[{"day":"01","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_published":"2019-09-01T00:00:00Z","article_type":"original","publication":"Journal of the ACM","citation":{"ista":"Lenzen C, Rybicki J. 2019. Self-stabilising Byzantine clock synchronisation is almost as easy as consensus. Journal of the ACM. 66(5), 32.","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","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","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.","mla":"Lenzen, Christoph, and Joel Rybicki. “Self-Stabilising Byzantine Clock Synchronisation Is Almost as Easy as Consensus.” Journal 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)."},"abstract":[{"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 f16th International Conference on Quantitative Evaluation of Systems, vol. 11785, Springer Nature, 2019, pp. 109–28, 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.","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.","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","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.","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","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."},"publication":"16th International Conference on Quantitative Evaluation of Systems"},{"publication_identifier":{"issn":["0370-2693"]},"month":"11","doi":"10.1016/j.physletb.2019.135016","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000494939000086"],"arxiv":["1904.00913"]},"quality_controlled":"1","isi":1,"file_date_updated":"2020-07-14T12:47:46Z","article_number":"135016","author":[{"first_name":"C.H.","last_name":"Schmickler","full_name":"Schmickler, C.H."},{"full_name":"Hammer, H.-W.","first_name":"H.-W.","last_name":"Hammer"},{"full_name":"Volosniev, Artem","first_name":"Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525"}],"volume":798,"date_updated":"2023-08-30T07:06:42Z","date_created":"2019-10-18T18:33:32Z","year":"2019","publisher":"Elsevier","department":[{"_id":"MiLe"}],"publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"10","scopus_import":"1","date_published":"2019-11-10T00:00:00Z","citation":{"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.","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.","short":"C.H. Schmickler, H.-W. Hammer, A. Volosniev, Physics Letters B 798 (2019).","ista":"Schmickler CH, Hammer H-W, Volosniev A. 2019. Universal physics of bound states of a few charged particles. Physics Letters B. 798, 135016.","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.","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"},"publication":"Physics Letters B","article_type":"original","abstract":[{"lang":"eng","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."}],"type":"journal_article","file":[{"file_name":"2019_PhysicsLettersB_Schmickler.pdf","access_level":"open_access","content_type":"application/pdf","file_size":528362,"creator":"dernst","relation":"main_file","file_id":"6974","date_updated":"2020-07-14T12:47:46Z","date_created":"2019-10-25T12:47:04Z","checksum":"d27f983b34ea7dafdf356afbf9472fbf"}],"oa_version":"Published Version","_id":"6955","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 798","ddc":["530"],"status":"public","title":"Universal physics of bound states of a few charged particles"},{"file":[{"file_size":4334962,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_JournNeurochemistry_Cheung.pdf","checksum":"ec1fb2aebb874009bc309adaada6e1d7","date_created":"2020-02-05T10:30:02Z","date_updated":"2020-07-14T12:47:47Z","relation":"main_file","file_id":"7452"}],"oa_version":"Published Version","_id":"7005","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 151","status":"public","ddc":["570"],"title":"Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction","issue":"5","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"}],"type":"journal_article","date_published":"2019-12-01T00:00:00Z","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","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.","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.","short":"G.T. Cheung, M.A. Cousin, Journal of Neurochemistry 151 (2019) 570–583.","mla":"Cheung, Giselle T., and Michael A. Cousin. “Synaptic Vesicle Generation from Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent Dynamin–Syndapin Interaction.” Journal of Neurochemistry, vol. 151, no. 5, Wiley, 2019, pp. 570–83, doi: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."},"publication":"Journal of Neurochemistry","page":"570-583","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","author":[{"orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung","first_name":"Giselle T","full_name":"Cheung, Giselle T"},{"first_name":"Michael A.","last_name":"Cousin","full_name":"Cousin, Michael A."}],"volume":151,"date_created":"2019-11-12T14:37:08Z","date_updated":"2023-08-30T07:21:50Z","pmid":1,"year":"2019","department":[{"_id":"SiHi"}],"publisher":"Wiley","publication_status":"published","file_date_updated":"2020-07-14T12:47:47Z","doi":"10.1111/jnc.14862","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000490703100001"],"pmid":["31479508"]},"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["1471-4159"],"issn":["0022-3042"]},"month":"12"},{"publication_identifier":{"eissn":["1807-0302"],"issn":["2238-3603"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1007/s40314-019-0955-9","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1007/s40314-019-0955-9","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2101.09081"],"isi":["000488973100005"]},"ec_funded":1,"article_number":"161","volume":38,"date_created":"2019-11-12T12:41:44Z","date_updated":"2023-08-30T07:20:32Z","author":[{"id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9224-7139","first_name":"Yekini","last_name":"Shehu","full_name":"Shehu, Yekini"},{"full_name":"Iyiola, Olaniyi S.","last_name":"Iyiola","first_name":"Olaniyi S."},{"full_name":"Li, Xiao-Huan","first_name":"Xiao-Huan","last_name":"Li"},{"full_name":"Dong, Qiao-Li","last_name":"Dong","first_name":"Qiao-Li"}],"department":[{"_id":"VlKo"}],"publisher":"Springer Nature","publication_status":"published","year":"2019","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-12-01T00:00:00Z","article_type":"original","citation":{"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","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.","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","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.","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.","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","issue":"4","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."}],"type":"journal_article","oa_version":"Published Version","intvolume":" 38","title":"Convergence analysis of projection method for variational inequalities","ddc":["510","515","518"],"status":"public","_id":"7000","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"publication_identifier":{"eissn":["1471-0080"],"issn":["1471-0072"]},"month":"12","doi":"10.1038/s41580-019-0172-9","language":[{"iso":"eng"}],"external_id":{"isi":["000497966900007"],"pmid":["31582855"]},"quality_controlled":"1","isi":1,"author":[{"last_name":"Yamada","first_name":"KM","full_name":"Yamada, KM"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"}],"volume":20,"date_created":"2019-11-12T14:54:42Z","date_updated":"2023-08-30T07:22:20Z","pmid":1,"year":"2019","department":[{"_id":"MiSi"}],"publisher":"Springer Nature","publication_status":"published","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-12-01T00:00:00Z","citation":{"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.","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.","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","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.","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"},"publication":"Nature Reviews Molecular Cell Biology","page":"738–752","article_type":"review","issue":"12","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."}],"type":"journal_article","oa_version":"None","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7009","intvolume":" 20","title":"Mechanisms of 3D cell migration","status":"public"},{"doi":"10.1016/j.it.2019.08.004","language":[{"iso":"eng"}],"external_id":{"pmid":["31601520"],"isi":["000493292100005"]},"project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["1471-4906"]},"month":"10","author":[{"last_name":"Nicolai","first_name":"Leo","full_name":"Nicolai, Leo"},{"full_name":"Gärtner, Florian R","last_name":"Gärtner","first_name":"Florian R","orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Steffen","last_name":"Massberg","full_name":"Massberg, Steffen"}],"volume":40,"date_created":"2019-11-04T16:27:36Z","date_updated":"2023-08-30T07:19:23Z","pmid":1,"year":"2019","department":[{"_id":"MiSi"}],"publisher":"Cell Press","publication_status":"published","ec_funded":1,"date_published":"2019-10-01T00:00:00Z","citation":{"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.","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","ista":"Nicolai L, Gärtner FR, Massberg S. 2019. Platelets in host defense: Experimental and clinical insights. Trends in Immunology. 40(10), 922–938.","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.","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."},"publication":"Trends in Immunology","page":"922-938","article_type":"review","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"None","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6988","intvolume":" 40","title":"Platelets in host defense: Experimental and clinical insights","status":"public","issue":"10","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."}],"type":"journal_article"},{"month":"07","publication_identifier":{"issn":["0730-0301"]},"external_id":{"isi":["000475740600011"]},"isi":1,"quality_controlled":"1","project":[{"_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841","name":"Distributed 3D Object Design","call_identifier":"H2020"}],"doi":"10.1145/3306346.3323009","language":[{"iso":"eng"}],"article_number":"37","ec_funded":1,"year":"2019","publication_status":"published","publisher":"ACM","department":[{"_id":"ChWo"}],"author":[{"full_name":"Kondapaneni, Ivo","last_name":"Kondapaneni","first_name":"Ivo"},{"full_name":"Vevoda, Petr","first_name":"Petr","last_name":"Vevoda"},{"full_name":"Grittmann, Pascal","first_name":"Pascal","last_name":"Grittmann"},{"id":"486A5A46-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","last_name":"Skrivan","full_name":"Skrivan, Tomas"},{"last_name":"Slusallek","first_name":"Philipp","full_name":"Slusallek, Philipp"},{"full_name":"Křivánek, Jaroslav","first_name":"Jaroslav","last_name":"Křivánek"}],"date_updated":"2023-08-30T07:21:25Z","date_created":"2019-11-12T13:05:40Z","volume":38,"scopus_import":"1","day":"01","article_processing_charge":"No","publication":"ACM Transactions on Graphics","citation":{"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","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.","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","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.","short":"I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, J. Křivánek, ACM Transactions on Graphics 38 (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."},"article_type":"original","date_published":"2019-07-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Multiple Importance Sampling (MIS) is a key technique for achieving robustness of Monte Carlo estimators in computer graphics and other fields. We derive optimal weighting functions for MIS that provably minimize the variance of an MIS estimator, given a set of sampling techniques. We show that the resulting variance reduction over the balance heuristic can be higher than predicted by the variance bounds derived by Veach and Guibas, who assumed only non-negative weights in their proof. We theoretically analyze the variance of the optimal MIS weights and show the relation to the variance of the balance heuristic. Furthermore, we establish a connection between the new weighting functions and control variates as previously applied to mixture sampling. We apply the new optimal weights to integration problems in light transport and show that they allow for new design considerations when choosing the appropriate sampling techniques for a given integration problem.","lang":"eng"}],"issue":"4","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7002","title":"Optimal multiple importance sampling","status":"public","intvolume":" 38","oa_version":"None"},{"author":[{"full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010","first_name":"Nazmi B","last_name":"Budanur"},{"first_name":"Akshunna","last_name":"Dogra","full_name":"Dogra, Akshunna"},{"full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-30T07:20:03Z","date_created":"2019-11-04T10:04:01Z","volume":4,"year":"2019","publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"American Physical Society","doi":"10.1103/PhysRevFluids.4.102401","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1810.02211"],"isi":["000493510400001"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.02211"}],"isi":1,"quality_controlled":"1","month":"10","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6978","status":"public","title":"Geometry of transient chaos in streamwise-localized pipe flow turbulence","intvolume":" 4","abstract":[{"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.","lang":"eng"}],"issue":"10","type":"journal_article","date_published":"2019-10-01T00:00:00Z","publication":"Physical Review Fluids","citation":{"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.","short":"N.B. Budanur, A. Dogra, B. Hof, Physical Review Fluids 4 (2019) 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.","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","ista":"Budanur NB, Dogra A, Hof B. 2019. Geometry of transient chaos in streamwise-localized pipe flow turbulence. Physical Review Fluids. 4(10), 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"},"article_type":"original","page":"102401","day":"01","article_processing_charge":"No","scopus_import":"1"},{"doi":"10.1016/j.cels.2019.10.004","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000499495400003"]},"project":[{"call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["2405-4712"]},"month":"11","author":[{"id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6549-4177","first_name":"Martin","last_name":"Lukacisin","full_name":"Lukacisin, Martin"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Tobias"}],"volume":9,"date_created":"2019-11-15T10:51:42Z","date_updated":"2023-08-30T07:24:58Z","year":"2019","department":[{"_id":"ToBo"}],"publisher":"Cell Press","publication_status":"published","file_date_updated":"2020-07-14T12:47:48Z","date_published":"2019-11-27T00:00:00Z","citation":{"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","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.","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.","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","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.","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."},"publication":"Cell Systems","page":"423-433.e1-e3","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"27","scopus_import":"1","file":[{"relation":"main_file","file_id":"7027","checksum":"7a11d6c2f9523d65b049512d61733178","date_updated":"2020-07-14T12:47:48Z","date_created":"2019-11-15T10:57:42Z","access_level":"open_access","file_name":"2019_CellSystems_Lukacisin.pdf","file_size":4238460,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7026","intvolume":" 9","ddc":["570"],"title":"Emergent gene expression responses to drug combinations predict higher-order drug interactions","status":"public","issue":"5","abstract":[{"lang":"eng","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."}],"type":"journal_article"},{"month":"10","publication_identifier":{"eissn":["1439-6912"],"issn":["0209-9683"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00493-019-3905-7","quality_controlled":"1","isi":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.00508"}],"oa":1,"external_id":{"arxiv":["1709.00508"],"isi":["000493267200003"]},"ec_funded":1,"date_created":"2019-11-18T14:29:50Z","date_updated":"2023-08-30T07:26:25Z","volume":39,"author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","first_name":"Radoslav","last_name":"Fulek","full_name":"Fulek, Radoslav"},{"full_name":"Kynčl, Jan","last_name":"Kynčl","first_name":"Jan"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"UlWa"}],"year":"2019","day":"29","article_processing_charge":"No","scopus_import":"1","date_published":"2019-10-29T00:00:00Z","article_type":"original","page":"1267-1279","publication":"Combinatorica","citation":{"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.","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.","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"},"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"}],"issue":"6","type":"journal_article","oa_version":"Preprint","title":"Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4","status":"public","intvolume":" 39","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7034"},{"scopus_import":"1","month":"10","day":"17","publication_identifier":{"isbn":["9781728104690"]},"article_processing_charge":"No","quality_controlled":"1","isi":1,"publication":"2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference","citation":{"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.","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.","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.","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","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.","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"},"external_id":{"isi":["000630002701617"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2019-06-27","start_date":"2019-06-23","location":"Munich, Germany","name":"CLEO: Conference on Lasers and Electro-Optics Europe"},"date_published":"2019-10-17T00:00:00Z","doi":"10.1109/cleoe-eqec.2019.8873300","article_number":"8873300","type":"conference","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"}],"status":"public","title":"Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators","publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"IEEE","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7032","year":"2019","date_updated":"2023-08-30T07:26:01Z","date_created":"2019-11-18T13:58:22Z","oa_version":"None","author":[{"last_name":"Rueda Sanchez","first_name":"Alfredo R","orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","full_name":"Rueda Sanchez, Alfredo R"},{"full_name":"Sedlmeir, Florian","last_name":"Sedlmeir","first_name":"Florian"},{"full_name":"Leuchs, Gerd","last_name":"Leuchs","first_name":"Gerd"},{"last_name":"Kuamri","first_name":"Madhuri","full_name":"Kuamri, Madhuri"},{"last_name":"Schwefel","first_name":"Harald G. L.","full_name":"Schwefel, Harald G. L."