[{"abstract":[{"lang":"eng","text":"Malaria, a disease caused by parasites of the Plasmodium genus, begins when Plasmodium-infected mosquitoes inject malaria sporozoites while searching for blood. Sporozoites migrate from the skin via blood to the liver, infect hepatocytes, and form liver stages which in mice 48 h later escape into blood and cause clinical malaria. Vaccine-induced activated or memory CD8 T cells are capable of locating and eliminating all liver stages in 48 h, thus preventing the blood-stage disease. However, the rules of how CD8 T cells are able to locate all liver stages within a relatively short time period remains poorly understood. We recently reported formation of clusters consisting of variable numbers of activated CD8 T cells around Plasmodium yoelii (Py)-infected hepatocytes. Using a combination of experimental data and mathematical models we now provide additional insights into mechanisms of formation of these clusters. First, we show that a model in which cluster formation is driven exclusively by T-cell-extrinsic factors, such as variability in “attractiveness” of different liver stages, cannot explain distribution of cluster sizes in different experimental conditions. In contrast, the model in which cluster formation is driven by the positive feedback loop (i.e., larger clusters attract more CD8 T cells) can accurately explain the available data. Second, while both Py-specific CD8 T cells and T cells of irrelevant specificity (non-specific CD8 T cells) are attracted to the clusters, we found no evidence that non-specific CD8 T cells play a role in cluster formation. Third and finally, mathematical modeling suggested that formation of clusters occurs rapidly, within few hours after adoptive transfer of CD8 T cells, thus illustrating high efficiency of CD8 T cells in locating their targets in complex peripheral organs, such as the liver. Taken together, our analysis provides novel insights into and attempts to discriminate between alternative mechanisms driving the formation of clusters of antigen-specific CD8 T cells in the liver."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"09","intvolume":" 10","publication_identifier":{"issn":["1664-3224"]},"publication_status":"published","file":[{"date_created":"2019-11-04T15:54:00Z","file_name":"2019_FrontiersImmonology_Kelemen.pdf","date_updated":"2020-07-14T12:47:46Z","file_size":2083061,"creator":"dernst","file_id":"6984","checksum":"68d1708f7aa412544159b498ef17a6b9","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"volume":10,"_id":"6983","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-30T07:18:23Z","ddc":["570"],"department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:47:46Z","publisher":"Frontiers","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2019","day":"20","publication":"Frontiers in Immunology","date_published":"2019-09-20T00:00:00Z","doi":"10.3389/fimmu.2019.02153","date_created":"2019-11-04T15:50:06Z","article_number":"2153","citation":{"mla":"Kelemen, Réka K., et al. “Clustering of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” Frontiers in Immunology, vol. 10, 2153, Frontiers, 2019, doi:10.3389/fimmu.2019.02153.","ieee":"R. K. Kelemen, H. Rajakaruna, I. Cockburn, and V. Ganusov, “Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells,” Frontiers in Immunology, vol. 10. Frontiers, 2019.","short":"R.K. Kelemen, H. Rajakaruna, I. Cockburn, V. Ganusov, Frontiers in Immunology 10 (2019).","apa":"Kelemen, R. K., Rajakaruna, H., Cockburn, I., & Ganusov, V. (2019). Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. Frontiers. https://doi.org/10.3389/fimmu.2019.02153","ama":"Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. 2019;10. doi:10.3389/fimmu.2019.02153","chicago":"Kelemen, Réka K, H Rajakaruna, IA Cockburn, and VV Ganusov. “Clustering of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” Frontiers in Immunology. Frontiers, 2019. https://doi.org/10.3389/fimmu.2019.02153.","ista":"Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. 2019. Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. 10, 2153."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Kelemen","orcid":"0000-0002-8489-9281","full_name":"Kelemen, Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","first_name":"Réka K"},{"first_name":"H","full_name":"Rajakaruna, H","last_name":"Rajakaruna"},{"first_name":"IA","full_name":"Cockburn, IA","last_name":"Cockburn"},{"last_name":"Ganusov","full_name":"Ganusov, VV","first_name":"VV"}],"external_id":{"isi":["000487187000001"],"pmid":["31616407"]},"article_processing_charge":"No","title":"Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells"},{"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"6972","file_date_updated":"2020-07-14T12:47:46Z","department":[{"_id":"DaAl"}],"date_updated":"2023-08-30T07:07:23Z","ddc":["000"],"scopus_import":"1","month":"09","intvolume":" 66","abstract":[{"lang":"eng","text":"We give fault-tolerant algorithms for establishing synchrony in distributed systems in which each of thennodes has its own clock. Our algorithms operate in a very strong fault model: we require self-stabilisation, i.e.,the initial state of the system may be arbitrary, and there can be up to fJournal of the ACM, vol. 66, no. 5, 32, ACM, 2019, doi:10.1145/3339471.","short":"C. Lenzen, J. Rybicki, Journal of the ACM 66 (2019).","ieee":"C. Lenzen and J. Rybicki, “Self-stabilising Byzantine clock synchronisation is almost as easy as consensus,” Journal of the ACM, vol. 66, no. 5. ACM, 2019.","ama":"Lenzen C, Rybicki J. Self-stabilising Byzantine clock synchronisation is almost as easy as consensus. Journal of the ACM. 2019;66(5). doi:10.1145/3339471","apa":"Lenzen, C., & Rybicki, J. (2019). Self-stabilising Byzantine clock synchronisation is almost as easy as consensus. Journal of the ACM. ACM. https://doi.org/10.1145/3339471","chicago":"Lenzen, Christoph, and Joel Rybicki. “Self-Stabilising Byzantine Clock Synchronisation Is Almost as Easy as Consensus.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3339471.","ista":"Lenzen C, Rybicki J. 2019. Self-stabilising Byzantine clock synchronisation is almost as easy as consensus. Journal of the ACM. 66(5), 32."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"ACM","quality_controlled":"1","oa":1,"date_published":"2019-09-01T00:00:00Z","doi":"10.1145/3339471","date_created":"2019-10-24T17:12:48Z","isi":1,"has_accepted_license":"1","year":"2019","day":"01","publication":"Journal of the ACM"},{"department":[{"_id":"KrCh"},{"_id":"ChLa"}],"date_updated":"2023-08-30T06:59:36Z","type":"conference","conference":{"name":"QEST: Quantitative Evaluation of Systems","location":"Glasgow, United Kingdom","end_date":"2019-09-12","start_date":"2019-09-10"},"status":"public","_id":"6942","volume":11785,"publication_identifier":{"eisbn":["9783030302818"],"issn":["0302-9743"],"isbn":["9783030302801"]},"publication_status":"published","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.08178"}],"month":"09","intvolume":" 11785","abstract":[{"text":"Graph games and Markov decision processes (MDPs) are standard models in reactive synthesis and verification of probabilistic systems with nondeterminism. The class of 𝜔 -regular winning conditions; e.g., safety, reachability, liveness, parity conditions; provides a robust and expressive specification formalism for properties that