi.org/10.1016/j.cels.2019.10.004\">https://doi.org/10.1016/j.cels.2019.10.004</a>.","mla":"Lukacisin, Martin, and Mark Tobias Bollenbach. “Emergent Gene Expression Responses to Drug Combinations Predict Higher-Order Drug Interactions.” <i>Cell Systems</i>, vol. 9, no. 5, Cell Press, 2019, pp. 423-433.e1-e3, doi:<a href=\"https://doi.org/10.1016/j.cels.2019.10.004\">10.1016/j.cels.2019.10.004</a>."},"day":"27","quality_controlled":"1","publication":"Cell Systems","_id":"7026","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"relation":"main_file","checksum":"7a11d6c2f9523d65b049512d61733178","file_name":"2019_CellSystems_Lukacisin.pdf","file_id":"7027","file_size":4238460,"date_updated":"2020-07-14T12:47:48Z","creator":"dernst","content_type":"application/pdf","access_level":"open_access","date_created":"2019-11-15T10:57:42Z"}],"publication_status":"published","has_accepted_license":"1","status":"public","title":"Emergent gene expression responses to drug combinations predict higher-order drug interactions","year":"2019","abstract":[{"text":"Effective design of combination therapies requires understanding the changes in cell physiology that result from drug interactions. Here, we show that the genome-wide transcriptional response to combinations of two drugs, measured at a rigorously controlled growth rate, can predict higher-order antagonism with a third drug in Saccharomyces cerevisiae. Using isogrowth profiling, over 90% of the variation in cellular response can be decomposed into three principal components (PCs) that have clear biological interpretations. We demonstrate that the third PC captures emergent transcriptional programs that are dependent on both drugs and can predict antagonism with a third drug targeting the emergent pathway. We further show that emergent gene expression patterns are most pronounced at a drug ratio where the drug interaction is strongest, providing a guideline for future measurements. Our results provide a readily applicable recipe for uncovering emergent responses in other systems and for higher-order drug combinations. A record of this paper’s transparent peer review process is included in the Supplemental Information.","lang":"eng"}],"page":"423-433.e1-e3","type":"journal_article","isi":1,"month":"11","date_published":"2019-11-27T00:00:00Z","doi":"10.1016/j.cels.2019.10.004","publication_identifier":{"issn":["2405-4712"]},"external_id":{"isi":["000499495400003"]},"volume":9,"ddc":["570"],"file_date_updated":"2020-07-14T12:47:48Z","publisher":"Cell Press","oa_version":"Published Version","article_type":"original","date_created":"2019-11-15T10:51:42Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2025-04-15T08:09:37Z","project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22"},{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013"}],"fulldoi":"https://doi.org/10.1016/j.cels.2019.10.004","intvolume":"         9","issue":"5","language":[{"iso":"eng"}],"department":[{"_id":"ToBo"}],"article_processing_charge":"No","author":[{"orcid":"0000-0001-6549-4177","first_name":"Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisin, Martin","last_name":"Lukacisin"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","full_name":"Bollenbach, Tobias"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"oa":1,"scopus_import":"1"},{"date_updated":"2023-08-30T07:26:01Z","conference":{"start_date":"2019-06-23","location":"Munich, Germany","end_date":"2019-06-27","name":"CLEO: Conference on Lasers and Electro-Optics Europe"},"date_created":"2019-11-18T13:58:22Z","title":"Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators","status":"public","abstract":[{"text":"Optical frequency combs (OFCs) are light sources whose spectra consists of equally spaced frequency lines in the optical domain [1]. They have great potential for improving high-capacity data transfer, all-optical atomic clocks, spectroscopy, and high-precision measurements [2].","lang":"eng"}],"year":"2019","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"IEEE","publication_status":"published","oa_version":"None","publication":"2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference","quality_controlled":"1","day":"17","citation":{"ista":"Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kuamri M, Schwefel HGL. 2019. Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators. 2019 Conference on Lasers and Electro-Optics Europe &#38; European Quantum Electronics Conference. CLEO: Conference on Lasers and Electro-Optics Europe, 8873300.","short":"A.R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kuamri, H.G.L. Schwefel, in:, 2019 Conference on Lasers and Electro-Optics Europe &#38; European Quantum Electronics Conference, IEEE, 2019.","mla":"Rueda Sanchez, Alfredo R., et al. “Electro-Optic Frequency Comb Generation in Lithium Niobate Whispering Gallery Mode Resonators.” <i>2019 Conference on Lasers and Electro-Optics Europe &#38; European Quantum Electronics Conference</i>, 8873300, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/cleoe-eqec.2019.8873300\">10.1109/cleoe-eqec.2019.8873300</a>.","chicago":"Rueda Sanchez, Alfredo R, Florian Sedlmeir, Gerd Leuchs, Madhuri Kuamri, and Harald G. L. Schwefel. “Electro-Optic Frequency Comb Generation in Lithium Niobate Whispering Gallery Mode Resonators.” In <i>2019 Conference on Lasers and Electro-Optics Europe &#38; European Quantum Electronics Conference</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/cleoe-eqec.2019.8873300\">https://doi.org/10.1109/cleoe-eqec.2019.8873300</a>.","apa":"Rueda Sanchez, A. R., Sedlmeir, F., Leuchs, G., Kuamri, M., &#38; Schwefel, H. G. L. (2019). Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators. In <i>2019 Conference on Lasers and Electro-Optics Europe &#38; European Quantum Electronics Conference</i>. Munich, Germany: IEEE. <a href=\"https://doi.org/10.1109/cleoe-eqec.2019.8873300\">https://doi.org/10.1109/cleoe-eqec.2019.8873300</a>","ieee":"A. R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kuamri, and H. G. L. Schwefel, “Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators,” in <i>2019 Conference on Lasers and Electro-Optics Europe &#38; European Quantum Electronics Conference</i>, Munich, Germany, 2019.","ama":"Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kuamri M, Schwefel HGL. Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators. In: <i>2019 Conference on Lasers and Electro-Optics Europe &#38; European Quantum Electronics Conference</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/cleoe-eqec.2019.8873300\">10.1109/cleoe-eqec.2019.8873300</a>"},"_id":"7032","publication_identifier":{"isbn":["9781728104690"]},"article_number":"8873300","external_id":{"isi":["000630002701617"]},"department":[{"_id":"JoFi"}],"article_processing_charge":"No","author":[{"orcid":"0000-0001-6249-5860","first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","full_name":"Rueda Sanchez, Alfredo R","last_name":"Rueda Sanchez"},{"first_name":"Florian","last_name":"Sedlmeir","full_name":"Sedlmeir, Florian"},{"full_name":"Leuchs, Gerd","last_name":"Leuchs","first_name":"Gerd"},{"first_name":"Madhuri","full_name":"Kuamri, Madhuri","last_name":"Kuamri"},{"full_name":"Schwefel, Harald G. L.","last_name":"Schwefel","first_name":"Harald G. L."}],"scopus_import":"1","doi":"10.1109/cleoe-eqec.2019.8873300","date_published":"2019-10-17T00:00:00Z","month":"10","isi":1,"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1109/cleoe-eqec.2019.8873300","type":"conference"},{"status":"public","title":"Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4","abstract":[{"lang":"eng","text":"We find a graph of genus 5 and its drawing on the orientable surface of genus 4 with every pair of independent edges crossing an even number of times. This shows that the strong Hanani–Tutte theorem cannot be extended to the orientable surface of genus 4. As a base step in the construction we use a counterexample to an extension of the unified Hanani–Tutte theorem on the torus."}],"year":"2019","quality_controlled":"1","publication":"Combinatorica","day":"29","citation":{"ista":"Fulek R, Kynčl J. 2019. Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4. Combinatorica. 39(6), 1267–1279.","short":"R. Fulek, J. Kynčl, Combinatorica 39 (2019) 1267–1279.","mla":"Fulek, Radoslav, and Jan Kynčl. “Counterexample to an Extension of the Hanani-Tutte Theorem on the Surface of Genus 4.” <i>Combinatorica</i>, vol. 39, no. 6, Springer Nature, 2019, pp. 1267–79, doi:<a href=\"https://doi.org/10.1007/s00493-019-3905-7\">10.1007/s00493-019-3905-7</a>.","chicago":"Fulek, Radoslav, and Jan Kynčl. “Counterexample to an Extension of the Hanani-Tutte Theorem on the Surface of Genus 4.” <i>Combinatorica</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/s00493-019-3905-7\">https://doi.org/10.1007/s00493-019-3905-7</a>.","apa":"Fulek, R., &#38; Kynčl, J. (2019). Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4. <i>Combinatorica</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00493-019-3905-7\">https://doi.org/10.1007/s00493-019-3905-7</a>","ieee":"R. Fulek and J. Kynčl, “Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4,” <i>Combinatorica</i>, vol. 39, no. 6. Springer Nature, pp. 1267–1279, 2019.","ama":"Fulek R, Kynčl J. Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4. <i>Combinatorica</i>. 2019;39(6):1267-1279. doi:<a href=\"https://doi.org/10.1007/s00493-019-3905-7\">10.1007/s00493-019-3905-7</a>"},"_id":"7034","publication_status":"published","arxiv":1,"doi":"10.1007/s00493-019-3905-7","date_published":"2019-10-29T00:00:00Z","publication_identifier":{"issn":["0209-9683"],"eissn":["1439-6912"]},"external_id":{"isi":["000493267200003"],"arxiv":["1709.00508"]},"page":"1267-1279","ec_funded":1,"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.00508"}],"month":"10","isi":1,"date_created":"2019-11-18T14:29:50Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2025-04-14T13:52:37Z","volume":39,"publisher":"Springer Nature","article_type":"original","oa_version":"Preprint","article_processing_charge":"No","author":[{"full_name":"Fulek, Radoslav","last_name":"Fulek","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774"},{"last_name":"Kynčl","full_name":"Kynčl, Jan","first_name":"Jan"}],"department":[{"_id":"UlWa"}],"oa":1,"scopus_import":"1","fulldoi":"https://doi.org/10.1007/s00493-019-3905-7","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs","grant_number":"M02281"}],"issue":"6","intvolume":"        39","language":[{"iso":"eng"}]},{"conference":{"name":"Research on isometries as preserver problems and related topics","end_date":"2019-01-30","location":"Kyoto, Japan","start_date":"2019-01-28"},"OA_place":"repository","acknowledgement":"This paper is part of a long term collaboration investigating the isometric structure of Wasserstein\r\nspaces. The authors would like to thank the warm hospitality and generosity of László Erdós and his\r\ngroup at Institute of Science and Technology Austria.