[{"oa_version":"Published Version","status":"public","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"scopus_import":"1","citation":{"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.","ieee":"D. Huang et al., “Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 42. Proceedings of the National Academy of Sciences, pp. 21274–21284, 2019.","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.","mla":"Huang, D., et al. “Salicylic Acid-Mediated Plasmodesmal Closure via Remorin-Dependent Lipid Organization.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 42, Proceedings of the National Academy of Sciences, 2019, pp. 21274–84, doi:10.1073/pnas.1911892116.","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.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1911892116.","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. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1911892116","ama":"Huang D, Sun Y, Ma Z, et al. Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(42):21274-21284. doi:10.1073/pnas.1911892116"},"publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"15","publisher":"Proceedings of the National Academy of Sciences","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","external_id":{"isi":["000490183000068"],"pmid":["31575745"]},"file":[{"relation":"main_file","file_name":"2019_PNAS_Huang.pdf","date_created":"2019-11-13T08:22:28Z","content_type":"application/pdf","file_size":3287466,"date_updated":"2020-07-14T12:47:46Z","access_level":"open_access","file_id":"7012","creator":"dernst","checksum":"258c666bc6253eab81961f61169eefae"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1073/pnas.2004738117"}]},"pmid":1,"issue":"42","publication_status":"published","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"department":[{"_id":"JiFr"}],"oa":1,"intvolume":" 116","doi":"10.1073/pnas.1911892116","title":"Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization","_id":"6999","month":"10","date_published":"2019-10-15T00:00:00Z","isi":1,"page":"21274-21284","article_type":"original","volume":116,"author":[{"first_name":"D","last_name":"Huang","full_name":"Huang, D"},{"last_name":"Sun","full_name":"Sun, Y","first_name":"Y"},{"first_name":"Z","last_name":"Ma","full_name":"Ma, Z"},{"full_name":"Ke, M","last_name":"Ke","first_name":"M"},{"first_name":"Y","full_name":"Cui, Y","last_name":"Cui"},{"full_name":"Chen, Z","last_name":"Chen","first_name":"Z"},{"first_name":"C","full_name":"Chen, C","last_name":"Chen"},{"first_name":"C","full_name":"Ji, C","last_name":"Ji"},{"first_name":"TM","last_name":"Tran","full_name":"Tran, TM"},{"first_name":"L","full_name":"Yang, L","last_name":"Yang"},{"last_name":"Lam","full_name":"Lam, SM","first_name":"SM"},{"last_name":"Han","full_name":"Han, Y","first_name":"Y"},{"first_name":"G","full_name":"Shu, G","last_name":"Shu"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"Y","full_name":"Miao, Y","last_name":"Miao"},{"last_name":"Jiang","full_name":"Jiang, L","first_name":"L"},{"first_name":"X","full_name":"Chen, X","last_name":"Chen"}],"ddc":["580"],"has_accepted_license":"1","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-10-17T12:32:37Z","file_date_updated":"2020-07-14T12:47:46Z","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"}],"type":"journal_article","date_created":"2019-11-12T11:42:05Z","quality_controlled":"1","language":[{"iso":"eng"}],"article_processing_charge":"No"},{"doi":"10.1007/s40314-019-0955-9","intvolume":" 38","month":"12","_id":"7000","title":"Convergence analysis of projection method for variational inequalities","date_published":"2019-12-01T00:00:00Z","ec_funded":1,"isi":1,"article_type":"original","volume":38,"author":[{"full_name":"Shehu, Yekini","last_name":"Shehu","orcid":"0000-0001-9224-7139","first_name":"Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87"},{"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"}],"ddc":["510","515","518"],"has_accepted_license":"1","year":"2019","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-30T07:20:32Z","article_number":"161","project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"}],"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"}],"date_created":"2019-11-12T12:41:44Z","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1007/s40314-019-0955-9","open_access":"1"}],"quality_controlled":"1","language":[{"iso":"eng"}],"article_processing_charge":"No","oa_version":"Published Version","status":"public","publication_identifier":{"eissn":["1807-0302"],"issn":["2238-3603"]},"scopus_import":"1","citation":{"short":"Y. Shehu, O.S. Iyiola, X.-H. Li, Q.-L. Dong, Computational and Applied Mathematics 38 (2019).","mla":"Shehu, Yekini, et al. “Convergence Analysis of Projection Method for Variational Inequalities.” Computational and Applied Mathematics, vol. 38, no. 4, 161, Springer Nature, 2019, doi:10.1007/s40314-019-0955-9.","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.","ieee":"Y. Shehu, O. S. Iyiola, X.-H. Li, and Q.-L. Dong, “Convergence analysis of projection method for variational inequalities,” Computational and Applied Mathematics, vol. 38, no. 4. Springer Nature, 2019.","ama":"Shehu Y, Iyiola OS, Li X-H, Dong Q-L. Convergence analysis of projection method for variational inequalities. Computational and Applied Mathematics. 2019;38(4). doi:10.1007/s40314-019-0955-9","apa":"Shehu, Y., Iyiola, O. S., Li, X.-H., & Dong, Q.-L. (2019). Convergence analysis of projection method for variational inequalities. Computational and Applied Mathematics. Springer Nature. https://doi.org/10.1007/s40314-019-0955-9","chicago":"Shehu, Yekini, Olaniyi S. Iyiola, Xiao-Huan Li, and Qiao-Li Dong. “Convergence Analysis of Projection Method for Variational Inequalities.” Computational and Applied Mathematics. Springer Nature, 2019. https://doi.org/10.1007/s40314-019-0955-9."},"publication":"Computational and Applied Mathematics","publisher":"Springer Nature","day":"01","external_id":{"isi":["000488973100005"],"arxiv":["2101.09081"]},"arxiv":1,"issue":"4","publication_status":"published","department":[{"_id":"VlKo"}],"oa":1},{"ddc":["570"],"has_accepted_license":"1","article_type":"original","volume":179,"author":[{"id":"3436488C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5130-2226","first_name":"Cornelia","full_name":"Schwayer, Cornelia","last_name":"Schwayer"},{"first_name":"Shayan","last_name":"Shamipour","full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","first_name":"Kornelija","full_name":"Pranjic-Ferscha, Kornelija","last_name":"Pranjic-Ferscha"},{"id":"30A536BA-F248-11E8-B48F-1D18A9856A87","last_name":"Schauer","full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142","first_name":"Alexandra"},{"full_name":"Balda, M","last_name":"Balda","first_name":"M"},{"first_name":"M","last_name":"Tada","full_name":"Tada, M"},{"first_name":"K","full_name":"Matter, K","last_name":"Matter"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"date_published":"2019-10-31T00:00:00Z","isi":1,"page":"937-952.e18","intvolume":" 179","doi":"10.1016/j.cell.2019.10.006","_id":"7001","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"month":"10","title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","language":[{"iso":"eng"}],"article_processing_charge":"No","quality_controlled":"1","file_date_updated":"2020-10-21T07:09:45Z","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020"}],"date_created":"2019-11-12T12:51:06Z","type":"journal_article","year":"2019","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2024-03-25T23:30:21Z","external_id":{"pmid":["31675500"],"isi":["000493898000012"]},"day":"31","publisher":"Cell Press","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"citation":{"short":"C. Schwayer, S. Shamipour, K. Pranjic-Ferscha, A. Schauer, M. Balda, M. Tada, K. Matter, C.