arise in analysis of reactive systems. The resolutions of nondeterminism in games and MDPs are represented as strategies, and we consider succinct representation of such strategies. The decision-tree data structure from machine learning retains the flavor of decisions of strategies and allows entropy-based minimization to obtain succinct trees. However, in contrast to traditional machine-learning problems where small errors are allowed, for winning strategies in graph games and MDPs no error is allowed, and the decision tree must represent the entire strategy. In this work we propose decision trees with linear classifiers for representation of strategies in graph games and MDPs. We have implemented strategy representation using this data structure and we present experimental results for problems on graph games and MDPs, which show that this new data structure presents a much more efficient strategy representation as compared to standard decision trees.","lang":"eng"}],"oa_version":"Preprint","author":[{"last_name":"Ashok","full_name":"Ashok, Pranav","first_name":"Pranav"},{"first_name":"Tomáš","last_name":"Brázdil","full_name":"Brázdil, Tomáš"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Křetínský, Jan","last_name":"Křetínský","first_name":"Jan"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert"},{"orcid":"0000-0001-9036-063X","full_name":"Toman, Viktor","last_name":"Toman","first_name":"Viktor","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["1906.08178"],"isi":["000679281300007"]},"title":"Strategy representation by decision trees with linear classifiers","citation":{"mla":"Ashok, Pranav, et al. “Strategy Representation by Decision Trees with Linear Classifiers.” 16th International Conference on Quantitative Evaluation of Systems, vol. 11785, Springer Nature, 2019, pp. 109–28, doi:10.1007/978-3-030-30281-8_7.","apa":"Ashok, P., Brázdil, T., Chatterjee, K., Křetínský, J., Lampert, C., & Toman, V. (2019). Strategy representation by decision trees with linear classifiers. In 16th International Conference on Quantitative Evaluation of Systems (Vol. 11785, pp. 109–128). Glasgow, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-030-30281-8_7","ama":"Ashok P, Brázdil T, Chatterjee K, Křetínský J, Lampert C, Toman V. Strategy representation by decision trees with linear classifiers. In: 16th International Conference on Quantitative Evaluation of Systems. Vol 11785. Springer Nature; 2019:109-128. doi:10.1007/978-3-030-30281-8_7","short":"P. Ashok, T. Brázdil, K. Chatterjee, J. Křetínský, C. Lampert, V. Toman, in:, 16th International Conference on Quantitative Evaluation of Systems, Springer Nature, 2019, pp. 109–128.","ieee":"P. Ashok, T. Brázdil, K. Chatterjee, J. Křetínský, C. Lampert, and V. Toman, “Strategy representation by decision trees with linear classifiers,” in 16th International Conference on Quantitative Evaluation of Systems, Glasgow, United Kingdom, 2019, vol. 11785, pp. 109–128.","chicago":"Ashok, Pranav, Tomáš Brázdil, Krishnendu Chatterjee, Jan Křetínský, Christoph Lampert, and Viktor Toman. “Strategy Representation by Decision Trees with Linear Classifiers.” In 16th International Conference on Quantitative Evaluation of Systems, 11785:109–28. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-30281-8_7.","ista":"Ashok P, Brázdil T, Chatterjee K, Křetínský J, Lampert C, Toman V. 2019. Strategy representation by decision trees with linear classifiers. 16th International Conference on Quantitative Evaluation of Systems. QEST: Quantitative Evaluation of Systems, LNCS, vol. 11785, 109–128."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23","name":"Rigorous Systems Engineering"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"page":"109-128","doi":"10.1007/978-3-030-30281-8_7","date_published":"2019-09-04T00:00:00Z","date_created":"2019-10-14T06:57:49Z","isi":1,"year":"2019","day":"04","publication":"16th International Conference on Quantitative Evaluation of Systems","quality_controlled":"1","publisher":"Springer Nature","oa":1},{"volume":798,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"6974","checksum":"d27f983b34ea7dafdf356afbf9472fbf","file_size":528362,"date_updated":"2020-07-14T12:47:46Z","creator":"dernst","file_name":"2019_PhysicsLettersB_Schmickler.pdf","date_created":"2019-10-25T12:47:04Z"}],"publication_status":"published","publication_identifier":{"issn":["0370-2693"]},"intvolume":" 798","month":"11","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We study few-body bound states of charged particles subject to attractive zero-range/short-range plus repulsive Coulomb interparticle forces. The characteristic length scales of the system at zero energy are set by the Coulomb length scale D and the Coulomb-modified effective range r eff. We study shallow bound states of charged particles with D >> r eff and show that these systems obey universal scaling laws different from neutral particles. An accurate description of these states requires both the Coulomb-modified scattering length and the effective range unless the Coulomb interaction is very weak (D -> ). Our findings are relevant for bound states whose spatial extent is significantly larger than the range of the attractive potential. These states enjoy universality – their character is independent of the shape of the short-range potential.","lang":"eng"}],"department":[{"_id":"MiLe"}],"file_date_updated":"2020-07-14T12:47:46Z","ddc":["530"],"date_updated":"2023-08-30T07:06:42Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"6955","date_created":"2019-10-18T18:33:32Z","doi":"10.1016/j.physletb.2019.135016","date_published":"2019-11-10T00:00:00Z","publication":"Physics Letters B","day":"10","year":"2019","has_accepted_license":"1","isi":1,"oa":1,"publisher":"Elsevier","quality_controlled":"1","title":"Universal physics of bound states of a few charged particles","external_id":{"arxiv":["1904.00913"],"isi":["000494939000086"]},"article_processing_charge":"No","author":[{"full_name":"Schmickler, C.H.","last_name":"Schmickler","first_name":"C.H."},{"last_name":"Hammer","full_name":"Hammer, H.-W.","first_name":"H.-W."},{"last_name":"Volosniev","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"C. H. Schmickler, H.-W. Hammer, and A. Volosniev, “Universal physics of bound states of a few charged particles,” Physics Letters B, vol. 798. Elsevier, 2019.","short":"C.H. Schmickler, H.-W. Hammer, A. Volosniev, Physics Letters B 798 (2019).","apa":"Schmickler, C. H., Hammer, H.-W., & Volosniev, A. (2019). Universal physics of bound states of a few charged particles. Physics Letters B. Elsevier. https://doi.org/10.1016/j.physletb.2019.135016","ama":"Schmickler CH, Hammer H-W, Volosniev A. Universal physics of bound states of a few charged particles. Physics Letters B. 2019;798. doi:10.1016/j.physletb.2019.135016","mla":"Schmickler, C. H., et al. “Universal Physics of Bound States of a Few Charged Particles.” Physics Letters B, vol. 798, 135016, Elsevier, 2019, doi:10.1016/j.physletb.2019.135016.","ista":"Schmickler CH, Hammer H-W, Volosniev A. 2019. Universal physics of bound states of a few charged particles. Physics Letters B. 798, 135016.","chicago":"Schmickler, C.H., H.-W. Hammer, and Artem Volosniev. “Universal Physics of Bound States of a Few Charged Particles.” Physics Letters B. Elsevier, 2019. https://doi.org/10.1016/j.physletb.2019.135016."