\r\nT. Titkos wants to thank Oriental Business and Innovation Center ‐ OBIC for providing financial\r\nsupport to participate in the symposium at the Kyoto RIMS.\r\nGy. P. Gehér was supported by the Leverhulme Trust Early Career Fellowship (ECF‐2018‐125),\r\nand also by the Hungarian National Research, Development and Innovation Office (K115383). T.\r\nTitkos was supported by the Hungarian National Research, Development and Innovation Office‐ NKFIH\r\n(PD128374), by the János Bolyai Research Scholarship of the Hungarian Academy of Sciences, and by the\r\nUNKP‐18‐4‐BGE‐3 New National Excellence Program of the Ministry of Human Capacities. D. Virosztek\r\nwas supported by the ISTFELLOW program of the Institute of Science and Technology Austria (project\r\ncode IC1027FELL01 ) and partially supported by the Hungarian National Research, Development and\r\nInnovation Office NKFIH (grant no. K124152 and grant no. KH129601)","corr_author":"1","status":"public","title":"Dirac masses and isometric rigidity","abstract":[{"text":"The aim of this short note is to expound one particular issue that was discussed during the talk [10] given at the symposium ”Researches on isometries as preserver problems and related topics” at Kyoto RIMS. That is,  the role of Dirac masses by  describing  the  isometry group of various metric spaces  of probability  measures.   This  article  is  of  survey  character,  and  it  does  not  contain  any  essentially  new results.From an isometric point of view, in some cases, metric spaces of measures are similar to C(K)-type function  spaces.   Similarity  means  here  that  their  isometries  are  driven  by  some  nice  transformations of  the  underlying  space.   Of  course,  it  depends  on  the  particular  choice  of  the  metric  how  nice  these transformations should be.  Sometimes, as we will see, being a homeomorphism is enough to generate an isometry.  But sometimes we need more:  the transformation must preserve the underlying distance as well.  Statements claiming that isometries in questions are necessarily induced by homeomorphisms are called Banach-Stone-type results, while results asserting that the underlying transformation is necessarily an isometry are termed as isometric rigidity results.As  Dirac  masses  can  be  considered  as  building  bricks  of  the  set  of  all  Borel  measures,  a  natural question arises:Is it enough to understand how an isometry acts on the set of Dirac masses?  Does this action extend uniquely to all measures?In what follows, we will thoroughly investigate this question.","lang":"eng"}],"year":"2019","publication_status":"published","quality_controlled":"1","publication":"Kyoto RIMS Kôkyûroku","citation":{"ieee":"G. P. Geher, T. Titkos, and D. Virosztek, “Dirac masses and isometric rigidity,” in <i>Kyoto RIMS Kôkyûroku</i>, Kyoto, Japan, 2019, vol. 2125, pp. 34–41.","ama":"Geher GP, Titkos T, Virosztek D. Dirac masses and isometric rigidity. In: <i>Kyoto RIMS Kôkyûroku</i>. Vol 2125. Research Institute for Mathematical Sciences, Kyoto University; 2019:34-41.","apa":"Geher, G. P., Titkos, T., &#38; Virosztek, D. (2019). Dirac masses and isometric rigidity. In <i>Kyoto RIMS Kôkyûroku</i> (Vol. 2125, pp. 34–41). Kyoto, Japan: Research Institute for Mathematical Sciences, Kyoto University.","mla":"Geher, Gyorgy Pal, et al. “Dirac Masses and Isometric Rigidity.” <i>Kyoto RIMS Kôkyûroku</i>, vol. 2125, Research Institute for Mathematical Sciences, Kyoto University, 2019, pp. 34–41.","chicago":"Geher, Gyorgy Pal, Tamas Titkos, and Daniel Virosztek. “Dirac Masses and Isometric Rigidity.” In <i>Kyoto RIMS Kôkyûroku</i>, 2125:34–41. Research Institute for Mathematical Sciences, Kyoto University, 2019.","ista":"Geher GP, Titkos T, Virosztek D. 2019. Dirac masses and isometric rigidity. Kyoto RIMS Kôkyûroku. Research on isometries as preserver problems and related topics vol. 2125, 34–41.","short":"G.P. Geher, T. Titkos, D. Virosztek, in:, Kyoto RIMS Kôkyûroku, Research Institute for Mathematical Sciences, Kyoto University, 2019, pp. 34–41."},"day":"30","_id":"7035","date_published":"2019-01-30T00:00:00Z","month":"01","page":"34-41","ec_funded":1,"type":"conference","main_file_link":[{"open_access":"1","url":"http://www.kurims.kyoto-u.ac.jp/~kyodo/kokyuroku/contents/2125.html"}],"date_updated":"2025-06-30T09:55:30Z","date_created":"2019-11-18T15:39:53Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Research Institute for Mathematical Sciences, Kyoto University","oa_version":"Submitted Version","volume":2125,"OA_type":"green","author":[{"last_name":"Geher","full_name":"Geher, Gyorgy Pal","first_name":"Gyorgy Pal"},{"full_name":"Titkos, Tamas","last_name":"Titkos","first_name":"Tamas"},{"orcid":"0000-0003-1109-5511","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Virosztek","full_name":"Virosztek, Daniel"}],"article_processing_charge":"No","department":[{"_id":"LaEr"}],"oa":1,"language":[{"iso":"eng"}],"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"intvolume":"      2125"},{"publication":"Journal of Computational Geometry","quality_controlled":"1","citation":{"chicago":"Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of Triangulated 3-Manifolds.” <i>Journal of Computational Geometry</i>. Computational Geometry Laborartoy, 2019. <a href=\"https://doi.org/10.20382/JOGC.V10I2A5\">https://doi.org/10.20382/JOGC.V10I2A5</a>.","mla":"Huszár, Kristóf, et al. “On the Treewidth of Triangulated 3-Manifolds.” <i>Journal of Computational Geometry</i>, vol. 10, no. 2, Computational Geometry Laborartoy, 2019, pp. 70–98, doi:<a href=\"https://doi.org/10.20382/JOGC.V10I2A5\">10.20382/JOGC.V10I2A5</a>.","short":"K. Huszár, J. Spreer, U. Wagner, Journal of Computational Geometry 10 (2019) 70–98.","ista":"Huszár K, Spreer J, Wagner U. 2019. On the treewidth of triangulated 3-manifolds. Journal of Computational Geometry. 