}]},{"intvolume":" 9","title":"Completion of BAX recruitment correlates with mitochondrial fission during apoptosis","ddc":["570"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7095","oa_version":"Published Version","file":[{"creator":"dernst","file_size":6467393,"content_type":"application/pdf","file_name":"2019_ScientificReports_Maes.pdf","access_level":"open_access","date_created":"2019-11-25T07:49:52Z","date_updated":"2020-07-14T12:47:49Z","checksum":"9ab397ed9c1c454b34bffb8cc863d734","file_id":"7096","relation":"main_file"}],"type":"journal_article","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"}],"article_type":"original","citation":{"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.","short":"M.E. Maes, J.A. Grosser, R.L. Fehrman, C.L. Schlamp, R.W. Nickells, Scientific Reports 9 (2019).","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.","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","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.","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","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."},"publication":"Scientific Reports","date_published":"2019-11-12T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"12","department":[{"_id":"SaSi"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2019","volume":9,"date_created":"2019-11-25T07:45:17Z","date_updated":"2023-08-30T07:26:54Z","author":[{"orcid":"0000-0001-9642-1085","id":"3838F452-F248-11E8-B48F-1D18A9856A87","last_name":"Maes","first_name":"Margaret E","full_name":"Maes, Margaret E"},{"full_name":"Grosser, J. A.","last_name":"Grosser","first_name":"J. A."},{"first_name":"R. L.","last_name":"Fehrman","full_name":"Fehrman, R. L."},{"full_name":"Schlamp, C. L.","first_name":"C. L.","last_name":"Schlamp"},{"first_name":"R. W.","last_name":"Nickells","full_name":"Nickells, R. W."}],"article_number":"16565","file_date_updated":"2020-07-14T12:47:49Z","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31719602"],"isi":["000495857600019"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41598-019-53049-w","publication_identifier":{"eissn":["2045-2322"]},"month":"11"},{"article_type":"original","citation":{"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.","short":"M. Nagano, J.Y. Toshima, D.E. Siekhaus, J. Toshima, Communications Biology 2 (2019).","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","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.","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."},"publication":"Communications Biology","date_published":"2019-11-15T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"15","intvolume":" 2","title":"Rab5-mediated endosome formation is regulated at the trans-Golgi network","status":"public","ddc":["570"],"_id":"7097","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-25T07:58:05Z","checksum":"c63c69a264fc8a0e52f2b0d482f3bdae","relation":"main_file","file_id":"7098","content_type":"application/pdf","file_size":2626069,"creator":"dernst","file_name":"2019_CommunicBiology_Nagano.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","issue":"1","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"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000496767800005"]},"language":[{"iso":"eng"}],"doi":"10.1038/s42003-019-0670-5","publication_identifier":{"issn":["2399-3642"]},"month":"11","publisher":"Springer Nature","department":[{"_id":"DaSi"}],"publication_status":"published","year":"2019","volume":2,"date_updated":"2023-08-30T07:27:55Z","date_created":"2019-11-25T07:55:01Z","author":[{"first_name":"Makoto","last_name":"Nagano","full_name":"Nagano, Makoto"},{"full_name":"Toshima, Junko Y.","last_name":"Toshima","first_name":"Junko Y."},{"full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus"},{"full_name":"Toshima, Jiro","last_name":"Toshima","first_name":"Jiro"}],"article_number":"419","file_date_updated":"2020-07-14T12:47:49Z"},{"type":"journal_article","issue":"4","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7099","status":"public","title":"Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning","ddc":["571","599"],"intvolume":" 104","oa_version":"Published Version","scopus_import":"1","day":"20","article_processing_charge":"No","has_accepted_license":"1","publication":"Neuron","citation":{"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.","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.","short":"Y. Kasugai, E. Vogel, H. Hörtnagl, S. Schönherr, E. Paradiso, M. Hauschild, G. Göbel, I. Milenkovic, Y. Peterschmitt, R. Tasan, G. Sperk, R. Shigemoto, W. Sieghart, N. Singewald, A. Lüthi, F. Ferraguti, Neuron 104 (2019) 781–794.e4.","ista":"Kasugai Y, Vogel E, Hörtnagl H, Schönherr S, Paradiso E, Hauschild M, Göbel G, Milenkovic I, Peterschmitt Y, Tasan R, Sperk G, Shigemoto R, Sieghart W, Singewald N, Lüthi A, Ferraguti F. 2019. Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. Neuron. 104(4), 781–794.e4.","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.","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","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"},"article_type":"original","page":"781-794.e4","date_published":"2019-11-20T00:00:00Z","acknowledgement":"The authors thank Gabi Schmid for excellent technical support. We also thank\r\nDr. H. Harada, Dr. W. Kaufmann, and Dr. B. Kapelari for testing the specificity\r\nof some of the antibodies used in this study on replicas. Funding was provided\r\nby the Austrian Science Fund (Fonds zur Fo¨ rderung der Wissenschaftlichen\r\nForschung) Sonderforschungsbereich grants F44-17 (to F.jF.), F44-10 and\r\nP25375-B24 (to N.S.), and P26680 (to G.S.) and by the Novartis Research\r\nFoundation and the Swiss National Science Foundation (to A.L). We also thank\r\nProf. M. Capogna for reading a previous version of the manuscript.","year":"2019","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"RySh"}],"author":[{"full_name":"Kasugai, Yu","last_name":"Kasugai","first_name":"Yu"},{"full_name":"Vogel, Elisabeth","last_name":"Vogel","first_name":"Elisabeth"},{"full_name":"Hörtnagl, Heide","last_name":"Hörtnagl","first_name":"Heide"},{"first_name":"Sabine","last_name":"Schönherr","full_name":"Schönherr, Sabine"},{"last_name":"Paradiso","first_name":"Enrica","full_name":"Paradiso, Enrica"},{"full_name":"Hauschild, Markus","first_name":"Markus","last_name":"Hauschild"},{"full_name":"Göbel, Georg","first_name":"Georg","last_name":"Göbel"},{"first_name":"Ivan","last_name":"Milenkovic","full_name":"Milenkovic, Ivan"},{"first_name":"Yvan","last_name":"Peterschmitt","full_name":"Peterschmitt, Yvan"},{"first_name":"Ramon","last_name":"Tasan","full_name":"Tasan, Ramon"},{"full_name":"Sperk, Günther","last_name":"Sperk","first_name":"Günther"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sieghart","first_name":"Werner","full_name":"Sieghart, Werner"},{"full_name":"Singewald, Nicolas","first_name":"Nicolas","last_name":"Singewald"},{"full_name":"Lüthi, Andreas","first_name":"Andreas","last_name":"Lüthi"},{"first_name":"Francesco","last_name":"Ferraguti","full_name":"Ferraguti, Francesco"}],"date_updated":"2023-08-30T07:28:22Z","date_created":"2019-11-25T08:02:39Z","volume":104,"month":"11","publication_identifier":{"issn":["0896-6273"]},"external_id":{"isi":["000497963500017"],"pmid":["31543297"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2019.08.013"}],"quality_controlled":"1","isi":1,"doi":"10.1016/j.neuron.2019.08.013","language":[{"iso":"eng"}]},{"date_published":"2019-05-10T00:00:00Z","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.","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","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","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.","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.","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)."},"publication":"Science","article_type":"original","article_processing_charge":"No","day":"10","scopus_import":"1","oa_version":"Published Version","_id":"6455","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 364","title":"Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex","status":"public","issue":"6440","abstract":[{"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.","lang":"eng"}],"type":"journal_article","doi":"10.1126/science.aav2522","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000467631800034"],"pmid":["31073041"]},"main_file_link":[{"open_access":"1","url":"https://orbi.uliege.be/bitstream/2268/239604/1/Telley_Agirman_Science2019.pdf"}],"project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780"},{"call_identifier":"FWF","name":"Role of Eed in neural stem cell lineage progression","grant_number":"T0101031","_id":"268F8446-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"month":"05","related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-to-generate-a-brain-of-correct-size-and-composition/","description":"News on IST Homepage","relation":"press_release"}]},"author":[{"first_name":"L","last_name":"Telley","full_name":"Telley, L"},{"full_name":"Agirman, G","first_name":"G","last_name":"Agirman"},{"full_name":"Prados, J","last_name":"Prados","first_name":"J"},{"full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","first_name":"Nicole","last_name":"Amberg"},{"full_name":"Fièvre, S","first_name":"S","last_name":"Fièvre"},{"full_name":"Oberst, P","last_name":"Oberst","first_name":"P"},{"full_name":"Bartolini, G","first_name":"G","last_name":"Bartolini"},{"first_name":"I","last_name":"Vitali","full_name":"Vitali, I"},{"last_name":"Cadilhac","first_name":"C","full_name":"Cadilhac, C"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"},{"full_name":"Nguyen, L","last_name":"Nguyen","first_name":"L"},{"last_name":"Dayer","first_name":"A","full_name":"Dayer, A"},{"full_name":"Jabaudon, D","last_name":"Jabaudon","first_name":"D"}],"volume":364,"date_updated":"2023-09-05T11:51:09Z","date_created":"2019-05-14T13:07:47Z","pmid":1,"year":"2019","department":[{"_id":"SiHi"}],"publisher":"AAAS","publication_status":"published","ec_funded":1,"article_number":"eaav2522"},{"isi":1,"quality_controlled":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"external_id":{"pmid":["31017419 "],"isi":["000469292300004"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1021/jacs.9b01394","month":"04","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"publication_status":"published","department":[{"_id":"MaIb"}],"publisher":"American Chemical Society","year":"2019","pmid":1,"date_updated":"2023-09-05T12:03:45Z","date_created":"2019-06-25T11:53:35Z","volume":141,"author":[{"orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria","full_name":"Ibáñez, Maria"},{"first_name":"Roger","last_name":"Hasler","full_name":"Hasler, Roger"},{"last_name":"Genç","first_name":"Aziz","full_name":"Genç, Aziz"},{"last_name":"Liu","first_name":"Yu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Yu"},{"full_name":"Kuster, Beatrice","last_name":"Kuster","first_name":"Beatrice"},{"last_name":"Schuster","first_name":"Maximilian","full_name":"Schuster, Maximilian"},{"full_name":"Dobrozhan, Oleksandr","first_name":"Oleksandr","last_name":"Dobrozhan"},{"first_name":"Doris","last_name":"Cadavid","full_name":"Cadavid, Doris"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"},{"full_name":"Kovalenko, Maksym V.","first_name":"Maksym V.","last_name":"Kovalenko"}],"file_date_updated":"2020-07-14T12:47:34Z","ec_funded":1,"article_type":"original","page":"8025-8029","publication":"Journal of the American Chemical Society","citation":{"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.","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.","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.","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","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.","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","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."},"date_published":"2019-04-19T00:00:00Z","scopus_import":"1","day":"19","article_processing_charge":"No","has_accepted_license":"1","ddc":["540"],"status":"public","title":"Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion","intvolume":" 141","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6586","oa_version":"Published Version","file":[{"checksum":"34d7ec837869cc6a07996b54f75696b7","date_created":"2019-06-25T11:59:00Z","date_updated":"2020-07-14T12:47:34Z","relation":"main_file","file_id":"6587","content_type":"application/pdf","file_size":6234004,"creator":"cpetz","access_level":"open_access","file_name":"JACS_April2019.pdf"}],"type":"journal_article","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."}],"issue":"20"},{"article_number":"094205","date_updated":"2023-09-05T12:11:13Z","date_created":"2019-03-25T07:32:08Z","volume":99,"author":[{"full_name":"Dumitrescu, Philipp T.","first_name":"Philipp T.","last_name":"Dumitrescu"},{"full_name":"Goremykina, Anna","last_name":"Goremykina","first_name":"Anna"},{"last_name":"Parameswaran","first_name":"Siddharth A.","full_name":"Parameswaran, Siddharth A."},{"first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"},{"full_name":"Vasseur, Romain","first_name":"Romain","last_name":"Vasseur"}],"publication_status":"published","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","year":"2019","month":"03","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"language":[{"iso":"eng"}],"doi":"10.1103/physrevb.99.094205","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.03103"}],"external_id":{"isi":["000462883200001"],"arxiv":["1811.03103"]},"abstract":[{"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.","lang":"eng"}],"issue":"9","type":"journal_article","oa_version":"Preprint","title":"Kosterlitz-Thouless scaling at many-body localization phase transitions","status":"public","intvolume":" 99","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6174","day":"22","article_processing_charge":"No","scopus_import":"1","date_published":"2019-03-22T00:00:00Z","article_type":"original","publication":"Physical Review B","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.","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.","short":"P.T. Dumitrescu, A. Goremykina, S.A. Parameswaran, M. Serbyn, R. Vasseur, Physical Review B 99 (2019).","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.","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.","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","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"}},{"month":"06","publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"doi":"10.1104/pp.18.01377","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["31000634"],"isi":["000470086100019"]},"main_file_link":[{"url":"www.doi.org/10.1104/pp.18.01377","open_access":"1"}],"isi":1,"quality_controlled":"1","author":[{"full_name":"Bellstaedt, Julia","last_name":"Bellstaedt","first_name":"Julia"},{"first_name":"Jana","last_name":"Trenner","full_name":"Trenner, Jana"},{"last_name":"Lippmann","first_name":"Rebecca","full_name":"Lippmann, Rebecca"},{"full_name":"Poeschl, Yvonne","last_name":"Poeschl","first_name":"Yvonne"},{"full_name":"Zhang, Xixi","first_name":"Xixi","last_name":"Zhang","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"first_name":"Marcel","last_name":"Quint","full_name":"Quint, Marcel"},{"full_name":"Delker, Carolin","first_name":"Carolin","last_name":"Delker"}],"date_created":"2019-04-30T15:24:22Z","date_updated":"2023-09-05T12:25:19Z","volume":180,"year":"2019","pmid":1,"publication_status":"published","publisher":"ASPB","department":[{"_id":"JiFr"}],"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-06-01T00:00:00Z","publication":"Plant Physiology","citation":{"short":"J. Bellstaedt, J. Trenner, R. Lippmann, Y. Poeschl, X. Zhang, J. Friml, M. Quint, C. Delker, Plant Physiology 180 (2019) 757–766.","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.","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.","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","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.","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."},"article_type":"original","page":"757-766","abstract":[{"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.","lang":"eng"}],"issue":"2","type":"journal_article","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6366","status":"public","title":"A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls","intvolume":" 180"},{"ec_funded":1,"year":"2019","publisher":"AMS","department":[{"_id":"TaHa"}],"publication_status":"published","author":[{"first_name":"Penghui","last_name":"Li","id":"42A24CCC-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Penghui"}],"volume":147,"date_created":"2019-11-04T16:10:50Z","date_updated":"2023-09-05T12:22:21Z","publication_identifier":{"eissn":["1088-6826"],"issn":["0002-9939"]},"month":"11","external_id":{"arxiv":["1810.07039"],"isi":["000488621700004"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.07039"}],"project":[{"grant_number":"320593","_id":"25E549F4-B435-11E9-9278-68D0E5697425","name":"Arithmetic and physics of Higgs moduli spaces","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","doi":"10.1090/proc/14586","language":[{"iso":"eng"}],"type":"journal_article","issue":"11","abstract":[{"text":"Li-Nadler proposed a conjecture about traces of Hecke categories, which implies the semistable part of the Betti geometric Langlands conjecture of Ben-Zvi-Nadler in genus 1. We prove a Weyl group analogue of this conjecture. Our theorem holds in the natural generality of reflection groups in Euclidean or hyperbolic space. As a corollary, we give an expression of the centralizer of a finite order element in a reflection group using homotopy theory. ","lang":"eng"}],"_id":"6986","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 147","title":"A colimit of traces of reflection groups","status":"public","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"ama":"Li P. A colimit of traces of reflection groups. Proceedings of the American Mathematical Society. 2019;147(11):4597-4604. doi:10.1090/proc/14586","ista":"Li P. 2019. A colimit of traces of reflection groups. Proceedings of the American Mathematical Society. 147(11), 4597–4604.","apa":"Li, P. (2019). A colimit of traces of reflection groups. Proceedings of the American Mathematical Society. AMS. https://doi.org/10.1090/proc/14586","ieee":"P. Li, “A colimit of traces of reflection groups,” Proceedings of the American Mathematical Society, vol. 147, no. 11. AMS, pp. 4597–4604, 2019.","mla":"Li, Penghui. “A Colimit of Traces of Reflection Groups.” Proceedings of the American Mathematical Society, vol. 147, no. 11, AMS, 2019, pp. 4597–604, doi:10.1090/proc/14586.","short":"P. Li, Proceedings of the American Mathematical Society 147 (2019) 4597–4604.","chicago":"Li, Penghui. “A Colimit of Traces of Reflection Groups.” Proceedings of the American Mathematical Society. AMS, 2019. https://doi.org/10.1090/proc/14586."},"publication":"Proceedings of the American Mathematical Society","page":"4597-4604","article_type":"original","date_published":"2019-11-01T00:00:00Z"},{"scopus_import":"1","day":"03","article_processing_charge":"No","has_accepted_license":"1","publication":"Neuron","citation":{"short":"G. Ortiz-Álvarez, M. Daclin, A. Shihavuddin, P. Lansade, A. Fortoul, M. Faucourt, S. Clavreul, M. Lalioti, S. Taraviras, S. Hippenmeyer, J. Livet, A. Meunier, A. Genovesio, N. Spassky, Neuron 102 (2019) 159–172.e7.","mla":"Ortiz-Álvarez, G., et al. “Adult Neural Stem Cells and Multiciliated Ependymal Cells Share a Common Lineage Regulated by the Geminin Family Members.” Neuron, vol. 102, no. 1, Elsevier, 2019, p. 159–172.e7, doi:10.1016/j.neuron.2019.01.051.","chicago":"Ortiz-Álvarez, G, M Daclin, A Shihavuddin, P Lansade, A Fortoul, M Faucourt, S Clavreul, et al. “Adult Neural Stem Cells and Multiciliated Ependymal Cells Share a Common Lineage Regulated by the Geminin Family Members.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.01.051.","ama":"Ortiz-Álvarez G, Daclin M, Shihavuddin A, et al. Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. Neuron. 2019;102(1):159-172.e7. doi:10.1016/j.neuron.2019.01.051","apa":"Ortiz-Álvarez, G., Daclin, M., Shihavuddin, A., Lansade, P., Fortoul, A., Faucourt, M., … Spassky, N. (2019). Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.01.051","ieee":"G. Ortiz-Álvarez et al., “Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members,” Neuron, vol. 102, no. 1. Elsevier, p. 159–172.e7, 2019.","ista":"Ortiz-Álvarez G, Daclin M, Shihavuddin A, Lansade P, Fortoul A, Faucourt M, Clavreul S, Lalioti M, Taraviras S, Hippenmeyer S, Livet J, Meunier A, Genovesio A, Spassky N. 2019. Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. Neuron. 102(1), 159–172.e7."},"page":"159-172.e7","date_published":"2019-04-03T00:00:00Z","type":"journal_article","abstract":[{"text":"Adult neural stem cells and multiciliated ependymalcells are glial cells essential for neurological func-tions. Together, they make up the adult neurogenicniche. Using both high-throughput clonal analysisand single-cell resolution of progenitor division pat-terns and fate, we show that these two componentsof the neurogenic niche are lineally related: adult neu-ral stem cells are sister cells to ependymal cells,whereas most ependymal cells arise from the termi-nal symmetric divisions of the lineage. Unexpectedly,we found that the antagonist regulators of DNA repli-cation, GemC1 and Geminin, can tune the proportionof neural stem cells and ependymal cells. Our find-ings reveal the controlled dynamic of the neurogenicniche ontogeny and identify the Geminin familymembers as key regulators of the initial pool of adultneural stem cells.","lang":"eng"}],"issue":"1","_id":"6454","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members","ddc":["570"],"intvolume":" 102","file":[{"file_name":"2019_Neuron_Ortiz.pdf","access_level":"open_access","file_size":7288572,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6457","date_updated":"2020-07-14T12:47:30Z","date_created":"2019-05-15T09:28:41Z","checksum":"1fb6e195c583eb0c5cabf26f69ff6675"}],"oa_version":"Published Version","month":"04","publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"external_id":{"pmid":["30824354"],"isi":["000463337900018"]},"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"doi":"10.1016/j.neuron.2019.01.051","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:30Z","ec_funded":1,"year":"2019","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"SiHi"}],"author":[{"full_name":"Ortiz-Álvarez, G","first_name":"G","last_name":"Ortiz-Álvarez"},{"full_name":"Daclin, M","last_name":"Daclin","first_name":"M"},{"full_name":"Shihavuddin, A","first_name":"A","last_name":"Shihavuddin"},{"full_name":"Lansade, P","last_name":"Lansade","first_name":"P"},{"full_name":"Fortoul, A","last_name":"Fortoul","first_name":"A"},{"full_name":"Faucourt, M","last_name":"Faucourt","first_name":"M"},{"full_name":"Clavreul, S","first_name":"S","last_name":"Clavreul"},{"first_name":"ME","last_name":"Lalioti","full_name":"Lalioti, ME"},{"first_name":"S","last_name":"Taraviras","full_name":"Taraviras, S"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Livet, J","last_name":"Livet","first_name":"J"},{"last_name":"Meunier","first_name":"A","full_name":"Meunier, A"},{"first_name":"A","last_name":"Genovesio","full_name":"Genovesio, A"},{"full_name":"Spassky, N","first_name":"N","last_name":"Spassky"}],"date_created":"2019-05-14T13:06:30Z","date_updated":"2023-09-05T13:02:21Z","volume":102},{"publisher":"Cell Press","department":[{"_id":"MiSi"}],"publication_status":"published","pmid":1,"year":"2019","volume":29,"date_created":"2019-11-04T15:18:29Z","date_updated":"2023-09-05T12:43:43Z","author":[{"id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2187-6656","first_name":"Aglaja","last_name":"Kopf","full_name":"Kopf, Aglaja"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"}],"publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"month":"10","isi":1,"quality_controlled":"1","external_id":{"pmid":["31639357"],"isi":["000491286200016"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2019.08.068","type":"journal_article","issue":"20","intvolume":" 29","title":"Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6979","oa_version":"None","scopus_import":"1","article_processing_charge":"No","day":"21","page":"R1091-R1093","article_type":"original","citation":{"apa":"Kopf, A., & Sixt, M. K. (2019). Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2019.08.068","ieee":"A. Kopf and M. K. Sixt, “Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal,” Current Biology, vol. 29, no. 20. Cell Press, pp. R1091–R1093, 2019.","ista":"Kopf A, Sixt MK. 2019. Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal. Current Biology. 29(20), R1091–R1093.","ama":"Kopf A, Sixt MK. Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal. Current Biology. 2019;29(20):R1091-R1093. doi:10.1016/j.cub.2019.08.068","chicago":"Kopf, Aglaja, and Michael K Sixt. “Gut Homeostasis: Active Migration of Intestinal Epithelial Cells in Tissue Renewal.” Current Biology. Cell Press, 2019. https://doi.org/10.1016/j.cub.2019.08.068.","short":"A. Kopf, M.K. Sixt, Current Biology 29 (2019) R1091–R1093.","mla":"Kopf, Aglaja, and Michael K. Sixt. “Gut Homeostasis: Active Migration of Intestinal Epithelial Cells in Tissue Renewal.” Current Biology, vol. 29, no. 20, Cell Press, 2019, pp. R1091–93, doi:10.1016/j.cub.2019.08.068."},"publication":"Current Biology","date_published":"2019-10-21T00:00:00Z"},{"issue":"20","abstract":[{"lang":"eng","text":"Tissue morphogenesis in multicellular organisms is brought about by spatiotemporal coordination of mechanical and chemical signals. Extensive work on how mechanical forces together with the well‐established morphogen signalling pathways can actively shape living tissues has revealed evolutionary conserved mechanochemical features of embryonic development. More recently, attention has been drawn to the description of tissue material properties and how they can influence certain morphogenetic processes. Interestingly, besides the role of tissue material properties in determining how much tissues deform in response to force application, there is increasing theoretical and experimental evidence, suggesting that tissue material properties can abruptly and drastically change in development. These changes resemble phase transitions, pointing at the intriguing possibility that important morphogenetic processes in development, such as symmetry breaking and self‐organization, might be mediated by tissue phase transitions. In this review, we summarize recent findings on the regulation and role of tissue material properties in the context of the developing embryo. We posit that abrupt changes of tissue rheological properties may have important implications in maintaining the balance between robustness and adaptability during embryonic development."}],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_Embo_Petridou.pdf","creator":"dernst","file_size":847356,"content_type":"application/pdf","file_id":"6981","relation":"main_file","checksum":"76f7f4e79ab6d850c30017a69726fd85","date_updated":"2020-07-14T12:47:46Z","date_created":"2019-11-04T15:30:08Z"}],"intvolume":" 38","ddc":["570"],"status":"public","title":"Tissue rheology in embryonic organization","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6980","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"15","scopus_import":"1","date_published":"2019-10-15T00:00:00Z","article_type":"review","citation":{"short":"N. Petridou, C.-P.J. Heisenberg, The EMBO Journal 38 (2019).","mla":"Petridou, Nicoletta, and Carl-Philipp J. Heisenberg. “Tissue Rheology in Embryonic Organization.” The EMBO Journal, vol. 38, no. 20, e102497, EMBO, 2019, doi:10.15252/embj.2019102497.","chicago":"Petridou, Nicoletta, and Carl-Philipp J Heisenberg. “Tissue Rheology in Embryonic Organization.” The EMBO Journal. EMBO, 2019. https://doi.org/10.15252/embj.2019102497.","ama":"Petridou N, Heisenberg C-PJ. Tissue rheology in embryonic organization. The EMBO Journal. 2019;38(20). doi:10.15252/embj.2019102497","ieee":"N. Petridou and C.-P. J. Heisenberg, “Tissue rheology in embryonic organization,” The EMBO Journal, vol. 38, no. 20. EMBO, 2019.","apa":"Petridou, N., & Heisenberg, C.-P. J. (2019). Tissue rheology in embryonic organization. The EMBO Journal. EMBO. https://doi.org/10.15252/embj.2019102497","ista":"Petridou N, Heisenberg C-PJ. 2019. Tissue rheology in embryonic organization. The EMBO Journal. 38(20), e102497."},"publication":"The EMBO Journal","ec_funded":1,"file_date_updated":"2020-07-14T12:47:46Z","article_number":"e102497","volume":38,"date_created":"2019-11-04T15:24:29Z","date_updated":"2023-09-05T13:04:13Z","author":[{"orcid":"0000-0002-8451-1195","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","last_name":"Petridou","first_name":"Nicoletta","full_name":"Petridou, Nicoletta"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"publisher":"EMBO","department":[{"_id":"CaHe"}],"publication_status":"published","pmid":1,"year":"2019","publication_identifier":{"eissn":["1460-2075"],"issn":["0261-4189"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.15252/embj.2019102497","project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"_id":"2693FD8C-B435-11E9-9278-68D0E5697425","grant_number":"V00736","call_identifier":"FWF","name":"Tissue material properties in embryonic development"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["31512749"],"isi":["000485561900001"]}},{"issue":"9","abstract":[{"text":"Due to the importance of zero-shot learning, i.e. classifying images where there is a lack of labeled training data, the number of proposed approaches has recently increased steadily. We argue that it is time to take a step back and to analyze the status quo of the area. The purpose of this paper is three-fold. First, given the fact that there is no agreed upon zero-shot learning benchmark, we first define a new benchmark by unifying both the evaluation protocols and data splits of publicly available datasets used for this task. This is an important contribution as published results are often not comparable and sometimes even flawed due to, e.g. pre-training on zero-shot test classes. Moreover, we propose a new zero-shot learning dataset, the Animals with Attributes 2 (AWA2) dataset which we make publicly available both in terms of image features and the images themselves. Second, we compare and analyze a significant number of the state-of-the-art methods in depth, both in the classic zero-shot setting but also in the more realistic generalized zero-shot setting. Finally, we discuss in detail the limitations of the current status of the area which can be taken as a basis for advancing it.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 41","status":"public","title":"Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6554","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-09-01T00:00:00Z","page":"2251 - 2265","article_type":"original","citation":{"ama":"Xian Y, Lampert C, Schiele B, Akata Z. Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2019;41(9):2251-2265. doi:10.1109/tpami.2018.2857768","ieee":"Y. Xian, C. Lampert, B. Schiele, and Z. Akata, “Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 41, no. 9. Institute of Electrical and Electronics Engineers (IEEE), pp. 2251–2265, 2019.","apa":"Xian, Y., Lampert, C., Schiele, B., & Akata, Z. (2019). Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly. IEEE Transactions on Pattern Analysis and Machine Intelligence. Institute of Electrical and Electronics Engineers (IEEE). https://doi.org/10.1109/tpami.2018.2857768","ista":"Xian Y, Lampert C, Schiele B, Akata Z. 2019. Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly. IEEE Transactions on Pattern Analysis and Machine Intelligence. 41(9), 2251–2265.","short":"Y. Xian, C. Lampert, B. Schiele, Z. Akata, IEEE Transactions on Pattern Analysis and Machine Intelligence 41 (2019) 2251–2265.","mla":"Xian, Yongqin, et al. “Zero-Shot Learning - A Comprehensive Evaluation of the Good, the Bad and the Ugly.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 41, no. 9, Institute of Electrical and Electronics Engineers (IEEE), 2019, pp. 2251–65, doi:10.1109/tpami.2018.2857768.","chicago":"Xian, Yongqin, Christoph Lampert, Bernt Schiele, and Zeynep Akata. “Zero-Shot Learning - A Comprehensive Evaluation of the Good, the Bad and the Ugly.” IEEE Transactions on Pattern Analysis and Machine Intelligence. Institute of Electrical and Electronics Engineers (IEEE), 2019. https://doi.org/10.1109/tpami.2018.2857768."},"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","volume":41,"date_created":"2019-06-11T14:05:59Z","date_updated":"2023-09-05T13:18:09Z","author":[{"full_name":"Xian, Yongqin","first_name":"Yongqin","last_name":"Xian"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph"},{"full_name":"Schiele, Bernt","last_name":"Schiele","first_name":"Bernt"},{"last_name":"Akata","first_name":"Zeynep","full_name":"Akata, Zeynep"}],"publisher":"Institute of Electrical and Electronics Engineers (IEEE)","department":[{"_id":"ChLa"}],"publication_status":"published","year":"2019","publication_identifier":{"issn":["0162-8828"],"eissn":["1939-3539"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1109/tpami.2018.2857768","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1707.00600","open_access":"1"}],"external_id":{"isi":["000480343900015"],"arxiv":["1707.00600"]},"oa":1},{"date_published":"2019-04-11T00:00:00Z","article_type":"original","page":"240-243","publication":"Nature","citation":{"ista":"Cao M, Chen R, Li P, Yu Y, Zheng R, Ge D, Zheng W, Wang X, Gu Y, Gelová Z, Friml J, Zhang H, Liu R, He J, Xu T. 2019. TMK1-mediated auxin signalling regulates differential growth of the apical hook. Nature. 568, 240–243.","apa":"Cao, M., Chen, R., Li, P., Yu, Y., Zheng, R., Ge, D., … Xu, T. (2019). TMK1-mediated auxin signalling regulates differential growth of the apical hook. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1069-7","ieee":"M. Cao et al., “TMK1-mediated auxin signalling regulates differential growth of the apical hook,” Nature, vol. 568. Springer Nature, pp. 240–243, 2019.","ama":"Cao M, Chen R, Li P, et al. TMK1-mediated auxin signalling regulates differential growth of the apical hook. Nature. 2019;568:240-243. doi:10.1038/s41586-019-1069-7","chicago":"Cao, Min, Rong Chen, Pan Li, Yongqiang Yu, Rui Zheng, Danfeng Ge, Wei Zheng, et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth of the Apical Hook.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1069-7.","mla":"Cao, Min, et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth of the Apical Hook.” Nature, vol. 568, Springer Nature, 2019, pp. 240–43, doi:10.1038/s41586-019-1069-7.","short":"M. Cao, R. Chen, P. Li, Y. Yu, R. Zheng, D. Ge, W. Zheng, X. Wang, Y. Gu, Z. Gelová, J. Friml, H. Zhang, R. Liu, J. He, T. Xu, Nature 568 (2019) 240–243."},"day":"11","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"date_updated":"2020-11-13T07:37:41Z","date_created":"2020-11-13T07:37:41Z","success":1,"checksum":"6b84ab602a34382cf0340a37a1378c75","file_id":"8751","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":4321328,"file_name":"2019_Nature _Cao_accepted.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","title":"TMK1-mediated auxin signalling regulates differential growth of the apical hook","status":"public","ddc":["580"],"intvolume":" 568","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6259","abstract":[{"text":"The plant hormone auxin has crucial roles in almost all aspects of plant growth and development. Concentrations of auxin vary across different tissues, mediating distinct developmental outcomes and contributing to the functional diversity of auxin. However, the mechanisms that underlie these activities are poorly understood. Here we identify an auxin signalling mechanism, which acts in parallel to the canonical auxin pathway based on the transport inhibitor response1 (TIR1) and other auxin receptor F-box (AFB) family proteins (TIR1/AFB receptors)1,2, that translates levels of cellular auxin to mediate differential growth during apical-hook development. This signalling mechanism operates at the concave side of the apical hook, and involves auxin-mediated C-terminal cleavage of transmembrane kinase 1 (TMK1). The cytosolic and nucleus-translocated C terminus of TMK1 specifically interacts with and phosphorylates two non-canonical transcriptional repressors of the auxin or indole-3-acetic acid (Aux/IAA) family (IAA32 and IAA34), thereby regulating ARF transcription factors. In contrast to the degradation of Aux/IAA transcriptional repressors in the canonical pathway, the newly identified mechanism stabilizes the non-canonical IAA32 and IAA34 transcriptional repressors to regulate gene expression and ultimately inhibit growth. The auxin–TMK1 signalling pathway originates at the cell surface, is triggered by high levels of auxin and shares a partially overlapping set of transcription factors with the TIR1/AFB signalling pathway. This allows distinct interpretations of different concentrations of cellular auxin, and thus enables this versatile signalling molecule to mediate complex developmental outcomes.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41586-019-1069-7","quality_controlled":"1","isi":1,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["000464412700050"],"pmid":["30944466"]},"month":"04","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"date_created":"2019-04-09T08:37:05Z","date_updated":"2023-09-05T14:58:41Z","volume":568,"author":[{"full_name":"Cao, Min","last_name":"Cao","first_name":"Min"},{"first_name":"Rong","last_name":"Chen","full_name":"Chen, Rong"},{"first_name":"Pan","last_name":"Li","full_name":"Li, Pan"},{"first_name":"Yongqiang","last_name":"Yu","full_name":"Yu, Yongqiang"},{"full_name":"Zheng, Rui","first_name":"Rui","last_name":"Zheng"},{"full_name":"Ge, Danfeng","first_name":"Danfeng","last_name":"Ge"},{"full_name":"Zheng, Wei","last_name":"Zheng","first_name":"Wei"},{"first_name":"Xuhui","last_name":"Wang","full_name":"Wang, Xuhui"},{"first_name":"Yangtao","last_name":"Gu","full_name":"Gu, Yangtao"},{"id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","orcid":"0000-0003-4783-1752","first_name":"Zuzana","last_name":"Gelová","full_name":"Gelová, Zuzana"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"},{"last_name":"Zhang","first_name":"Heng","full_name":"Zhang, Heng"},{"full_name":"Liu, Renyi","first_name":"Renyi","last_name":"Liu"},{"full_name":"He, Jun","first_name":"Jun","last_name":"He"},{"full_name":"Xu, Tongda","last_name":"Xu","first_name":"Tongda"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/newly-discovered-mechanism-of-plant-hormone-auxin-acts-the-opposite-way/","description":"News on IST Homepage","relation":"press_release"}]},"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","year":"2019","pmid":1,"file_date_updated":"2020-11-13T07:37:41Z","ec_funded":1},{"alternative_title":["RESULTS"],"type":"book_chapter","abstract":[{"lang":"eng","text":"Cells are arranged into species-specific patterns during early embryogenesis. Such cell division patterns are important since they often reflect the distribution of localized cortical factors from eggs/fertilized eggs to specific cells as well as the emergence of organismal form. However, it has proven difficult to reveal the mechanisms that underlie the emergence of cell positioning patterns that underlie embryonic shape, likely because a systems-level approach is required that integrates cell biological, genetic, developmental, and mechanical parameters. The choice of organism to address such questions is also important. Because ascidians display the most extreme form of invariant cleavage pattern among the metazoans, we have been analyzing the cell biological mechanisms that underpin three aspects of cell division (unequal cell division (UCD), oriented cell division (OCD), and asynchronous cell cycles) which affect the overall shape of the blastula-stage ascidian embryo composed of 64 cells. In ascidians, UCD creates two small cells at the 16-cell stage that in turn undergo two further successive rounds of UCD. Starting at the 16-cell stage, the cell cycle becomes asynchronous, whereby the vegetal half divides before the animal half, thus creating 24-, 32-, 44-, and then 64-cell stages. Perturbing either UCD or the alternate cell division rhythm perturbs cell position. We propose that dynamic cell shape changes propagate throughout the embryo via cell-cell contacts to create the ascidian-specific invariant cleavage pattern."