-P.J. Heisenberg, Cell 179 (2019) 937–952.e18.","mla":"Schwayer, Cornelia, et al. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Cell, vol. 179, no. 4, Cell Press, 2019, p. 937–952.e18, doi:10.1016/j.cell.2019.10.006.","ieee":"C. Schwayer et al., “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” Cell, vol. 179, no. 4. Cell Press, p. 937–952.e18, 2019.","ista":"Schwayer C, Shamipour S, Pranjic-Ferscha K, Schauer A, Balda M, Tada M, Matter K, Heisenberg C-PJ. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 179(4), 937–952.e18.","ama":"Schwayer C, Shamipour S, Pranjic-Ferscha K, et al. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 2019;179(4):937-952.e18. doi:10.1016/j.cell.2019.10.006","apa":"Schwayer, C., Shamipour, S., Pranjic-Ferscha, K., Schauer, A., Balda, M., Tada, M., … Heisenberg, C.-P. J. (2019). Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. Cell Press. https://doi.org/10.1016/j.cell.2019.10.006","chicago":"Schwayer, Cornelia, Shayan Shamipour, Kornelija Pranjic-Ferscha, Alexandra Schauer, M Balda, M Tada, K Matter, and Carl-Philipp J Heisenberg. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Cell. Cell Press, 2019. https://doi.org/10.1016/j.cell.2019.10.006."},"scopus_import":"1","publication":"Cell","oa_version":"Submitted Version","status":"public","department":[{"_id":"CaHe"},{"_id":"BjHo"}],"oa":1,"issue":"4","publication_status":"published","pmid":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"7186"},{"relation":"dissertation_contains","id":"8350","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/biochemistry-meets-mechanics-the-sensitive-nature-of-cell-cell-contact-formation-in-embryo-development/","relation":"press_release","description":"News auf IST Website"}]},"file":[{"content_type":"application/pdf","date_updated":"2020-10-21T07:09:45Z","file_size":8805878,"relation":"main_file","file_name":"2019_Cell_Schwayer_accepted.pdf","date_created":"2020-10-21T07:09:45Z","creator":"dernst","checksum":"33dac4bb77ee630e2666e936b4d57980","success":1,"access_level":"open_access","file_id":"8684"}]},{"department":[{"_id":"ChWo"}],"issue":"4","publication_status":"published","external_id":{"isi":["000475740600011"]},"publisher":"ACM","day":"01","publication_identifier":{"issn":["0730-0301"]},"citation":{"mla":"Kondapaneni, Ivo, et al. “Optimal Multiple Importance Sampling.” ACM Transactions on Graphics, vol. 38, no. 4, 37, ACM, 2019, doi:10.1145/3306346.3323009.","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.","ieee":"I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, and J. Křivánek, “Optimal multiple importance sampling,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.","ama":"Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J. Optimal multiple importance sampling. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3323009","chicago":"Kondapaneni, Ivo, Petr Vevoda, Pascal Grittmann, Tomas Skrivan, Philipp Slusallek, and Jaroslav Křivánek. “Optimal Multiple Importance Sampling.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3323009.","apa":"Kondapaneni, I., Vevoda, P., Grittmann, P., Skrivan, T., Slusallek, P., & Křivánek, J. (2019). Optimal multiple importance sampling. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3323009","short":"I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, J. Křivánek, ACM Transactions on Graphics 38 (2019)."},"scopus_import":"1","publication":"ACM Transactions on Graphics","oa_version":"None","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","quality_controlled":"1","project":[{"_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841","name":"Distributed 3D Object Design","call_identifier":"H2020"}],"abstract":[{"lang":"eng","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."}],"date_created":"2019-11-12T13:05:40Z","type":"journal_article","year":"2019","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"37","date_updated":"2023-08-30T07:21:25Z","article_type":"original","volume":38,"author":[{"first_name":"Ivo","full_name":"Kondapaneni, Ivo","last_name":"Kondapaneni"},{"first_name":"Petr","last_name":"Vevoda","full_name":"Vevoda, Petr"},{"first_name":"Pascal","last_name":"Grittmann","full_name":"Grittmann, Pascal"},{"id":"486A5A46-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","full_name":"Skrivan, Tomas","last_name":"Skrivan"},{"last_name":"Slusallek","full_name":"Slusallek, Philipp","first_name":"Philipp"},{"last_name":"Křivánek","full_name":"Křivánek, Jaroslav","first_name":"Jaroslav"}],"ec_funded":1,"date_published":"2019-07-01T00:00:00Z","isi":1,"intvolume":" 38","doi":"10.1145/3306346.3323009","_id":"7002","month":"07","title":"Optimal multiple importance sampling"},{"oa":1,"department":[{"_id":"SiHi"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","issue":"5","pmid":1,"file":[{"date_created":"2020-02-05T10:30:02Z","relation":"main_file","file_name":"2019_JournNeurochemistry_Cheung.pdf","date_updated":"2020-07-14T12:47:47Z","file_size":4334962,"content_type":"application/pdf","file_id":"7452","access_level":"open_access","checksum":"ec1fb2aebb874009bc309adaada6e1d7","creator":"dernst"}],"external_id":{"pmid":["31479508"],"isi":["000490703100001"]},"day":"01","publisher":"Wiley","publication":"Journal of Neurochemistry","scopus_import":"1","citation":{"ama":"Cheung GT, Cousin MA. Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. Journal of Neurochemistry. 2019;151(5):570-583. doi:10.1111/jnc.14862","apa":"Cheung, G. T., & Cousin, M. A. (2019). Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. Journal of Neurochemistry. Wiley. https://doi.org/10.1111/jnc.14862","chicago":"Cheung, Giselle T, and Michael A. Cousin. “Synaptic Vesicle Generation from Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent Dynamin–Syndapin Interaction.” Journal of Neurochemistry. Wiley, 2019. https://doi.org/10.1111/jnc.14862.","mla":"Cheung, Giselle T., and Michael A. Cousin. “Synaptic Vesicle Generation from Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent Dynamin–Syndapin Interaction.” Journal of Neurochemistry, vol. 151, no. 5, Wiley, 2019, pp. 570–83, doi:10.1111/jnc.14862.","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.","ieee":"G. T. Cheung and M. A. Cousin, “Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction,” Journal of Neurochemistry, vol. 151, no. 5. Wiley, pp. 570–583, 2019.","short":"G.T. Cheung, M.A. Cousin, Journal of Neurochemistry 151 (2019) 570–583."},"publication_identifier":{"issn":["0022-3042"],"eissn":["1471-4159"]},"status":"public","oa_version":"Published Version","article_processing_charge":"No","language":[{"iso":"eng"}],"quality_controlled":"1","date_created":"2019-11-12T14:37:08Z","type":"journal_article","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"}],"file_date_updated":"2020-07-14T12:47:47Z","date_updated":"2023-08-30T07:21:50Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2019","has_accepted_license":"1","ddc":["570"],"author":[{"last_name":"Cheung","full_name":"Cheung, Giselle T","first_name":"Giselle T","orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cousin","full_name":"Cousin, Michael A.","first_name":"Michael A."