},"article_number":"135016"},{"oa":1,"quality_controlled":"1","publisher":"Wiley","year":"2019","isi":1,"has_accepted_license":"1","publication":"Journal of Neurochemistry","day":"01","page":"570-583","date_created":"2019-11-12T14:37:08Z","doi":"10.1111/jnc.14862","date_published":"2019-12-01T00:00:00Z","citation":{"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.","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","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000490703100001"],"pmid":["31479508"]},"author":[{"orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T","last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T"},{"last_name":"Cousin","full_name":"Cousin, Michael A.","first_name":"Michael A."}],"title":"Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction","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"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 151","month":"12","publication_status":"published","publication_identifier":{"eissn":["1471-4159"],"issn":["0022-3042"]},"language":[{"iso":"eng"}],"file":[{"file_id":"7452","checksum":"ec1fb2aebb874009bc309adaada6e1d7","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-02-05T10:30:02Z","file_name":"2019_JournNeurochemistry_Cheung.pdf","date_updated":"2020-07-14T12:47:47Z","file_size":4334962,"creator":"dernst"}],"volume":151,"issue":"5","_id":"7005","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-30T07:21:50Z","ddc":["570"],"department":[{"_id":"SiHi"}],"file_date_updated":"2020-07-14T12:47:47Z"},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1807-0302"],"issn":["2238-3603"]},"ec_funded":1,"volume":38,"issue":"4","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"intvolume":" 38","month":"12","main_file_link":[{"url":"https://doi.org/10.1007/s40314-019-0955-9","open_access":"1"}],"scopus_import":"1","ddc":["510","515","518"],"date_updated":"2023-08-30T07:20:32Z","department":[{"_id":"VlKo"}],"_id":"7000","status":"public","type":"journal_article","article_type":"original","publication":"Computational and Applied Mathematics","day":"01","year":"2019","isi":1,"has_accepted_license":"1","date_created":"2019-11-12T12:41:44Z","date_published":"2019-12-01T00:00:00Z","doi":"10.1007/s40314-019-0955-9","oa":1,"publisher":"Springer Nature","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","short":"Y. Shehu, O.S. Iyiola, X.-H. Li, Q.-L. Dong, Computational and Applied Mathematics 38 (2019).","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.","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.","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."},"title":"Convergence analysis of projection method for variational inequalities","external_id":{"isi":["000488973100005"],"arxiv":["2101.09081"]},"article_processing_charge":"No","author":[{"full_name":"Shehu, Yekini","orcid":"0000-0001-9224-7139","last_name":"Shehu","first_name":"Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Iyiola, Olaniyi S.","last_name":"Iyiola","first_name":"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"}],"article_number":"161","project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"_id":"7009","status":"public","type":"journal_article","article_type":"review","date_updated":"2023-08-30T07:22:20Z","department":[{"_id":"MiSi"}],"pmid":1,"oa_version":"None","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."}],"month":"12","intvolume":" 20","scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1471-0072"],"eissn":["1471-0080"]},"publication_status":"published","issue":"12","volume":20,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Yamada K, Sixt MK. 2019. Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. 20(12), 738–752.","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.","short":"K. Yamada, M.K. Sixt, Nature Reviews Molecular Cell Biology 20 (2019) 738–752.","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.","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","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."},"title":"Mechanisms of 3D cell migration","author":[{"first_name":"KM","last_name":"Yamada","full_name":"Yamada, KM"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"external_id":{"isi":["000497966900007"],"pmid":["31582855"]},"article_processing_charge":"No","publisher":"Springer Nature","quality_controlled":"1","day":"01","publication":"Nature Reviews Molecular Cell Biology","isi":1,"year":"2019","doi":"10.1038/s41580-019-0172-9","date_published":"2019-12-01T00:00:00Z","date_created":"2019-11-12T14:54:42Z","page":"738–752"},{"ec_funded":1,"issue":"10","volume":40,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1471-4906"]},"intvolume":" 40","month":"10","scopus_import":"1","pmid":1,"oa_version":"None","abstract":[{"lang":"eng","text":"Platelets are central players in thrombosis and hemostasis but are increasingly recognized as key components of the immune system. They shape ensuing immune responses by recruiting leukocytes, and support the development of adaptive immunity. Recent data shed new light on the complex role of platelets in immunity. Here, we summarize experimental and clinical data on the role of platelets in host defense against bacteria. Platelets bind, contain, and kill bacteria directly; however, platelet proinflammatory effector functions and cross-talk with the coagulation system, can also result in damage to the host (e.g., acute lung injury and sepsis). Novel clinical insights support this dichotomy: platelet inhibition/thrombocytopenia can be either harmful or protective, depending on pathophysiological context. Clinical studies are currently addressing this aspect in greater depth."}],"department":[{"_id":"MiSi"}],"date_updated":"2023-08-30T07:19:23Z","status":"public","type":"journal_article","article_type":"review","_id":"6988","date_created":"2019-11-04T16:27:36Z","date_published":"2019-10-01T00:00:00Z","doi":"10.1016/j.it.2019.08.004","page":"922-938","publication":"Trends in Immunology","day":"01","year":"2019","isi":1,"publisher":"Cell Press","quality_controlled":"1","title":"Platelets in host defense: Experimental and clinical insights","external_id":{"isi":["000493292100005"],"pmid":["31601520"]},"article_processing_charge":"No","author":[{"first_name":"Leo","full_name":"Nicolai, Leo","last_name":"Nicolai"},{"first_name":"Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","last_name":"Gärtner","orcid":"0000-0001-6120-3723","full_name":"Gärtner, Florian R"},{"first_name":"Steffen","last_name":"Massberg","full_name":"Massberg, Steffen"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Nicolai L, Gärtner FR, Massberg S. 2019. Platelets in host defense: Experimental and clinical insights. Trends in Immunology. 40(10), 922–938.","chicago":"Nicolai, Leo, Florian R Gärtner, and Steffen Massberg. “Platelets in Host Defense: Experimental and Clinical Insights.” Trends in Immunology. Cell Press, 2019. https://doi.org/10.1016/j.it.2019.08.004.","apa":"Nicolai, L., Gärtner, F. R., & Massberg, S. (2019). Platelets in host defense: Experimental and clinical insights. Trends in Immunology. Cell Press. https://doi.org/10.1016/j.it.2019.08.004","ama":"Nicolai L, Gärtner FR, Massberg S. Platelets in host defense: Experimental and clinical insights. Trends in Immunology. 