}],"intvolume":" 68","title":"Emergence of embryo shape during cleavage divisions","status":"public","ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6987","file":[{"date_updated":"2020-07-14T12:47:46Z","date_created":"2020-05-14T10:09:30Z","checksum":"7f43e1e3706d15061475c5c57efc2786","relation":"main_file","file_id":"7829","content_type":"application/pdf","file_size":19317348,"creator":"dernst","file_name":"2019_RESULTS_McDougall.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"10","page":"127-154","citation":{"mla":"McDougall, Alex, et al. “Emergence of Embryo Shape during Cleavage Divisions.” Evo-Devo: Non-Model Species in Cell and Developmental Biology, edited by Waclaw Tworzydlo and Szczepan M. Bilinski, vol. 68, Springer Nature, 2019, pp. 127–54, doi:10.1007/978-3-030-23459-1_6.","short":"A. McDougall, J. Chenevert, B.G. Godard, R. Dumollard, in:, W. Tworzydlo, S.M. Bilinski (Eds.), Evo-Devo: Non-Model Species in Cell and Developmental Biology, Springer Nature, 2019, pp. 127–154.","chicago":"McDougall, Alex, Janet Chenevert, Benoit G Godard, and Remi Dumollard. “Emergence of Embryo Shape during Cleavage Divisions.” In Evo-Devo: Non-Model Species in Cell and Developmental Biology, edited by Waclaw Tworzydlo and Szczepan M. Bilinski, 68:127–54. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-23459-1_6.","ama":"McDougall A, Chenevert J, Godard BG, Dumollard R. Emergence of embryo shape during cleavage divisions. In: Tworzydlo W, Bilinski SM, eds. Evo-Devo: Non-Model Species in Cell and Developmental Biology. Vol 68. Springer Nature; 2019:127-154. doi:10.1007/978-3-030-23459-1_6","ista":"McDougall A, Chenevert J, Godard BG, Dumollard R. 2019.Emergence of embryo shape during cleavage divisions. In: Evo-Devo: Non-model species in cell and developmental biology. RESULTS, vol. 68, 127–154.","ieee":"A. McDougall, J. Chenevert, B. G. Godard, and R. Dumollard, “Emergence of embryo shape during cleavage divisions,” in Evo-Devo: Non-model species in cell and developmental biology, vol. 68, W. Tworzydlo and S. M. Bilinski, Eds. Springer Nature, 2019, pp. 127–154.","apa":"McDougall, A., Chenevert, J., Godard, B. G., & Dumollard, R. (2019). Emergence of embryo shape during cleavage divisions. In W. Tworzydlo & S. M. Bilinski (Eds.), Evo-Devo: Non-model species in cell and developmental biology (Vol. 68, pp. 127–154). Springer Nature. https://doi.org/10.1007/978-3-030-23459-1_6"},"publication":"Evo-Devo: Non-model species in cell and developmental biology","date_published":"2019-10-10T00:00:00Z","file_date_updated":"2020-07-14T12:47:46Z","editor":[{"full_name":"Tworzydlo, Waclaw","first_name":"Waclaw","last_name":"Tworzydlo"},{"last_name":"Bilinski","first_name":"Szczepan M.","full_name":"Bilinski, Szczepan M."}],"publisher":"Springer Nature","department":[{"_id":"CaHe"}],"publication_status":"published","pmid":1,"year":"2019","volume":68,"date_updated":"2023-09-05T15:01:12Z","date_created":"2019-11-04T16:20:19Z","author":[{"full_name":"McDougall, Alex","last_name":"McDougall","first_name":"Alex"},{"first_name":"Janet","last_name":"Chenevert","full_name":"Chenevert, Janet"},{"full_name":"Godard, Benoit G","last_name":"Godard","first_name":"Benoit G","id":"33280250-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Remi","last_name":"Dumollard","full_name":"Dumollard, Remi"}],"publication_identifier":{"eissn":["1861-0412"],"isbn":["9783030234584","9783030234591"],"issn":["0080-1844"]},"month":"10","quality_controlled":"1","external_id":{"pmid":["31598855"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-23459-1_6"},{"publication_status":"published","publisher":"SIAM","department":[{"_id":"JuFi"}],"year":"2019","date_updated":"2023-09-05T15:05:45Z","date_created":"2019-08-04T21:59:21Z","volume":17,"author":[{"full_name":"Friesecke, Gero","last_name":"Friesecke","first_name":"Gero"},{"id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5645-4333","first_name":"Michael","last_name":"Kniely","full_name":"Kniely, Michael"}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.04200"}],"external_id":{"isi":["000487931800002"],"arxiv":["1808.04200"]},"language":[{"iso":"eng"}],"doi":"10.1137/18M1207272","month":"07","publication_identifier":{"eissn":["15403467"],"issn":["15403459"]},"status":"public","title":"New optimal control problems in density functional theory motivated by photovoltaics","intvolume":" 17","_id":"6762","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We present and study novel optimal control problems motivated by the search for photovoltaic materials with high power-conversion efficiency. The material must perform the first step: convert light (photons) into electronic excitations. We formulate various desirable properties of the excitations as mathematical control goals at the Kohn-Sham-DFT level\r\nof theory, with the control being given by the nuclear charge distribution. We prove that nuclear distributions exist which give rise to optimal HOMO-LUMO excitations, and present illustrative numerical simulations for 1D finite nanocrystals. We observe pronounced goal-dependent features such as large electron-hole separation, and a hierarchy of length scales: internal HOMO and LUMO wavelengths < atomic spacings < (irregular) fluctuations of the doping profiles < system size."}],"issue":"3","page":"926-947","publication":"Multiscale Modeling and Simulation","citation":{"apa":"Friesecke, G., & Kniely, M. (2019). New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. SIAM. https://doi.org/10.1137/18M1207272","ieee":"G. Friesecke and M. Kniely, “New optimal control problems in density functional theory motivated by photovoltaics,” Multiscale Modeling and Simulation, vol. 17, no. 3. SIAM, pp. 926–947, 2019.","ista":"Friesecke G, Kniely M. 2019. New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. 17(3), 926–947.","ama":"Friesecke G, Kniely M. New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. 2019;17(3):926-947. doi:10.1137/18M1207272","chicago":"Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation. SIAM, 2019. https://doi.org/10.1137/18M1207272.","short":"G. Friesecke, M. Kniely, Multiscale Modeling and Simulation 17 (2019) 926–947.","mla":"Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation, vol. 17, no. 3, SIAM, 2019, pp. 926–47, doi:10.1137/18M1207272."},"date_published":"2019-07-16T00:00:00Z","scopus_import":"1","day":"16","article_processing_charge":"No"},{"article_processing_charge":"No","day":"02","keyword":["Algebra and Number Theory"],"scopus_import":"1","date_published":"2019-01-02T00:00:00Z","article_type":"original","citation":{"chicago":"Ionica, Sorina, Pınar Kılıçer, Kristin Lauter, Elisa Lorenzo García, Maria-Adelina Manzateanu, Maike Massierer, and Christelle Vincent. “Modular Invariants for Genus 3 Hyperelliptic Curves.” Research in Number Theory. Springer Nature, 2019. https://doi.org/10.1007/s40993-018-0146-6.","short":"S. Ionica, P. Kılıçer, K. Lauter, E. Lorenzo García, M.-A. Manzateanu, M. Massierer, C. Vincent, Research in Number Theory 5 (2019).","mla":"Ionica, Sorina, et al. “Modular Invariants for Genus 3 Hyperelliptic Curves.” Research in Number Theory, vol. 5, 9, Springer Nature, 2019, doi:10.1007/s40993-018-0146-6.","apa":"Ionica, S., Kılıçer, P., Lauter, K., Lorenzo García, E., Manzateanu, M.-A., Massierer, M., & Vincent, C. (2019). Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. Springer Nature. https://doi.org/10.1007/s40993-018-0146-6","ieee":"S. Ionica et al., “Modular invariants for genus 3 hyperelliptic curves,” Research in Number Theory, vol. 5. Springer Nature, 2019.","ista":"Ionica S, Kılıçer P, Lauter K, Lorenzo García E, Manzateanu M-A, Massierer M, Vincent C. 2019. Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. 5, 9.","ama":"Ionica S, Kılıçer P, Lauter K, et al. Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. 2019;5. doi:10.1007/s40993-018-0146-6"},"publication":"Research in Number Theory","abstract":[{"lang":"eng","text":"In this article we prove an analogue of a theorem of Lachaud, Ritzenthaler, and Zykin, which allows us to connect invariants of binary octics to Siegel modular forms of genus 3. We use this connection to show that certain modular functions, when restricted to the hyperelliptic locus, assume values whose denominators are products of powers of primes of bad reduction for the associated hyperelliptic curves. We illustrate our theorem with explicit computations. This work is motivated by the study of the values of these modular functions at CM points of the Siegel upper half-space, which, if their denominators are known, can be used to effectively compute models of (hyperelliptic, in our case) curves with CM."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 5","title":"Modular invariants for genus 3 hyperelliptic curves","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10874","publication_identifier":{"eissn":["2363-9555"],"issn":["2522-0160"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1007/s40993-018-0146-6","quality_controlled":"1","oa":1,"external_id":{"arxiv":["1807.08986"]},"main_file_link":[{"url":"https://arxiv.org/abs/1807.08986","open_access":"1"}],"article_number":"9","volume":5,"date_updated":"2023-09-05T15:39:31Z","date_created":"2022-03-18T12:09:48Z","author":[{"first_name":"Sorina","last_name":"Ionica","full_name":"Ionica, Sorina"},{"first_name":"Pınar","last_name":"Kılıçer","full_name":"Kılıçer, Pınar"},{"last_name":"Lauter","first_name":"Kristin","full_name":"Lauter, Kristin"},{"first_name":"Elisa","last_name":"Lorenzo García","full_name":"Lorenzo García, Elisa"},{"full_name":"Manzateanu, Maria-Adelina","id":"be8d652e-a908-11ec-82a4-e2867729459c","last_name":"Manzateanu","first_name":"Maria-Adelina"},{"last_name":"Massierer","first_name":"Maike","full_name":"Massierer, Maike"},{"full_name":"Vincent, Christelle","first_name":"Christelle","last_name":"Vincent"}],"publisher":"Springer Nature","department":[{"_id":"TiBr"}],"publication_status":"published","acknowledgement":"The authors would like to thank the Lorentz Center in Leiden for hosting the Women in Numbers Europe 2 workshop and providing a productive and enjoyable environment for our initial work on this project. We are grateful to the organizers of WIN-E2, Irene Bouw, Rachel Newton and Ekin Ozman, for making this conference and this collaboration possible. We\r\nthank Irene Bouw and Christophe Ritzenhaler for helpful discussions. Ionica acknowledges support from the Thomas Jefferson Fund of the Embassy of France in the United States and the FACE Foundation. Most of Kılıçer’s work was carried out during her stay in Universiteit Leiden and Carl von Ossietzky Universität Oldenburg. Massierer was supported by the Australian Research Council (DP150101689). Vincent is supported by the National Science Foundation under Grant No. DMS-1802323 and by the Thomas Jefferson Fund of the Embassy of France in the United States and the FACE Foundation. ","year":"2019"},{"_id":"7100","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 372","status":"public","title":"Derivation of the time dependent Gross–Pitaevskii equation in two dimensions","ddc":["510"],"file":[{"creator":"dernst","content_type":"application/pdf","file_size":884469,"access_level":"open_access","file_name":"2019_CommMathPhys_Jeblick.pdf","checksum":"cd283b475dd739e04655315abd46f528","date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-25T08:11:11Z","file_id":"7101","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"text":"We present microscopic derivations of the defocusing two-dimensional cubic nonlinear Schrödinger equation and the Gross–Pitaevskii equation starting froman interacting N-particle system of bosons. We consider the interaction potential to be given either by Wβ(x)=N−1+2βW(Nβx), for any β>0, or to be given by VN(x)=e2NV(eNx), for some spherical symmetric, nonnegative and compactly supported W,V∈L∞(R2,R). In both cases we prove the convergence of the reduced density corresponding to the exact time evolution to the projector onto the solution of the corresponding nonlinear Schrödinger equation in trace norm. For the latter potential VN we show that it is crucial to take the microscopic structure of the condensate into account in order to obtain the correct dynamics.","lang":"eng"}],"citation":{"short":"M. Jeblick, N.K. Leopold, P. Pickl, Communications in Mathematical Physics 372 (2019) 1–69.","mla":"Jeblick, Maximilian, et al. “Derivation of the Time Dependent Gross–Pitaevskii Equation in Two Dimensions.” Communications in Mathematical Physics, vol. 372, no. 1, Springer Nature, 2019, pp. 1–69, doi:10.1007/s00220-019-03599-x.","chicago":"Jeblick, Maximilian, Nikolai K Leopold, and Peter Pickl. “Derivation of the Time Dependent Gross–Pitaevskii Equation in Two Dimensions.” Communications in Mathematical Physics. Springer Nature, 2019. https://doi.org/10.1007/s00220-019-03599-x.","ama":"Jeblick M, Leopold NK, Pickl P. Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical Physics. 2019;372(1):1-69. doi:10.1007/s00220-019-03599-x","ieee":"M. Jeblick, N. K. Leopold, and P. Pickl, “Derivation of the time dependent Gross–Pitaevskii equation in two dimensions,” Communications in Mathematical Physics, vol. 372, no. 1. Springer Nature, pp. 1–69, 2019.","apa":"Jeblick, M., Leopold, N. K., & Pickl, P. (2019). Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03599-x","ista":"Jeblick M, Leopold NK, Pickl P. 2019. Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical Physics. 372(1), 1–69."},"publication":"Communications in Mathematical Physics","page":"1-69","article_type":"original","date_published":"2019-11-08T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"08","acknowledgement":"OA fund by IST Austria","year":"2019","department":[{"_id":"RoSe"}],"publisher":"Springer Nature","publication_status":"published","author":[{"last_name":"Jeblick","first_name":"Maximilian","full_name":"Jeblick, Maximilian"},{"full_name":"Leopold, Nikolai K","first_name":"Nikolai K","last_name":"Leopold","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0495-6822"},{"first_name":"Peter","last_name":"Pickl","full_name":"Pickl, Peter"}],"volume":372,"date_created":"2019-11-25T08:08:02Z","date_updated":"2023-09-06T10:47:43Z","ec_funded":1,"file_date_updated":"2020-07-14T12:47:49Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000495193700002"]},"oa":1,"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"isi":1,"quality_controlled":"1","doi":"10.1007/s00220-019-03599-x","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"month":"11"},{"date_published":"2019-11-01T00:00:00Z","article_type":"original","page":"1114-1119","publication":"Nature Plants","citation":{"mla":"Skokan, Roman, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte Evolution.” Nature Plants, vol. 5, no. 11, Springer Nature, 2019, pp. 1114–19, doi:10.1038/s41477-019-0542-5.","short":"R. Skokan, E. Medvecká, T. Viaene, S. Vosolsobě, M. Zwiewka, K. Müller, P. Skůpa, M. Karady, Y. Zhang, D.P. Janacek, U.Z. Hammes, K. Ljung, T. Nodzyński, J. Petrášek, J. Friml, Nature Plants 5 (2019) 1114–1119.","chicago":"Skokan, Roman, Eva Medvecká, Tom Viaene, Stanislav Vosolsobě, Marta Zwiewka, Karel Müller, Petr Skůpa, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte Evolution.” Nature Plants. Springer Nature, 2019. https://doi.org/10.1038/s41477-019-0542-5.","ama":"Skokan R, Medvecká E, Viaene T, et al. PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. 2019;5(11):1114-1119. doi:10.1038/s41477-019-0542-5","ista":"Skokan R, Medvecká E, Viaene T, Vosolsobě S, Zwiewka M, Müller K, Skůpa P, Karady M, Zhang Y, Janacek DP, Hammes UZ, Ljung K, Nodzyński T, Petrášek J, Friml J. 2019. PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. 5(11), 1114–1119.","apa":"Skokan, R., Medvecká, E., Viaene, T., Vosolsobě, S., Zwiewka, M., Müller, K., … Friml, J. (2019). PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-019-0542-5","ieee":"R. Skokan et al., “PIN-driven auxin transport emerged early in streptophyte evolution,” Nature Plants, vol. 5, no. 11. Springer Nature, pp. 1114–1119, 2019."},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"creator":"dernst","file_size":1980851,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_NaturePlants_Skokan_accepted.pdf","success":1,"checksum":"94e0426856aad9a9bd0135d5436efbf1","date_updated":"2020-10-14T08:54:49Z","date_created":"2020-10-14T08:54:49Z","file_id":"8660","relation":"main_file"}],"oa_version":"Submitted Version","ddc":["580"],"title":"PIN-driven auxin transport emerged early in streptophyte evolution","status":"public","intvolume":" 5","_id":"7106","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"PIN-FORMED (PIN) transporters mediate directional, intercellular movement of the phytohormone auxin in land plants. To elucidate the evolutionary origins of this developmentally crucial mechanism, we analysed the single PIN homologue of a simple green alga Klebsormidium flaccidum. KfPIN functions as a plasma membrane-localized auxin exporter in land plants and heterologous models. While its role in algae remains unclear, PIN-driven auxin export is probably an ancient and conserved trait within streptophytes.","lang":"eng"}],"issue":"11","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41477-019-0542-5","quality_controlled":"1","isi":1,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"external_id":{"isi":["000496526100010"],"pmid":["31712756"]},"oa":1,"month":"11","publication_identifier":{"issn":["2055-0278"]},"date_updated":"2023-09-06T11:09:49Z","date_created":"2019-11-25T09:08:04Z","volume":5,"author":[{"last_name":"Skokan","first_name":"Roman","full_name":"Skokan, Roman"},{"first_name":"Eva","last_name":"Medvecká","full_name":"Medvecká, Eva"},{"last_name":"Viaene","first_name":"Tom","full_name":"Viaene, Tom"},{"first_name":"Stanislav","last_name":"Vosolsobě","full_name":"Vosolsobě, Stanislav"},{"last_name":"Zwiewka","first_name":"Marta","full_name":"Zwiewka, Marta"},{"full_name":"Müller, Karel","first_name":"Karel","last_name":"Müller"},{"full_name":"Skůpa, Petr","first_name":"Petr","last_name":"Skůpa"},{"first_name":"Michal","last_name":"Karady","full_name":"Karady, Michal"},{"first_name":"Yuzhou","last_name":"Zhang","full_name":"Zhang, Yuzhou"},{"full_name":"Janacek, Dorina P.","last_name":"Janacek","first_name":"Dorina P."},{"last_name":"Hammes","first_name":"Ulrich Z.","full_name":"Hammes, Ulrich Z."