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PNAS. 2018;115(42):10690-10695. doi:10.1073/pnas.1721061115","short":"J. Rybicki, E. Kisdi, J. Anttila, PNAS 115 (2018) 10690–10695.","apa":"Rybicki, J., Kisdi, E., & Anttila, J. (2018). Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1721061115","mla":"Rybicki, Joel, et al. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” PNAS, vol. 115, no. 42, National Academy of Sciences, 2018, pp. 10690–95, doi:10.1073/pnas.1721061115.","ista":"Rybicki J, Kisdi E, Anttila J. 2018. Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. 115(42), 10690–10695."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"author":[{"last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","full_name":"Rybicki, Joel","first_name":"Joel","orcid":"0000-0002-6432-6646"},{"last_name":"Kisdi","first_name":"Eva","full_name":"Kisdi, Eva"},{"last_name":"Anttila","first_name":"Jani","full_name":"Anttila, Jani"}],"pubrep_id":"1063","type":"journal_article","external_id":{"isi":["000447491300057"]},"file_date_updated":"2020-07-14T12:46:26Z","scopus_import":"1","_id":"43","year":"2018","publication":"PNAS","volume":115,"article_processing_charge":"No","ddc":["570","577"],"date_created":"2018-12-11T11:44:19Z","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"date_published":"2018-10-02T00:00:00Z","title":"Model of bacterial toxin-dependent pathogenesis explains infective dose","quality_controlled":"1","acknowledgement":"J.R. and J.V.A. were also supported by the Academy of Finland Grants 1273253 and 267541.","publication_status":"published","day":"02","ec_funded":1,"isi":1,"month":"10","issue":"42","publist_id":"8011","abstract":[{"text":"The initial amount of pathogens required to start an infection within a susceptible host is called the infective dose and is known to vary to a large extent between different pathogen species. We investigate the hypothesis that the differences in infective doses are explained by the mode of action in the underlying mechanism of pathogenesis: Pathogens with locally acting mechanisms tend to have smaller infective doses than pathogens with distantly acting mechanisms. While empirical evidence tends to support the hypothesis, a formal theoretical explanation has been lacking. We give simple analytical models to gain insight into this phenomenon and also investigate a stochastic, spatially explicit, mechanistic within-host model for toxin-dependent bacterial infections. The model shows that pathogens secreting locally acting toxins have smaller infective doses than pathogens secreting diffusive toxins, as hypothesized. While local pathogenetic mechanisms require smaller infective doses, pathogens with distantly acting toxins tend to spread faster and may cause more damage to the host. The proposed model can serve as a basis for the spatially explicit analysis of various virulence factors also in the context of other problems in infection dynamics.","lang":"eng"}],"doi":"10.1073/pnas.1721061115","status":"public","language":[{"iso":"eng"}],"intvolume":" 115","page":"10690 - 10695","publisher":"National Academy of Sciences"},{"page":"1351 - 1355","intvolume":" 208","language":[{"iso":"eng"}],"publisher":"Genetics Society of America","month":"04","isi":1,"day":"01","publication_status":"published","status":"public","publist_id":"7393","doi":"10.1534/genetics.118.300786","abstract":[{"text":"In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to sev- eral human examples ( Racimo et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary ge neticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for c hanges in allele frequencies. By aggregating small signal s of change across many such loci, directional natural selection is now in principle detect- able using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accom- panying test of polygenic selection. However, it is important to be aware of complications th at arise in interpretation, especially given that these studies may easily be misinter- preted both in and outside the evolutionary genetics commu- nity. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are inter- preted and reported upon more broadly.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by/4.0/","issue":"4","date_created":"2018-12-11T11:46:26Z","ddc":["576"],"volume":208,"article_processing_charge":"No","publication":"Genetics","year":"2018","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","date_published":"2018-04-01T00:00:00Z","title":"Tread lightly interpreting polygenic tests of selection","type":"journal_article","pubrep_id":"1012","author":[{"last_name":"Novembre","first_name":"John","full_name":"Novembre, John"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"}],"oa":1,"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Novembre, J., & Barton, N. H. (2018). Tread lightly interpreting polygenic tests of selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300786","mla":"Novembre, John, and Nicholas H. Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1351–55, doi:10.1534/genetics.118.300786.","ista":"Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of selection. Genetics. 208(4), 1351–1355.","chicago":"Novembre, John, and Nicholas H Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300786.","ama":"Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection. Genetics. 2018;208(4):1351-1355. doi:10.1534/genetics.118.300786","short":"J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355.","ieee":"J. Novembre and N. H. Barton, “Tread lightly interpreting polygenic tests of selection,” Genetics, vol. 208, no. 4. Genetics Society of America, pp. 1351–1355, 2018."},"department":[{"_id":"NiBa"}],"file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:46:26Z","file_size":500129,"file_name":"IST-2018-1012-v1+1_2018_Barton_Tread.pdf","file_id":"4958","date_created":"2018-12-12T10:12:40Z","access_level":"open_access","creator":"system","checksum":"3d838dc285df394376555b794b6a5ad1","relation":"main_file"}],"oa_version":"Published Version","date_updated":"2023-09-19T10:17:30Z","_id":"430","scopus_import":"1","file_date_updated":"2020-07-14T12:46:26Z","external_id":{"isi":["000429094400005"]}},{"type":"conference","oa_version":"Submitted Version","date_updated":"2023-08-24T14:39:32Z","department":[{"_id":"UlWa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"R. Fulek and J. Pach, “Thrackles: An improved upper bound,” presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States, 2018, vol. 10692, pp. 160–166.","chicago":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound,” 10692:160–66. Springer, 2018. https://doi.org/10.1007/978-3-319-73915-1_14.","short":"R. Fulek, J. Pach, in:, Springer, 2018, pp. 160–166.","ama":"Fulek R, Pach J. Thrackles: An improved upper bound. In: Vol 10692. Springer; 2018:160-166. doi:10.1007/978-3-319-73915-1_14","apa":"Fulek, R., & Pach, J. (2018). Thrackles: An improved upper bound (Vol. 10692, pp. 160–166). Presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States: Springer. https://doi.org/10.1007/978-3-319-73915-1_14","mla":"Fulek, Radoslav, and János Pach. Thrackles: An Improved Upper Bound. Vol. 10692, Springer, 2018, pp. 160–66, doi:10.1007/978-3-319-73915-1_14.","ista":"Fulek R, Pach J. 2018. Thrackles: An improved upper bound. GD 2017: Graph Drawing and Network Visualization, LNCS, vol. 10692, 160–166."