2019;40(10):922-938. doi:10.1016/j.it.2019.08.004","ieee":"L. Nicolai, F. R. Gärtner, and S. Massberg, “Platelets in host defense: Experimental and clinical insights,” Trends in Immunology, vol. 40, no. 10. Cell Press, pp. 922–938, 2019.","short":"L. Nicolai, F.R. Gärtner, S. Massberg, Trends in Immunology 40 (2019) 922–938.","mla":"Nicolai, Leo, et al. “Platelets in Host Defense: Experimental and Clinical Insights.” Trends in Immunology, vol. 40, no. 10, Cell Press, 2019, pp. 922–38, doi:10.1016/j.it.2019.08.004."},"project":[{"call_identifier":"H2020","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","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","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).","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.","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.","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."},"title":"Optimal multiple importance sampling","external_id":{"isi":["000475740600011"]},"article_processing_charge":"No","author":[{"first_name":"Ivo","full_name":"Kondapaneni, Ivo","last_name":"Kondapaneni"},{"full_name":"Vevoda, Petr","last_name":"Vevoda","first_name":"Petr"},{"full_name":"Grittmann, Pascal","last_name":"Grittmann","first_name":"Pascal"},{"first_name":"Tomas","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","full_name":"Skrivan, Tomas","last_name":"Skrivan"},{"first_name":"Philipp","last_name":"Slusallek","full_name":"Slusallek, Philipp"},{"first_name":"Jaroslav","last_name":"Křivánek","full_name":"Křivánek, Jaroslav"}],"article_number":"37","project":[{"call_identifier":"H2020","_id":"2508E324-B435-11E9-9278-68D0E5697425","name":"Distributed 3D Object Design","grant_number":"642841"}],"publication":"ACM Transactions on Graphics","day":"01","year":"2019","isi":1,"date_created":"2019-11-12T13:05:40Z","date_published":"2019-07-01T00:00:00Z","doi":"10.1145/3306346.3323009","quality_controlled":"1","publisher":"ACM","date_updated":"2023-08-30T07:21:25Z","department":[{"_id":"ChWo"}],"_id":"7002","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0730-0301"]},"ec_funded":1,"volume":38,"issue":"4","oa_version":"None","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."}],"intvolume":" 38","month":"07","scopus_import":"1"},{"volume":4,"issue":"10","publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.02211"}],"month":"10","intvolume":" 4","abstract":[{"lang":"eng","text":"In pipes and channels, the onset of turbulence is initially dominated by localizedtransients, which lead to sustained turbulence through their collective dynamics. In thepresent work, we study numerically the localized turbulence in pipe flow and elucidate astate space structure that gives rise to transient chaos. Starting from the basin boundaryseparating laminar and turbulent flow, we identify transverse homoclinic orbits, thepresence of which necessitates a homoclinic tangle and chaos. A direct consequence ofthe homoclinic tangle is the fractal nature of the laminar-turbulent boundary, which wasconjectured in various earlier studies. By mapping the transverse intersections between thestable and unstable manifold of a periodic orbit, we identify the gateways that promote anescape from turbulence."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Preprint","department":[{"_id":"BjHo"}],"date_updated":"2023-08-30T07:20:03Z","type":"journal_article","article_type":"original","status":"public","_id":"6978","page":"102401","date_published":"2019-10-01T00:00:00Z","doi":"10.1103/PhysRevFluids.4.102401","date_created":"2019-11-04T10:04:01Z","isi":1,"year":"2019","day":"01","publication":"Physical Review Fluids","quality_controlled":"1","publisher":"American Physical Society","oa":1,"author":[{"first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","last_name":"Budanur","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010"},{"full_name":"Dogra, Akshunna","last_name":"Dogra","first_name":"Akshunna"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["1810.02211"],"isi":["000493510400001"]},"title":"Geometry of transient chaos in streamwise-localized pipe flow turbulence","citation":{"short":"N.B. Budanur, A. Dogra, B. Hof, Physical Review Fluids 4 (2019) 102401.","ieee":"N. B. Budanur, A. Dogra, and B. Hof, “Geometry of transient chaos in streamwise-localized pipe flow turbulence,” Physical Review Fluids, vol. 4, no. 10. American Physical Society, p. 102401, 2019.","apa":"Budanur, N. B., Dogra, A., & Hof, B. (2019). Geometry of transient chaos in streamwise-localized pipe flow turbulence. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.4.102401","ama":"Budanur NB, Dogra A, Hof B. Geometry of transient chaos in streamwise-localized pipe flow turbulence. Physical Review Fluids. 2019;4(10):102401. doi:10.1103/PhysRevFluids.4.102401","mla":"Budanur, Nazmi B., et al. “Geometry of Transient Chaos in Streamwise-Localized Pipe Flow Turbulence.” Physical Review Fluids, vol. 4, no. 10, American Physical Society, 2019, p. 102401, doi:10.1103/PhysRevFluids.4.102401.","ista":"Budanur NB, Dogra A, Hof B. 2019. Geometry of transient chaos in streamwise-localized pipe flow turbulence. Physical Review Fluids. 4(10), 102401.","chicago":"Budanur, Nazmi B, Akshunna Dogra, and Björn Hof. “Geometry of Transient Chaos in Streamwise-Localized Pipe Flow Turbulence.” Physical Review Fluids. American Physical Society, 2019. https://doi.org/10.1103/PhysRevFluids.4.102401."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"_id":"7026","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-08-30T07:24:58Z","department":[{"_id":"ToBo"}],"file_date_updated":"2020-07-14T12:47:48Z","oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"}],"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"}],"month":"11","intvolume":" 9","scopus_import":"1","file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:48Z","file_size":4238460,"date_created":"2019-11-15T10:57:42Z","file_name":"2019_CellSystems_Lukacisin.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"7a11d6c2f9523d65b049512d61733178","file_id":"7027"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2405-4712"]},"publication_status":"published","volume":9,"issue":"5","project":[{"call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22"},{"name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.” Cell Systems. Cell Press, 2019. https://doi.org/10.1016/j.cels.2019.10.004.","short":"M. Lukacisin, M.T. Bollenbach, Cell Systems 9 (2019) 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.","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","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","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."