}],"volume":151,"article_type":"original","page":"570-583","isi":1,"date_published":"2019-12-01T00:00:00Z","_id":"7005","month":"12","title":"Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction","doi":"10.1111/jnc.14862","intvolume":" 151"},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"MaMo"}],"oa":1,"issue":"10","publication_status":"published","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"6675"}]},"file":[{"checksum":"267756d8f9db572f496cd1663c89d59a","creator":"dernst","file_id":"7008","access_level":"open_access","file_size":696791,"date_updated":"2020-07-14T12:47:47Z","content_type":"application/pdf","date_created":"2019-11-12T14:48:45Z","file_name":"2019_Algorithms_Mondelli.pdf","relation":"main_file"}],"external_id":{"arxiv":["1801.03153"]},"arxiv":1,"publisher":"MDPI","day":"18","publication_identifier":{"issn":["1999-4893"]},"scopus_import":1,"citation":{"apa":"Mondelli, M., Hassani, S. H., & Urbanke, R. (2019). A new coding paradigm for the primitive relay channel. Algorithms. MDPI. https://doi.org/10.3390/a12100218","chicago":"Mondelli, Marco, S. Hamed Hassani, and Rüdiger Urbanke. “A New Coding Paradigm for the Primitive Relay Channel.” Algorithms. MDPI, 2019. https://doi.org/10.3390/a12100218.","ama":"Mondelli M, Hassani SH, Urbanke R. A new coding paradigm for the primitive relay channel. Algorithms. 2019;12(10). doi:10.3390/a12100218","ieee":"M. Mondelli, S. H. Hassani, and R. Urbanke, “A new coding paradigm for the primitive relay channel,” Algorithms, vol. 12, no. 10. MDPI, 2019.","ista":"Mondelli M, Hassani SH, Urbanke R. 2019. A new coding paradigm for the primitive relay channel. Algorithms. 12(10), 218.","mla":"Mondelli, Marco, et al. “A New Coding Paradigm for the Primitive Relay Channel.” Algorithms, vol. 12, no. 10, 218, MDPI, 2019, doi:10.3390/a12100218.","short":"M. Mondelli, S.H. Hassani, R. Urbanke, Algorithms 12 (2019)."},"publication":"Algorithms","oa_version":"Published Version","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","file_date_updated":"2020-07-14T12:47:47Z","abstract":[{"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.","lang":"eng"}],"type":"journal_article","date_created":"2019-11-12T14:46:19Z","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T12:49:28Z","article_number":"218","ddc":["510"],"has_accepted_license":"1","article_type":"original","volume":12,"author":[{"id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","first_name":"Marco","last_name":"Mondelli","full_name":"Mondelli, Marco"},{"first_name":"S. Hamed","full_name":"Hassani, S. Hamed","last_name":"Hassani"},{"full_name":"Urbanke, Rüdiger","last_name":"Urbanke","first_name":"Rüdiger"}],"date_published":"2019-10-18T00:00:00Z","intvolume":" 12","doi":"10.3390/a12100218","_id":"7007","month":"10","title":"A new coding paradigm for the primitive relay channel"},{"publication_status":"published","issue":"12","department":[{"_id":"MiSi"}],"pmid":1,"day":"01","publisher":"Springer Nature","external_id":{"isi":["000497966900007"],"pmid":["31582855"]},"status":"public","oa_version":"None","publication":"Nature Reviews Molecular Cell Biology","publication_identifier":{"issn":["1471-0072"],"eissn":["1471-0080"]},"citation":{"short":"K. Yamada, M.K. Sixt, Nature Reviews Molecular Cell Biology 20 (2019) 738–752.","ama":"Yamada K, Sixt MK. Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. 2019;20(12):738–752. doi:10.1038/s41580-019-0172-9","apa":"Yamada, K., & Sixt, M. K. (2019). Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. Springer Nature. https://doi.org/10.1038/s41580-019-0172-9","chicago":"Yamada, KM, and Michael K Sixt. “Mechanisms of 3D Cell Migration.” Nature Reviews Molecular Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41580-019-0172-9.","mla":"Yamada, KM, and Michael K. Sixt. “Mechanisms of 3D Cell Migration.” Nature Reviews Molecular Cell Biology, vol. 20, no. 12, Springer Nature, 2019, pp. 738–752, doi:10.1038/s41580-019-0172-9.","ieee":"K. Yamada and M. K. Sixt, “Mechanisms of 3D cell migration,” Nature Reviews Molecular Cell Biology, vol. 20, no. 12. Springer Nature, pp. 738–752, 2019.","ista":"Yamada K, Sixt MK. 2019. Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. 20(12), 738–752."},"scopus_import":"1","quality_controlled":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-30T07:22:20Z","year":"2019","abstract":[{"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.","lang":"eng"}],"type":"journal_article","date_created":"2019-11-12T14:54:42Z","volume":20,"author":[{"first_name":"KM","full_name":"Yamada, KM","last_name":"Yamada"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"article_type":"review","_id":"7009","month":"12","title":"Mechanisms of 3D cell migration","doi":"10.1038/s41580-019-0172-9","intvolume":" 20","page":"738–752","date_published":"2019-12-01T00:00:00Z","isi":1},{"article_number":"110760V","date_updated":"2023-08-29T06:54:38Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2019","date_created":"2019-11-12T15:10:18Z","type":"conference","abstract":[{"lang":"eng","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."}],"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-02368135/file/110760V.pdf"}],"quality_controlled":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"7010","month":"07","title":"Blood cell-vessel wall interactions probed by reflection interference contrast microscopy","intvolume":" 11076","doi":"10.1117/12.2527058","isi":1,"date_published":"2019-07-22T00:00:00Z","author":[{"full_name":"Davies, Heather S.","last_name":"Davies","first_name":"Heather S."},{"full_name":"Baranova, Natalia S.","last_name":"Baranova","first_name":"Natalia S.","orcid":"0000-0002-3086-9124","id":"38661662-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nouha","last_name":"El Amri","full_name":"El Amri, Nouha"},{"first_name":"Liliane","full_name":"Coche-Guérente, Liliane","last_name":"Coche-Guérente"},{"first_name":"Claude","full_name":"Verdier, Claude","last_name":"Verdier"},{"full_name":"Bureau, Lionel","last_name":"Bureau","first_name":"Lionel"},{"first_name":"Ralf P.","last_name":"Richter","full_name":"Richter, Ralf P."},{"last_name":"Débarre","full_name":"Débarre, Delphine","first_name":"Delphine"}],"volume":11076,"publication_status":"published","oa":1,"department":[{"_id":"MaLo"}],"status":"public","oa_version":"Published Version","publication":"Advances in Microscopic Imaging II","citation":{"mla":"Davies, Heather S., et al. “Blood Cell-Vessel Wall Interactions Probed by Reflection Interference Contrast Microscopy.” Advances in Microscopic Imaging II, vol. 11076, 110760V, SPIE, 2019, doi:10.1117/12.2527058.","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.","ieee":"H. S. Davies et al., “Blood cell-vessel wall interactions probed by reflection interference contrast microscopy,” in Advances in Microscopic Imaging II, Munich, Germany, 2019, vol. 11076.","ama":"Davies HS, Baranova NS, El Amri N, et al. Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. In: Advances in Microscopic Imaging II. Vol 11076. SPIE; 2019. doi:10.1117/12.2527058","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 Advances in Microscopic Imaging II (Vol. 11076). Munich, Germany: SPIE. https://doi.org/10.1117/12.2527058","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 Advances in Microscopic Imaging II, Vol. 11076. SPIE, 2019. https://doi.org/10.1117/12.2527058.","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."