10(2), 70–98.","ieee":"K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,” <i>Journal of Computational Geometry</i>, vol. 10, no. 2. Computational Geometry Laborartoy, pp. 70–98, 2019.","ama":"Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds. <i>Journal of Computational Geometry</i>. 2019;10(2):70–98. doi:<a href=\"https://doi.org/10.20382/JOGC.V10I2A5\">10.20382/JOGC.V10I2A5</a>","apa":"Huszár, K., Spreer, J., &#38; Wagner, U. (2019). On the treewidth of triangulated 3-manifolds. <i>Journal of Computational Geometry</i>. Computational Geometry Laborartoy. <a href=\"https://doi.org/10.20382/JOGC.V10I2A5\">https://doi.org/10.20382/JOGC.V10I2A5</a>"},"day":"01","_id":"7093","file":[{"file_size":857590,"date_updated":"2020-07-14T12:47:49Z","creator":"khuszar","content_type":"application/pdf","access_level":"open_access","date_created":"2019-11-23T12:35:16Z","relation":"main_file","checksum":"c872d590d38d538404782bca20c4c3f5","file_name":"479-1917-1-PB.pdf","file_id":"7094"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published","has_accepted_license":"1","title":"On the treewidth of triangulated 3-manifolds","status":"public","abstract":[{"lang":"eng","text":"In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how \"simple\" or \"thin\" a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth.\r\nIn view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs).\r\nWe derive these results from work of Agol, of Scharlemann and Thompson, and of Scharlemann, Schultens and Saito by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 18(k+1) (resp. 4(3k+1))."}],"year":"2019","page":"70–98","type":"journal_article","month":"11","arxiv":1,"doi":"10.20382/JOGC.V10I2A5","date_published":"2019-11-01T00:00:00Z","publication_identifier":{"issn":["1920-180X"]},"external_id":{"arxiv":["1712.00434"]},"volume":10,"ddc":["514"],"file_date_updated":"2020-07-14T12:47:49Z","publisher":"Computational Geometry Laborartoy","article_type":"original","oa_version":"Published Version","date_created":"2019-11-23T12:14:09Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2026-04-08T07:21:27Z","related_material":{"record":[{"status":"public","id":"285","relation":"earlier_version"},{"id":"8032","relation":"part_of_dissertation","status":"public"}]},"fulldoi":"https://doi.org/10.20382/JOGC.V10I2A5","intvolume":"        10","issue":"2","language":[{"iso":"eng"}],"department":[{"_id":"UlWa"}],"author":[{"last_name":"Huszár","full_name":"Huszár, Kristóf","orcid":"0000-0002-5445-5057","id":"33C26278-F248-11E8-B48F-1D18A9856A87","first_name":"Kristóf"},{"first_name":"Jonathan","last_name":"Spreer","full_name":"Spreer, Jonathan"},{"last_name":"Wagner","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","orcid":"0000-0002-1494-0568"}],"article_processing_charge":"No","oa":1,"scopus_import":"1"},{"date_updated":"2023-08-30T07:26:54Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-11-25T07:45:17Z","oa_version":"Published Version","article_type":"original","pmid":1,"publisher":"Springer Nature","ddc":["570"],"file_date_updated":"2020-07-14T12:47:49Z","volume":9,"article_number":"16565","scopus_import":"1","oa":1,"article_processing_charge":"No","department":[{"_id":"SaSi"}],"author":[{"id":"3838F452-F248-11E8-B48F-1D18A9856A87","first_name":"Margaret E","orcid":"0000-0001-9642-1085","last_name":"Maes","full_name":"Maes, Margaret E"},{"first_name":"J. A.","full_name":"Grosser, J. A.","last_name":"Grosser"},{"last_name":"Fehrman","full_name":"Fehrman, R. L.","first_name":"R. L."},{"last_name":"Schlamp","full_name":"Schlamp, C. L.","first_name":"C. L."},{"full_name":"Nickells, R. W.","last_name":"Nickells","first_name":"R. W."}],"language":[{"iso":"eng"}],"intvolume":"         9","fulldoi":"https://doi.org/10.1038/s41598-019-53049-w","year":"2019","abstract":[{"lang":"eng","text":"BAX, a member of the BCL2 gene family, controls the committed step of the intrinsic apoptotic program. Mitochondrial fragmentation is a commonly observed feature of apoptosis, which occurs through the process of mitochondrial fission. BAX has consistently been associated with mitochondrial fission, yet how BAX participates in the process of mitochondrial fragmentation during apoptosis remains to be tested. Time-lapse imaging of BAX recruitment and mitochondrial fragmentation demonstrates that rapid mitochondrial fragmentation during apoptosis occurs after the complete recruitment of BAX to the mitochondrial outer membrane (MOM). The requirement of a fully functioning BAX protein for the fission process was demonstrated further in BAX/BAK-deficient HCT116 cells expressing a P168A mutant of BAX. The mutant performed fusion to restore the mitochondrial network. but was not demonstrably recruited to the MOM after apoptosis induction. Under these conditions, mitochondrial fragmentation was blocked. Additionally, we show that loss of the fission protein, dynamin-like protein 1 (DRP1), does not temporally affect the initiation time or rate of BAX recruitment, but does reduce the final level of BAX recruited to the MOM during the late phase of BAX recruitment. These correlative observations suggest a model where late-stage BAX oligomers play a functional part of the mitochondrial fragmentation machinery in apoptotic cells."