},{"first_name":"Karin","last_name":"Ljung","full_name":"Ljung, Karin"},{"first_name":"Tomasz","last_name":"Nodzyński","full_name":"Nodzyński, Tomasz"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JiFr"}],"year":"2019","pmid":1,"file_date_updated":"2020-10-14T08:54:49Z","ec_funded":1},{"month":"11","publication_identifier":{"issn":["1465-7392"],"eissn":["1476-4679"]},"oa":1,"external_id":{"pmid":["31685997"],"isi":["000495888300009"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7025891"}],"isi":1,"quality_controlled":"1","doi":"10.1038/s41556-019-0411-5","language":[{"iso":"eng"}],"year":"2019","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"MiSi"}],"author":[{"full_name":"Yolland, Lawrence","last_name":"Yolland","first_name":"Lawrence"},{"first_name":"Mubarik","last_name":"Burki","full_name":"Burki, Mubarik"},{"full_name":"Marcotti, Stefania","last_name":"Marcotti","first_name":"Stefania"},{"full_name":"Luchici, Andrei","last_name":"Luchici","first_name":"Andrei"},{"last_name":"Kenny","first_name":"Fiona N.","full_name":"Kenny, Fiona N."},{"last_name":"Davis","first_name":"John Robert","full_name":"Davis, John Robert"},{"full_name":"Serna-Morales, Eduardo","first_name":"Eduardo","last_name":"Serna-Morales"},{"id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","first_name":"Jan","last_name":"Müller","full_name":"Müller, Jan"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"},{"full_name":"Davidson, Andrew","last_name":"Davidson","first_name":"Andrew"},{"last_name":"Wood","first_name":"Will","full_name":"Wood, Will"},{"full_name":"Schumacher, Linus J.","first_name":"Linus J.","last_name":"Schumacher"},{"last_name":"Endres","first_name":"Robert G.","full_name":"Endres, Robert G."},{"first_name":"Mark","last_name":"Miodownik","full_name":"Miodownik, Mark"},{"first_name":"Brian M.","last_name":"Stramer","full_name":"Stramer, Brian M."}],"date_created":"2019-11-25T08:55:00Z","date_updated":"2023-09-06T11:08:52Z","volume":21,"scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Nature Cell Biology","citation":{"ama":"Yolland L, Burki M, Marcotti S, et al. Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. 2019;21(11):1370-1381. doi:10.1038/s41556-019-0411-5","ista":"Yolland L, Burki M, Marcotti S, Luchici A, Kenny FN, Davis JR, Serna-Morales E, Müller J, Sixt MK, Davidson A, Wood W, Schumacher LJ, Endres RG, Miodownik M, Stramer BM. 2019. Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. 21(11), 1370–1381.","apa":"Yolland, L., Burki, M., Marcotti, S., Luchici, A., Kenny, F. N., Davis, J. R., … Stramer, B. M. (2019). Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-019-0411-5","ieee":"L. Yolland et al., “Persistent and polarized global actin flow is essential for directionality during cell migration,” Nature Cell Biology, vol. 21, no. 11. Springer Nature, pp. 1370–1381, 2019.","mla":"Yolland, Lawrence, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” Nature Cell Biology, vol. 21, no. 11, Springer Nature, 2019, pp. 1370–81, doi:10.1038/s41556-019-0411-5.","short":"L. Yolland, M. Burki, S. Marcotti, A. Luchici, F.N. Kenny, J.R. Davis, E. Serna-Morales, J. Müller, M.K. Sixt, A. Davidson, W. Wood, L.J. Schumacher, R.G. Endres, M. Miodownik, B.M. Stramer, Nature Cell Biology 21 (2019) 1370–1381.","chicago":"Yolland, Lawrence, Mubarik Burki, Stefania Marcotti, Andrei Luchici, Fiona N. Kenny, John Robert Davis, Eduardo Serna-Morales, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” Nature Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41556-019-0411-5."},"article_type":"original","page":"1370-1381","date_published":"2019-11-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Cell migration is hypothesized to involve a cycle of behaviours beginning with leading edge extension. However, recent evidence suggests that the leading edge may be dispensable for migration, raising the question of what actually controls cell directionality. Here, we exploit the embryonic migration of Drosophila macrophages to bridge the different temporal scales of the behaviours controlling motility. This approach reveals that edge fluctuations during random motility are not persistent and are weakly correlated with motion. In contrast, flow of the actin network behind the leading edge is highly persistent. Quantification of actin flow structure during migration reveals a stable organization and asymmetry in the cell-wide flowfield that strongly correlates with cell directionality. This organization is regulated by a gradient of actin network compression and destruction, which is controlled by myosin contraction and cofilin-mediated disassembly. It is this stable actin-flow polarity, which integrates rapid fluctuations of the leading edge, that controls inherent cellular persistence.","lang":"eng"}],"issue":"11","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7105","status":"public","title":"Persistent and polarized global actin flow is essential for directionality during cell migration","intvolume":" 21","oa_version":"Submitted Version"},{"month":"05","publication_identifier":{"issn":["0004-5411"]},"language":[{"iso":"eng"}],"doi":"10.1145/3286976","isi":1,"quality_controlled":"1","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000495406300005"]},"article_number":"19","date_created":"2019-11-26T10:22:32Z","date_updated":"2023-09-06T11:11:56Z","volume":66,"author":[{"first_name":"Thomas","last_name":"Ferrere","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas"},{"last_name":"Maler","first_name":"Oded","full_name":"Maler, Oded"},{"full_name":"Ničković, Dejan","first_name":"Dejan","last_name":"Ničković"},{"last_name":"Pnueli","first_name":"Amir","full_name":"Pnueli, Amir"}],"publication_status":"published","publisher":"ACM","department":[{"_id":"ToHe"}],"year":"2019","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-05-01T00:00:00Z","article_type":"original","publication":"Journal of the ACM","citation":{"ista":"Ferrere T, Maler O, Ničković D, Pnueli A. 2019. From real-time logic to timed automata. Journal of the ACM. 66(3), 19.","ieee":"T. Ferrere, O. Maler, D. Ničković, and A. Pnueli, “From real-time logic to timed automata,” Journal of the ACM, vol. 66, no. 3. ACM, 2019.","apa":"Ferrere, T., Maler, O., Ničković, D., & Pnueli, A. (2019). From real-time logic to timed automata. Journal of the ACM. ACM. https://doi.org/10.1145/3286976","ama":"Ferrere T, Maler O, Ničković D, Pnueli A. From real-time logic to timed automata. Journal of the ACM. 2019;66(3). doi:10.1145/3286976","chicago":"Ferrere, Thomas, Oded Maler, Dejan Ničković, and Amir Pnueli. “From Real-Time Logic to Timed Automata.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3286976.","mla":"Ferrere, Thomas, et al. “From Real-Time Logic to Timed Automata.” Journal of the ACM, vol. 66, no. 3, 19, ACM, 2019, doi:10.1145/3286976.","short":"T. Ferrere, O. Maler, D. Ničković, A. Pnueli, Journal of the ACM 66 (2019)."},"abstract":[{"lang":"eng","text":"We show how to construct temporal testers for the logic MITL, a prominent linear-time logic for real-time systems. A temporal tester is a transducer that inputs a signal holding the Boolean value of atomic propositions and outputs the truth value of a formula along time. Here we consider testers over continuous-time Boolean signals that use clock variables to enforce duration constraints, as in timed automata. We first rewrite the MITL formula into a “simple” formula using a limited set of temporal modalities. We then build testers for these specific modalities and show how to compose testers for simple formulae into complex ones. Temporal testers can be turned into acceptors, yielding a compositional translation from MITL to timed automata. This construction is much simpler than previously known and remains asymptotically optimal. It supports both past and future operators and can easily be extended."}],"issue":"3","type":"journal_article","oa_version":"None","status":"public","title":"From real-time logic to timed automata","intvolume":" 66","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7109"},{"article_number":"21","volume":66,"date_created":"2019-11-26T10:13:59Z","date_updated":"2023-09-06T11:10:58Z","related_material":{"record":[{"id":"184","status":"public","relation":"earlier_version"}]},"author":[{"last_name":"Goaoc","first_name":"Xavier","full_name":"Goaoc, Xavier"},{"full_name":"Patak, Pavel","last_name":"Patak","first_name":"Pavel","id":"B593B804-1035-11EA-B4F1-947645A5BB83"},{"orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87","last_name":"Patakova","first_name":"Zuzana","full_name":"Patakova, Zuzana"},{"full_name":"Tancer, Martin","first_name":"Martin","last_name":"Tancer"},{"first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"publisher":"ACM","department":[{"_id":"UlWa"}],"publication_status":"published","year":"2019","publication_identifier":{"issn":["0004-5411"]},"month":"06","language":[{"iso":"eng"}],"doi":"10.1145/3314024","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/pdf/1711.08436.pdf","open_access":"1"}],"external_id":{"arxiv":["1711.08436"],"isi":["000495406300007"]},"oa":1,"issue":"3","abstract":[{"lang":"eng","text":"We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes. Another simple corollary of our result is that it is NP-hard to decide whether a given poset is CL-shellable."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 66","title":"Shellability is NP-complete","status":"public","_id":"7108","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-06-01T00:00:00Z","article_type":"original","citation":{"apa":"Goaoc, X., Patak, P., Patakova, Z., Tancer, M., & Wagner, U. (2019). Shellability is NP-complete. Journal of the ACM. ACM. https://doi.org/10.1145/3314024","ieee":"X. Goaoc, P. Patak, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” Journal of the ACM, vol. 66, no. 3. ACM, 2019.","ista":"Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. 2019. Shellability is NP-complete. Journal of the ACM. 66(3), 21.","ama":"Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. Journal of the ACM. 2019;66(3). doi:10.1145/3314024","chicago":"Goaoc, Xavier, Pavel Patak, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3314024.","short":"X. Goaoc, P. Patak, Z. Patakova, M. Tancer, U. Wagner, Journal of the ACM 66 (2019).","mla":"Goaoc, Xavier, et al. “Shellability Is NP-Complete.” Journal of the ACM, vol. 66, no. 3, 21, ACM, 2019, doi:10.1145/3314024."},"publication":"Journal of the ACM"},{"scopus_import":"1","day":"17","article_processing_charge":"No","publication":"17th International Conference on Computational Methods in Systems Biology","citation":{"short":"C.C. Guet, T.A. Henzinger, C. Igler, T. Petrov, A. Sezgin, in:, 17th International Conference on Computational Methods in Systems Biology, Springer Nature, 2019, pp. 155–187.","mla":"Guet, Calin C., et al. “Transient Memory in Gene Regulation.” 17th International Conference on Computational Methods in Systems Biology, vol. 11773, Springer Nature, 2019, pp. 155–87, doi:10.1007/978-3-030-31304-3_9.","chicago":"Guet, Calin C, Thomas A Henzinger, Claudia Igler, Tatjana Petrov, and Ali Sezgin. “Transient Memory in Gene Regulation.” In 17th International Conference on Computational Methods in Systems Biology, 11773:155–87. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-31304-3_9.","ama":"Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. Transient memory in gene regulation. In: 17th International Conference on Computational Methods in Systems Biology. Vol 11773. Springer Nature; 2019:155-187. doi:10.1007/978-3-030-31304-3_9","ieee":"C. C. Guet, T. A. Henzinger, C. Igler, T. Petrov, and A. Sezgin, “Transient memory in gene regulation,” in 17th International Conference on Computational Methods in Systems Biology, Trieste, Italy, 2019, vol. 11773, pp. 155–187.","apa":"Guet, C. C., Henzinger, T. A., Igler, C., Petrov, T., & Sezgin, A. (2019). Transient memory in gene regulation. In 17th International Conference on Computational Methods in Systems Biology (Vol. 11773, pp. 155–187). Trieste, Italy: Springer Nature. https://doi.org/10.1007/978-3-030-31304-3_9","ista":"Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. 2019. Transient memory in gene regulation. 17th International Conference on Computational Methods in Systems Biology. CMSB: Computational Methods in Systems Biology, LNCS, vol. 11773, 155–187."},"page":"155-187","date_published":"2019-09-17T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"The expression of a gene is characterised by its transcription factors and the function processing them. If the transcription factors are not affected by gene products, the regulating function is often represented as a combinational logic circuit, where the outputs (product) are determined by current input values (transcription factors) only, and are hence independent on their relative arrival times. However, the simultaneous arrival of transcription factors (TFs) in genetic circuits is a strong assumption, given that the processes of transcription and translation of a gene into a protein introduce intrinsic time delays and that there is no global synchronisation among the arrival times of different molecular species at molecular targets.\r\n\r\nIn this paper, we construct an experimentally implementable genetic circuit with two inputs and a single output, such that, in presence of small delays in input arrival, the circuit exhibits qualitatively distinct observable phenotypes. In particular, these phenotypes are long lived transients: they all converge to a single value, but so slowly, that they seem stable for an extended time period, longer than typical experiment duration. We used rule-based language to prototype our circuit, and we implemented a search for finding the parameter combinations raising the phenotypes of interest.\r\n\r\nThe behaviour of our prototype circuit has wide implications. First, it suggests that GRNs can exploit event timing to create phenotypes. Second, it opens the possibility that GRNs are using event timing to react to stimuli and memorise events, without explicit feedback in regulation. From the modelling perspective, our prototype circuit demonstrates the critical importance of analysing the transient dynamics at the promoter binding sites of the DNA, before applying rapid equilibrium assumptions.","lang":"eng"}],"_id":"7147","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Transient memory in gene regulation","intvolume":" 11773","oa_version":"None","month":"09","publication_identifier":{"isbn":["9783030313036","9783030313043"],"eissn":["1611-3349"],"issn":["0302-9743"]},"external_id":{"isi":["000557875100009"]},"quality_controlled":"1","isi":1,"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"Design principles underlying genetic switch architecture","_id":"251EE76E-B435-11E9-9278-68D0E5697425","grant_number":"24573"}],"conference":{"location":"Trieste, Italy","start_date":"2019-09-18","end_date":"2019-09-20","name":"CMSB: Computational Methods in Systems Biology"},"doi":"10.1007/978-3-030-31304-3_9","language":[{"iso":"eng"}],"year":"2019","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"author":[{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia","last_name":"Igler"},{"full_name":"Petrov, Tatjana","first_name":"Tatjana","last_name":"Petrov","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9041-0905"},{"id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","last_name":"Sezgin","first_name":"Ali","full_name":"Sezgin, Ali"}],"date_updated":"2023-09-06T11:18:08Z","date_created":"2019-12-04T16:07:50Z","volume":11773},{"doi":"10.1109/isit.2019.8849240","conference":{"end_date":"2019-07-12","start_date":"2019-07-07","location":"Paris, France","name":"ISIT: International Symposium on Information Theory"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.08476"}],"external_id":{"isi":["000489100301043"],"arxiv":["1702.08476"]},"oa":1,"quality_controlled":"1","isi":1,"publication_identifier":{"isbn":["9781538692912"]},"month":"07","author":[{"full_name":"Skórski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","last_name":"Skórski"}],"date_created":"2019-11-28T10:19:21Z","date_updated":"2023-09-06T11:15:41Z","year":"2019","publisher":"IEEE","department":[{"_id":"KrPi"}],"publication_status":"published","article_number":"8849240","date_published":"2019-07-01T00:00:00Z","citation":{"ista":"Skórski M. 2019. Strong chain rules for min-entropy under few bits spoiled. 2019 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory, 8849240.","apa":"Skórski, M. (2019). Strong chain rules for min-entropy under few bits spoiled. In 2019 IEEE International Symposium on Information Theory. Paris, France: IEEE. https://doi.org/10.1109/isit.2019.8849240","ieee":"M. Skórski, “Strong chain rules for min-entropy under few bits spoiled,” in 2019 IEEE International Symposium on Information Theory, Paris, France, 2019.","ama":"Skórski M. Strong chain rules for min-entropy under few bits spoiled. In: 2019 IEEE International Symposium on Information Theory. IEEE; 2019. doi:10.1109/isit.2019.8849240","chicago":"Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.” In 2019 IEEE International Symposium on Information Theory. IEEE, 2019. https://doi.org/10.1109/isit.2019.8849240.","mla":"Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.” 2019 IEEE International Symposium on Information Theory, 8849240, IEEE, 2019, doi:10.1109/isit.2019.8849240.","short":"M. Skórski, in:, 2019 IEEE International Symposium on Information Theory, IEEE, 2019."},"publication":"2019 IEEE International Symposium on Information Theory","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7136","title":"Strong chain rules for min-entropy under few bits spoiled","status":"public","abstract":[{"lang":"eng","text":"It is well established that the notion of min-entropy fails to satisfy the \\emph{chain rule} of the form H(X,Y)=H(X|Y)+H(Y), known for Shannon Entropy. Such a property would help to analyze how min-entropy is split among smaller blocks. Problems of this kind arise for example when constructing extractors and dispersers.\r\nWe show that any sequence of variables exhibits a very strong strong block-source structure (conditional distributions of blocks are nearly flat) when we \\emph{spoil few correlated bits}. This implies, conditioned on the spoiled bits, that \\emph{splitting-recombination properties} hold. In particular, we have many nice properties that min-entropy doesn't obey in general, for example strong chain rules, \"information can't hurt\" inequalities, equivalences of average and worst-case conditional entropy definitions and others. Quantitatively, for any sequence X1,…,Xt of random variables over an alphabet X we prove that, when conditioned on m=t⋅O(loglog|X|+loglog(1/ϵ)+logt) bits of auxiliary information, all conditional distributions of the form Xi|X2018 IEEE Conference on Decision and Control, 8619625, IEEE, 2019, doi:10.1109/cdc.2018.8619625.","chicago":"Khirirat, Sarit, Mikael Johansson, and Dan-Adrian Alistarh. “Gradient Compression for Communication-Limited Convex Optimization.” In 2018 IEEE Conference on Decision and Control. IEEE, 2019. https://doi.org/10.1109/cdc.2018.8619625.","ama":"Khirirat S, Johansson M, Alistarh D-A. Gradient compression for communication-limited convex optimization. In: 2018 IEEE Conference on Decision and Control. IEEE; 2019. doi:10.1109/cdc.2018.8619625","apa":"Khirirat, S., Johansson, M., & Alistarh, D.-A. (2019). Gradient compression for communication-limited convex optimization. In 2018 IEEE Conference on Decision and Control. Miami Beach, FL, United States: IEEE. https://doi.org/10.1109/cdc.2018.8619625","ieee":"S. Khirirat, M. Johansson, and D.