},"title":"Emergent gene expression responses to drug combinations predict higher-order drug interactions","author":[{"first_name":"Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6549-4177","full_name":"Lukacisin, Martin","last_name":"Lukacisin"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias","last_name":"Bollenbach"}],"article_processing_charge":"No","external_id":{"isi":["000499495400003"]},"publisher":"Cell Press","quality_controlled":"1","oa":1,"day":"27","publication":"Cell Systems","has_accepted_license":"1","isi":1,"year":"2019","doi":"10.1016/j.cels.2019.10.004","date_published":"2019-11-27T00:00:00Z","date_created":"2019-11-15T10:51:42Z","page":"423-433.e1-e3"},{"publication_status":"published","publication_identifier":{"eissn":["1439-6912"],"issn":["0209-9683"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":39,"issue":"6","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"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.00508"}],"scopus_import":"1","intvolume":" 39","month":"10","date_updated":"2023-08-30T07:26:25Z","department":[{"_id":"UlWa"}],"_id":"7034","type":"journal_article","article_type":"original","status":"public","year":"2019","isi":1,"publication":"Combinatorica","day":"29","page":"1267-1279","date_created":"2019-11-18T14:29:50Z","date_published":"2019-10-29T00:00:00Z","doi":"10.1007/s00493-019-3905-7","oa":1,"quality_controlled":"1","publisher":"Springer Nature","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","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","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.","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.” Combinatorica, vol. 39, no. 6, Springer Nature, 2019, pp. 1267–79, 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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"arxiv":["1709.00508"],"isi":["000493267200003"]},"author":[{"first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774"},{"first_name":"Jan","full_name":"Kynčl, Jan","last_name":"Kynčl"}],"title":"Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"M02281","name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425"}]},{"type":"conference","conference":{"name":"CLEO: Conference on Lasers and Electro-Optics Europe","location":"Munich, Germany","end_date":"2019-06-27","start_date":"2019-06-23"},"status":"public","_id":"7032","article_number":"8873300","author":[{"last_name":"Rueda Sanchez","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Florian","full_name":"Sedlmeir, Florian","last_name":"Sedlmeir"},{"last_name":"Leuchs","full_name":"Leuchs, Gerd","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."}],"external_id":{"isi":["000630002701617"]},"article_processing_charge":"No","department":[{"_id":"JoFi"}],"title":"Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators","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 & European Quantum Electronics Conference. CLEO: Conference on Lasers and Electro-Optics Europe, 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.","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: 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. IEEE; 2019. doi:10.1109/cleoe-eqec.2019.8873300","apa":"Rueda Sanchez, A. R., Sedlmeir, F., Leuchs, G., Kuamri, M., & Schwefel, H. G. L. (2019). 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. Munich, Germany: IEEE. https://doi.org/10.1109/cleoe-eqec.2019.8873300","short":"A.R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kuamri, H.G.L. Schwefel, in:, 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, IEEE, 2019.","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 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, Munich, Germany, 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."},"date_updated":"2023-08-30T07:26:01Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","scopus_import":"1","publisher":"IEEE","month":"10","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"}],"oa_version":"None","date_published":"2019-10-17T00:00:00Z","doi":"10.1109/cleoe-eqec.2019.8873300","date_created":"2019-11-18T13:58:22Z","isi":1,"publication_identifier":{"isbn":["9781728104690"]},"publication_status":"published","year":"2019","day":"17","publication":"2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference","language":[{"iso":"eng"}]},{"oa":1,"quality_controlled":"1","publisher":"Springer Nature","date_created":"2019-11-25T07:45:17Z","date_published":"2019-11-12T00:00:00Z","doi":"10.1038/s41598-019-53049-w","year":"2019","isi":1,"has_accepted_license":"1","publication":"Scientific Reports","day":"12","article_number":"16565","article_processing_charge":"No","external_id":{"pmid":["31719602"],"isi":["000495857600019"]},"author":[{"first_name":"Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","last_name":"Maes","full_name":"Maes, Margaret E","orcid":"0000-0001-9642-1085"},{"last_name":"Grosser","full_name":"Grosser, J. A.","first_name":"J. A."},{"first_name":"R. L.","full_name":"Fehrman, R. L.","last_name":"Fehrman"},{"last_name":"Schlamp","full_name":"Schlamp, C. L.","first_name":"C. L."},{"last_name":"Nickells","full_name":"Nickells, R. W.","first_name":"R. W."}],"title":"Completion of BAX recruitment correlates with mitochondrial fission during apoptosis","citation":{"ama":"Maes ME, Grosser JA, Fehrman RL, Schlamp CL, Nickells RW. Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. Scientific Reports. 2019;9. doi:10.1038/s41598-019-53049-w","apa":"Maes, M. E., Grosser, J. A., Fehrman, R. L., Schlamp, C. L., & Nickells, R. W. (2019). Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-019-53049-w","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,” Scientific Reports, vol. 9. Springer Nature, 2019.","mla":"Maes, Margaret E., et al. “Completion of BAX Recruitment Correlates with Mitochondrial Fission during Apoptosis.” Scientific Reports, vol. 9, 16565, Springer Nature, 2019, doi:10.1038/s41598-019-53049-w.","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.","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.” Scientific Reports. Springer Nature, 2019. https://doi.org/10.1038/s41598-019-53049-w."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","intvolume":" 9","month":"11","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"volume":9,"publication_status":"published","publication_identifier":{"eissn":["2045-2322"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"9ab397ed9c1c454b34bffb8cc863d734","file_id":"7096","creator":"dernst","file_size":6467393,"date_updated":"2020-07-14T12:47:49Z","file_name":"2019_ScientificReports_Maes.pdf","date_created":"2019-11-25T07:49:52Z"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"7095","file_date_updated":"2020-07-14T12:47:49Z","department":[{"_id":"SaSi"}],"date_updated":"2023-08-30T07:26:54Z","ddc":["570"]},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"7097","department":[{"_id":"DaSi"}],"file_date_updated":"2020-07-14T12:47:49Z","date_updated":"2023-08-30T07:27:55Z","ddc":["570"],"scopus_import":"1","intvolume":" 2","month":"11","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","volume":2,"issue":"1","publication_status":"published","publication_identifier":{"issn":["2399-3642"]},"language":[{"iso":"eng"}],"file":[{"checksum":"c63c69a264fc8a0e52f2b0d482f3bdae","file_id":"7098","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-11-25T07:58:05Z","file_name":"2019_CommunicBiology_Nagano.pdf","date_updated":"2020-07-14T12:47:49Z","file_size":2626069,"creator":"dernst"}],"article_number":"419","external_id":{"isi":["000496767800005"]},"article_processing_charge":"No","author":[{"first_name":"Makoto","full_name":"Nagano, Makoto","last_name":"Nagano"},{"full_name":"Toshima, Junko Y.","last_name":"Toshima","first_name":"Junko Y."},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E"},{"last_name":"Toshima","full_name":"Toshima, Jiro","first_name":"Jiro"}],"title":"Rab5-mediated endosome formation is regulated at the trans-Golgi network","citation":{"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.","chicago":"Nagano, Makoto, Junko Y. Toshima, Daria E Siekhaus, and Jiro Toshima. “Rab5-Mediated Endosome Formation Is Regulated at the Trans-Golgi Network.” Communications Biology. Springer Nature, 2019. https://doi.org/10.1038/s42003-019-0670-5.","ama":"Nagano M, Toshima JY, Siekhaus DE, Toshima J. Rab5-mediated endosome formation is regulated at the trans-Golgi network. Communications Biology. 