},"oa":1,"author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek"},{"last_name":"Pach","first_name":"János","full_name":"Pach, János"}],"_id":"433","external_id":{"arxiv":["1708.08037"]},"scopus_import":1,"date_created":"2018-12-11T11:46:27Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08037"}],"year":"2018","volume":10692,"conference":{"location":"Boston, MA, United States","start_date":"201-09-25","end_date":"2017-09-27","name":"GD 2017: Graph Drawing and Network Visualization"},"date_published":"2018-01-21T00:00:00Z","title":"Thrackles: An improved upper bound","quality_controlled":"1","alternative_title":["LNCS"],"month":"01","related_material":{"record":[{"relation":"later_version","id":"5857","status":"public"}]},"publication_status":"published","day":"21","status":"public","abstract":[{"text":"A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is 3/2(n-1), and that this bound is best possible for infinitely many values of n.","lang":"eng"}],"publist_id":"7390","doi":"10.1007/978-3-319-73915-1_14","intvolume":" 10692","page":"160 - 166","arxiv":1,"language":[{"iso":"eng"}],"publisher":"Springer"},{"publisher":"IEEE","language":[{"iso":"eng"}],"intvolume":" 19","page":"3320 - 3333","issue":"10","doi":"10.1109/TITS.2017.2778077","abstract":[{"lang":"eng","text":"In this paper, we present a formal model-driven design approach to establish a safety-assured implementation of multifunction vehicle bus controller (MVBC), which controls the data transmission among the devices of the vehicle. First, the generic models and safety requirements described in International Electrotechnical Commission Standard 61375 are formalized as time automata and timed computation tree logic formulas, respectively. With model checking tool Uppaal, we verify whether or not the constructed timed automata satisfy the formulas and several logic inconsistencies in the original standard are detected and corrected. Then, we apply the code generation tool Times to generate C code from the verified model, which is later synthesized into a real MVBC chip, with some handwriting glue code. Furthermore, the runtime verification tool RMOR is applied on the integrated code, to verify some safety requirements that cannot be formalized on the timed automata. For evaluation, we compare the proposed approach with existing MVBC design methods, such as BeagleBone, Galsblock, and Simulink. Experiments show that more ambiguousness or bugs in the standard are detected during Uppaal verification, and the generated code of Times outperforms the C code generated by others in terms of the synthesized binary code size. The errors in the standard have been confirmed and the resulting MVBC has been deployed in the real train communication network."}],"publist_id":"7389","status":"public","publication_status":"published","day":"01","month":"01","related_material":{"record":[{"relation":"earlier_version","id":"1205","status":"public"}]},"isi":1,"date_published":"2018-01-01T00:00:00Z","title":"Safety-assured model-driven design of the multifunction vehicle bus controller","quality_controlled":"1","year":"2018","volume":19,"article_processing_charge":"No","publication":"IEEE Transactions on Intelligent Transportation Systems","date_created":"2018-12-11T11:46:27Z","external_id":{"isi":["000446651100020"]},"scopus_import":"1","_id":"434","department":[{"_id":"ToHe"}],"oa_version":"None","date_updated":"2023-09-18T08:12:49Z","author":[{"first_name":"Yu","full_name":"Jiang, Yu","last_name":"Jiang"},{"first_name":"Han","full_name":"Liu, Han","last_name":"Liu"},{"first_name":"Huobing","full_name":"Song, Huobing","last_name":"Song"},{"id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","full_name":"Kong, Hui","first_name":"Hui","orcid":"0000-0002-3066-6941","last_name":"Kong"},{"last_name":"Wang","full_name":"Wang, Rui","first_name":"Rui"},{"last_name":"Guan","full_name":"Guan, Yong","first_name":"Yong"},{"last_name":"Sha","full_name":"Sha, Lui","first_name":"Lui"}],"citation":{"ama":"Jiang Y, Liu H, Song H, et al. Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. 2018;19(10):3320-3333. doi:10.1109/TITS.2017.2778077","short":"Y. Jiang, H. Liu, H. Song, H. Kong, R. Wang, Y. Guan, L. Sha, IEEE Transactions on Intelligent Transportation Systems 19 (2018) 3320–3333.","chicago":"Jiang, Yu, Han Liu, Huobing Song, Hui Kong, Rui Wang, Yong Guan, and Lui Sha. “Safety-Assured Model-Driven Design of the Multifunction Vehicle Bus Controller.” IEEE Transactions on Intelligent Transportation Systems. IEEE, 2018. https://doi.org/10.1109/TITS.2017.2778077.","ieee":"Y. Jiang et al., “Safety-assured model-driven design of the multifunction vehicle bus controller,” IEEE Transactions on Intelligent Transportation Systems, vol. 19, no. 10. IEEE, pp. 3320–3333, 2018.","ista":"Jiang Y, Liu H, Song H, Kong H, Wang R, Guan Y, Sha L. 2018. Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. 19(10), 3320–3333.","apa":"Jiang, Y., Liu, H., Song, H., Kong, H., Wang, R., Guan, Y., & Sha, L. (2018). Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. IEEE. https://doi.org/10.1109/TITS.2017.2778077","mla":"Jiang, Yu, et al. “Safety-Assured Model-Driven Design of the Multifunction Vehicle Bus Controller.” IEEE Transactions on Intelligent Transportation Systems, vol. 19, no. 10, IEEE, 2018, pp. 3320–33, doi:10.1109/TITS.2017.2778077."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article"},{"status":"public","issue":"3","publist_id":"7388","doi":"10.1364/OL.43.000607","abstract":[{"text":"It is shown that two fundamentally different phenomena, the bound states in continuum and the spectral singularity (or time-reversed spectral singularity), can occur simultaneously. This can be achieved in a rectangular core dielectric waveguide with an embedded active (or absorbing) layer. In such a system a two-dimensional bound state in a continuum is created in the plane of a waveguide cross section, and it is emitted or absorbed along the waveguide core. The idea can be used for experimental implementation of a laser or a coherent-perfect-absorber for a photonic bound state that resides in a continuous spectrum.","lang":"eng"}],"isi":1,"month":"02","acknowledgement":"Seventh Framework Programme (FP7) People: Marie-Curie Actions (PEOPLE) (291734). B. M. acknowledges the financial support by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/ 2007-2013) under REA.","publication_status":"published","day":"01","ec_funded":1,"publisher":"Optica Publishing Group","intvolume":" 43","page":"607 - 610","arxiv":1,"language":[{"iso":"eng"}],"_id":"435","external_id":{"arxiv":["1711.01986"],"isi":["000423776600066"]},"scopus_import":"1","type":"journal_article","date_updated":"2023-10-17T12:15:06Z","oa_version":"Preprint","department":[{"_id":"MiLe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"B. Midya and V. Konotop, “Coherent-perfect-absorber and laser for bound states in a continuum,” Optics Letters, vol. 43, no. 3. Optica Publishing Group, pp. 607–610, 2018.","chicago":"Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and Laser for Bound States in a Continuum.” Optics Letters. Optica Publishing Group, 2018. https://doi.org/10.1364/OL.43.000607.","ama":"Midya B, Konotop V. Coherent-perfect-absorber and laser for bound states in a continuum. Optics Letters. 2018;43(3):607-610. doi:10.1364/OL.43.000607","short":"B. Midya, V. Konotop, Optics Letters 43 (2018) 607–610.","apa":"Midya, B., & Konotop, V. (2018). Coherent-perfect-absorber and laser for bound states in a continuum. Optics Letters. Optica Publishing Group. https://doi.org/10.1364/OL.43.000607","mla":"Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and Laser for Bound States in a Continuum.” Optics Letters, vol. 43, no. 3, Optica Publishing Group, 2018, pp. 607–10, doi:10.1364/OL.43.000607.","ista":"Midya B, Konotop V. 2018. Coherent-perfect-absorber and laser for bound states in a continuum. Optics Letters. 43(3), 607–610."},"author":[{"first_name":"Bikashkali","full_name":"Midya, Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87","last_name":"Midya"},{"last_name":"Konotop","full_name":"Konotop, Vladimir","first_name":"Vladimir"}],"oa":1,"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"title":"Coherent-perfect-absorber and laser for bound states in a continuum","date_published":"2018-02-01T00:00:00Z","quality_controlled":"1","date_created":"2018-12-11T11:46:27Z","main_file_link":[{"url":"https://arxiv.org/abs/1711.01986","open_access":"1"}],"year":"2018","publication":"Optics Letters","article_processing_charge":"No","volume":43},{"quality_controlled":"1","project":[{"name":"Hybrid Optomechanical Technologies","grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","grant_number":"707438"}],"title":"Manipulating the flow of thermal noise in quantum devices","date_published":"2018-02-07T00:00:00Z","publication":"Physical Review Letters","article_processing_charge":"No","volume":120,"year":"2018","main_file_link":[{"url":"https://arxiv.org/abs/1706.09051","open_access":"1"}],"date_created":"2018-12-11T11:46:28Z","scopus_import":"1","external_id":{"isi":["000424382100004"],"arxiv":["1706.09051"]},"_id":"436","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Barzanjeh S, Aquilina M, Xuereb A. 2018. Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. 120(6), 060601.","apa":"Barzanjeh, S., Aquilina, M., & Xuereb, A. (2018). Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.120.060601","mla":"Barzanjeh, Shabir, et al. “Manipulating the Flow of Thermal Noise in Quantum Devices.” Physical Review Letters, vol. 120, no. 6, 060601, American Physical Society, 2018, doi:10.1103/PhysRevLett.120.060601.","ieee":"S. Barzanjeh, M. Aquilina, and A. Xuereb, “Manipulating the flow of thermal noise in quantum devices,” Physical Review Letters, vol. 120, no. 6. American Physical Society, 2018.","short":"S. Barzanjeh, M. Aquilina, A. Xuereb, Physical Review Letters 120 (2018).","ama":"Barzanjeh S, Aquilina M, Xuereb A. Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. 2018;120(6). doi:10.1103/PhysRevLett.120.060601","chicago":"Barzanjeh, Shabir, Matteo Aquilina, and André Xuereb. “Manipulating the Flow of Thermal Noise in Quantum Devices.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.120.060601."},"oa":1,"author":[{"last_name":"Barzanjeh","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir"},{"first_name":"Matteo","full_name":"Aquilina, Matteo","last_name":"Aquilina"},{"full_name":"Xuereb, André","first_name":"André","last_name":"Xuereb"}],"date_updated":"2023-09-13T08:52:27Z","oa_version":"Preprint","department":[{"_id":"JoFi"}],"type":"journal_article","publisher":"American Physical Society","language":[{"iso":"eng"}],"arxiv":1,"article_number":"060601 ","intvolume":" 120","abstract":[{"lang":"eng","text":"There has been significant interest recently in using complex quantum systems to create effective nonreciprocal dynamics. Proposals have been put forward for the realization of artificial magnetic fields for photons and phonons; experimental progress is fast making these proposals a reality. Much work has concentrated on the use of such systems for controlling the flow of signals, e.g., to create isolators or directional amplifiers for optical signals. In this Letter, we build on this work but move in a different direction. We develop the theory of and discuss a potential realization for the controllable flow of thermal noise in quantum systems. We demonstrate theoretically that the unidirectional flow of thermal noise is possible within quantum cascaded systems. Viewing an optomechanical platform as a cascaded system we show here that one can ultimately control the direction of the flow of thermal noise. By appropriately engineering the mechanical resonator, which acts as an artificial reservoir, the flow of thermal noise can be constrained to a desired direction, yielding a thermal rectifier. The proposed quantum thermal noise rectifier could potentially be used to develop devices such as a thermal modulator, a thermal router, and a thermal amplifier for nanoelectronic devices and superconducting circuits."}],"doi":"10.1103/PhysRevLett.120.060601","publist_id":"7387","issue":"6","status":"public","day":"07","ec_funded":1,"publication_status":"published","isi":1,"month":"02","related_material":{"link":[{"url":"https://ist.ac.at/en/news/interference-as-a-new-method-for-cooling-quantum-devices/","relation":"press_release","description":"News on IST Homepage"}]}},{"ec_funded":1,"day":"13","publication_status":"published","acknowledgement":"This work was supported by grants of the European Research Council (ERC CoG 724373) and the Austrian Science Fund (FWF) to M.S. We thank the scientific support units at IST Austria for excellent technical support.\r\nWe thank the scientific support units at IST Austria for excellent technical support. ","month":"02","isi":1,"doi":"10.1002/eji.201747358","abstract":[{"text":"Dendritic cells (DCs) are sentinels of the adaptive immune system that reside in peripheral organs of mammals. Upon pathogen encounter, they undergo maturation and up-regulate the chemokine receptor CCR7 that guides them along gradients of its chemokine ligands CCL19 and 21 to the next draining lymph node. There, DCs present peripherally acquired antigen to naïve T cells, thereby triggering adaptive immunity.","lang":"eng"}],"publist_id":"7386","issue":"6","license":"https://creativecommons.org/licenses/by-nc/4.0/","acknowledged_ssus":[{"_id":"SSU"}],"status":"public","language":[{"iso":"eng"}],"page":"1074 - 1077","intvolume":" 48","publisher":"Wiley-Blackwell","oa":1,"author":[{"last_name":"Leithner","full_name":"Leithner, Alexander F","first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1073-744X"},{"last_name":"Renkawitz","orcid":"0000-0003-2856-3369","first_name":"Jörg","full_name":"Renkawitz, Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"De Vries","full_name":"De Vries, Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild"},{"first_name":"Hans","full_name":"Haecker, Hans","last_name":"Haecker"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","citation":{"ista":"Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. 2018. Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. European Journal of Immunology. 48(6), 1074–1077.","apa":"Leithner, A. F., Renkawitz, J., de Vries, I., Hauschild, R., Haecker, H., & Sixt, M. K. (2018). Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. European Journal of Immunology. Wiley-Blackwell. https://doi.org/10.1002/eji.201747358","mla":"Leithner, Alexander F., et al. “Fast and Efficient Genetic Engineering of Hematopoietic Precursor Cells for the Study of Dendritic Cell Migration.” European Journal of Immunology, vol. 48, no. 6, Wiley-Blackwell, 2018, pp. 1074–77, doi:10.1002/eji.201747358.","short":"A.F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, M.K. Sixt, European Journal of Immunology 48 (2018) 1074–1077.","ama":"Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. European Journal of Immunology. 2018;48(6):1074-1077. doi:10.1002/eji.201747358","chicago":"Leithner, Alexander F, Jörg Renkawitz, Ingrid de Vries, Robert Hauschild, Hans Haecker, and Michael K Sixt. “Fast and Efficient Genetic Engineering of Hematopoietic Precursor Cells for the Study of Dendritic Cell Migration.” European Journal of Immunology. Wiley-Blackwell, 2018. https://doi.org/10.1002/eji.201747358.","ieee":"A. F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, and M. K. Sixt, “Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration,” European Journal of Immunology, vol. 48, no. 6. Wiley-Blackwell, pp. 1074–1077, 2018."},"file":[{"checksum":"9d5b74cd016505aeb9a4c2d33bbedaeb","relation":"main_file","creator":"system","access_level":"open_access","file_id":"5044","date_created":"2018-12-12T10:13:56Z","file_name":"IST-2018-1067-v1+2_Leithner_et_al-2018-European_Journal_of_Immunology.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:27Z","file_size":590106}],"department":[{"_id":"MiSi"},{"_id":"Bio"}],"date_updated":"2023-09-11T14:01:18Z","oa_version":"Published Version","type":"journal_article","pubrep_id":"1067","scopus_import":"1","file_date_updated":"2020-07-14T12:46:27Z","external_id":{"isi":["000434963700016"]},"_id":"437","volume":48,"article_processing_charge":"Yes (via OA deal)","publication":"European Journal of Immunology","year":"2018","date_created":"2018-12-11T11:46:28Z","ddc":["570"],"quality_controlled":"1","date_published":"2018-02-13T00:00:00Z","title":"Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration","project":[{"grant_number":"724373","name":"Cellular navigation along spatial gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"}},{"external_id":{"isi":["000429009500021"]},"scopus_import":"1","file_date_updated":"2020-07-14T12:46:27Z","_id":"438","file":[{"date_created":"2018-12-12T10:15:30Z","file_id":"5151","access_level":"open_access","file_size":5027978,"content_type":"application/pdf","date_updated":"2020-07-14T12:46:27Z","file_name":"IST-2018-971-v1+1_2018_Nikoloc_Autoregulation_of.pdf","creator":"system","relation":"main_file","checksum":"3ff4f545c27e11a4cd20ccb30778793e"}],"department":[{"_id":"CaGu"}],"date_updated":"2024-02-21T13:44:45Z","oa_version":"Published Version","oa":1,"author":[{"first_name":"Nela","full_name":"Nikolic, Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9068-6090","last_name":"Nikolic"},{"last_name":"Bergmiller","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","first_name":"Tobias"},{"full_name":"Vandervelde, Alexandra","first_name":"Alexandra","last_name":"Vandervelde"},{"last_name":"Albanese","full_name":"Albanese, Tanino","first_name":"Tanino"},{"first_name":"Lendert","full_name":"Gelens, Lendert","last_name":"Gelens"},{"last_name":"Moll","full_name":"Moll, Isabella","first_name":"Isabella"}],"has_accepted_license":"1","citation":{"mla":"Nikolic, Nela, et al. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.” Nucleic Acids Research, vol. 46, no. 6, Oxford University Press, 2018, pp. 2918–31, doi:10.1093/nar/gky079.","apa":"Nikolic, N., Bergmiller, T., Vandervelde, A., Albanese, T., Gelens, L., & Moll, I. (2018). Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gky079","ista":"Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. 2018. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. 46(6), 2918–2931.","ieee":"N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, and I. Moll, “Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations,” Nucleic Acids Research, vol. 46, no. 6. Oxford University Press, pp. 2918–2931, 2018.","chicago":"Nikolic, Nela, Tobias Bergmiller, Alexandra Vandervelde, Tanino Albanese, Lendert Gelens, and Isabella Moll. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.” Nucleic Acids Research. Oxford University Press, 2018. https://doi.org/10.1093/nar/gky079.","ama":"Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. 2018;46(6):2918-2931. doi:10.1093/nar/gky079","short":"N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, I. Moll, Nucleic Acids Research 46 (2018) 2918–2931."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","pubrep_id":"971","type":"journal_article","title":"Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations","date_published":"2018-04-06T00:00:00Z","project":[{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"}],"quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2018","article_processing_charge":"Yes (in subscription journal)","volume":46,"publication":"Nucleic Acids Research","date_created":"2018-12-11T11:46:29Z","ddc":["576"],"issue":"6","doi":"10.1093/nar/gky079","abstract":[{"lang":"eng","text":"The MazF toxin sequence-specifically cleaves single-stranded RNA upon various stressful conditions, and it is activated as a part of the mazEF toxin–antitoxin module in Escherichia coli. Although autoregulation of mazEF expression through the MazE antitoxin-dependent transcriptional repression has been biochemically characterized, less is known about post-transcriptional autoregulation, as well as how both of these autoregulatory features affect growth of single cells during conditions that promote MazF production. Here, we demonstrate post-transcriptional autoregulation of mazF expression dynamics by MazF cleaving its own transcript. Single-cell analyses of bacterial populations during ectopic MazF production indicated that two-level autoregulation of mazEF expression influences cell-to-cell growth rate heterogeneity. The increase in growth rate heterogeneity is governed by the MazE antitoxin, and tuned by the MazF-dependent mazF mRNA cleavage. Also, both autoregulatory features grant rapid exit from the stress caused by mazF overexpression. Time-lapse microscopy revealed that MazF-mediated cleavage of mazF mRNA leads to increased temporal variability in length of individual cells during ectopic mazF overexpression, as explained by a stochastic model indicating that mazEF mRNA cleavage underlies temporal fluctuations in MazF levels during stress."}],"status":"public","publication_status":"published","day":"06","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5569"}]},"month":"04","isi":1,"publisher":"Oxford University Press","language":[{"iso":"eng"}],"intvolume":" 46","page":"2918-2931"},{"title":"Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations","date_published":"2018-10-22T00:00:00Z","quality_controlled":"1","date_created":"2018-12-11T11:44:19Z","year":"2018","main_file_link":[{"url":"https://arxiv.org/abs/1806.10933","open_access":"1"}],"publication":"Physical Review B","article_processing_charge":"No","volume":98,"_id":"44","external_id":{"arxiv":["1806.10933"],"isi":["000447919100001"]},"scopus_import":"1","type":"journal_article","date_updated":"2023-10-10T13:28:49Z","oa_version":"Preprint","department":[{"_id":"MaSe"}],"citation":{"ieee":"C. J. Turner, A. Michailidis, D. A. Abanin, M. Serbyn, and Z. Papić, “Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations,” Physical Review B, vol. 98, no. 15. American Physical Society, 2018.","chicago":"Turner, C J, Alexios Michailidis, D A Abanin, Maksym Serbyn, and Z Papić. “Quantum Scarred Eigenstates in a Rydberg Atom Chain: Entanglement, Breakdown of Thermalization, and Stability to Perturbations.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.98.155134.","ama":"Turner CJ, Michailidis A, Abanin DA, Serbyn M, Papić Z. Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations. Physical Review B. 2018;98(15). doi:10.1103/PhysRevB.98.155134","short":"C.J. Turner, A. Michailidis, D.A. Abanin, M. Serbyn, Z. Papić, Physical Review B 98 (2018).","mla":"Turner, C. J., et al. “Quantum Scarred Eigenstates in a Rydberg Atom Chain: Entanglement, Breakdown of Thermalization, and Stability to Perturbations.” Physical Review B, vol. 98, no. 15, 155134, American Physical Society, 2018, doi:10.1103/PhysRevB.98.155134.","apa":"Turner, C. J., Michailidis, A., Abanin, D. A., Serbyn, M., & Papić, Z. (2018). Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.98.155134","ista":"Turner CJ, Michailidis A, Abanin DA, Serbyn M, Papić Z. 2018. Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations. Physical Review B. 98(15), 155134."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"first_name":"C J","full_name":"Turner, C J","last_name":"Turner"},{"first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064","last_name":"Michailidis"},{"first_name":"D A","full_name":"Abanin, D A","last_name":"Abanin"},{"last_name":"Serbyn","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","orcid":"0000-0002-2399-5827"},{"full_name":"Papić, Z","first_name":"Z","last_name":"Papić"}],"publisher":"American Physical Society","article_number":"155134","intvolume":" 98","language":[{"iso":"eng"}],"arxiv":1,"status":"public","acknowledged_ssus":[{"_id":"ScienComp"}],"issue":"15","doi":"10.1103/PhysRevB.98.155134","abstract":[{"lang":"eng","text":"Recent realization of a kinetically constrained chain of Rydberg atoms by Bernien et al., [Nature (London) 551, 579 (2017)] resulted in the observation of unusual revivals in the many-body quantum dynamics. In our previous work [C. J. Turner et al., Nat. Phys. 14, 745 (2018)], such dynamics was attributed to the existence of “quantum scarred” eigenstates in the many-body spectrum of the experimentally realized model. Here, we present a detailed study of the eigenstate properties of the same model. We find that the majority of the eigenstates exhibit anomalous thermalization: the observable expectation values converge to their Gibbs ensemble values, but parametrically slower compared to the predictions of the eigenstate thermalization hypothesis (ETH). Amidst the thermalizing spectrum, we identify nonergodic eigenstates that strongly violate the ETH, whose number grows polynomially with system size. Previously, the same eigenstates were identified via large overlaps with certain product states, and were used to explain the revivals observed in experiment. Here, we find that these eigenstates, in addition to highly atypical expectation values of local observables, also exhibit subthermal entanglement entropy that scales logarithmically with the system size. Moreover, we identify an additional class of quantum scarred eigenstates, and discuss their manifestations in the dynamics starting from initial product states. We use forward scattering approximation to describe the structure and physical properties of quantum scarred eigenstates. Finally, we discuss the stability of quantum scars to various perturbations. We observe that quantum scars remain robust when the introduced perturbation is compatible with the forward scattering approximation. In contrast, the perturbations which most efficiently destroy quantum scars also lead to the restoration of “canonical” thermalization."