-A. Alistarh, “Gradient compression for communication-limited convex optimization,” in 2018 IEEE Conference on Decision and Control, Miami Beach, FL, United States, 2019.","ista":"Khirirat S, Johansson M, Alistarh D-A. 2019. Gradient compression for communication-limited convex optimization. 2018 IEEE Conference on Decision and Control. CDC: Conference on Decision and Control, 8619625."},"quality_controlled":"1","isi":1,"conference":{"end_date":"2018-12-19","location":"Miami Beach, FL, United States","start_date":"2018-12-17","name":"CDC: Conference on Decision and Control"},"date_published":"2019-01-21T00:00:00Z","doi":"10.1109/cdc.2018.8619625","language":[{"iso":"eng"}],"article_number":"8619625","type":"conference","abstract":[{"text":"Data-rich applications in machine-learning and control have motivated an intense research on large-scale optimization. Novel algorithms have been proposed and shown to have optimal convergence rates in terms of iteration counts. However, their practical performance is severely degraded by the cost of exchanging high-dimensional gradient vectors between computing nodes. Several gradient compression heuristics have recently been proposed to reduce communications, but few theoretical results exist that quantify how they impact algorithm convergence. This paper establishes and strengthens the convergence guarantees for gradient descent under a family of gradient compression techniques. For convex optimization problems, we derive admissible step sizes and quantify both the number of iterations and the number of bits that need to be exchanged to reach a target accuracy. Finally, we validate the performance of different gradient compression techniques in simulations. The numerical results highlight the properties of different gradient compression algorithms and confirm that fast convergence with limited information exchange is possible.","lang":"eng"}],"_id":"7122","year":"2019","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","title":"Gradient compression for communication-limited convex optimization","status":"public","department":[{"_id":"DaAl"}],"publisher":"IEEE","author":[{"first_name":"Sarit","last_name":"Khirirat","full_name":"Khirirat, Sarit"},{"first_name":"Mikael","last_name":"Johansson","full_name":"Johansson, Mikael"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"}],"date_created":"2019-11-26T15:07:49Z","date_updated":"2023-09-06T11:14:55Z","oa_version":"None"},{"ec_funded":1,"author":[{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"date_created":"2019-12-04T16:05:25Z","date_updated":"2023-09-06T11:18:59Z","volume":3,"year":"2019","publication_status":"published","department":[{"_id":"BeVi"}],"publisher":"Springer Nature","month":"11","publication_identifier":{"issn":["2397-334X"]},"doi":"10.1038/s41559-019-1050-8","language":[{"iso":"eng"}],"external_id":{"isi":["000500728800009"]},"quality_controlled":"1","isi":1,"project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Prevailing models of sex-chromosome evolution were largely inspired by the stable and highly differentiated XY pairs of model organisms, such as those of mammals and flies. Recent work has uncovered an incredible diversity of sex-determining systems, bringing some of the assumptions of these traditional models into question. One particular question that has arisen is what drives some sex chromosomes to be maintained over millions of years and differentiate fully, while others are replaced by new sex-determining chromosomes before differentiation has occurred. Here, I review recent data on the variability of sex-determining genes and sex chromosomes in different non-model vertebrates and invertebrates, and discuss some theoretical models that have been put forward to account for this diversity.","lang":"eng"}],"issue":"12","type":"journal_article","oa_version":"None","_id":"7146","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Molecular and evolutionary dynamics of animal sex-chromosome turnover","intvolume":" 3","day":"25","article_processing_charge":"No","scopus_import":"1","date_published":"2019-11-25T00:00:00Z","publication":"Nature Ecology & Evolution","citation":{"chicago":"Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome Turnover.” Nature Ecology & Evolution. Springer Nature, 2019. https://doi.org/10.1038/s41559-019-1050-8.","mla":"Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome Turnover.” Nature Ecology & Evolution, vol. 3, no. 12, Springer Nature, 2019, pp. 1632–41, doi:10.1038/s41559-019-1050-8.","short":"B. Vicoso, Nature Ecology & Evolution 3 (2019) 1632–1641.","ista":"Vicoso B. 2019. Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology & Evolution. 3(12), 1632–1641.","ieee":"B. Vicoso, “Molecular and evolutionary dynamics of animal sex-chromosome turnover,” Nature Ecology & Evolution, vol. 3, no. 12. Springer Nature, pp. 1632–1641, 2019.","apa":"Vicoso, B. (2019). Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-019-1050-8","ama":"Vicoso B. Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology & Evolution. 2019;3(12):1632-1641. doi:10.1038/s41559-019-1050-8"},"article_type":"original","page":"1632-1641"},{"oa_version":"Published Version","intvolume":" 29","status":"public","title":"Defying gravity: a plant's quest for moisture","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7143","abstract":[{"text":"Roots grow downwards parallel to the gravity vector, to anchor a plant in soil and acquire water and nutrients, using a gravitropic mechanism dependent on the asymmetric distribution of the phytohormone auxin. Recently, Chang et al. demonstrate that asymmetric distribution of another phytohormone, cytokinin, directs root growth towards higher water content.","lang":"eng"}],"type":"journal_article","date_published":"2019-12-01T00:00:00Z","page":"965-966","article_type":"original","citation":{"short":"S.A. Sinclair, J. Friml, Cell Research 29 (2019) 965–966.","mla":"Sinclair, Scott A., and Jiří Friml. “Defying Gravity: A Plant’s Quest for Moisture.” Cell Research, vol. 29, Springer Nature, 2019, pp. 965–66, doi:10.1038/s41422-019-0254-4.","chicago":"Sinclair, Scott A, and Jiří Friml. “Defying Gravity: A Plant’s Quest for Moisture.” Cell Research. Springer Nature, 2019. https://doi.org/10.1038/s41422-019-0254-4.","ama":"Sinclair SA, Friml J. Defying gravity: a plant’s quest for moisture. Cell Research. 2019;29:965-966. doi:10.1038/s41422-019-0254-4","apa":"Sinclair, S. A., & Friml, J. (2019). Defying gravity: a plant’s quest for moisture. Cell Research. Springer Nature. https://doi.org/10.1038/s41422-019-0254-4","ieee":"S. A. Sinclair and J. Friml, “Defying gravity: a plant’s quest for moisture,” Cell Research, vol. 29. Springer Nature, pp. 965–966, 2019.","ista":"Sinclair SA, Friml J. 2019. Defying gravity: a plant’s quest for moisture. Cell Research. 29, 965–966."},"publication":"Cell Research","article_processing_charge":"No","day":"01","scopus_import":"1","volume":29,"date_updated":"2023-09-06T11:20:58Z","date_created":"2019-12-02T12:30:48Z","author":[{"id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4566-0593","first_name":"Scott A","last_name":"Sinclair","full_name":"Sinclair, Scott A"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"department":[{"_id":"JiFr"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2019","language":[{"iso":"eng"}],"doi":"10.1038/s41422-019-0254-4","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41422-019-0254-4"}],"external_id":{"isi":["000500749600001"],"pmid":["31745287"]},"oa":1,"publication_identifier":{"eissn":["1748-7838"],"issn":["1001-0602"]},"month":"12"},{"type":"journal_article","abstract":[{"lang":"eng","text":"We propose an efficient microwave-photonic modulator as a resource for stationary entangled microwave-optical fields and develop the theory for deterministic entanglement generation and quantum state transfer in multi-resonant electro-optic systems. The device is based on a single crystal whispering gallery mode resonator integrated into a 3D-microwave cavity. The specific design relies on a new combination of thin-film technology and conventional machining that is optimized for the lowest dissipation rates in the microwave, optical, and mechanical domains. We extract important device properties from finite-element simulations and predict continuous variable entanglement generation rates on the order of a Mebit/s for optical pump powers of only a few tens of microwatts. We compare the quantum state transfer fidelities of coherent, squeezed, and non-Gaussian cat states for both teleportation and direct conversion protocols under realistic conditions. Combining the unique capabilities of circuit quantum electrodynamics with the resilience of fiber optic communication could facilitate long-distance solid-state qubit networks, new methods for quantum signal synthesis, quantum key distribution, and quantum enhanced detection, as well as more power-efficient classical sensing and modulation."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7156","title":"Electro-optic entanglement source for microwave to telecom quantum state transfer","status":"public","ddc":["530"],"intvolume":" 5","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":1580132,"creator":"dernst","access_level":"open_access","file_name":"2019_NPJ_Rueda.pdf","checksum":"13e0ea1d4f9b5f5710780d9473364f58","date_updated":"2020-07-14T12:47:50Z","date_created":"2019-12-09T08:25:06Z","relation":"main_file","file_id":"7157"}],"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication":"npj Quantum Information","citation":{"mla":"Rueda Sanchez, Alfredo R., et al. “Electro-Optic Entanglement Source for Microwave to Telecom Quantum State Transfer.” Npj Quantum Information, vol. 5, 108, Springer Nature, 2019, doi:10.1038/s41534-019-0220-5.","short":"A.R. Rueda Sanchez, W.J. Hease, S. Barzanjeh, J.M. Fink, Npj Quantum Information 5 (2019).","chicago":"Rueda Sanchez, Alfredo R, William J Hease, Shabir Barzanjeh, and Johannes M Fink. “Electro-Optic Entanglement Source for Microwave to Telecom Quantum State Transfer.” Npj Quantum Information. Springer Nature, 2019. https://doi.org/10.1038/s41534-019-0220-5.","ama":"Rueda Sanchez AR, Hease WJ, Barzanjeh S, Fink JM. Electro-optic entanglement source for microwave to telecom quantum state transfer. npj Quantum Information. 2019;5. doi:10.1038/s41534-019-0220-5","ista":"Rueda Sanchez AR, Hease WJ, Barzanjeh S, Fink JM. 2019. Electro-optic entanglement source for microwave to telecom quantum state transfer. npj Quantum Information. 5, 108.","apa":"Rueda Sanchez, A. R., Hease, W. J., Barzanjeh, S., & Fink, J. M. (2019). Electro-optic entanglement source for microwave to telecom quantum state transfer. Npj Quantum Information. Springer Nature. https://doi.org/10.1038/s41534-019-0220-5","ieee":"A. R. Rueda Sanchez, W. J. Hease, S. Barzanjeh, and J. M. Fink, “Electro-optic entanglement source for microwave to telecom quantum state transfer,” npj Quantum Information, vol. 5. Springer Nature, 2019."},"article_type":"original","date_published":"2019-12-01T00:00:00Z","article_number":"108","file_date_updated":"2020-07-14T12:47:50Z","ec_funded":1,"year":"2019","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JoFi"}],"author":[{"full_name":"Rueda Sanchez, Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","first_name":"Alfredo R","last_name":"Rueda Sanchez"},{"full_name":"Hease, William J","last_name":"Hease","first_name":"William J","orcid":"0000-0001-9868-2166","id":"29705398-F248-11E8-B48F-1D18A9856A87"},{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","first_name":"Shabir","last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M"}],"date_updated":"2023-09-06T11:22:39Z","date_created":"2019-12-09T08:18:56Z","volume":5,"month":"12","publication_identifier":{"issn":["2056-6387"]},"external_id":{"arxiv":["1909.01470"],"isi":["000502996200003"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"call_identifier":"H2020","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438"},{"grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425","name":"Hybrid Optomechanical Technologies","call_identifier":"H2020"},{"_id":"26927A52-B435-11E9-9278-68D0E5697425","grant_number":"F07105","call_identifier":"FWF","name":"Integrating superconducting quantum circuits"}],"doi":"10.1038/s41534-019-0220-5","language":[{"iso":"eng"}]},{"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"month":"12","doi":"10.1242/dev.176297","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31784457"],"isi":["000507575700004"]},"project":[{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037","call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord"}],"quality_controlled":"1","isi":1,"ec_funded":1,"file_date_updated":"2020-07-14T12:47:50Z","article_number":"dev176297","author":[{"last_name":"Guerrero","first_name":"Pilar","full_name":"Guerrero, Pilar"},{"first_name":"Ruben","last_name":"Perez-Carrasco","full_name":"Perez-Carrasco, Ruben"},{"id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7896-7762","first_name":"Marcin P","last_name":"Zagórski","full_name":"Zagórski, Marcin P"},{"full_name":"Page, David","last_name":"Page","first_name":"David"},{"first_name":"Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna"},{"full_name":"Briscoe, James","last_name":"Briscoe","first_name":"James"},{"full_name":"Page, Karen M.","last_name":"Page","first_name":"Karen M."}],"volume":146,"date_updated":"2023-09-06T11:26:36Z","date_created":"2019-12-10T14:39:50Z","pmid":1,"year":"2019","publisher":"The Company of Biologists","department":[{"_id":"AnKi"}],"publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"04","scopus_import":"1","date_published":"2019-12-04T00:00:00Z","citation":{"ama":"Guerrero P, Perez-Carrasco R, Zagórski MP, et al. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. 2019;146(23). doi:10.1242/dev.176297","apa":"Guerrero, P., Perez-Carrasco, R., Zagórski, M. P., Page, D., Kicheva, A., Briscoe, J., & Page, K. M. (2019). Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. The Company of Biologists. https://doi.org/10.1242/dev.176297","ieee":"P. Guerrero et al., “Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium,” Development, vol. 146, no. 23. The Company of Biologists, 2019.","ista":"Guerrero P, Perez-Carrasco R, Zagórski MP, Page D, Kicheva A, Briscoe J, Page KM. 2019. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. 146(23), dev176297.","short":"P. Guerrero, R. Perez-Carrasco, M.P. Zagórski, D. Page, A. Kicheva, J. Briscoe, K.M. Page, Development 146 (2019).","mla":"Guerrero, Pilar, et al. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” Development, vol. 146, no. 23, dev176297, The Company of Biologists, 2019, doi:10.1242/dev.176297.","chicago":"Guerrero, Pilar, Ruben Perez-Carrasco, Marcin P Zagórski, David Page, Anna Kicheva, James Briscoe, and Karen M. Page. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” Development. The Company of Biologists, 2019. https://doi.org/10.1242/dev.176297."},"publication":"Development","article_type":"original","issue":"23","abstract":[{"lang":"eng","text":"Cell division, movement and differentiation contribute to pattern formation in developing tissues. This is the case in the vertebrate neural tube, in which neurons differentiate in a characteristic pattern from a highly dynamic proliferating pseudostratified epithelium. To investigate how progenitor proliferation and differentiation affect cell arrangement and growth of the neural tube, we used experimental measurements to develop a mechanical model of the apical surface of the neuroepithelium that incorporates the effect of interkinetic nuclear movement and spatially varying rates of neuronal differentiation. Simulations predict that tissue growth and the shape of lineage-related clones of cells differ with the rate of differentiation. Growth is isotropic in regions of high differentiation, but dorsoventrally biased in regions of low differentiation. This is consistent with experimental observations. The absence of directional signalling in the simulations indicates that global mechanical constraints are sufficient to explain the observed differences in anisotropy. This provides insight into how the tissue growth rate affects cell dynamics and growth anisotropy and opens up possibilities to study the coupling between mechanics, pattern formation and growth in the neural tube."}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","file_size":7797881,"content_type":"application/pdf","file_name":"2019_Development_Guerrero.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:50Z","date_created":"2019-12-13T07:34:06Z","checksum":"b6533c37dc8fbd803ffeca216e0a8b8a","file_id":"7177","relation":"main_file"}],"_id":"7165","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 146","status":"public","ddc":["570"],"title":"Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium"},{"year":"2019","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"publication_status":"published","author":[{"full_name":"Ničković, Dejan","first_name":"Dejan","last_name":"Ničković"},{"first_name":"Xin","last_name":"Qin","full_name":"Qin, Xin"},{"full_name":"Ferrere, Thomas","last_name":"Ferrere","first_name":"Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mateis, Cristinel","first_name":"Cristinel","last_name":"Mateis"},{"first_name":"Jyotirmoy","last_name":"Deshmukh","full_name":"Deshmukh, Jyotirmoy"}],"volume":11757,"date_created":"2019-12-09T08:47:55Z","date_updated":"2023-09-06T11:24:10Z","publication_identifier":{"isbn":["9783030320782","9783030320799"],"issn":["0302-9743"]},"month":"10","external_id":{"isi":["000570006300017"]},"project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"}],"isi":1,"quality_controlled":"1","doi":"10.1007/978-3-030-32079-9_17","conference":{"name":"RV: Runtime Verification","location":"Porto, Portugal","start_date":"2019-10-08","end_date":"2019-10-11"},"language":[{"iso":"eng"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Cyber-physical systems (CPS) and the Internet-of-Things (IoT) result in a tremendous amount of generated, measured and recorded time-series data. Extracting temporal segments that encode patterns with useful information out of these huge amounts of data is an extremely difficult problem. We propose shape expressions as a declarative formalism for specifying, querying and extracting sophisticated temporal patterns from possibly noisy data. Shape expressions are regular expressions with arbitrary (linear, exponential, sinusoidal, etc.) shapes with parameters as atomic predicates and additional constraints on these parameters. We equip shape expressions with a novel noisy semantics that combines regular expression matching semantics with statistical regression. We characterize essential properties of the formalism and propose an efficient approximate shape expression matching procedure. We demonstrate the wide applicability of this technique on two case studies. "}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7159","intvolume":" 11757","status":"public","title":"Shape expressions for specifying and extracting signal features","oa_version":"None","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"chicago":"Ničković, Dejan, Xin Qin, Thomas Ferrere, Cristinel Mateis, and Jyotirmoy Deshmukh. “Shape Expressions for Specifying and Extracting Signal Features.” In 19th International Conference on Runtime Verification, 11757:292–309. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-32079-9_17.","short":"D. Ničković, X. Qin, T. Ferrere, C. Mateis, J. Deshmukh, in:, 19th International Conference on Runtime Verification, Springer Nature, 2019, pp. 292–309.","mla":"Ničković, Dejan, et al. “Shape Expressions for Specifying and Extracting Signal Features.” 