2019;2(1). doi:10.1038/s42003-019-0670-5","apa":"Nagano, M., Toshima, J. Y., Siekhaus, D. E., & Toshima, J. (2019). Rab5-mediated endosome formation is regulated at the trans-Golgi network. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-019-0670-5","ieee":"M. Nagano, J. Y. Toshima, D. E. Siekhaus, and J. Toshima, “Rab5-mediated endosome formation is regulated at the trans-Golgi network,” Communications Biology, vol. 2, no. 1. Springer Nature, 2019.","short":"M. Nagano, J.Y. Toshima, D.E. Siekhaus, J. Toshima, Communications Biology 2 (2019).","mla":"Nagano, Makoto, et al. “Rab5-Mediated Endosome Formation Is Regulated at the Trans-Golgi Network.” Communications Biology, vol. 2, no. 1, 419, Springer Nature, 2019, doi:10.1038/s42003-019-0670-5."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"Springer Nature","quality_controlled":"1","date_created":"2019-11-25T07:55:01Z","doi":"10.1038/s42003-019-0670-5","date_published":"2019-11-15T00:00:00Z","year":"2019","has_accepted_license":"1","isi":1,"publication":"Communications Biology","day":"15"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Kasugai Y, Vogel E, Hörtnagl H, et al. Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. Neuron. 2019;104(4):781-794.e4. doi:10.1016/j.neuron.2019.08.013","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. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.08.013","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.","ieee":"Y. Kasugai et al., “Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning,” Neuron, vol. 104, no. 4. Elsevier, p. 781–794.e4, 2019.","mla":"Kasugai, Yu, et al. “Structural and Functional Remodeling of Amygdala GABAergic Synapses in Associative Fear Learning.” Neuron, vol. 104, no. 4, Elsevier, 2019, p. 781–794.e4, doi:10.1016/j.neuron.2019.08.013.","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.","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.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.08.013."},"title":"Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning","author":[{"full_name":"Kasugai, Yu","last_name":"Kasugai","first_name":"Yu"},{"last_name":"Vogel","full_name":"Vogel, Elisabeth","first_name":"Elisabeth"},{"full_name":"Hörtnagl, Heide","last_name":"Hörtnagl","first_name":"Heide"},{"full_name":"Schönherr, Sabine","last_name":"Schönherr","first_name":"Sabine"},{"full_name":"Paradiso, Enrica","last_name":"Paradiso","first_name":"Enrica"},{"first_name":"Markus","full_name":"Hauschild, Markus","last_name":"Hauschild"},{"last_name":"Göbel","full_name":"Göbel, Georg","first_name":"Georg"},{"first_name":"Ivan","full_name":"Milenkovic, Ivan","last_name":"Milenkovic"},{"first_name":"Yvan","full_name":"Peterschmitt, Yvan","last_name":"Peterschmitt"},{"full_name":"Tasan, Ramon","last_name":"Tasan","first_name":"Ramon"},{"last_name":"Sperk","full_name":"Sperk, Günther","first_name":"Günther"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"first_name":"Werner","full_name":"Sieghart, Werner","last_name":"Sieghart"},{"last_name":"Singewald","full_name":"Singewald, Nicolas","first_name":"Nicolas"},{"full_name":"Lüthi, Andreas","last_name":"Lüthi","first_name":"Andreas"},{"first_name":"Francesco","last_name":"Ferraguti","full_name":"Ferraguti, Francesco"}],"article_processing_charge":"No","external_id":{"isi":["000497963500017"],"pmid":["31543297"]},"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.","publisher":"Elsevier","quality_controlled":"1","oa":1,"day":"20","publication":"Neuron","isi":1,"has_accepted_license":"1","year":"2019","doi":"10.1016/j.neuron.2019.08.013","date_published":"2019-11-20T00:00:00Z","date_created":"2019-11-25T08:02:39Z","page":"781-794.e4","_id":"7099","status":"public","article_type":"original","type":"journal_article","ddc":["571","599"],"date_updated":"2023-08-30T07:28:22Z","department":[{"_id":"RySh"}],"pmid":1,"oa_version":"Published Version","month":"11","intvolume":" 104","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2019.08.013"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0896-6273"]},"publication_status":"published","volume":104,"issue":"4"},{"publication_status":"published","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"6440","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/how-to-generate-a-brain-of-correct-size-and-composition/"}]},"volume":364,"abstract":[{"lang":"eng","text":"During corticogenesis, distinct subtypes of neurons are sequentially born from ventricular zone progenitors. How these cells are molecularly temporally patterned is poorly understood. We used single-cell RNA sequencing at high temporal resolution to trace the lineage of the molecular identities of successive generations of apical progenitors (APs) and their daughter neurons in mouse embryos. We identified a core set of evolutionarily conserved, temporally patterned genes that drive APs from internally driven to more exteroceptive states. We found that the Polycomb repressor complex 2 (PRC2) epigenetically regulates AP temporal progression. Embryonic age–dependent AP molecular states are transmitted to their progeny as successive ground states, onto which essentially conserved early postmitotic differentiation programs are applied, and are complemented by later-occurring environment-dependent signals. Thus, epigenetically regulated temporal molecular birthmarks present in progenitors act in their postmitotic progeny to seed adult neuronal diversity."}],"oa_version":"Published Version","pmid":1,"main_file_link":[{"url":"https://orbi.uliege.be/bitstream/2268/239604/1/Telley_Agirman_Science2019.pdf","open_access":"1"}],"scopus_import":"1","intvolume":" 364","month":"05","date_updated":"2023-09-05T11:51:09Z","department":[{"_id":"SiHi"}],"_id":"6455","type":"journal_article","article_type":"original","status":"public","year":"2019","isi":1,"publication":"Science","day":"10","date_created":"2019-05-14T13:07:47Z","date_published":"2019-05-10T00:00:00Z","doi":"10.1126/science.aav2522","oa":1,"publisher":"AAAS","quality_controlled":"1","citation":{"ista":"Telley L, Agirman G, Prados J, Amberg N, Fièvre S, Oberst P, Bartolini G, Vitali I, Cadilhac C, Hippenmeyer S, Nguyen L, Dayer A, Jabaudon D. 2019. Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. Science. 364(6440), eaav2522.","chicago":"Telley, L, G Agirman, J Prados, Nicole Amberg, S Fièvre, P Oberst, G Bartolini, et al. “Temporal Patterning of Apical Progenitors and Their Daughter Neurons in the Developing Neocortex.” Science. AAAS, 2019. https://doi.org/10.1126/science.aav2522.","short":"L. Telley, G. Agirman, J. Prados, N. Amberg, S. Fièvre, P. Oberst, G. Bartolini, I. Vitali, C. Cadilhac, S. Hippenmeyer, L. Nguyen, A. Dayer, D. Jabaudon, Science 364 (2019).","ieee":"L. Telley et al., “Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex,” Science, vol. 364, no. 6440. AAAS, 2019.","ama":"Telley L, Agirman G, Prados J, et al. Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. Science. 2019;364(6440). doi:10.1126/science.aav2522","apa":"Telley, L., Agirman, G., Prados, J., Amberg, N., Fièvre, S., Oberst, P., … Jabaudon, D. (2019). Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. Science. AAAS. https://doi.org/10.1126/science.aav2522","mla":"Telley, L., et al. “Temporal Patterning of Apical Progenitors and Their Daughter Neurons in the Developing Neocortex.” Science, vol. 364, no. 6440, eaav2522, AAAS, 2019, doi:10.1126/science.aav2522."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"pmid":["31073041"],"isi":["000467631800034"]},"article_processing_charge":"No","author":[{"first_name":"L","last_name":"Telley","full_name":"Telley, L"},{"full_name":"Agirman, G","last_name":"Agirman","first_name":"G"},{"full_name":"Prados, J","last_name":"Prados","first_name":"J"},{"last_name":"Amberg","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole"},{"last_name":"Fièvre","full_name":"Fièvre, S","first_name":"S"},{"first_name":"P","full_name":"Oberst, P","last_name":"Oberst"},{"first_name":"G","last_name":"Bartolini","full_name":"Bartolini, G"},{"last_name":"Vitali","full_name":"Vitali, I","first_name":"I"},{"last_name":"Cadilhac","full_name":"Cadilhac, C","first_name":"C"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"},{"full_name":"Nguyen, L","last_name":"Nguyen","first_name":"L"},{"full_name":"Dayer, A","last_name":"Dayer","first_name":"A"},{"last_name":"Jabaudon","full_name":"Jabaudon, D","first_name":"D"}],"title":"Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex","article_number":"eaav2522","project":[{"call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"_id":"268F8446-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"T0101031","name":"Role of Eed in neural stem cell lineage progression"}]},{"publication":"Journal of the American Chemical Society","day":"19","year":"2019","has_accepted_license":"1","isi":1,"date_created":"2019-06-25T11:53:35Z","doi":"10.1021/jacs.9b01394","date_published":"2019-04-19T00:00:00Z","page":"8025-8029","oa":1,"publisher":"American Chemical Society","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Ibáñez, Maria, Roger Hasler, Aziz Genç, Yu Liu, Beatrice Kuster, Maximilian Schuster, Oleksandr Dobrozhan, et al. “Ligand-Mediated Band Engineering in Bottom-up Assembled SnTe Nanocomposites for Thermoelectric Energy Conversion.” Journal of the American Chemical Society. American Chemical Society, 2019. https://doi.org/10.1021/jacs.9b01394.","ista":"Ibáñez M, Hasler R, Genç A, Liu Y, Kuster B, Schuster M, Dobrozhan O, Cadavid D, Arbiol J, Cabot A, Kovalenko MV. 2019. Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion. Journal of the American Chemical Society. 141(20), 8025–8029.","mla":"Ibáñez, Maria, et al. “Ligand-Mediated Band Engineering in Bottom-up Assembled SnTe Nanocomposites for Thermoelectric Energy Conversion.” Journal of the American Chemical Society, vol. 141, no. 20, American Chemical Society, 2019, pp. 8025–29, doi:10.1021/jacs.9b01394.","apa":"Ibáñez, M., Hasler, R., Genç, A., Liu, Y., Kuster, B., Schuster, M., … Kovalenko, M. V. (2019). Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.9b01394","ama":"Ibáñez M, Hasler R, Genç A, et al. Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion. Journal of the American Chemical Society. 2019;141(20):8025-8029. doi:10.1021/jacs.9b01394","short":"M. Ibáñez, R. Hasler, A. Genç, Y. Liu, B. Kuster, M. Schuster, O. Dobrozhan, D. Cadavid, J. Arbiol, A. Cabot, M.V. Kovalenko, Journal of the American Chemical Society 141 (2019) 8025–8029.","ieee":"M. Ibáñez et al., “Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion,” Journal of the American Chemical Society, vol. 141, no. 20. American Chemical Society, pp. 8025–8029, 2019."},"title":"Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion","article_processing_charge":"No","external_id":{"isi":["000469292300004"],"pmid":["31017419 "]},"author":[{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"},{"last_name":"Hasler","full_name":"Hasler, Roger","first_name":"Roger"},{"first_name":"Aziz","full_name":"Genç, Aziz","last_name":"Genç"},{"last_name":"Liu","full_name":"Liu, Yu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","first_name":"Yu"},{"first_name":"Beatrice","last_name":"Kuster","full_name":"Kuster, Beatrice"},{"full_name":"Schuster, Maximilian","last_name":"Schuster","first_name":"Maximilian"},{"full_name":"Dobrozhan, Oleksandr","last_name":"Dobrozhan","first_name":"Oleksandr"},{"first_name":"Doris","full_name":"Cadavid, Doris","last_name":"Cadavid"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"},{"full_name":"Kovalenko, Maksym V.","last_name":"Kovalenko","first_name":"Maksym V."}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"language":[{"iso":"eng"}],"file":[{"file_name":"JACS_April2019.pdf","date_created":"2019-06-25T11:59:00Z","creator":"cpetz","file_size":6234004,"date_updated":"2020-07-14T12:47:34Z","file_id":"6587","checksum":"34d7ec837869cc6a07996b54f75696b7","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"ec_funded":1,"issue":"20","volume":141,"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The bottom-up assembly of colloidal nanocrystals is a versatile methodology to produce composite nanomaterials with precisely tuned electronic properties. Beyond the synthetic control over crystal domain size, shape, crystal phase, and composition, solution-processed nanocrystals allow exquisite surface engineering. This provides additional means to modulate the nanomaterial characteristics and particularly its electronic transport properties. For instance, inorganic surface ligands can be used to tune the type and concentration of majority carriers or to modify the electronic band structure. Herein, we report the thermoelectric properties of SnTe nanocomposites obtained from the consolidation of surface-engineered SnTe nanocrystals into macroscopic pellets. A CdSe-based ligand is selected to (i) converge the light and heavy bands through partial Cd alloying and (ii) generate CdSe nanoinclusions as a secondary phase within the SnTe matrix, thereby reducing the thermal conductivity. These SnTe-CdSe nanocomposites possess thermoelectric figures of merit of up to 1.3 at 850 K, which is, to the best of our knowledge, the highest thermoelectric figure of merit reported for solution-processed SnTe."}],"intvolume":" 141","month":"04","scopus_import":"1","ddc":["540"],"date_updated":"2023-09-05T12:03:45Z","department":[{"_id":"MaIb"}],"file_date_updated":"2020-07-14T12:47:34Z","_id":"6586","status":"public","article_type":"original","type":"journal_article"},{"issue":"9","volume":99,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"publication_status":"published","month":"03","intvolume":" 99","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1811.03103","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We propose a scaling theory for the many-body localization (MBL) phase transition in one dimension, building on the idea that it proceeds via a “quantum avalanche.” We argue that the critical properties can be captured at a coarse-grained level by a Kosterlitz-Thouless (KT) renormalization group (RG) flow. On phenomenological grounds, we identify the scaling variables as the density of thermal regions and the length scale that controls the decay of typical matrix elements. Within this KT picture, the MBL phase is a line of fixed points that terminates at the delocalization transition. We discuss two possible scenarios distinguished by the distribution of rare, fractal thermal inclusions within the MBL phase. In the first scenario, these regions have a stretched exponential distribution in the MBL phase. In the second scenario, the near-critical MBL phase hosts rare thermal regions that are power-law-distributed in size. This points to the existence of a second transition within the MBL phase, at which these power laws change to the stretched exponential form expected at strong disorder. We numerically simulate two different phenomenological RGs previously proposed to describe the MBL transition. Both RGs display a universal power-law length distribution of thermal regions at the transition with a critical exponent αc=2, and continuously varying exponents in the MBL phase consistent with the KT picture."