},"scopus_import":"1","publication_identifier":{"isbn":["9781510628458"],"issn":["1605-7422"]},"conference":{"start_date":"2019-06-26","end_date":"2019-06-27","name":"European Conferences on Biomedical Optics","location":"Munich, Germany"},"publisher":"SPIE","day":"22","external_id":{"isi":["000535353000023"]}},{"article_processing_charge":"No","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.04043"}],"quality_controlled":"1","type":"journal_article","date_created":"2019-11-13T08:25:48Z","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"}],"article_number":"134504","date_updated":"2024-02-28T13:13:13Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","author":[{"first_name":"Tuure","full_name":"Orell, Tuure","last_name":"Orell"},{"last_name":"Michailidis","full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064","first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maksym","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Silveri, Matti","last_name":"Silveri","first_name":"Matti"}],"volume":100,"article_type":"original","isi":1,"date_published":"2019-10-01T00:00:00Z","_id":"7013","month":"10","title":"Probing the many-body localization phase transition with superconducting circuits","intvolume":" 100","doi":"10.1103/physrevb.100.134504","oa":1,"department":[{"_id":"MaSe"}],"publication_status":"published","issue":"13","arxiv":1,"external_id":{"arxiv":["1907.04043"],"isi":["000489036500004"]},"publisher":"American Physical Society","day":"01","publication":"Physical Review B","scopus_import":"1","citation":{"ama":"Orell T, Michailidis A, Serbyn M, Silveri M. Probing the many-body localization phase transition with superconducting circuits. Physical Review B. 2019;100(13). doi:10.1103/physrevb.100.134504","chicago":"Orell, Tuure, Alexios Michailidis, Maksym Serbyn, and Matti Silveri. “Probing the Many-Body Localization Phase Transition with Superconducting Circuits.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.134504.","apa":"Orell, T., Michailidis, A., Serbyn, M., & Silveri, M. (2019). Probing the many-body localization phase transition with superconducting circuits. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.100.134504","mla":"Orell, Tuure, et al. “Probing the Many-Body Localization Phase Transition with Superconducting Circuits.” Physical Review B, vol. 100, no. 13, 134504, American Physical Society, 2019, doi:10.1103/physrevb.100.134504.","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.","ieee":"T. Orell, A. Michailidis, M. Serbyn, and M. Silveri, “Probing the many-body localization phase transition with superconducting circuits,” Physical Review B, vol. 100, no. 13. American Physical Society, 2019.","short":"T. Orell, A. Michailidis, M. Serbyn, M. Silveri, Physical Review B 100 (2019)."},"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"status":"public","oa_version":"Preprint"},{"author":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"}],"volume":41,"article_type":"original","isi":1,"date_published":"2019-10-01T00:00:00Z","ec_funded":1,"title":"Non-polynomial worst-case analysis of recursive programs","_id":"7014","month":"10","intvolume":" 41","doi":"10.1145/3339984","article_processing_charge":"No","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.00317"}],"quality_controlled":"1","type":"journal_article","date_created":"2019-11-13T08:33:43Z","abstract":[{"lang":"eng","text":"We study the problem of developing efficient approaches for proving\r\nworst-case bounds of non-deterministic recursive programs. Ranking functions\r\nare sound and complete for proving termination and worst-case bounds of\r\nnonrecursive programs. First, we apply ranking functions to recursion,\r\nresulting in measure functions. We show that measure functions provide a sound\r\nand complete approach to prove worst-case bounds of non-deterministic recursive\r\nprograms. Our second contribution is the synthesis of measure functions in\r\nnonpolynomial forms. We show that non-polynomial measure functions with\r\nlogarithm and exponentiation can be synthesized through abstraction of\r\nlogarithmic or exponentiation terms, Farkas' Lemma, and Handelman's Theorem\r\nusing linear programming. While previous methods obtain worst-case polynomial\r\nbounds, our approach can synthesize bounds of the form $\\mathcal{O}(n\\log n)$\r\nas well as $\\mathcal{O}(n^r)$ where $r$ is not an integer. We present\r\nexperimental results to demonstrate that our approach can obtain efficiently\r\nworst-case bounds of classical recursive algorithms such as (i) Merge-Sort, the\r\ndivide-and-conquer algorithm for the Closest-Pair problem, where we obtain\r\n$\\mathcal{O}(n \\log n)$ worst-case bound, and (ii) Karatsuba's algorithm for\r\npolynomial multiplication and Strassen's algorithm for matrix multiplication,\r\nwhere we obtain $\\mathcal{O}(n^r)$ bound such that $r$ is not an integer and\r\nclose to the best-known bounds for the respective algorithms."}],"project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"}],"article_number":"20","date_updated":"2025-06-02T08:53:47Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2019","arxiv":1,"external_id":{"isi":["000564108400001"],"arxiv":["1705.00317"]},"publisher":"ACM","day":"01","publication":"ACM Transactions on Programming Languages and Systems","citation":{"short":"K. Chatterjee, H. Fu, A.K. Goharshady, ACM Transactions on Programming Languages and Systems 41 (2019).","ista":"Chatterjee K, Fu H, Goharshady AK. 2019. Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. 41(4), 20.","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Non-polynomial worst-case analysis of recursive programs,” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4. ACM, 2019.","mla":"Chatterjee, Krishnendu, et al. “Non-Polynomial Worst-Case Analysis of Recursive Programs.” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4, 20, ACM, 2019, doi:10.1145/3339984.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Non-Polynomial Worst-Case Analysis of Recursive Programs.” ACM Transactions on Programming Languages and Systems. ACM, 2019. https://doi.org/10.1145/3339984.","apa":"Chatterjee, K., Fu, H., & Goharshady, A. K. (2019). Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. ACM. https://doi.org/10.1145/3339984","ama":"Chatterjee K, Fu H, Goharshady AK. Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. 2019;41(4). doi:10.1145/3339984"},"scopus_import":"1","status":"public","oa_version":"Preprint","oa":1,"department":[{"_id":"KrCh"}],"publication_status":"published","issue":"4","related_material":{"record":[{"status":"public","id":"639","relation":"earlier_version"},{"relation":"dissertation_contains","status":"public","id":"8934"}]}},{"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."}],"date_created":"2019-11-13T08:41:48Z","type":"journal_article","project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-28T13:13:23Z","article_number":"035127","year":"2019","article_processing_charge":"No","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1905.09138","open_access":"1"}],"quality_controlled":"1","date_published":"2019-07-25T00:00:00Z","ec_funded":1,"isi":1,"title":"Floating Wigner crystal with no boundary charge fluctuations","_id":"7015","month":"07","doi":"10.1103/physrevb.100.035127","intvolume":" 100","volume":100,"author":[{"first_name":"Mathieu","last_name":"Lewin","full_name":"Lewin, Mathieu"},{"first_name":"Elliott H.","last_name":"Lieb","full_name":"Lieb, Elliott H."},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"article_type":"original","department":[{"_id":"RoSe"}],"oa":1,"publication_status":"published","issue":"3","publication":"Physical Review B","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"citation":{"short":"M. Lewin, E.H. Lieb, R. Seiringer, Physical Review B 100 (2019).","ama":"Lewin M, Lieb EH, Seiringer R. Floating Wigner crystal with no boundary charge fluctuations. Physical Review B. 2019;100(3). doi:10.1103/physrevb.100.035127","chicago":"Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “Floating Wigner Crystal with No Boundary Charge Fluctuations.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.035127.","apa":"Lewin, M., Lieb, E. H., & Seiringer, R. (2019). Floating Wigner crystal with no boundary charge fluctuations. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.100.035127","mla":"Lewin, Mathieu, et al. “Floating Wigner Crystal with No Boundary Charge Fluctuations.” Physical Review B, vol. 100, no. 3, 035127, American Physical Society, 2019, doi:10.1103/physrevb.100.035127.","ieee":"M. Lewin, E. H. Lieb, and R. Seiringer, “Floating Wigner crystal with no boundary charge fluctuations,” Physical Review B, vol. 100, no. 3. American Physical Society, 2019.","ista":"Lewin M, Lieb EH, Seiringer R. 2019. Floating Wigner crystal with no boundary charge fluctuations. Physical Review B. 100(3), 035127."},"scopus_import":"1","status":"public","oa_version":"Preprint","external_id":{"arxiv":["1905.09138"],"isi":["000477888200001"]},"arxiv":1,"publisher":"American Physical Society","day":"25"},{"ddc":["576"],"has_accepted_license":"1","author":[{"orcid":"0000-0001-6197-363X","first_name":"Isabella","last_name":"Tomanek","full_name":"Tomanek, Isabella","id":"3981F020-F248-11E8-B48F-1D18A9856A87"}],"day":"13","publisher":"Institute of Science and Technology Austria","citation":{"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, 10.15479/AT:ISTA:7016.","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.","mla":"Tomanek, Isabella. Data for the Paper “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7016.","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. https://doi.org/10.15479/AT:ISTA:7016","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. https://doi.org/10.15479/AT:ISTA:7016.","ama":"Tomanek I. Data for the paper “Gene amplification as a form of population-level gene expression regulation.” 2019. doi:10.15479/AT:ISTA:7016","short":"I. 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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."}],"year":"2019","file":[{"description":"Illumina whole genome sequence data for Locus 1 - amplified.","file_id":"7017","access_level":"open_access","checksum":"72441055043eda4cbf1398a422e2c118","creator":"itomanek","date_created":"2019-11-13T08:52:21Z","file_name":"D8_S35_R2_001.fastq","relation":"main_file","title":"Locus1_amplified","file_size":2456192500,"date_updated":"2020-07-14T12:47:47Z","content_type":"application/octet-stream"},{"creator":"itomanek","checksum":"a4ac50bf655d9c751f0305ade5c2ee16","access_level":"open_access","description":"Illumina whole genome sequence data for Locus 1 - ancestral.","file_id":"7018","content_type":"application/octet-stream","file_size":2833452234,"date_updated":"2020-07-14T12:47:47Z","title":"Locus1_ancestral","relation":"main_file","file_name":"IT028_S11_R2_001.fastq","date_created":"2019-11-13T08:52:59Z"},{"date_created":"2019-11-13T08:54:10Z","file_name":"D8-DOG1_S47_R2_001.fastq","relation":"main_file","date_updated":"2020-07-14T12:47:47Z","file_size":2878017264,"title":"Locus1_amplified_DOG","content_type":"application/octet-stream","description":"Illumina whole genome sequence data for Locus 1 - 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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"}],"type":"journal_article","date_created":"2019-11-15T10:51:42Z","file_date_updated":"2020-07-14T12:47:48Z","project":[{"call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions"},{"name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"}],"volume":9,"author":[{"first_name":"Martin","orcid":"0000-0001-6549-4177","full_name":"Lukacisin, Martin","last_name":"Lukacisin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4398-476X","first_name":"Tobias","full_name":"Bollenbach, Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","has_accepted_license":"1","ddc":["570"],"_id":"7026","acknowledged_ssus":[{"_id":"LifeSc"}],"title":"Emergent gene expression responses to drug combinations predict higher-order drug interactions","month":"11","intvolume":" 9","doi":"10.1016/j.cels.2019.10.004","page":"423-433.e1-e3","date_published":"2019-11-27T00:00:00Z","isi":1,"publication_status":"published","issue":"5","department":[{"_id":"ToBo"}],"oa":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"access_level":"open_access","file_id":"7027","creator":"dernst","checksum":"7a11d6c2f9523d65b049512d61733178","file_name":"2019_CellSystems_Lukacisin.pdf","relation":"main_file","date_created":"2019-11-15T10:57:42Z","content_type":"application/pdf","date_updated":"2020-07-14T12:47:48Z","file_size":4238460}],"publisher":"Cell Press","day":"27","external_id":{"isi":["000499495400003"]},"status":"public","oa_version":"Published Version","publication":"Cell Systems","publication_identifier":{"issn":["2405-4712"]},"scopus_import":"1","citation":{"ama":"Lukacisin M, Bollenbach MT. Emergent gene expression responses to drug combinations predict higher-order drug interactions. Cell Systems. 2019;9(5):423-433.e1-e3. doi:10.1016/j.cels.2019.10.004","apa":"Lukacisin, M., & Bollenbach, M. T. (2019). Emergent gene expression responses to drug combinations predict higher-order drug interactions. Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2019.10.004","chicago":"Lukacisin, Martin, and Mark Tobias Bollenbach. “Emergent Gene Expression Responses to Drug Combinations Predict Higher-Order Drug Interactions.” Cell Systems. Cell Press, 2019. https://doi.org/10.1016/j.cels.2019.10.004.","mla":"Lukacisin, Martin, and Mark Tobias Bollenbach. “Emergent Gene Expression Responses to Drug Combinations Predict Higher-Order Drug Interactions.” Cell Systems, vol. 9, no. 5, Cell Press, 2019, pp. 423-433.e1-e3, doi:10.1016/j.cels.2019.10.004.","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.","ieee":"M. Lukacisin and M. T. Bollenbach, “Emergent gene expression responses to drug combinations predict higher-order drug interactions,” Cell Systems, 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."}},{"date_published":"2019-10-17T00:00:00Z","publication_identifier":{"isbn":["9781728104690"]},"isi":1,"citation":{"short":"A.R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kuamri, H.G.L. Schwefel, in:, 2019 Conference on Lasers and Electro-Optics Europe & 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.” 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, 8873300, IEEE, 2019, doi:10.1109/cleoe-eqec.2019.8873300.","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 & European Quantum Electronics Conference. CLEO: Conference on Lasers and Electro-Optics Europe, 8873300.","ieee":"A. R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kuamri, and H. G. L. 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Munich, Germany: IEEE. https://doi.org/10.1109/cleoe-eqec.2019.8873300","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 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. IEEE, 2019. https://doi.org/10.1109/cleoe-eqec.2019.8873300."},"scopus_import":"1","publication":"2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference","doi":"10.1109/cleoe-eqec.2019.8873300","oa_version":"None","_id":"7032","title":"Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators","status":"public","month":"10","external_id":{"isi":["000630002701617"]},"publisher":"IEEE","day":"17","conference":{"end_date":"2019-06-27","location":"Munich, Germany","name":"CLEO: Conference on Lasers and Electro-Optics Europe","start_date":"2019-06-23"},"author":[{"full_name":"Rueda Sanchez, Alfredo R","last_name":"Rueda Sanchez","orcid":"0000-0001-6249-5860","first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sedlmeir, Florian","last_name":"Sedlmeir","first_name":"Florian"},{"first_name":"Gerd","last_name":"Leuchs","full_name":"Leuchs, Gerd"},{"first_name":"Madhuri","last_name":"Kuamri","full_name":"Kuamri, Madhuri"},{"first_name":"Harald G. L.","full_name":"Schwefel, Harald G. L.","last_name":"Schwefel"}],"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"}],"type":"conference","date_created":"2019-11-18T13:58:22Z","year":"2019","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"8873300","date_updated":"2023-08-30T07:26:01Z","language":[{"iso":"eng"}],"department":[{"_id":"JoFi"}],"article_processing_charge":"No","publication_status":"published","quality_controlled":"1"},{"oa":1,"department":[{"_id":"UlWa"}],"issue":"6","publication_status":"published","citation":{"apa":"Fulek, R., & Kynčl, J. (2019). Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4. Combinatorica. Springer Nature. https://doi.org/10.1007/s00493-019-3905-7","chicago":"Fulek, Radoslav, and Jan Kynčl. “Counterexample to an Extension of the Hanani-Tutte Theorem on the Surface of Genus 4.” Combinatorica. Springer Nature, 2019. https://doi.org/10.1007/s00493-019-3905-7.","ama":"Fulek R, Kynčl J. Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4. Combinatorica. 2019;39(6):1267-1279. doi:10.1007/s00493-019-3905-7","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.","ieee":"R. Fulek and J. Kynčl, “Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4,” Combinatorica, vol. 39, no. 6. Springer Nature, pp. 1267–1279, 2019.","mla":"Fulek, Radoslav, and Jan Kynčl. “Counterexample to an Extension of the Hanani-Tutte Theorem on the Surface of Genus 4.” Combinatorica, vol. 39, no. 6, Springer Nature, 2019, pp. 1267–79, doi:10.1007/s00493-019-3905-7.","short":"R. Fulek, J. Kynčl, Combinatorica 39 (2019) 1267–1279."},"scopus_import":"1","publication_identifier":{"issn":["0209-9683"],"eissn":["1439-6912"]},"publication":"Combinatorica","oa_version":"Preprint","status":"public","arxiv":1,"external_id":{"arxiv":["1709.00508"],"isi":["000493267200003"]},"publisher":"Springer Nature","day":"29","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","grant_number":"M02281","name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF"}],"type":"journal_article","date_created":"2019-11-18T14:29:50Z","abstract":[{"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.","lang":"eng"}],"year":"2019","date_updated":"2023-08-30T07:26:25Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"article_processing_charge":"No","main_file_link":[{"url":"https://arxiv.org/abs/1709.00508","open_access":"1"}],"quality_controlled":"1","isi":1,"ec_funded":1,"date_published":"2019-10-29T00:00:00Z","page":"1267-1279","doi":"10.1007/s00493-019-3905-7","intvolume":" 39","_id":"7034","month":"10","title":"Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4","article_type":"original","author":[{"orcid":"0000-0001-8485-1774","first_name":"Radoslav","last_name":"Fulek","full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kynčl, Jan","last_name":"Kynčl","first_name":"Jan"}],"volume":39},{"date_created":"2019-11-18T15:39:53Z","type":"conference","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"}],"date_updated":"2021-01-12T08:11:33Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","oa":1,"article_processing_charge":"No","department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://www.kurims.kyoto-u.ac.jp/~kyodo/kokyuroku/contents/2125.html"}],"quality_controlled":"1","publication_status":"published","publication":"Kyoto RIMS Kôkyûroku","page":"34-41","citation":{"short":"G.P. Geher, T. Titkos, D. Virosztek, in:, Kyoto RIMS Kôkyûroku, Research Institute for Mathematical Sciences, Kyoto University, 2019, pp. 34–41.","ieee":"G. P. Geher, T. Titkos, and D. Virosztek, “Dirac masses and isometric rigidity,” in Kyoto RIMS Kôkyûroku, Kyoto, Japan, 2019, vol. 2125, pp. 34–41.","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.","mla":"Geher, Gyorgy Pal, et al. “Dirac Masses and Isometric Rigidity.” Kyoto RIMS Kôkyûroku, vol. 2125, Research Institute for Mathematical Sciences, Kyoto University, 2019, pp. 34–41.","apa":"Geher, G. P., Titkos, T., & Virosztek, D. (2019). Dirac masses and isometric rigidity. In Kyoto RIMS Kôkyûroku (Vol. 2125, pp. 34–41). Kyoto, Japan: Research Institute for Mathematical Sciences, Kyoto University.","chicago":"Geher, Gyorgy Pal, Tamas Titkos, and Daniel Virosztek. “Dirac Masses and Isometric Rigidity.” In Kyoto RIMS Kôkyûroku, 2125:34–41. Research Institute for Mathematical Sciences, Kyoto University, 2019.","ama":"Geher GP, Titkos T, Virosztek D. Dirac masses and isometric rigidity. In: Kyoto RIMS Kôkyûroku. Vol 2125. Research Institute for Mathematical Sciences, Kyoto University; 2019:34-41."},"date_published":"2019-01-30T00:00:00Z","_id":"7035","status":"public","month":"01","title":"Dirac masses and isometric rigidity","oa_version":"Submitted Version","intvolume":" 2125","author":[{"first_name":"Gyorgy Pal","last_name":"Geher","full_name":"Geher, Gyorgy Pal"},{"last_name":"Titkos","full_name":"Titkos, Tamas","first_name":"Tamas"},{"id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1109-5511","first_name":"Daniel","last_name":"Virosztek","full_name":"Virosztek, Daniel"}],"conference":{"end_date":"2019-01-30","location":"Kyoto, Japan","name":"Research on isometries as preserver problems and related topics","start_date":"2019-01-28"},"day":"30","volume":2125,"publisher":"Research Institute for Mathematical Sciences, Kyoto University"},{"publication_identifier":{"issn":["2166-532X"]},"citation":{"short":"K.R. Shirer, K.A. Modic, T. Zimmerling, M.D. Bachmann, M. König, P.J.W. Moll, L. Schoop, A.P. Mackenzie, APL Materials 7 (2019).","mla":"Shirer, Kent R., et al. “Out-of-Plane Transport in ZrSiS and ZrSiSe Microstructures.” APL Materials, vol. 7, no. 10, 101116, AIP, 2019, doi:10.1063/1.5124568.","ista":"Shirer KR, Modic KA, Zimmerling T, Bachmann MD, König M, Moll PJW, Schoop L, Mackenzie AP. 2019. Out-of-plane transport in ZrSiS and ZrSiSe microstructures. APL Materials. 7(10), 101116.","ieee":"K. R. Shirer et al., “Out-of-plane transport in ZrSiS and ZrSiSe microstructures,” APL Materials, vol. 7, no. 10. AIP, 2019.","ama":"Shirer KR, Modic KA, Zimmerling T, et al. Out-of-plane transport in ZrSiS and ZrSiSe microstructures. APL Materials. 2019;7(10). doi:10.1063/1.5124568","chicago":"Shirer, Kent R., Kimberly A Modic, Tino Zimmerling, Maja D. Bachmann, Markus König, Philip J. W. Moll, Leslie Schoop, and Andrew P. Mackenzie. “Out-of-Plane Transport in ZrSiS and ZrSiSe Microstructures.” APL Materials. AIP, 2019. https://doi.org/10.1063/1.5124568.","apa":"Shirer, K. R., Modic, K. A., Zimmerling, T., Bachmann, M. D., König, M., Moll, P. J. W., … Mackenzie, A. P. (2019). Out-of-plane transport in ZrSiS and ZrSiSe microstructures. APL Materials. AIP. https://doi.org/10.1063/1.5124568"},"publication":"APL Materials","oa_version":"Published Version","status":"public","publisher":"AIP","day":"17","file":[{"date_created":"2019-11-20T12:27:01Z","file_name":"2019_APL_Shirer.pdf","relation":"main_file","date_updated":"2020-07-14T12:47:48Z","file_size":2453220,"content_type":"application/pdf","file_id":"7087","access_level":"open_access","checksum":"142fe7b3e37d8e916071743bb194360d","creator":"dernst"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"issue":"10","publication_status":"published","date_published":"2019-10-17T00:00:00Z","intvolume":" 7","doi":"10.1063/1.5124568","month":"10","_id":"7055","title":"Out-of-plane transport in ZrSiS and ZrSiSe microstructures","ddc":["530"],"has_accepted_license":"1","article_type":"original","extern":"1","volume":7,"author":[{"first_name":"Kent R.","last_name":"Shirer","full_name":"Shirer, Kent R."},{"first_name":"Kimberly A","orcid":"0000-0001-9760-3147","last_name":"Modic","full_name":"Modic, Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425"},{"last_name":"Zimmerling","full_name":"Zimmerling, Tino","first_name":"Tino"},{"first_name":"Maja D.","last_name":"Bachmann","full_name":"Bachmann, Maja D."},{"last_name":"König","full_name":"König, Markus","first_name":"Markus"},{"last_name":"Moll","full_name":"Moll, Philip J. W.","first_name":"Philip J. W."