}],"publist_id":"8010","isi":1,"month":"10","publication_status":"published","day":"22"},{"ec_funded":1,"day":"05","acknowledgement":"This protocol was adapted from Fendrych et al., 2016. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385, and Austrian Science Fund (FWF) [M 2128-B21]. ","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","id":"10083","status":"public"}]},"month":"01","doi":"10.21769/BioProtoc.2685","abstract":[{"lang":"eng","text":"The rapid auxin-triggered growth of the Arabidopsis hypocotyls involves the nuclear TIR1/AFB-Aux/IAA signaling and is accompanied by acidification of the apoplast and cell walls (Fendrych et al., 2016). Here, we describe in detail the method for analysis of the elongation and the TIR1/AFB-Aux/IAA-dependent auxin response in hypocotyl segments as well as the determination of relative values of the cell wall pH."}],"publist_id":"7381","issue":"1","publication_identifier":{"eissn":["2331-8325"]},"status":"public","language":[{"iso":"eng"}],"article_type":"original","intvolume":" 8","publisher":"Bio-protocol","oa":1,"author":[{"last_name":"Li","orcid":"0000-0002-5607-272X","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin"},{"full_name":"Krens, Gabriel","first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","last_name":"Krens"},{"orcid":"0000-0002-9767-8699","first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","full_name":"Fendrych, Matyas","last_name":"Fendrych"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","citation":{"ieee":"L. Li, G. Krens, M. Fendrych, and J. Friml, “Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls,” Bio-protocol, vol. 8, no. 1. Bio-protocol, 2018.","ama":"Li L, Krens G, Fendrych M, Friml J. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-protocol. 2018;8(1). doi:10.21769/BioProtoc.2685","short":"L. Li, G. Krens, M. Fendrych, J. Friml, Bio-Protocol 8 (2018).","chicago":"Li, Lanxin, Gabriel Krens, Matyas Fendrych, and Jiří Friml. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” Bio-Protocol. Bio-protocol, 2018. https://doi.org/10.21769/BioProtoc.2685.","ista":"Li L, Krens G, Fendrych M, Friml J. 2018. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-protocol. 8(1).","mla":"Li, Lanxin, et al. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” Bio-Protocol, vol. 8, no. 1, Bio-protocol, 2018, doi:10.21769/BioProtoc.2685.","apa":"Li, L., Krens, G., Fendrych, M., & Friml, J. (2018). Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-Protocol. Bio-protocol. https://doi.org/10.21769/BioProtoc.2685"},"file":[{"date_created":"2018-12-12T10:17:43Z","file_id":"5299","access_level":"open_access","file_size":11352389,"content_type":"application/pdf","date_updated":"2020-07-14T12:46:29Z","file_name":"IST-2018-970-v1+1_2018_Lanxin_Real-time_analysis.pdf","creator":"system","relation":"main_file","checksum":"6644ba698206eda32b0abf09128e63e3"}],"department":[{"_id":"JiFr"},{"_id":"Bio"}],"date_updated":"2024-10-29T10:22:43Z","oa_version":"Published Version","type":"journal_article","pubrep_id":"970","file_date_updated":"2020-07-14T12:46:29Z","_id":"442","volume":8,"article_processing_charge":"No","publication":"Bio-protocol","year":"2018","date_created":"2018-12-11T11:46:30Z","ddc":["576","581"],"quality_controlled":"1","date_published":"2018-01-05T00:00:00Z","title":"Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"intvolume":" 71","article_type":"original","page":"577 - 614","arxiv":1,"language":[{"iso":"eng"}],"publisher":"Wiley-Blackwell","isi":1,"month":"03","acknowledgement":"We thank the referee for helpful suggestions that improved the presentation of the paper. We also acknowledge partial support by National Science Foundation Grant DMS-1363432 (R.L.F.), Austrian Science Fund (FWF) Project Nr. P 27533-N27 (P.T.N.), CONICYT (Chile) through CONICYT–PCHA/ Doctorado Nacional/2014, and Iniciativa Científica Milenio (Chile) through Millenium Nucleus RC–120002 “Física Matemática” (H.V.D.B.).\r\n","publication_status":"published","day":"01","status":"public","issue":"3","abstract":[{"text":"We prove that in Thomas–Fermi–Dirac–von Weizsäcker theory, a nucleus of charge Z > 0 can bind at most Z + C electrons, where C is a universal constant. This result is obtained through a comparison with Thomas-Fermi theory which, as a by-product, gives bounds on the screened nuclear potential and the radius of the minimizer. A key ingredient of the proof is a novel technique to control the particles in the exterior region, which also applies to the liquid drop model with a nuclear background potential.","lang":"eng"}],"doi":"10.1002/cpa.21717","publist_id":"7377","date_created":"2018-12-11T11:46:31Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.07355"}],"year":"2018","publication":"Communications on Pure and Applied Mathematics","volume":71,"article_processing_charge":"No","title":"The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory","date_published":"2018-03-01T00:00:00Z","quality_controlled":"1","type":"journal_article","oa_version":"Preprint","date_updated":"2023-09-19T10:09:40Z","department":[{"_id":"RoSe"}],"citation":{"ieee":"R. Frank, P. Nam, and H. Van Den Bosch, “The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory,” Communications on Pure and Applied Mathematics, vol. 71, no. 3. Wiley-Blackwell, pp. 577–614, 2018.","short":"R. Frank, P. Nam, H. Van Den Bosch, Communications on Pure and Applied Mathematics 71 (2018) 577–614.","ama":"Frank R, Nam P, Van Den Bosch H. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 2018;71(3):577-614. doi:10.1002/cpa.21717","chicago":"Frank, Rupert, Phan Nam, and Hanne Van Den Bosch. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2018. https://doi.org/10.1002/cpa.21717.","ista":"Frank R, Nam P, Van Den Bosch H. 2018. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 71(3), 577–614.","mla":"Frank, Rupert, et al. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” Communications on Pure and Applied Mathematics, vol. 71, no. 3, Wiley-Blackwell, 2018, pp. 577–614, doi:10.1002/cpa.21717.","apa":"Frank, R., Nam, P., & Van Den Bosch, H. (2018). The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21717"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"author":[{"last_name":"Frank","full_name":"Frank, Rupert","first_name":"Rupert"},{"first_name":"Nam","full_name":"Phan Thanh, Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87","last_name":"Phan Thanh"},{"last_name":"Van Den Bosch","full_name":"Van Den Bosch, Hanne","first_name":"Hanne"}],"_id":"446","external_id":{"arxiv":["1606.07355"],"isi":["000422675800004"]}},{"external_id":{"isi":["000426559600026"]},"file_date_updated":"2020-07-14T12:46:30Z","scopus_import":"1","_id":"448","date_updated":"2023-09-11T14:10:57Z","oa_version":"Published Version","file":[{"file_name":"IST-2018-969-v1+1_2018_Huylmans_Hemimetabolous_genomes.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:30Z","file_size":3730583,"access_level":"open_access","file_id":"4731","date_created":"2018-12-12T10:09:08Z","checksum":"874953136ac125e65f37971d3cabc5b7","relation":"main_file","creator":"system"}],"department":[{"_id":"BeVi"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"M. Harrison et al., “Hemimetabolous genomes reveal molecular basis of termite eusociality,” Nature Ecology and Evolution, vol. 2, no. 3. Springer Nature, pp. 557–566, 2018.","short":"M. Harrison, E. Jongepier, H. Robertson, N. Arning, T. Bitard Feildel, H. Chao, C. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner, Y. Han, H. Hu, D. Hughes, A.K. Huylmans, K. Kemena, L. Kremer, S. Lee, A. López Ezquerra, L. Mallet, J. Monroy Kuhn, A. Moser, S. Murali, D. Muzny, S. Otani, M. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada Katsumata, K. Worley, Q. Xie, G. Ylla, M. Poulsen, R. Gibbs, C. Schal, S. Richards, X. Belles, J. Korb, E. Bornberg Bauer, Nature Ecology and Evolution 2 (2018) 557–566.","ama":"Harrison M, Jongepier E, Robertson H, et al. Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology and Evolution. 2018;2(3):557-566. doi:10.1038/s41559-017-0459-1","chicago":"Harrison, Mark, Evelien Jongepier, Hugh Robertson, Nicolas Arning, Tristan Bitard Feildel, Hsu Chao, Christopher Childers, et al. “Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Nature Ecology and Evolution. Springer Nature, 2018. https://doi.org/10.1038/s41559-017-0459-1.","ista":"Harrison M, Jongepier E, Robertson H, Arning N, Bitard Feildel T, Chao H, Childers C, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu H, Hughes D, Huylmans AK, Kemena K, Kremer L, Lee S, López Ezquerra A, Mallet L, Monroy Kuhn J, Moser A, Murali S, Muzny D, Otani S, Piulachs M, Poelchau M, Qu J, Schaub F, Wada Katsumata A, Worley K, Xie Q, Ylla G, Poulsen M, Gibbs R, Schal C, Richards S, Belles X, Korb J, Bornberg Bauer E. 2018. Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology and Evolution. 2(3), 557–566.","mla":"Harrison, Mark, et al. “Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Nature Ecology and Evolution, vol. 2, no. 3, Springer Nature, 2018, pp. 557–66, doi:10.1038/s41559-017-0459-1.","apa":"Harrison, M., Jongepier, E., Robertson, H., Arning, N., Bitard Feildel, T., Chao, H., … Bornberg Bauer, E. (2018). Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-017-0459-1"},"has_accepted_license":"1","author":[{"last_name":"Harrison","full_name":"Harrison, Mark","first_name":"Mark"},{"last_name":"Jongepier","full_name":"Jongepier, Evelien","first_name":"Evelien"},{"first_name":"Hugh","full_name":"Robertson, Hugh","last_name":"Robertson"},{"last_name":"Arning","first_name":"Nicolas","full_name":"Arning, Nicolas"},{"last_name":"Bitard Feildel","first_name":"Tristan","full_name":"Bitard Feildel, Tristan"},{"last_name":"Chao","full_name":"Chao, Hsu","first_name":"Hsu"},{"last_name":"Childers","first_name":"Christopher","full_name":"Childers, Christopher"},{"last_name":"Dinh","first_name":"Huyen","full_name":"Dinh, Huyen"},{"full_name":"Doddapaneni, Harshavardhan","first_name":"Harshavardhan","last_name":"Doddapaneni"},{"last_name":"Dugan","first_name":"Shannon","full_name":"Dugan, Shannon"},{"last_name":"Gowin","full_name":"Gowin, Johannes","first_name":"Johannes"},{"last_name":"Greiner","full_name":"Greiner, Carolin","first_name":"Carolin"},{"full_name":"Han, Yi","first_name":"Yi","last_name":"Han"},{"last_name":"Hu","first_name":"Haofu","full_name":"Hu, Haofu"},{"last_name":"Hughes","first_name":"Daniel","full_name":"Hughes, Daniel"},{"orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","full_name":"Huylmans, Ann K","last_name":"Huylmans"},{"full_name":"Kemena, Karsten","first_name":"Karsten","last_name":"Kemena"},{"last_name":"Kremer","full_name":"Kremer, Lukas","first_name":"Lukas"},{"full_name":"Lee, Sandra","first_name":"Sandra","last_name":"Lee"},{"last_name":"López Ezquerra","full_name":"López Ezquerra, Alberto","first_name":"Alberto"},{"full_name":"Mallet, Ludovic","first_name":"Ludovic","last_name":"Mallet"},{"full_name":"Monroy Kuhn, Jose","first_name":"Jose","last_name":"Monroy Kuhn"},{"full_name":"Moser, Annabell","first_name":"Annabell","last_name":"Moser"},{"full_name":"Murali, Shwetha","first_name":"Shwetha","last_name":"Murali"},{"last_name":"Muzny","first_name":"Donna","full_name":"Muzny, Donna"},{"first_name":"Saria","full_name":"Otani, Saria","last_name":"Otani"},{"full_name":"Piulachs, Maria","first_name":"Maria","last_name":"Piulachs"},{"last_name":"Poelchau","full_name":"Poelchau, Monica","first_name":"Monica"},{"last_name":"Qu","full_name":"Qu, Jiaxin","first_name":"Jiaxin"},{"full_name":"Schaub, Florentine","first_name":"Florentine","last_name":"Schaub"},{"last_name":"Wada Katsumata","first_name":"Ayako","full_name":"Wada Katsumata, Ayako"},{"last_name":"Worley","first_name":"Kim","full_name":"Worley, Kim"},{"first_name":"Qiaolin","full_name":"Xie, Qiaolin","last_name":"Xie"},{"last_name":"Ylla","first_name":"Guillem","full_name":"Ylla, Guillem"},{"last_name":"Poulsen","first_name":"Michael","full_name":"Poulsen, Michael"},{"last_name":"Gibbs","full_name":"Gibbs, Richard","first_name":"Richard"},{"last_name":"Schal","full_name":"Schal, Coby","first_name":"Coby"},{"last_name":"Richards","full_name":"Richards, Stephen","first_name":"Stephen"},{"last_name":"Belles","full_name":"Belles, Xavier","first_name":"Xavier"},{"last_name":"Korb","full_name":"Korb, Judith","first_name":"Judith"},{"last_name":"Bornberg Bauer","first_name":"Erich","full_name":"Bornberg Bauer, Erich"}],"oa":1,"pubrep_id":"969","type":"journal_article","date_published":"2018-02-05T00:00:00Z","title":"Hemimetabolous genomes reveal molecular basis of termite eusociality","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2018","publication":"Nature Ecology and Evolution","article_processing_charge":"No","volume":2,"ddc":["576"],"date_created":"2018-12-11T11:46:32Z","issue":"3","doi":"10.1038/s41559-017-0459-1","abstract":[{"text":"Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity.","lang":"eng"}],"publist_id":"7375","status":"public","acknowledgement":"We thank O. Niehuis for allowing use of the unpublished E. danica genome, J. Gadau and C. Smith for comments and advice on the manuscript, and J. Schmitz for assistance with analyses and proofreading the manuscript. J.K. thanks Charles Darwin University (Australia), especially S. Garnett and the Horticulture and Aquaculture team, for providing logistic support to collect C. secundus. The Parks and Wildlife Commission, Northern Territory, the Department of the Environment, Water, Heritage and the Arts gave permission to collect (Permit number 36401) and export (Permit WT2010-6997) the termites. USDA is an equal opportunity provider and employer. M.C.H. and E.J. are supported by DFG grant BO2544/11-1 to E.B.-B. J.K. is supported by University of Osnabrück and DFG grant KO1895/16-1. X.B. and M.-D.P. are supported by Spanish Ministerio de Economía y Competitividad (CGL2012-36251 and CGL2015-64727-P to X.B., and CGL2016-76011-R to M.-D.P.), including FEDER funds, and by Catalan Government (2014 SGR 619). C.S. is supported by grants from the US Department of Housing and Urban Development (NCHHU-0017-13), the National Science Foundation (IOS-1557864), the Alfred P. Sloan Foundation (2013-5-35 MBE), the National Institute of Environmental Health Sciences (P30ES025128) to the Center for Human Health and the Environment, and the Blanton J. Whitmire Endowment. M.P. is supported by a Villum Kann Rasmussen Young Investigator Fellowship (VKR10101).","publication_status":"published","day":"05","isi":1,"related_material":{"record":[{"status":"public","id":"9841","relation":"research_data"}]},"month":"02","publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":" 2","page":"557-566"},{"status":"public","issue":"1","publist_id":"7373","doi":"10.1371/journal.pgen.1007177","abstract":[{"lang":"eng","text":"Auxin is unique among plant hormones due to its directional transport that is mediated by the polarly distributed PIN auxin transporters at the plasma membrane. The canalization hypothesis proposes that the auxin feedback on its polar flow is a crucial, plant-specific mechanism mediating multiple self-organizing developmental processes. Here, we used the auxin effect on the PIN polar localization in Arabidopsis thaliana roots as a proxy for the auxin feedback on the PIN polarity during canalization. We performed microarray experiments to find regulators of this process that act downstream of auxin. We identified genes that were transcriptionally regulated by auxin in an AXR3/IAA17- and ARF7/ARF19-dependent manner. Besides the known components of the PIN polarity, such as PID and PIP5K kinases, a number of potential new regulators were detected, among which the WRKY23 transcription factor, which was characterized in more detail. Gain- and loss-of-function mutants confirmed a role for WRKY23 in mediating the auxin effect on the PIN polarity. Accordingly, processes requiring auxin-mediated PIN polarity rearrangements, such as vascular tissue development during leaf venation, showed a higher WRKY23 expression and required the WRKY23 activity. Our results provide initial insights into the auxin transcriptional network acting upstream of PIN polarization and, potentially, canalization-mediated plant development."