19th International Conference on Runtime Verification, vol. 11757, Springer Nature, 2019, pp. 292–309, doi:10.1007/978-3-030-32079-9_17.","ieee":"D. Ničković, X. Qin, T. Ferrere, C. Mateis, and J. Deshmukh, “Shape expressions for specifying and extracting signal features,” in 19th International Conference on Runtime Verification, Porto, Portugal, 2019, vol. 11757, pp. 292–309.","apa":"Ničković, D., Qin, X., Ferrere, T., Mateis, C., & Deshmukh, J. (2019). Shape expressions for specifying and extracting signal features. In 19th International Conference on Runtime Verification (Vol. 11757, pp. 292–309). Porto, Portugal: Springer Nature. https://doi.org/10.1007/978-3-030-32079-9_17","ista":"Ničković D, Qin X, Ferrere T, Mateis C, Deshmukh J. 2019. Shape expressions for specifying and extracting signal features. 19th International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 11757, 292–309.","ama":"Ničković D, Qin X, Ferrere T, Mateis C, Deshmukh J. Shape expressions for specifying and extracting signal features. In: 19th International Conference on Runtime Verification. Vol 11757. Springer Nature; 2019:292-309. doi:10.1007/978-3-030-32079-9_17"},"publication":"19th International Conference on Runtime Verification","page":"292-309","date_published":"2019-10-01T00:00:00Z"},{"date_published":"2019-10-21T00:00:00Z","citation":{"ieee":"T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, and D. Velan, “Deciding fast termination for probabilistic VASS with nondeterminism,” in International Symposium on Automated Technology for Verification and Analysis, Taipei, Taiwan, 2019, vol. 11781, pp. 462–478.","apa":"Brázdil, T., Chatterjee, K., Kucera, A., Novotný, P., & Velan, D. (2019). Deciding fast termination for probabilistic VASS with nondeterminism. In International Symposium on Automated Technology for Verification and Analysis (Vol. 11781, pp. 462–478). Taipei, Taiwan: Springer Nature. https://doi.org/10.1007/978-3-030-31784-3_27","ista":"Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. 2019. Deciding fast termination for probabilistic VASS with nondeterminism. International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated TEchnology for Verification and Analysis, LNCS, vol. 11781, 462–478.","ama":"Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. Deciding fast termination for probabilistic VASS with nondeterminism. In: International Symposium on Automated Technology for Verification and Analysis. Vol 11781. Springer Nature; 2019:462-478. doi:10.1007/978-3-030-31784-3_27","chicago":"Brázdil, Tomás, Krishnendu Chatterjee, Antonín Kucera, Petr Novotný, and Dominik Velan. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” In International Symposium on Automated Technology for Verification and Analysis, 11781:462–78. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-31784-3_27.","short":"T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, D. Velan, in:, International Symposium on Automated Technology for Verification and Analysis, Springer Nature, 2019, pp. 462–478.","mla":"Brázdil, Tomás, et al. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” International Symposium on Automated Technology for Verification and Analysis, vol. 11781, Springer Nature, 2019, pp. 462–78, doi:10.1007/978-3-030-31784-3_27."},"publication":"International Symposium on Automated Technology for Verification and Analysis","page":"462-478","article_processing_charge":"No","day":"21","scopus_import":"1","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7183","intvolume":" 11781","status":"public","title":"Deciding fast termination for probabilistic VASS with nondeterminism","abstract":[{"text":"A probabilistic vector addition system with states (pVASS) is a finite state Markov process augmented with non-negative integer counters that can be incremented or decremented during each state transition, blocking any behaviour that would cause a counter to decrease below zero. The pVASS can be used as abstractions of probabilistic programs with many decidable properties. The use of pVASS as abstractions requires the presence of nondeterminism in the model. In this paper, we develop techniques for checking fast termination of pVASS with nondeterminism. That is, for every initial configuration of size n, we consider the worst expected number of transitions needed to reach a configuration with some counter negative (the expected termination time). We show that the problem whether the asymptotic expected termination time is linear is decidable in polynomial time for a certain natural class of pVASS with nondeterminism. Furthermore, we show the following dichotomy: if the asymptotic expected termination time is not linear, then it is at least quadratic, i.e., in Ω(n2).","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"doi":"10.1007/978-3-030-31784-3_27","conference":{"name":"ATVA: Automated TEchnology for Verification and Analysis","end_date":"2019-10-31","start_date":"2019-10-28","location":"Taipei, Taiwan"},"language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000723515700027"],"arxiv":["1907.11010"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.11010"}],"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"quality_controlled":"1","isi":1,"publication_identifier":{"isbn":["9783030317836"],"eissn":["16113349"],"issn":["03029743"]},"month":"10","author":[{"first_name":"Tomás","last_name":"Brázdil","full_name":"Brázdil, Tomás"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kucera, Antonín","first_name":"Antonín","last_name":"Kucera"},{"full_name":"Novotný, Petr","last_name":"Novotný","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Velan","first_name":"Dominik","full_name":"Velan, Dominik"}],"volume":11781,"date_created":"2019-12-15T23:00:44Z","date_updated":"2023-09-06T12:40:58Z","year":"2019","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"publication_status":"published"},{"has_accepted_license":"1","article_processing_charge":"No","day":"14","scopus_import":"1","date_published":"2019-11-14T00:00:00Z","citation":{"apa":"Alcântara, A., Bosch, J., Nazari, F., Hoffmann, G., Gallei, M. C., Uhse, S., … Djamei, A. (2019). Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2019.01437","ieee":"A. Alcântara et al., “Systematic Y2H screening reveals extensive effector-complex formation,” Frontiers in Plant Science, vol. 10, no. 11. Frontiers, 2019.","ista":"Alcântara A, Bosch J, Nazari F, Hoffmann G, Gallei MC, Uhse S, Darino MA, Olukayode T, Reumann D, Baggaley L, Djamei A. 2019. Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. 10(11), 1437.","ama":"Alcântara A, Bosch J, Nazari F, et al. Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. 2019;10(11). doi:10.3389/fpls.2019.01437","chicago":"Alcântara, André, Jason Bosch, Fahimeh Nazari, Gesa Hoffmann, Michelle C Gallei, Simon Uhse, Martin A. Darino, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” Frontiers in Plant Science. Frontiers, 2019. https://doi.org/10.3389/fpls.2019.01437.","short":"A. Alcântara, J. Bosch, F. Nazari, G. Hoffmann, M.C. Gallei, S. Uhse, M.A. Darino, T. Olukayode, D. Reumann, L. Baggaley, A. Djamei, Frontiers in Plant Science 10 (2019).","mla":"Alcântara, André, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” Frontiers in Plant Science, vol. 10, no. 11, 1437, Frontiers, 2019, doi:10.3389/fpls.2019.01437."},"publication":"Frontiers in Plant Science","article_type":"original","issue":"11","abstract":[{"lang":"eng","text":"During infection pathogens secrete small molecules, termed effectors, to manipulate and control the interaction with their specific hosts. Both the pathogen and the plant are under high selective pressure to rapidly adapt and co-evolve in what is usually referred to as molecular arms race. Components of the host’s immune system form a network that processes information about molecules with a foreign origin and damage-associated signals, integrating them with developmental and abiotic cues to adapt the plant’s responses. Both in the case of nucleotide-binding leucine-rich repeat receptors and leucine-rich repeat receptor kinases interaction networks have been extensively characterized. However, little is known on whether pathogenic effectors form complexes to overcome plant immunity and promote disease. Ustilago maydis, a biotrophic fungal pathogen that infects maize plants, produces effectors that target hubs in the immune network of the host cell. Here we assess the capability of U. maydis effector candidates to interact with each other, which may play a crucial role during the infection process. Using a systematic yeast-two-hybrid approach and based on a preliminary pooled screen, we selected 63 putative effectors for one-on-one matings with a library of nearly 300 effector candidates. We found that 126 of these effector candidates interacted either with themselves or other predicted effectors. Although the functional relevance of the observed interactions remains elusive, we propose that the observed abundance in complex formation between effectors adds an additional level of complexity to effector research and should be taken into consideration when studying effector evolution and function. Based on this fundamental finding, we suggest various scenarios which could evolutionarily drive the formation and stabilization of an effector interactome."}],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_FrontiersPlant_Alcantara.pdf","content_type":"application/pdf","file_size":1532505,"creator":"dernst","relation":"main_file","file_id":"7185","checksum":"995aa838aec2064d93550de82b40bbd1","date_updated":"2020-07-14T12:47:52Z","date_created":"2019-12-16T07:58:43Z"}],"_id":"7182","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 10","ddc":["580"],"title":"Systematic Y2H screening reveals extensive effector-complex formation","status":"public","publication_identifier":{"eissn":["1664462X"]},"month":"11","doi":"10.3389/fpls.2019.01437","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["31803201"],"isi":["000499821700001"]},"isi":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:47:52Z","article_number":"1437","author":[{"full_name":"Alcântara, André","first_name":"André","last_name":"Alcântara"},{"full_name":"Bosch, Jason","first_name":"Jason","last_name":"Bosch"},{"last_name":"Nazari","first_name":"Fahimeh","full_name":"Nazari, Fahimeh"},{"first_name":"Gesa","last_name":"Hoffmann","full_name":"Hoffmann, Gesa"},{"last_name":"Gallei","first_name":"Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C"},{"last_name":"Uhse","first_name":"Simon","full_name":"Uhse, Simon"},{"full_name":"Darino, Martin A.","first_name":"Martin A.","last_name":"Darino"},{"full_name":"Olukayode, Toluwase","first_name":"Toluwase","last_name":"Olukayode"},{"last_name":"Reumann","first_name":"Daniel","full_name":"Reumann, Daniel"},{"full_name":"Baggaley, Laura","first_name":"Laura","last_name":"Baggaley"},{"last_name":"Djamei","first_name":"Armin","full_name":"Djamei, Armin"}],"volume":10,"date_created":"2019-12-15T23:00:43Z","date_updated":"2023-09-06T14:33:46Z","pmid":1,"year":"2019","department":[{"_id":"JiFr"}],"publisher":"Frontiers","publication_status":"published"},{"month":"12","publication_identifier":{"eissn":["20411723"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-019-13543-1","quality_controlled":"1","isi":1,"project":[{"grant_number":"M02379","_id":"264CBBAC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modeling epithelial tissue mechanics during cell invasion"}],"external_id":{"pmid":["31797871"],"isi":["000500508100001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2020-07-14T12:47:52Z","article_number":"5516","date_created":"2019-12-15T23:00:43Z","date_updated":"2023-09-06T14:08:21Z","volume":10,"author":[{"full_name":"Retzer, Katarzyna","last_name":"Retzer","first_name":"Katarzyna"},{"last_name":"Akhmanova","first_name":"Maria","orcid":"0000-0003-1522-3162","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","full_name":"Akhmanova, Maria"},{"full_name":"Konstantinova, Nataliia","first_name":"Nataliia","last_name":"Konstantinova"},{"full_name":"Malínská, Kateřina","first_name":"Kateřina","last_name":"Malínská"},{"first_name":"Johannes","last_name":"Leitner","full_name":"Leitner, Johannes"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"last_name":"Luschnig","first_name":"Christian","full_name":"Luschnig, Christian"}],"publication_status":"published","department":[{"_id":"DaSi"}],"publisher":"Springer Nature","year":"2019","pmid":1,"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-12-01T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"ista":"Retzer K, Akhmanova M, Konstantinova N, Malínská K, Leitner J, Petrášek J, Luschnig C. 2019. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. 10, 5516.","apa":"Retzer, K., Akhmanova, M., Konstantinova, N., Malínská, K., Leitner, J., Petrášek, J., & Luschnig, C. (2019). Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-13543-1","ieee":"K. Retzer et al., “Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter,” Nature Communications, vol. 10. Springer Nature, 2019.","ama":"Retzer K, Akhmanova M, Konstantinova N, et al. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. 2019;10. doi:10.1038/s41467-019-13543-1","chicago":"Retzer, Katarzyna, Maria Akhmanova, Nataliia Konstantinova, Kateřina Malínská, Johannes Leitner, Jan Petrášek, and Christian Luschnig. “Brassinosteroid Signaling Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13543-1.","mla":"Retzer, Katarzyna, et al. “Brassinosteroid Signaling Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.” Nature Communications, vol. 10, 5516, Springer Nature, 2019, doi:10.1038/s41467-019-13543-1.","short":"K. Retzer, M. Akhmanova, N. Konstantinova, K. Malínská, J. Leitner, J. Petrášek, C. Luschnig, Nature Communications 10 (2019)."},"abstract":[{"text":"Arabidopsis PIN2 protein directs transport of the phytohormone auxin from the root tip into the root elongation zone. Variation in hormone transport, which depends on a delicate interplay between PIN2 sorting to and from polar plasma membrane domains, determines root growth. By employing a constitutively degraded version of PIN2, we identify brassinolides as antagonists of PIN2 endocytosis. This response does not require de novo protein synthesis, but involves early events in canonical brassinolide signaling. Brassinolide-controlled adjustments in PIN2 sorting and intracellular distribution governs formation of a lateral PIN2 gradient in gravistimulated roots, coinciding with adjustments in auxin signaling and directional root growth. Strikingly, simulations indicate that PIN2 gradient formation is no prerequisite for root bending but rather dampens asymmetric auxin flow and signaling. Crosstalk between brassinolide signaling and endocytic PIN2 sorting, thus, appears essential for determining the rate of gravity-induced root curvature via attenuation of differential cell elongation.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_NatureComm_Retzer.pdf","creator":"dernst","file_size":5156533,"content_type":"application/pdf","file_id":"7184","relation":"main_file","checksum":"77e8720a8e0f3091b98159f85be40893","date_updated":"2020-07-14T12:47:52Z","date_created":"2019-12-16T07:37:50Z"}],"status":"public","ddc":["570"],"title":"Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter","intvolume":" 10","_id":"7180","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"oa_version":"Submitted Version","_id":"7181","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 37","status":"public","title":"Large multiple sequence alignments with a root-to-leaf regressive method","issue":"12","abstract":[{"text":"Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary predictions1,2, but the complexity of aligning large datasets requires the use of approximate solutions3, including the progressive algorithm4. Progressive MSA methods start by aligning the most similar sequences and subsequently incorporate the remaining sequences, from leaf-to-root, based on a guide-tree. Their accuracy declines substantially as the number of sequences is scaled up5. We introduce a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard workstation and substantially improves accuracy on datasets larger than 10,000 sequences. Our regressive algorithm works the other way around to the progressive algorithm and begins by aligning the most dissimilar sequences. It uses an efficient divide-and-conquer strategy to run third-party alignment methods in linear time, regardless of their original complexity. Our approach will enable analyses of extremely large genomic datasets such as the recently announced Earth BioGenome Project, which comprises 1.5 million eukaryotic genomes6.","lang":"eng"}],"type":"journal_article","date_published":"2019-12-01T00:00:00Z","citation":{"ama":"Garriga E, Di Tommaso P, Magis C, et al. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 2019;37(12):1466-1470. doi:10.1038/s41587-019-0333-6","ieee":"E. Garriga et al., “Large multiple sequence alignments with a root-to-leaf regressive method,” Nature Biotechnology, vol. 37, no. 12. Springer Nature, pp. 1466–1470, 2019.","apa":"Garriga, E., Di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2019). Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-019-0333-6","ista":"Garriga E, Di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2019. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 37(12), 1466–1470.","short":"E. Garriga, P. Di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, Nature Biotechnology 37 (2019) 1466–1470.","mla":"Garriga, Edgar, et al. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology, vol. 37, no. 12, Springer Nature, 2019, pp. 1466–70, doi:10.1038/s41587-019-0333-6.","chicago":"Garriga, Edgar, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41587-019-0333-6."