},{"first_name":"Leslie","full_name":"Schoop, Leslie","last_name":"Schoop"},{"first_name":"Andrew P.","last_name":"Mackenzie","full_name":"Mackenzie, Andrew P."}],"file_date_updated":"2020-07-14T12:47:48Z","abstract":[{"lang":"eng","text":"A recent class of topological nodal-line semimetals with the general formula MSiX (M = Zr, Hf and X = S, Se, Te) has attracted much experimental and theoretical interest due to their properties, particularly their large magnetoresistances and high carrier mobilities. The plateletlike nature of the MSiX crystals and their extremely low residual resistivities make measurements of the resistivity along the [001] direction extremely challenging. To accomplish such measurements, microstructures of single crystals were prepared using focused ion beam techniques. Microstructures prepared in this manner have very well-defined geometries and maintain their high crystal quality, verified by the observations of quantum oscillations. We present magnetoresistance and quantum oscillation data for currents applied along both [001] and [100] in ZrSiS and ZrSiSe, which are consistent with the nontrivial topology of the Dirac line-node, as determined by a measured π Berry phase. Surprisingly, we find that, despite the three dimensional nature of both the Fermi surfaces of ZrSiS and ZrSiSe, both the resistivity anisotropy under applied magnetic fields and the in-plane angular dependent magnetoresistance differ considerably between the two compounds. Finally, we discuss the role microstructuring can play in the study of these materials and our ability to make these microstructures free-standing."}],"type":"journal_article","date_created":"2019-11-19T12:52:43Z","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:11:35Z","article_number":"101116","language":[{"iso":"eng"}],"article_processing_charge":"No","quality_controlled":"1"},{"date_published":"2019-09-03T00:00:00Z","_id":"7056","month":"09","title":"Persistent antiferromagnetic order in heavily overdoped Ca1−x La x FeAs2","doi":"10.1088/1361-648x/ab3b43","intvolume":" 31","volume":31,"extern":"1","author":[{"full_name":"Martino, Edoardo","last_name":"Martino","first_name":"Edoardo"},{"full_name":"Bachmann, Maja D","last_name":"Bachmann","first_name":"Maja D"},{"full_name":"Rossi, Lidia","last_name":"Rossi","first_name":"Lidia"},{"id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","full_name":"Modic, Kimberly A","last_name":"Modic","first_name":"Kimberly A","orcid":"0000-0001-9760-3147"},{"full_name":"Zivkovic, Ivica","last_name":"Zivkovic","first_name":"Ivica"},{"first_name":"Henrik M","full_name":"Rønnow, Henrik M","last_name":"Rønnow"},{"first_name":"Philip J W","last_name":"Moll","full_name":"Moll, Philip J W"},{"last_name":"Akrap","full_name":"Akrap, Ana","first_name":"Ana"},{"full_name":"Forró, László","last_name":"Forró","first_name":"László"},{"last_name":"Katrych","full_name":"Katrych, Sergiy","first_name":"Sergiy"}],"article_type":"original","abstract":[{"lang":"eng","text":"In the Ca1−x La x FeAs2 (1 1 2) family of pnictide superconductors, we have investigated a highly overdoped composition (x = 0.56), prepared by a high-pressure, high-temperature synthesis. Magnetic measurements show an antiferromagnetic transition at T N = 120 K, well above the one at lower doping (0.15 < x < 0.27).\r\n\r\nBelow the onset of long-range magnetic order at T N, the electrical resistivity is strongly reduced and is dominated by electron–electron interactions, as evident from its temperature dependence. The Seebeck coefficient shows a clear metallic behavior as in narrow band conductors. The temperature dependence of the Hall coefficient and the violation of Kohler's rule agree with the multiband character of the material. No superconductivity was observed down to 1.8 K. The success of the high-pressure synthesis encourages further investigations of the so far only partially explored phase diagram in this family of Iron-based high temperature superconductors.\r\n"}],"type":"journal_article","date_created":"2019-11-19T12:56:17Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:11:35Z","article_number":"485705","year":"2019","article_processing_charge":"No","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1905.08640","open_access":"1"}],"quality_controlled":"1","publication":"Journal of Physics: Condensed Matter","publication_identifier":{"eissn":["1361-648X"],"issn":["0953-8984"]},"citation":{"chicago":"Martino, Edoardo, Maja D Bachmann, Lidia Rossi, Kimberly A Modic, Ivica Zivkovic, Henrik M Rønnow, Philip J W Moll, Ana Akrap, László Forró, and Sergiy Katrych. “Persistent Antiferromagnetic Order in Heavily Overdoped Ca1−x La x FeAs2.” Journal of Physics: Condensed Matter. IOP Publishing, 2019. https://doi.org/10.1088/1361-648x/ab3b43.","apa":"Martino, E., Bachmann, M. D., Rossi, L., Modic, K. A., Zivkovic, I., Rønnow, H. M., … Katrych, S. (2019). Persistent antiferromagnetic order in heavily overdoped Ca1−x La x FeAs2. Journal of Physics: Condensed Matter. IOP Publishing. https://doi.org/10.1088/1361-648x/ab3b43","ama":"Martino E, Bachmann MD, Rossi L, et al. Persistent antiferromagnetic order in heavily overdoped Ca1−x La x FeAs2. Journal of Physics: Condensed Matter. 2019;31(48). doi:10.1088/1361-648x/ab3b43","ista":"Martino E, Bachmann MD, Rossi L, Modic KA, Zivkovic I, Rønnow HM, Moll PJW, Akrap A, Forró L, Katrych S. 2019. Persistent antiferromagnetic order in heavily overdoped Ca1−x La x FeAs2. Journal of Physics: Condensed Matter. 31(48), 485705.","ieee":"E. Martino et al., “Persistent antiferromagnetic order in heavily overdoped Ca1−x La x FeAs2,” Journal of Physics: Condensed Matter, vol. 31, no. 48. IOP Publishing, 2019.","mla":"Martino, Edoardo, et al. “Persistent Antiferromagnetic Order in Heavily Overdoped Ca1−x La x FeAs2.” Journal of Physics: Condensed Matter, vol. 31, no. 48, 485705, IOP Publishing, 2019, doi:10.1088/1361-648x/ab3b43.","short":"E. Martino, M.D. Bachmann, L. Rossi, K.A. Modic, I. Zivkovic, H.M. Rønnow, P.J.W. Moll, A. Akrap, L. Forró, S. Katrych, Journal of Physics: Condensed Matter 31 (2019)."},"status":"public","oa_version":"Preprint","external_id":{"arxiv":["1905.08640"]},"arxiv":1,"publisher":"IOP Publishing","day":"03","oa":1,"publication_status":"published","issue":"48"},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"issue":"1","publication_status":"published","file":[{"checksum":"3b5a7b316e1ff22aa0f89e8d1f1ace91","creator":"dernst","file_id":"7086","access_level":"open_access","date_updated":"2020-07-14T12:47:48Z","file_size":3256400,"content_type":"application/pdf","date_created":"2019-11-20T12:24:13Z","relation":"main_file","file_name":"2019_ScientificReports_Modic.pdf"}],"day":"14","publisher":"Springer Nature","citation":{"short":"K.A. Modic, T. Meng, F. Ronning, E.D. Bauer, P.J.W. Moll, B.J. Ramshaw, Scientific Reports 9 (2019).","ieee":"K. A. Modic, T. Meng, F. Ronning, E. D. Bauer, P. J. W. Moll, and B. J. Ramshaw, “Thermodynamic signatures of Weyl fermions in NbP,” Scientific Reports, vol. 9, no. 1. Springer Nature, 2019.","ista":"Modic KA, Meng T, Ronning F, Bauer ED, Moll PJW, Ramshaw BJ. 2019. Thermodynamic signatures of Weyl fermions in NbP. Scientific Reports. 9(1), 2095.","mla":"Modic, Kimberly A., et al. “Thermodynamic Signatures of Weyl Fermions in NbP.” Scientific Reports, vol. 9, no. 1, 2095, Springer Nature, 2019, doi:10.1038/s41598-018-38161-7.","chicago":"Modic, Kimberly A, Tobias Meng, Filip Ronning, Eric D. Bauer, Philip J. W. Moll, and B. J. Ramshaw. “Thermodynamic Signatures of Weyl Fermions in NbP.” Scientific Reports. Springer Nature, 2019. https://doi.org/10.1038/s41598-018-38161-7.","apa":"Modic, K. A., Meng, T., Ronning, F., Bauer, E. D., Moll, P. J. W., & Ramshaw, B. J. (2019). Thermodynamic signatures of Weyl fermions in NbP. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-018-38161-7","ama":"Modic KA, Meng T, Ronning F, Bauer ED, Moll PJW, Ramshaw BJ. Thermodynamic signatures of Weyl fermions in NbP. Scientific Reports. 2019;9(1). doi:10.1038/s41598-018-38161-7"},"publication_identifier":{"issn":["2045-2322"]},"publication":"Scientific Reports","oa_version":"Published Version","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:48Z","date_created":"2019-11-19T13:00:35Z","type":"journal_article","abstract":[{"lang":"eng","text":"We present a high magnetic field study of NbP—a member of the monopnictide Weyl semimetal (WSM) family. While the monoarsenides (NbAs and TaAs) have topologically distinct left and right-handed Weyl fermi surfaces, NbP is argued to be “topologically trivial” due to the fact that all pairs of Weyl nodes are encompassed by a single Fermi surface. We use torque magnetometry to measure the magnetic response of NbP up to 60 tesla and uncover a Berry paramagnetic response, characteristic of the topological Weyl nodes, across the entire field range. At the quantum limit B* (≈32 T), τ/B experiences a change in slope when the chemical potential enters the last Landau level. Our calculations confirm that this magnetic response arises from band topology of the Weyl pocket, even though the Fermi surface encompasses both Weyl nodes at zero magnetic field. We also find that the magnetic field pulls the chemical potential to the chiral n = 0 Landau level in the quantum limit, providing a disorder-free way of accessing chiral Weyl fermions in systems that are “not quite” WSMs in zero magnetic field."}],"year":"2019","date_updated":"2021-01-12T08:11:36Z","article_number":"2095","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"has_accepted_license":"1","article_type":"original","author":[{"id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","orcid":"0000-0001-9760-3147","first_name":"Kimberly A","last_name":"Modic","full_name":"Modic, Kimberly A"},{"first_name":"Tobias","last_name":"Meng","full_name":"Meng, Tobias"},{"full_name":"Ronning, Filip","last_name":"Ronning","first_name":"Filip"},{"last_name":"Bauer","full_name":"Bauer, Eric D.","first_name":"Eric D."},{"last_name":"Moll","full_name":"Moll, Philip J. W.","first_name":"Philip J. W."},{"full_name":"Ramshaw, B. J.","last_name":"Ramshaw","first_name":"B. J."}],"volume":9,"extern":"1","date_published":"2019-02-14T00:00:00Z","doi":"10.1038/s41598-018-38161-7","intvolume":" 9","month":"02","_id":"7057","title":"Thermodynamic signatures of Weyl fermions in NbP"},{"author":[{"first_name":"Maja D.","full_name":"Bachmann, Maja D.","last_name":"Bachmann"},{"full_name":"Ferguson, G. M.","last_name":"Ferguson","first_name":"G. M."},{"first_name":"Florian","last_name":"Theuss","full_name":"Theuss, Florian"},{"last_name":"Meng","full_name":"Meng, Tobias","first_name":"Tobias"},{"first_name":"Carsten","last_name":"Putzke","full_name":"Putzke, Carsten"},{"first_name":"Toni","full_name":"Helm, Toni","last_name":"Helm"},{"last_name":"Shirer","full_name":"Shirer, K. R.","first_name":"K. R."},{"full_name":"Li, You-Sheng","last_name":"Li","first_name":"You-Sheng"},{"first_name":"Kimberly A","orcid":"0000-0001-9760-3147","full_name":"Modic, Kimberly A","last_name":"Modic","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425"},{"last_name":"Nicklas","full_name":"Nicklas, Michael","first_name":"Michael"},{"first_name":"Markus","last_name":"König","full_name":"König, Markus"},{"last_name":"Low","full_name":"Low, D.","first_name":"D."},{"full_name":"Ghosh, Sayak","last_name":"Ghosh","first_name":"Sayak"},{"first_name":"Andrew P.","last_name":"Mackenzie","full_name":"Mackenzie, Andrew P."},{"first_name":"Frank","last_name":"Arnold","full_name":"Arnold, Frank"},{"first_name":"Elena","last_name":"Hassinger","full_name":"Hassinger, Elena"},{"first_name":"Ross D.","last_name":"McDonald","full_name":"McDonald, Ross D."},{"first_name":"Laurel E.","full_name":"Winter, Laurel E.","last_name":"Winter"},{"last_name":"Bauer","full_name":"Bauer, Eric D.","first_name":"Eric D."},{"first_name":"Filip","full_name":"Ronning, Filip","last_name":"Ronning"},{"first_name":"B. J.","full_name":"Ramshaw, B. J.","last_name":"Ramshaw"},{"first_name":"Katja C.","last_name":"Nowack","full_name":"Nowack, Katja C."},{"full_name":"Moll, Philip J. W.","last_name":"Moll","first_name":"Philip J. W."}],"day":"11","extern":"1","volume":366,"publisher":"AAAS","article_type":"original","publication":"Science","page":"221-226","citation":{"mla":"Bachmann, Maja D., et al. “Spatial Control of Heavy-Fermion Superconductivity in CeIrIn5.” Science, vol. 366, no. 6462, AAAS, 2019, pp. 221–26, doi:10.1126/science.aao6640.","ista":"Bachmann MD, Ferguson GM, Theuss F, Meng T, Putzke C, Helm T, Shirer KR, Li Y-S, Modic KA, Nicklas M, König M, Low D, Ghosh S, Mackenzie AP, Arnold F, Hassinger E, McDonald RD, Winter LE, Bauer ED, Ronning F, Ramshaw BJ, Nowack KC, Moll PJW. 2019. Spatial control of heavy-fermion superconductivity in CeIrIn5. Science. 366(6462), 221–226.","ieee":"M. D. Bachmann et al., “Spatial control of heavy-fermion superconductivity in CeIrIn5,” Science, vol. 366, no. 6462. AAAS, pp. 221–226, 2019.","ama":"Bachmann MD, Ferguson GM, Theuss F, et al. Spatial control of heavy-fermion superconductivity in CeIrIn5. Science. 2019;366(6462):221-226. doi:10.1126/science.aao6640","apa":"Bachmann, M. D., Ferguson, G. M., Theuss, F., Meng, T., Putzke, C., Helm, T., … Moll, P. J. W. (2019). Spatial control of heavy-fermion superconductivity in CeIrIn5. Science. AAAS. https://doi.org/10.1126/science.aao6640","chicago":"Bachmann, Maja D., G. M. Ferguson, Florian Theuss, Tobias Meng, Carsten Putzke, Toni Helm, K. R. Shirer, et al. “Spatial Control of Heavy-Fermion Superconductivity in CeIrIn5.” Science. AAAS, 2019. https://doi.org/10.1126/science.aao6640.","short":"M.D. Bachmann, G.M. Ferguson, F. Theuss, T. Meng, C. Putzke, T. Helm, K.R. Shirer, Y.-S. Li, K.A. Modic, M. Nicklas, M. König, D. Low, S. Ghosh, A.P. Mackenzie, F. Arnold, E. Hassinger, R.D. McDonald, L.E. Winter, E.D. Bauer, F. Ronning, B.J. Ramshaw, K.C. Nowack, P.J.W. Moll, Science 366 (2019) 221–226."},"date_published":"2019-10-11T00:00:00Z","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"_id":"7082","status":"public","title":"Spatial control of heavy-fermion superconductivity in CeIrIn5","month":"10","oa_version":"None","intvolume":" 366","doi":"10.1126/science.aao6640","article_processing_charge":"No","language":[{"iso":"eng"}],"quality_controlled":"1","publication_status":"published","issue":"6462","date_created":"2019-11-19T13:55:58Z","type":"journal_article","abstract":[{"text":"Although crystals of strongly correlated metals exhibit a diverse set of electronic ground states, few approaches exist for spatially modulating their properties. In this study, we demonstrate disorder-free control, on the micrometer scale, over the superconducting state in samples of the heavy-fermion superconductor CeIrIn5. We pattern crystals by focused ion beam milling to tailor the boundary conditions for the elastic deformation upon thermal contraction during cooling. The resulting nonuniform strain fields induce complex patterns of superconductivity, owing to the strong dependence of the transition temperature on the strength and direction of strain. These results showcase a generic approach to manipulating electronic order on micrometer length scales in strongly correlated matter without compromising the cleanliness, stoichiometry, or mean free path.","lang":"eng"}],"date_updated":"2021-01-12T08:11:46Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019"}]