}],"isi":1,"related_material":{"record":[{"id":"1127","relation":"dissertation_contains","status":"public"},{"status":"public","id":"7172","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"8822"}]},"month":"01","publication_status":"published","day":"29","ec_funded":1,"publisher":"Public Library of Science","intvolume":" 14","language":[{"iso":"eng"}],"_id":"449","external_id":{"isi":["000423718600034"]},"file_date_updated":"2020-07-14T12:46:30Z","scopus_import":"1","pubrep_id":"967","type":"journal_article","date_updated":"2025-05-07T11:12:28Z","oa_version":"Published Version","department":[{"_id":"JiFr"}],"file":[{"access_level":"open_access","date_created":"2018-12-12T10:10:52Z","file_id":"4843","file_name":"IST-2018-967-v1+1_journal.pgen.1007177.pdf","file_size":24709062,"date_updated":"2020-07-14T12:46:30Z","content_type":"application/pdf","relation":"main_file","checksum":"0276d66788ec076f4924164a39e6a712","creator":"system"}],"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Prat T, Hajny J, Grunewald W, Vasileva MK, Molnar G, Tejos R, Schmid M, Sauer M, Friml J. 2018. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. 14(1).","apa":"Prat, T., Hajny, J., Grunewald, W., Vasileva, M. K., Molnar, G., Tejos, R., … Friml, J. (2018). WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007177","mla":"Prat, Tomas, et al. “WRKY23 Is a Component of the Transcriptional Network Mediating Auxin Feedback on PIN Polarity.” PLoS Genetics, vol. 14, no. 1, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007177.","ama":"Prat T, Hajny J, Grunewald W, et al. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. 2018;14(1). doi:10.1371/journal.pgen.1007177","short":"T. Prat, J. Hajny, W. Grunewald, M.K. Vasileva, G. Molnar, R. Tejos, M. Schmid, M. Sauer, J. Friml, PLoS Genetics 14 (2018).","chicago":"Prat, Tomas, Jakub Hajny, Wim Grunewald, Mina K Vasileva, Gergely Molnar, Ricardo Tejos, Markus Schmid, Michael Sauer, and Jiří Friml. “WRKY23 Is a Component of the Transcriptional Network Mediating Auxin Feedback on PIN Polarity.” PLoS Genetics. Public Library of Science, 2018. https://doi.org/10.1371/journal.pgen.1007177.","ieee":"T. Prat et al., “WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity,” PLoS Genetics, vol. 14, no. 1. Public Library of Science, 2018."},"oa":1,"author":[{"id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","full_name":"Prat, Tomas","first_name":"Tomas","last_name":"Prat"},{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub","first_name":"Jakub","orcid":"0000-0003-2140-7195","last_name":"Hajny"},{"first_name":"Wim","full_name":"Grunewald, Wim","last_name":"Grunewald"},{"last_name":"Vasileva","id":"3407EB18-F248-11E8-B48F-1D18A9856A87","first_name":"Mina K","full_name":"Vasileva, Mina K"},{"last_name":"Molnar","full_name":"Molnar, Gergely","first_name":"Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tejos, Ricardo","first_name":"Ricardo","last_name":"Tejos"},{"full_name":"Schmid, Markus","first_name":"Markus","last_name":"Schmid"},{"first_name":"Michael","full_name":"Sauer, Michael","last_name":"Sauer"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"date_published":"2018-01-29T00:00:00Z","title":"WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity","quality_controlled":"1","ddc":["581"],"date_created":"2018-12-11T11:46:32Z","year":"2018","publication":"PLoS Genetics","volume":14,"article_processing_charge":"Yes"},{"intvolume":" 9","article_number":"555","language":[{"iso":"eng"}],"publisher":"Nature Publishing Group","month":"02","isi":1,"ec_funded":1,"day":"07","publication_status":"published","acknowledgement":"This work was supported by the European Research Council (ERC) start grant 279307: Graph Games (C.K.), Austrian Science Fund (FWF) grant no P23499-N23 (C.K.), FWF\r\nNFN grant no S11407-N23 RiSE/SHiNE (C.K.), Office of Naval Research grant N00014-16-1-2914 (M.A.N.), National Cancer Institute grant CA179991 (M.A.N.) and by the John Templeton Foundation. J.G.R. is supported by an Erwin Schrödinger fellowship\r\n(Austrian Science Fund FWF J-3996). C.H. acknowledges generous support from the\r\nISTFELLOW program. The Program for Evolutionary Dynamics is supported in part by\r\na gift from B Wu and Eric Larson.","status":"public","publist_id":"7368","doi":"10.1038/s41467-017-02721-8","abstract":[{"lang":"eng","text":"Direct reciprocity is a mechanism for cooperation among humans. Many of our daily interactions are repeated. We interact repeatedly with our family, friends, colleagues, members of the local and even global community. In the theory of repeated games, it is a tacit assumption that the various games that a person plays simultaneously have no effect on each other. Here we introduce a general framework that allows us to analyze “crosstalk” between a player’s concurrent games. In the presence of crosstalk, the action a person experiences in one game can alter the person’s decision in another. We find that crosstalk impedes the maintenance of cooperation and requires stronger levels of forgiveness. The magnitude of the effect depends on the population structure. In more densely connected social groups, crosstalk has a stronger effect. A harsh retaliator, such as Tit-for-Tat, is unable to counteract crosstalk. The crosstalk framework provides a unified interpretation of direct and upstream reciprocity in the context of repeated games."}],"issue":"1","date_created":"2018-12-11T11:46:34Z","ddc":["004"],"volume":9,"article_processing_charge":"No","publication":"Nature Communications","year":"2018","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","title":"Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness","date_published":"2018-02-07T00:00:00Z","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"type":"journal_article","pubrep_id":"964","author":[{"orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Reiter"},{"last_name":"Hilbe","first_name":"Christian","full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X"},{"first_name":"David","full_name":"Rand, David","last_name":"Rand"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","citation":{"apa":"Reiter, J., Hilbe, C., Rand, D., Chatterjee, K., & Nowak, M. (2018). Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-02721-8","mla":"Reiter, Johannes, et al. “Crosstalk in Concurrent Repeated Games Impedes Direct Reciprocity and Requires Stronger Levels of Forgiveness.” Nature Communications, vol. 9, no. 1, 555, Nature Publishing Group, 2018, doi:10.1038/s41467-017-02721-8.","ista":"Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. 2018. Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. 9(1), 555.","chicago":"Reiter, Johannes, Christian Hilbe, David Rand, Krishnendu Chatterjee, and Martin Nowak. “Crosstalk in Concurrent Repeated Games Impedes Direct Reciprocity and Requires Stronger Levels of Forgiveness.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-017-02721-8.","ama":"Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. 2018;9(1). doi:10.1038/s41467-017-02721-8","short":"J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, M. Nowak, Nature Communications 9 (2018).","ieee":"J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, and M. Nowak, “Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness,” Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018."