}],"title":"Completion of BAX recruitment correlates with mitochondrial fission during apoptosis","status":"public","has_accepted_license":"1","publication_status":"published","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_updated":"2020-07-14T12:47:49Z","file_size":6467393,"date_created":"2019-11-25T07:49:52Z","access_level":"open_access","content_type":"application/pdf","creator":"dernst","checksum":"9ab397ed9c1c454b34bffb8cc863d734","relation":"main_file","file_id":"7096","file_name":"2019_ScientificReports_Maes.pdf"}],"_id":"7095","citation":{"chicago":"Maes, Margaret E, J. A. Grosser, R. L. Fehrman, C. L. Schlamp, and R. W. Nickells. “Completion of BAX Recruitment Correlates with Mitochondrial Fission during Apoptosis.” <i>Scientific Reports</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41598-019-53049-w\">https://doi.org/10.1038/s41598-019-53049-w</a>.","mla":"Maes, Margaret E., et al. “Completion of BAX Recruitment Correlates with Mitochondrial Fission during Apoptosis.” <i>Scientific Reports</i>, vol. 9, 16565, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41598-019-53049-w\">10.1038/s41598-019-53049-w</a>.","ista":"Maes ME, Grosser JA, Fehrman RL, Schlamp CL, Nickells RW. 2019. Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. Scientific Reports. 9, 16565.","short":"M.E. Maes, J.A. Grosser, R.L. Fehrman, C.L. Schlamp, R.W. Nickells, Scientific Reports 9 (2019).","ieee":"M. E. Maes, J. A. Grosser, R. L. Fehrman, C. L. Schlamp, and R. W. Nickells, “Completion of BAX recruitment correlates with mitochondrial fission during apoptosis,” <i>Scientific Reports</i>, vol. 9. Springer Nature, 2019.","ama":"Maes ME, Grosser JA, Fehrman RL, Schlamp CL, Nickells RW. Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. <i>Scientific Reports</i>. 2019;9. doi:<a href=\"https://doi.org/10.1038/s41598-019-53049-w\">10.1038/s41598-019-53049-w</a>","apa":"Maes, M. E., Grosser, J. A., Fehrman, R. L., Schlamp, C. L., &#38; Nickells, R. W. (2019). Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-019-53049-w\">https://doi.org/10.1038/s41598-019-53049-w</a>"},"day":"12","publication":"Scientific Reports","quality_controlled":"1","external_id":{"isi":["000495857600019"],"pmid":["31719602"]},"publication_identifier":{"eissn":["2045-2322"]},"date_published":"2019-11-12T00:00:00Z","doi":"10.1038/s41598-019-53049-w","isi":1,"month":"11","type":"journal_article"},{"doi":"10.1038/s42003-019-0670-5","date_published":"2019-11-15T00:00:00Z","external_id":{"isi":["000496767800005"]},"publication_identifier":{"issn":["2399-3642"]},"type":"journal_article","isi":1,"month":"11","year":"2019","abstract":[{"lang":"eng","text":"Early endosomes, also called sorting endosomes, are known to mature into late endosomesvia the Rab5-mediated endolysosomal trafficking pathway. Thus, early endosome existence isthought to be maintained by the continual fusion of transport vesicles from the plasmamembrane and thetrans-Golgi network (TGN). Here we show instead that endocytosis isdispensable and post-Golgi vesicle transport is crucial for the formation of endosomes andthe subsequent endolysosomal traffic regulated by yeast Rab5 Vps21p. Fittingly, all threeproteins required for endosomal nucleotide exchange on Vps21p arefirst recruited to theTGN  before  transport  to  the  endosome,  namely  the  GEF  Vps9p and  the  epsin-relatedadaptors Ent3/5p. The TGN recruitment of these components is distinctly controlled, withVps9p appearing to require the Arf1p GTPase, and the Rab11s, Ypt31p/32p. These resultsprovide a different view of endosome formation and identify the TGN as a critical location forregulating progress through the endolysosomal trafficking pathway."}],"title":"Rab5-mediated endosome formation is regulated at the trans-Golgi network","status":"public","_id":"7097","citation":{"apa":"Nagano, M., Toshima, J. Y., Siekhaus, D. E., &#38; Toshima, J. (2019). Rab5-mediated endosome formation is regulated at the trans-Golgi network. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-019-0670-5\">https://doi.org/10.1038/s42003-019-0670-5</a>","ieee":"M. Nagano, J. Y. Toshima, D. E. Siekhaus, and J. Toshima, “Rab5-mediated endosome formation is regulated at the trans-Golgi network,” <i>Communications Biology</i>, vol. 2, no. 1. Springer Nature, 2019.","ama":"Nagano M, Toshima JY, Siekhaus DE, Toshima J. Rab5-mediated endosome formation is regulated at the trans-Golgi network. <i>Communications Biology</i>. 2019;2(1). doi:<a href=\"https://doi.org/10.1038/s42003-019-0670-5\">10.1038/s42003-019-0670-5</a>","short":"M. Nagano, J.Y. Toshima, D.E. Siekhaus, J. Toshima, Communications Biology 2 (2019).","ista":"Nagano M, Toshima JY, Siekhaus DE, Toshima J. 2019. Rab5-mediated endosome formation is regulated at the trans-Golgi network. Communications Biology. 