},"publication":"Nature Biotechnology","page":"1466-1470","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","related_material":{"record":[{"id":"13059","status":"public","relation":"research_data"}]},"author":[{"full_name":"Garriga, Edgar","last_name":"Garriga","first_name":"Edgar"},{"last_name":"Di Tommaso","first_name":"Paolo","full_name":"Di Tommaso, Paolo"},{"first_name":"Cedrik","last_name":"Magis","full_name":"Magis, Cedrik"},{"full_name":"Erb, Ionas","first_name":"Ionas","last_name":"Erb"},{"full_name":"Mansouri, Leila","first_name":"Leila","last_name":"Mansouri"},{"last_name":"Baltzis","first_name":"Athanasios","full_name":"Baltzis, Athanasios"},{"full_name":"Laayouni, Hafid","last_name":"Laayouni","first_name":"Hafid"},{"last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"},{"last_name":"Floden","first_name":"Evan","full_name":"Floden, Evan"},{"full_name":"Notredame, Cedric","last_name":"Notredame","first_name":"Cedric"}],"volume":37,"date_updated":"2023-09-06T14:32:52Z","date_created":"2019-12-15T23:00:43Z","pmid":1,"year":"2019","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"publication_status":"published","ec_funded":1,"doi":"10.1038/s41587-019-0333-6","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["31792410"],"isi":["000500748900021"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943/","open_access":"1"}],"project":[{"_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["15461696"],"issn":["10870156"]},"month":"12"},{"file":[{"creator":"dernst","file_size":2960543,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_eLife_Llorca.pdf","checksum":"b460ecc33e1a68265e7adea775021f3a","date_created":"2020-02-18T15:19:26Z","date_updated":"2020-07-14T12:47:53Z","file_id":"7503","relation":"main_file"}],"oa_version":"Published Version","intvolume":" 8","ddc":["570"],"status":"public","title":"A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture","_id":"7202","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"The cerebral cortex contains multiple areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have investigated the neuronal output of individual progenitor cells in the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. Our experimental results indicate that progenitor cells generate pyramidal cell lineages with a wide range of sizes and laminar configurations. Mathematical modelling indicates that these outcomes are compatible with a stochastic model of cortical neurogenesis in which progenitor cells undergo a series of probabilistic decisions that lead to the specification of very heterogeneous progenies. Our findings support a mechanism for cortical neurogenesis whose flexibility would make it capable to generate the diverse cytoarchitectures that characterize distinct neocortical areas.","lang":"eng"}],"type":"journal_article","date_published":"2019-11-18T00:00:00Z","article_type":"original","citation":{"chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong Kuan Wong, Giovanni Diana, Eleni Serafeimidou-Pouliou, Marian Fernández-Otero, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.51381.","mla":"Llorca, Alfredo, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” ELife, vol. 8, e51381, eLife Sciences Publications, 2019, doi:10.7554/eLife.51381.","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou-Pouliou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, ELife 8 (2019).","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou-Pouliou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. 2019. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. eLife. 8, e51381.","ieee":"A. Llorca et al., “A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture,” eLife, vol. 8. eLife Sciences Publications, 2019.","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou-Pouliou, E., … Marín, O. (2019). A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.51381","ama":"Llorca A, Ciceri G, Beattie RJ, et al. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. eLife. 2019;8. doi:10.7554/eLife.51381"},"publication":"eLife","article_processing_charge":"No","has_accepted_license":"1","day":"18","scopus_import":"1","volume":8,"date_created":"2019-12-22T23:00:42Z","date_updated":"2023-09-06T14:38:39Z","author":[{"full_name":"Llorca, Alfredo","first_name":"Alfredo","last_name":"Llorca"},{"full_name":"Ciceri, Gabriele","first_name":"Gabriele","last_name":"Ciceri"},{"orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","last_name":"Beattie","first_name":"Robert J","full_name":"Beattie, Robert J"},{"full_name":"Wong, Fong Kuan","first_name":"Fong Kuan","last_name":"Wong"},{"first_name":"Giovanni","last_name":"Diana","full_name":"Diana, Giovanni"},{"first_name":"Eleni","last_name":"Serafeimidou-Pouliou","full_name":"Serafeimidou-Pouliou, Eleni"},{"full_name":"Fernández-Otero, Marian","first_name":"Marian","last_name":"Fernández-Otero"},{"full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","first_name":"Carmen"},{"last_name":"Arnold","first_name":"Sebastian J.","full_name":"Arnold, Sebastian J."},{"first_name":"Martin","last_name":"Meyer","full_name":"Meyer, Martin"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon"},{"first_name":"Miguel","last_name":"Maravall","full_name":"Maravall, Miguel"},{"full_name":"Marín, Oscar","first_name":"Oscar","last_name":"Marín"}],"department":[{"_id":"SiHi"}],"publisher":"eLife Sciences Publications","publication_status":"published","pmid":1,"year":"2019","ec_funded":1,"file_date_updated":"2020-07-14T12:47:53Z","article_number":"e51381","language":[{"iso":"eng"}],"doi":"10.7554/eLife.51381","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"grant_number":"M02416","_id":"264E56E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31736464"],"isi":["000508156800001"]},"oa":1,"publication_identifier":{"eissn":["2050084X"]},"month":"11"},{"date_published":"2019-12-01T00:00:00Z","article_type":"original","page":"13734-13746","publication":"FASEB Journal","citation":{"mla":"Klotz, Lisa, et al. “Localization of Group II and III Metabotropic Glutamate Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.” FASEB Journal, vol. 33, no. 12, FASEB, 2019, pp. 13734–46, doi:10.1096/fj.201901543R.","short":"L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, R. Enz, FASEB Journal 33 (2019) 13734–13746.","chicago":"Klotz, Lisa, Olaf Wendler, Renato Frischknecht, Ryuichi Shigemoto, Holger Schulze, and Ralf Enz. “Localization of Group II and III Metabotropic Glutamate Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.” FASEB Journal. FASEB, 2019. https://doi.org/10.1096/fj.201901543R.","ama":"Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. 2019;33(12):13734-13746. doi:10.1096/fj.201901543R","ista":"Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. 2019. Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. 33(12), 13734–13746.","ieee":"L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, and R. Enz, “Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses,” FASEB Journal, vol. 33, no. 12. FASEB, pp. 13734–13746, 2019.","apa":"Klotz, L., Wendler, O., Frischknecht, R., Shigemoto, R., Schulze, H., & Enz, R. (2019). Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. FASEB. https://doi.org/10.1096/fj.201901543R"},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","file":[{"file_name":"Klotz et al 2019 EMBO Reports.pdf","access_level":"open_access","file_size":4766789,"content_type":"application/pdf","creator":"shigemot","relation":"main_file","file_id":"8922","date_updated":"2020-12-06T17:30:09Z","date_created":"2020-12-06T17:30:09Z","checksum":"79e3b72481dc32489911121cf3b7d8d0","success":1}],"status":"public","ddc":["571","599"],"title":"Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses","intvolume":" 33","_id":"7179","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Glutamate is the major excitatory neurotransmitter in the CNS binding to a variety of glutamate receptors. Metabotropic glutamate receptors (mGluR1 to mGluR8) can act excitatory or inhibitory, depending on associated signal cascades. Expression and localization of inhibitory acting mGluRs at inner hair cells (IHCs) in the cochlea are largely unknown. Here, we analyzed expression of mGluR2, mGluR3, mGluR4, mGluR6, mGluR7, and mGluR8 and investigated their localization with respect to the presynaptic ribbon of IHC synapses. We detected transcripts for mGluR2, mGluR3, and mGluR4 as well as for mGluR7a, mGluR7b, mGluR8a, and mGluR8b splice variants. Using receptor-specific antibodies in cochlear wholemounts, we found expression of mGluR2, mGluR4, and mGluR8b close to presynaptic ribbons. Super resolution and confocal microscopy in combination with 3-dimensional reconstructions indicated a postsynaptic localization of mGluR2 that overlaps with postsynaptic density protein 95 on dendrites of afferent type I spiral ganglion neurons. In contrast, mGluR4 and mGluR8b were expressed at the presynapse close to IHC ribbons. In summary, we localized in detail 3 mGluR types at IHC ribbon synapses, providing a fundament for new therapeutical strategies that could protect the cochlea against noxious stimuli and excitotoxicity."}],"issue":"12","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1096/fj.201901543R","quality_controlled":"1","isi":1,"external_id":{"isi":["000507466100054"],"pmid":["31585509"]},"oa":1,"month":"12","publication_identifier":{"eissn":["15306860"]},"date_created":"2019-12-15T23:00:42Z","date_updated":"2023-09-06T14:34:36Z","volume":33,"author":[{"full_name":"Klotz, Lisa","last_name":"Klotz","first_name":"Lisa"},{"full_name":"Wendler, Olaf","first_name":"Olaf","last_name":"Wendler"},{"first_name":"Renato","last_name":"Frischknecht","full_name":"Frischknecht, Renato"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto"},{"full_name":"Schulze, Holger","first_name":"Holger","last_name":"Schulze"},{"full_name":"Enz, Ralf","first_name":"Ralf","last_name":"Enz"}],"publication_status":"published","publisher":"FASEB","department":[{"_id":"RySh"}],"year":"2019","pmid":1,"file_date_updated":"2020-12-06T17:30:09Z"},{"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.08021"}],"external_id":{"isi":["000545976800011"],"arxiv":["1802.08021"]},"project":[{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"doi":"10.1145/3295500.3356222","conference":{"location":"Denver, CO, Unites States","start_date":"2019-11-17","end_date":"2019-11-19","name":"SC: Conference for High Performance Computing, Networking, Storage and Analysis"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["21674329"],"isbn":["9781450362290"],"eissn":["21674337"]},"month":"11","year":"2019","department":[{"_id":"DaAl"}],"publisher":"ACM","publication_status":"published","author":[{"full_name":"Renggli, Cedric","first_name":"Cedric","last_name":"Renggli"},{"full_name":"Ashkboos, Saleh","last_name":"Ashkboos","first_name":"Saleh","id":"0D0A9058-257B-11EA-A937-9341C3D8BC8A"},{"full_name":"Aghagolzadeh, Mehdi","last_name":"Aghagolzadeh","first_name":"Mehdi"},{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"},{"full_name":"Hoefler, Torsten","last_name":"Hoefler","first_name":"Torsten"}],"date_updated":"2023-09-06T14:37:55Z","date_created":"2019-12-22T23:00:42Z","article_number":"a11","ec_funded":1,"citation":{"mla":"Renggli, Cedric, et al. “SparCML: High-Performance Sparse Communication for Machine Learning.” International Conference for High Performance Computing, Networking, Storage and Analysis, SC, a11, ACM, 2019, doi:10.1145/3295500.3356222.","short":"C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, T. Hoefler, in:, International Conference for High Performance Computing, Networking, Storage and Analysis, SC, ACM, 2019.","chicago":"Renggli, Cedric, Saleh Ashkboos, Mehdi Aghagolzadeh, Dan-Adrian Alistarh, and Torsten Hoefler. “SparCML: High-Performance Sparse Communication for Machine Learning.” In International Conference for High Performance Computing, Networking, Storage and Analysis, SC. ACM, 2019. https://doi.org/10.1145/3295500.3356222.","ama":"Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. SparCML: High-performance sparse communication for machine learning. In: International Conference for High Performance Computing, Networking, Storage and Analysis, SC. ACM; 2019. doi:10.1145/3295500.3356222","ista":"Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. 2019. SparCML: High-performance sparse communication for machine learning. International Conference for High Performance Computing, Networking, Storage and Analysis, SC. SC: Conference for High Performance Computing, Networking, Storage and Analysis, a11.","ieee":"C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, and T. Hoefler, “SparCML: High-performance sparse communication for machine learning,” in International Conference for High Performance Computing, Networking, Storage and Analysis, SC, Denver, CO, Unites States, 2019.","apa":"Renggli, C., Ashkboos, S., Aghagolzadeh, M., Alistarh, D.-A., & Hoefler, T. (2019). SparCML: High-performance sparse communication for machine learning. In International Conference for High Performance Computing, Networking, Storage and Analysis, SC. Denver, CO, Unites States: ACM. https://doi.org/10.1145/3295500.3356222"},"publication":"International Conference for High Performance Computing, Networking, Storage and Analysis, SC","date_published":"2019-11-17T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"17","_id":"7201","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"SparCML: High-performance sparse communication for machine learning","status":"public","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"Applying machine learning techniques to the quickly growing data in science and industry requires highly-scalable algorithms. Large datasets are most commonly processed \"data parallel\" distributed across many nodes. Each node's contribution to the overall gradient is summed using a global allreduce. This allreduce is the single communication and thus scalability bottleneck for most machine learning workloads. We observe that frequently, many gradient values are (close to) zero, leading to sparse of sparsifyable communications. To exploit this insight, we analyze, design, and implement a set of communication-efficient protocols for sparse input data, in conjunction with efficient machine learning algorithms which can leverage these primitives. Our communication protocols generalize standard collective operations, by allowing processes to contribute arbitrary sparse input data vectors. Our generic communication library, SparCML1, extends MPI to support additional features, such as non-blocking (asynchronous) operations and low-precision data representations. As such, SparCML and its techniques will form the basis of future highly-scalable machine learning frameworks."}]},{"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7205"}]},"author":[{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"first_name":"Zuzanna","last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram"},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"}],"oa_version":"Published Version","date_created":"2023-05-23T16:36:27Z","date_updated":"2023-09-06T14:48:57Z","_id":"13067","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Dryad","department":[{"_id":"NiBa"}],"title":"Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?","ddc":["570"],"status":"public","abstract":[{"lang":"eng","text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis divergent selection forms strong barriers to gene flow, while the role of postzygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Postzygotic barriers might include genetic incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterised female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant postzygotic barriers contributing to ecotype divergence and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females."}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","type":"research_data_reference","date_published":"2019-12-02T00:00:00Z","doi":"10.5061/DRYAD.TB2RBNZWK","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes?” Dryad, 2019. https://doi.org/10.5061/DRYAD.TB2RBNZWK.","mla":"Johannesson, Kerstin, et al. Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes? Dryad, 2019, doi:10.5061/DRYAD.TB2RBNZWK.","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019).","ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?, Dryad, 10.5061/DRYAD.TB2RBNZWK.","apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. (2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? Dryad. https://doi.org/10.5061/DRYAD.TB2RBNZWK","ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. Butlin, “Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?” Dryad, 2019.","ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? 2019. doi:10.5061/DRYAD.TB2RBNZWK"},"oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.tb2rbnzwk","open_access":"1"}],"article_processing_charge":"No","month":"12","day":"02"},{"department":[{"_id":"DaAl"}],"publisher":"BMC","publication_status":"published","year":"2019","volume":20,"date_updated":"2023-09-06T14:51:06Z","date_created":"2019-12-29T23:00:46Z","author":[{"full_name":"Aganezov, Sergey","first_name":"Sergey","last_name":"Aganezov"},{"last_name":"Zban","first_name":"Ilya","full_name":"Zban, Ilya"},{"first_name":"Vitalii","last_name":"Aksenov","id":"2980135A-F248-11E8-B48F-1D18A9856A87","full_name":"Aksenov, Vitalii"},{"full_name":"Alexeev, Nikita","last_name":"Alexeev","first_name":"Nikita"},{"first_name":"Michael C.","last_name":"Schatz","full_name":"Schatz, Michael C."}],"article_number":"641","file_date_updated":"2020-07-14T12:47:54Z","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000511618800007"]},"language":[{"iso":"eng"}],"doi":"10.1186/s12859-019-3208-4","publication_identifier":{"eissn":["14712105"]},"month":"12","intvolume":" 20","ddc":["570"],"status":"public","title":"Recovering rearranged cancer chromosomes from karyotype graphs","_id":"7214","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_created":"2020-01-02T16:10:58Z","date_updated":"2020-07-14T12:47:54Z","checksum":"7a30357efdcf8f66587ed495c0927724","relation":"main_file","file_id":"7221","content_type":"application/pdf","file_size":1917374,"creator":"dernst","file_name":"2019_BMCBioinfo_Aganezov.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Background: Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale variations into a karyotype graph representation of the rearranged cancer genomes. Such a representation, however, does not directly describe the linear and/or circular structure of the underlying rearranged cancer chromosomes, thus limiting possible analysis of cancer genomes somatic evolutionary process as well as functional genomic changes brought by the large-scale genome rearrangements.\r\n\r\nResults: Here we address the aforementioned limitation by introducing a novel methodological framework for recovering rearranged cancer chromosomes from karyotype graphs. For a cancer karyotype graph we formulate an Eulerian Decomposition Problem (EDP) of finding a collection of linear and/or circular rearranged cancer chromosomes that are determined by the graph. We derive and prove computational complexities for several variations of the EDP. We then demonstrate that Eulerian decomposition of the cancer karyotype graphs is not always unique and present the Consistent Contig Covering Problem (CCCP) of recovering unambiguous cancer contigs from the cancer karyotype graph, and describe a novel algorithm CCR capable of solving CCCP in polynomial time. We apply CCR on a prostate cancer dataset and demonstrate that it is capable of consistently recovering large cancer contigs even when underlying cancer genomes are highly rearranged.\r\n\r\nConclusions: CCR can recover rearranged cancer contigs from karyotype graphs thereby addressing existing limitation in inferring chromosomal structures of rearranged cancer genomes and advancing our understanding of both patient/cancer-specific as well as the overall genetic instability in cancer."}],"article_type":"original","citation":{"ama":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 2019;20. doi:10.1186/s12859-019-3208-4","ista":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. 2019. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 20, 641.","ieee":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, and M. C. Schatz, “Recovering rearranged cancer chromosomes from karyotype graphs,” BMC Bioinformatics, vol. 20. BMC, 2019.","apa":"Aganezov, S., Zban, I., Aksenov, V., Alexeev, N., & Schatz, M. C. (2019). Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. BMC. https://doi.org/10.1186/s12859-019-3208-4","mla":"Aganezov, Sergey, et al. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC Bioinformatics, vol. 20, 641, BMC, 2019, doi:10.1186/s12859-019-3208-4.","short":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, M.C. Schatz, BMC Bioinformatics 20 (2019).","chicago":"Aganezov, Sergey, Ilya Zban, Vitalii Aksenov, Nikita Alexeev, and Michael C. Schatz. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC Bioinformatics. BMC, 2019. https://doi.org/10.1186/s12859-019-3208-4."},"publication":"BMC Bioinformatics","date_published":"2019-12-17T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"17"}]