}],"department":[{"_id":"MaSe"}],"date_updated":"2023-09-05T12:11:13Z","status":"public","article_type":"original","type":"journal_article","_id":"6174","date_published":"2019-03-22T00:00:00Z","doi":"10.1103/physrevb.99.094205","date_created":"2019-03-25T07:32:08Z","day":"22","publication":"Physical Review B","isi":1,"year":"2019","publisher":"American Physical Society","quality_controlled":"1","oa":1,"title":"Kosterlitz-Thouless scaling at many-body localization phase transitions","author":[{"full_name":"Dumitrescu, Philipp T.","last_name":"Dumitrescu","first_name":"Philipp T."},{"full_name":"Goremykina, Anna","last_name":"Goremykina","first_name":"Anna"},{"first_name":"Siddharth A.","last_name":"Parameswaran","full_name":"Parameswaran, Siddharth A."},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"},{"first_name":"Romain","last_name":"Vasseur","full_name":"Vasseur, Romain"}],"external_id":{"isi":["000462883200001"],"arxiv":["1811.03103"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Dumitrescu, Philipp T., Anna Goremykina, Siddharth A. Parameswaran, Maksym Serbyn, and Romain Vasseur. “Kosterlitz-Thouless Scaling at Many-Body Localization Phase Transitions.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.99.094205.","ista":"Dumitrescu PT, Goremykina A, Parameswaran SA, Serbyn M, Vasseur R. 2019. Kosterlitz-Thouless scaling at many-body localization phase transitions. Physical Review B. 99(9), 094205.","mla":"Dumitrescu, Philipp T., et al. “Kosterlitz-Thouless Scaling at Many-Body Localization Phase Transitions.” Physical Review B, vol. 99, no. 9, 094205, American Physical Society, 2019, doi:10.1103/physrevb.99.094205.","ama":"Dumitrescu PT, Goremykina A, Parameswaran SA, Serbyn M, Vasseur R. Kosterlitz-Thouless scaling at many-body localization phase transitions. Physical Review B. 2019;99(9). doi:10.1103/physrevb.99.094205","apa":"Dumitrescu, P. T., Goremykina, A., Parameswaran, S. A., Serbyn, M., & Vasseur, R. (2019). Kosterlitz-Thouless scaling at many-body localization phase transitions. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.99.094205","ieee":"P. T. Dumitrescu, A. Goremykina, S. A. Parameswaran, M. Serbyn, and R. Vasseur, “Kosterlitz-Thouless scaling at many-body localization phase transitions,” Physical Review B, vol. 99, no. 9. American Physical Society, 2019.","short":"P.T. Dumitrescu, A. Goremykina, S.A. Parameswaran, M. Serbyn, R. Vasseur, Physical Review B 99 (2019)."},"article_number":"094205"},{"_id":"6366","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-05T12:25:19Z","department":[{"_id":"JiFr"}],"abstract":[{"lang":"eng","text":"Plants have a remarkable capacity to adjust their growth and development to elevated ambient temperatures. Increased elongation growth of roots, hypocotyls and petioles in warm temperatures are hallmarks of seedling thermomorphogenesis. In the last decade, significant progress has been made to identify the molecular signaling components regulating these growth responses. Increased ambient temperature utilizes diverse components of the light sensing and signal transduction network to trigger growth adjustments. However, it remains unknown whether temperature sensing and responses are universal processes that occur uniformly in all plant organs. Alternatively, temperature sensing may be confined to specific tissues or organs, which would require a systemic signal that mediates responses in distal parts of the plant. Here we show that Arabidopsis (Arabidopsis thaliana) seedlings show organ-specific transcriptome responses to elevated temperatures, and that thermomorphogenesis involves both autonomous and organ-interdependent temperature sensing and signaling. Seedling roots can sense and respond to temperature in a shoot-independent manner, whereas shoot temperature responses require both local and systemic processes. The induction of cell elongation in hypocotyls requires temperature sensing in cotyledons, followed by generation of a mobile auxin signal. Subsequently, auxin travels to the hypocotyl where it triggers local brassinosteroid-induced cell elongation in seedling stems, which depends upon a distinct, permissive temperature sensor in the hypocotyl."}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"url":"www.doi.org/10.1104/pp.18.01377","open_access":"1"}],"scopus_import":"1","intvolume":" 180","month":"06","publication_status":"published","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"language":[{"iso":"eng"}],"issue":"2","volume":180,"citation":{"mla":"Bellstaedt, Julia, et al. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” Plant Physiology, vol. 180, no. 2, ASPB, 2019, pp. 757–66, doi:10.1104/pp.18.01377.","ieee":"J. Bellstaedt et al., “A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls,” Plant Physiology, vol. 180, no. 2. ASPB, pp. 757–766, 2019.","short":"J. Bellstaedt, J. Trenner, R. Lippmann, Y. Poeschl, X. Zhang, J. Friml, M. Quint, C. Delker, Plant Physiology 180 (2019) 757–766.","ama":"Bellstaedt J, Trenner J, Lippmann R, et al. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. 2019;180(2):757-766. doi:10.1104/pp.18.01377","apa":"Bellstaedt, J., Trenner, J., Lippmann, R., Poeschl, Y., Zhang, X., Friml, J., … Delker, C. (2019). A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. ASPB. https://doi.org/10.1104/pp.18.01377","chicago":"Bellstaedt, Julia, Jana Trenner, Rebecca Lippmann, Yvonne Poeschl, Xixi Zhang, Jiří Friml, Marcel Quint, and Carolin Delker. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.18.01377.","ista":"Bellstaedt J, Trenner J, Lippmann R, Poeschl Y, Zhang X, Friml J, Quint M, Delker C. 2019. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. 180(2), 757–766."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000470086100019"],"pmid":["31000634"]},"article_processing_charge":"No","author":[{"full_name":"Bellstaedt, Julia","last_name":"Bellstaedt","first_name":"Julia"},{"first_name":"Jana","last_name":"Trenner","full_name":"Trenner, Jana"},{"first_name":"Rebecca","last_name":"Lippmann","full_name":"Lippmann, Rebecca"},{"full_name":"Poeschl, Yvonne","last_name":"Poeschl","first_name":"Yvonne"},{"last_name":"Zhang","full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Quint, Marcel","last_name":"Quint","first_name":"Marcel"},{"full_name":"Delker, Carolin","last_name":"Delker","first_name":"Carolin"}],"title":"A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls","oa":1,"publisher":"ASPB","quality_controlled":"1","year":"2019","isi":1,"publication":"Plant Physiology","day":"01","page":"757-766","date_created":"2019-04-30T15:24:22Z","date_published":"2019-06-01T00:00:00Z","doi":"10.1104/pp.18.01377"}]