2(1), 419.","mla":"Nagano, Makoto, et al. “Rab5-Mediated Endosome Formation Is Regulated at the Trans-Golgi Network.” <i>Communications Biology</i>, vol. 2, no. 1, 419, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s42003-019-0670-5\">10.1038/s42003-019-0670-5</a>.","chicago":"Nagano, Makoto, Junko Y. Toshima, Daria E Siekhaus, and Jiro Toshima. “Rab5-Mediated Endosome Formation Is Regulated at the Trans-Golgi Network.” <i>Communications Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s42003-019-0670-5\">https://doi.org/10.1038/s42003-019-0670-5</a>."},"day":"15","publication":"Communications Biology","quality_controlled":"1","has_accepted_license":"1","publication_status":"published","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_size":2626069,"date_updated":"2020-07-14T12:47:49Z","access_level":"open_access","date_created":"2019-11-25T07:58:05Z","creator":"dernst","content_type":"application/pdf","relation":"main_file","checksum":"c63c69a264fc8a0e52f2b0d482f3bdae","file_id":"7098","file_name":"2019_CommunicBiology_Nagano.pdf"}],"scopus_import":"1","oa":1,"author":[{"first_name":"Makoto","last_name":"Nagano","full_name":"Nagano, Makoto"},{"first_name":"Junko Y.","last_name":"Toshima","full_name":"Toshima, Junko Y."},{"full_name":"Siekhaus, Daria E","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jiro","last_name":"Toshima","full_name":"Toshima, Jiro"}],"department":[{"_id":"DaSi"}],"article_processing_charge":"No","article_number":"419","intvolume":"         2","issue":"1","fulldoi":"https://doi.org/10.1038/s42003-019-0670-5","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-11-25T07:55:01Z","date_updated":"2023-08-30T07:27:55Z","file_date_updated":"2020-07-14T12:47:49Z","ddc":["570"],"volume":2,"oa_version":"Published Version","article_type":"original","publisher":"Springer Nature"},{"language":[{"iso":"eng"}],"issue":"4","intvolume":"       104","fulldoi":"https://doi.org/10.1016/j.neuron.2019.08.013","scopus_import":"1","oa":1,"article_processing_charge":"No","author":[{"last_name":"Kasugai","full_name":"Kasugai, Yu","first_name":"Yu"},{"last_name":"Vogel","full_name":"Vogel, Elisabeth","first_name":"Elisabeth"},{"full_name":"Hörtnagl, Heide","last_name":"Hörtnagl","first_name":"Heide"},{"first_name":"Sabine","last_name":"Schönherr","full_name":"Schönherr, Sabine"},{"first_name":"Enrica","full_name":"Paradiso, Enrica","last_name":"Paradiso"},{"first_name":"Markus","full_name":"Hauschild, Markus","last_name":"Hauschild"},{"first_name":"Georg","full_name":"Göbel, Georg","last_name":"Göbel"},{"full_name":"Milenkovic, Ivan","last_name":"Milenkovic","first_name":"Ivan"},{"first_name":"Yvan","full_name":"Peterschmitt, Yvan","last_name":"Peterschmitt"},{"first_name":"Ramon","full_name":"Tasan, Ramon","last_name":"Tasan"},{"first_name":"Günther","last_name":"Sperk","full_name":"Sperk, Günther"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"},{"last_name":"Sieghart","full_name":"Sieghart, Werner","first_name":"Werner"},{"first_name":"Nicolas","last_name":"Singewald","full_name":"Singewald, Nicolas"},{"last_name":"Lüthi","full_name":"Lüthi, Andreas","first_name":"Andreas"},{"first_name":"Francesco","last_name":"Ferraguti","full_name":"Ferraguti, Francesco"}],"department":[{"_id":"RySh"}],"oa_version":"Published Version","article_type":"original","publisher":"Elsevier","pmid":1,"ddc":["571","599"],"volume":104,"date_updated":"2023-08-30T07:28:22Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-11-25T08:02:39Z","isi":1,"month":"11","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2019.08.013"}],"type":"journal_article","page":"781-794.e4","external_id":{"pmid":["31543297"],"isi":["000497963500017"]},"publication_identifier":{"issn":["0896-6273"]},"doi":"10.1016/j.neuron.2019.08.013","date_published":"2019-11-20T00:00:00Z","publication_status":"published","has_accepted_license":"1","_id":"7099","citation":{"ieee":"Y. Kasugai <i>et al.</i>, “Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning,” <i>Neuron</i>, vol. 104, no. 4. Elsevier, p. 781–794.e4, 2019.","ama":"Kasugai Y, Vogel E, Hörtnagl H, et al. Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. <i>Neuron</i>. 2019;104(4):781-794.e4. doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.08.013\">10.1016/j.neuron.2019.08.013</a>","apa":"Kasugai, Y., Vogel, E., Hörtnagl, H., Schönherr, S., Paradiso, E., Hauschild, M., … Ferraguti, F. (2019). Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2019.08.013\">https://doi.org/10.1016/j.neuron.2019.08.013</a>","mla":"Kasugai, Yu, et al. “Structural and Functional Remodeling of Amygdala GABAergic Synapses in Associative Fear Learning.” <i>Neuron</i>, vol. 104, no. 4, Elsevier, 2019, p. 781–794.e4, doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.08.013\">10.1016/j.neuron.2019.08.013</a>.","chicago":"Kasugai, Yu, Elisabeth Vogel, Heide Hörtnagl, Sabine Schönherr, Enrica Paradiso, Markus Hauschild, Georg Göbel, et al. “Structural and Functional Remodeling of Amygdala GABAergic Synapses in Associative Fear Learning.” <i>Neuron</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.neuron.2019.08.013\">https://doi.org/10.1016/j.neuron.2019.08.013</a>.","short":"Y. Kasugai, E. Vogel, H. Hörtnagl, S. Schönherr, E. Paradiso, M. Hauschild, G. Göbel, I. Milenkovic, Y. Peterschmitt, R. Tasan, G. Sperk, R. Shigemoto, W. Sieghart, N. Singewald, A. Lüthi, F. Ferraguti, Neuron 104 (2019) 781–794.e4.","ista":"Kasugai Y, Vogel E, Hörtnagl H, Schönherr S, Paradiso E, Hauschild M, Göbel G, Milenkovic I, Peterschmitt Y, Tasan R, Sperk G, Shigemoto R, Sieghart W, Singewald N, Lüthi A, Ferraguti F. 2019. Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. Neuron. 104(4), 781–794.e4."},"day":"20","quality_controlled":"1","publication":"Neuron","acknowledgement":"The authors thank Gabi Schmid for excellent technical support. We also thank\r\nDr. H. Harada, Dr. W. Kaufmann, and Dr. B. Kapelari for testing the specificity\r\nof some of the antibodies used in this study on replicas. Funding was provided\r\nby the Austrian Science Fund (Fonds zur Fo¨ rderung der Wissenschaftlichen\r\nForschung) Sonderforschungsbereich grants F44-17 (to F.jF.), F44-10 and\r\nP25375-B24 (to N.S.), and P26680 (to G.S.) and by the Novartis Research\r\nFoundation and the Swiss National Science Foundation (to A.L). We also thank\r\nProf. M. Capogna for reading a previous version of the manuscript.","year":"2019","title":"Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning","status":"public"},{"_id":"7103","citation":{"chicago":"Wang, Jilin W. J. L., Fabrizio Lombardi, Xiyun Zhang, Christelle Anaclet, and Plamen Ch. Ivanov. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” <i>PLoS Computational Biology</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pcbi.1007268\">https://doi.org/10.1371/journal.pcbi.1007268</a>.","mla":"Wang, Jilin W. J. L., et al. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” <i>PLoS Computational Biology</i>, vol. 15, no. 11, e1007268, Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007268\">10.1371/journal.pcbi.1007268</a>.","ista":"Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. 2019. Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. 15(11), e1007268.","short":"J.W.J.L. Wang, F. Lombardi, X. Zhang, C. Anaclet, P.C. Ivanov, PLoS Computational Biology 15 (2019).","ama":"Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. <i>PLoS Computational Biology</i>. 2019;15(11). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007268\">10.1371/journal.pcbi.1007268</a>","ieee":"J. W. J. L. Wang, F. Lombardi, X. Zhang, C. Anaclet, and P. C. Ivanov, “Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture,” <i>PLoS Computational Biology</i>, vol. 15, no. 11. Public Library of Science, 2019.","apa":"Wang, J. W. J. L., Lombardi, F., Zhang, X., Anaclet, C., &#38; Ivanov, P. C. (2019). Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007268\">https://doi.org/10.1371/journal.pcbi.1007268</a>"},"day":"01","publication":"PLoS Computational Biology","quality_controlled":"1","has_accepted_license":"1","publication_status":"published","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_size":3982516,"date_updated":"2020-07-14T12:47:49Z","access_level":"open_access","date_created":"2019-11-25T08:24:01Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","checksum":"2a096a9c6dcc6eaa94077b2603bc6c12","file_id":"7104","file_name":"2019_PLOSComBio_Wang.pdf"}],"year":"2019","abstract":[{"lang":"eng","text":"Origin and functions of intermittent transitions among sleep stages, including short awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing the sleep-wake cycle results from an underlying non-equilibrium critical dynamics, bridging collective behaviors across spatio-temporal scales. We investigate θ and δ wave dynamics in control rats and in rats with lesions of sleep-promoting neurons in the parafacial zone. We demonstrate that intermittent bursts in θ and δ rhythms exhibit a complex temporal organization, with long-range power-law correlations and a robust duality of power law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, typical features of non-equilibrium systems self-organizing at criticality. Crucially, such temporal organization relates to anti-correlated coupling between θ- and δ-bursts, and is independent of the dominant physiologic state and lesions, a solid indication of a basic principle in sleep dynamics."}],"status":"public","title":"Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture","type":"journal_article","ec_funded":1,"isi":1,"month":"11","doi":"10.1371/journal.pcbi.1007268","date_published":"2019-11-01T00:00:00Z","external_id":{"isi":["000500976100014"],"pmid":["31725712"]},"publication_identifier":{"issn":["1553-7358"]},"ddc":["570","000"],"file_date_updated":"2020-07-14T12:47:49Z","volume":15,"oa_version":"Published Version","article_type":"original","publisher":"Public Library of Science","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-11-25T08:20:47Z","date_updated":"2025-04-14T07:44:06Z","intvolume":"        15","issue":"11","fulldoi":"https://doi.org/10.1371/journal.pcbi.1007268","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"language":[{"iso":"eng"}],"oa":1,"scopus_import":"1","department":[{"_id":"GaTk"}],"article_processing_charge":"No","author":[{"last_name":"Wang","full_name":"Wang, Jilin W. J. L.","first_name":"Jilin W. J. L."},{"first_name":"Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249","full_name":"Lombardi, Fabrizio","last_name":"Lombardi"},{"full_name":"Zhang, Xiyun","last_name":"Zhang","first_name":"Xiyun"},{"full_name":"Anaclet, Christelle","last_name":"Anaclet","first_name":"Christelle"},{"first_name":"Plamen Ch.","last_name":"Ivanov","full_name":"Ivanov, Plamen Ch."}],"article_number":"e1007268"},{"date_updated":"2023-09-06T11:08:52Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2019-11-25T08:55:00Z","oa_version":"Submitted Version","article_type":"original","publisher":"Springer Nature","pmid":1,"volume":21,"oa":1,"scopus_import":"1","department":[{"_id":"MiSi"}],"author":[{"first_name":"Lawrence","last_name":"Yolland","full_name":"Yolland, Lawrence"},{"first_name":"Mubarik","last_name":"Burki","full_name":"Burki, Mubarik"},{"last_name":"Marcotti","full_name":"Marcotti, Stefania","first_name":"Stefania"},{"first_name":"Andrei","last_name":"Luchici","full_name":"Luchici, Andrei"},{"first_name":"Fiona N.","full_name":"Kenny, Fiona N.","last_name":"Kenny"},{"first_name":"John Robert","last_name":"Davis","full_name":"Davis, John Robert"},{"full_name":"Serna-Morales, Eduardo","last_name":"Serna-Morales","first_name":"Eduardo"},{"first_name":"Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","full_name":"Müller, Jan","last_name":"Müller"},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"first_name":"Andrew","last_name":"Davidson","full_name":"Davidson, Andrew"},{"first_name":"Will","full_name":"Wood, Will","last_name":"Wood"},{"first_name":"Linus J.","last_name":"Schumacher","full_name":"Schumacher, Linus J."},{"first_name":"Robert G.","last_name":"Endres","full_name":"Endres, Robert G."},{"last_name":"Miodownik","full_name":"Miodownik, Mark","first_name":"Mark"},{"full_name":"Stramer, Brian M.","last_name":"Stramer","first_name":"Brian M."}],"article_processing_charge":"No","language":[{"iso":"eng"}],"issue":"11","intvolume":"        21","fulldoi":"https://doi.org/10.1038/s41556-019-0411-5","abstract":[{"lang":"eng","text":"Cell migration is hypothesized to involve a cycle of behaviours beginning with leading edge extension. However, recent evidence suggests that the leading edge may be dispensable for migration, raising the question of what actually controls cell directionality. Here, we exploit the embryonic migration of Drosophila macrophages to bridge the different temporal scales of the behaviours controlling motility. This approach reveals that edge fluctuations during random motility are not persistent and are weakly correlated with motion. In contrast, flow of the actin network behind the leading edge is highly persistent. Quantification of actin flow structure during migration reveals a stable organization and asymmetry in the cell-wide flowfield that strongly correlates with cell directionality. This organization is regulated by a gradient of actin network compression and destruction, which is controlled by myosin contraction and cofilin-mediated disassembly. It is this stable actin-flow polarity, which integrates rapid fluctuations of the leading edge, that controls inherent cellular persistence."}],"year":"2019","title":"Persistent and polarized global actin flow is essential for directionality during cell migration","status":"public","publication_status":"published","_id":"7105","citation":{"apa":"Yolland, L., Burki, M., Marcotti, S., Luchici, A., Kenny, F. N., Davis, J. R., … Stramer, B. M. (2019). Persistent and polarized global actin flow is essential for directionality during cell migration. <i>Nature Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41556-019-0411-5\">https://doi.org/10.1038/s41556-019-0411-5</a>","ieee":"L. Yolland <i>et al.</i>, “Persistent and polarized global actin flow is essential for directionality during cell migration,” <i>Nature Cell Biology</i>, vol. 21, no. 11. Springer Nature, pp. 1370–1381, 2019.","ama":"Yolland L, Burki M, Marcotti S, et al. Persistent and polarized global actin flow is essential for directionality during cell migration. <i>Nature Cell Biology</i>. 2019;21(11):1370-1381. doi:<a href=\"https://doi.org/10.1038/s41556-019-0411-5\">10.1038/s41556-019-0411-5</a>","ista":"Yolland L, Burki M, Marcotti S, Luchici A, Kenny FN, Davis JR, Serna-Morales E, Müller J, Sixt MK, Davidson A, Wood W, Schumacher LJ, Endres RG, Miodownik M, Stramer BM. 2019. Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. 21(11), 1370–1381.","short":"L. Yolland, M. Burki, S. Marcotti, A. Luchici, F.N. Kenny, J.R. Davis, E. Serna-Morales, J. Müller, M.K. Sixt, A. Davidson, W. Wood, L.J. Schumacher, R.G. Endres, M. Miodownik, B.M. Stramer, Nature Cell Biology 21 (2019) 1370–1381.","chicago":"Yolland, Lawrence, Mubarik Burki, Stefania Marcotti, Andrei Luchici, Fiona N. Kenny, John Robert Davis, Eduardo Serna-Morales, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” <i>Nature Cell Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41556-019-0411-5\">https://doi.org/10.1038/s41556-019-0411-5</a>.","mla":"Yolland, Lawrence, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” <i>Nature Cell Biology</i>, vol. 21, no. 11, Springer Nature, 2019, pp. 1370–81, doi:<a href=\"https://doi.org/10.1038/s41556-019-0411-5\">10.1038/s41556-019-0411-5</a>."},"day":"01","quality_controlled":"1","publication":"Nature Cell Biology","external_id":{"isi":["000495888300009"],"pmid":["31685997"]},"publication_identifier":{"eissn":["1476-4679"],"issn":["1465-7392"]},"date_published":"2019-11-01T00:00:00Z","doi":"10.1038/s41556-019-0411-5","isi":1,"month":"11","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7025891"}],"type":"journal_article","page":"1370-1381"}]