},"file":[{"relation":"main_file","checksum":"b6b90367545b4c615891c960ab0567f1","creator":"system","access_level":"open_access","date_created":"2018-12-12T10:09:18Z","file_id":"4741","file_name":"IST-2018-964-v1+1_2018_Hilbe_Crosstalk_in.pdf","file_size":843646,"content_type":"application/pdf","date_updated":"2020-07-14T12:46:31Z"}],"department":[{"_id":"KrCh"}],"oa_version":"Published Version","date_updated":"2023-09-11T12:51:03Z","_id":"454","scopus_import":"1","file_date_updated":"2020-07-14T12:46:31Z","external_id":{"isi":["000424318200001"]}},{"publication":"Annales Henri Poincare","article_processing_charge":"No","volume":19,"year":"2018","ddc":["510","539"],"date_created":"2018-12-11T11:46:34Z","quality_controlled":"1","title":"The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations","date_published":"2018-04-01T00:00:00Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"N. P. Benedikter, J. Sok, and J. Solovej, “The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations,” Annales Henri Poincare, vol. 19, no. 4. Birkhäuser, pp. 1167–1214, 2018.","chicago":"Benedikter, Niels P, Jérémy Sok, and Jan Solovej. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” Annales Henri Poincare. Birkhäuser, 2018. https://doi.org/10.1007/s00023-018-0644-z.","short":"N.P. Benedikter, J. Sok, J. Solovej, Annales Henri Poincare 19 (2018) 1167–1214.","ama":"Benedikter NP, Sok J, Solovej J. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. 2018;19(4):1167-1214. doi:10.1007/s00023-018-0644-z","apa":"Benedikter, N. P., Sok, J., & Solovej, J. (2018). The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. Birkhäuser. https://doi.org/10.1007/s00023-018-0644-z","mla":"Benedikter, Niels P., et al. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” Annales Henri Poincare, vol. 19, no. 4, Birkhäuser, 2018, pp. 1167–214, doi:10.1007/s00023-018-0644-z.","ista":"Benedikter NP, Sok J, Solovej J. 2018. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. 19(4), 1167–1214."},"has_accepted_license":"1","author":[{"full_name":"Benedikter, Niels P","first_name":"Niels P","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1071-6091","last_name":"Benedikter"},{"first_name":"Jérémy","full_name":"Sok, Jérémy","last_name":"Sok"},{"first_name":"Jan","full_name":"Solovej, Jan","last_name":"Solovej"}],"oa":1,"date_updated":"2023-09-19T10:07:41Z","oa_version":"Published Version","file":[{"file_name":"IST-2018-993-v1+1_2018_Benedikter_Dirac.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:31Z","file_size":923252,"access_level":"open_access","file_id":"4914","date_created":"2018-12-12T10:11:57Z","checksum":"883eeccba8384ad7fcaa28761d99a0fa","relation":"main_file","creator":"system"}],"department":[{"_id":"RoSe"}],"type":"journal_article","pubrep_id":"993","file_date_updated":"2020-07-14T12:46:31Z","scopus_import":"1","external_id":{"isi":["000427578900006"]},"_id":"455","language":[{"iso":"eng"}],"page":"1167 - 1214","intvolume":" 19","publisher":"Birkhäuser","day":"01","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors acknowledge support by ERC Advanced Grant 321029 and by VILLUM FONDEN via the QMATH Centre of Excellence (Grant No. 10059). The authors would like to thank Sébastien Breteaux, Enno Lenzmann, Mathieu Lewin and Jochen Schmid for comments and discussions about well-posedness of the Bogoliubov–de Gennes equations.","publication_status":"published","isi":1,"month":"04","alternative_title":["Annales Henri Poincare"],"doi":"10.1007/s00023-018-0644-z","abstract":[{"text":"The derivation of effective evolution equations is central to the study of non-stationary quantum many-body systems, and widely used in contexts such as superconductivity, nuclear physics, Bose–Einstein condensation and quantum chemistry. We reformulate the Dirac–Frenkel approximation principle in terms of reduced density matrices and apply it to fermionic and bosonic many-body systems. We obtain the Bogoliubov–de Gennes and Hartree–Fock–Bogoliubov equations, respectively. While we do not prove quantitative error estimates, our formulation does show that the approximation is optimal within the class of quasifree states. Furthermore, we prove well-posedness of the Bogoliubov–de Gennes equations in energy space and discuss conserved quantities","lang":"eng"}],"publist_id":"7367","issue":"4","status":"public"},{"title":"A faster approximation algorithm for the Gibbs partition function","date_published":"2017-12-27T00:00:00Z","project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"conference":{"name":"COLT: Annual Conference on Learning Theory ","start_date":"2018-07-06","end_date":"2018-07-09"},"year":"2017","volume":75,"article_processing_charge":"No","publication":"Proceedings of the 31st Conference On Learning Theory","date_created":"2018-12-11T11:45:33Z","ddc":["510"],"external_id":{"arxiv":["1608.04223"]},"file_date_updated":"2020-07-14T12:45:45Z","_id":"274","department":[{"_id":"VlKo"}],"file":[{"relation":"main_file","checksum":"89db06a0e8083524449cb59b56bf4e5b","creator":"dernst","file_name":"2018_PMLR_Kolmogorov.pdf","file_size":408974,"content_type":"application/pdf","date_updated":"2020-07-14T12:45:45Z","access_level":"open_access","date_created":"2020-05-12T09:23:27Z","file_id":"7820"}],"date_updated":"2023-10-17T12:32:13Z","oa_version":"Published Version","author":[{"first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","citation":{"chicago":"Kolmogorov, Vladimir. “A Faster Approximation Algorithm for the Gibbs Partition Function.” In Proceedings of the 31st Conference On Learning Theory, 75:228–49. ML Research Press, 2017.","ama":"Kolmogorov V. A faster approximation algorithm for the Gibbs partition function. In: Proceedings of the 31st Conference On Learning Theory. Vol 75. ML Research Press; 2017:228-249.","short":"V. Kolmogorov, in:, Proceedings of the 31st Conference On Learning Theory, ML Research Press, 2017, pp. 228–249.","ieee":"V. Kolmogorov, “A faster approximation algorithm for the Gibbs partition function,” in Proceedings of the 31st Conference On Learning Theory, 2017, vol. 75, pp. 228–249.","mla":"Kolmogorov, Vladimir. “A Faster Approximation Algorithm for the Gibbs Partition Function.” Proceedings of the 31st Conference On Learning Theory, vol. 75, ML Research Press, 2017, pp. 228–49.","apa":"Kolmogorov, V. (2017). A faster approximation algorithm for the Gibbs partition function. In Proceedings of the 31st Conference On Learning Theory (Vol. 75, pp. 228–249). ML Research Press.","ista":"Kolmogorov V. 2017. A faster approximation algorithm for the Gibbs partition function. Proceedings of the 31st Conference On Learning Theory. COLT: Annual Conference on Learning Theory vol. 75, 228–249."},"type":"conference","publisher":"ML Research Press","language":[{"iso":"eng"}],"arxiv":1,"intvolume":" 75","page":"228-249","abstract":[{"text":"We consider the problem of estimating the partition function Z(β)=∑xexp(−β(H(x)) of a Gibbs distribution with a Hamilton H(⋅), or more precisely the logarithm of the ratio q=lnZ(0)/Z(β). It has been recently shown how to approximate q with high probability assuming the existence of an oracle that produces samples from the Gibbs distribution for a given parameter value in [0,β]. The current best known approach due to Huber [9] uses O(qlnn⋅[lnq+lnlnn+ε−2]) oracle calls on average where ε is the desired accuracy of approximation and H(⋅) is assumed to lie in {0}∪[1,n]. We improve the complexity to O(qlnn⋅ε−2) oracle calls. We also show that the same complexity can be achieved if exact oracles are replaced with approximate sampling oracles that are within O(ε2qlnn) variation distance from exact oracles. Finally, we prove a lower bound of Ω(q⋅ε−2) oracle calls under a natural model of computation.","lang":"eng"}],"publist_id":"7628","status":"public","publication_status":"published","ec_funded":1,"day":"27","month":"12"},{"publisher":"American Physical Society","article_number":"012004","intvolume":" 999","arxiv":1,"language":[{"iso":"eng"}],"status":"public","publication_identifier":{"issn":["17426588"]},"issue":"1","doi":"10.1088/1742-6596/999/1/012004","abstract":[{"lang":"eng","text":"Tunneling of a particle through a potential barrier remains one of the most remarkable quantum phenomena. Owing to advances in laser technology, electric fields comparable to those electrons experience in atoms are readily generated and open opportunities to dynamically investigate the process of electron tunneling through the potential barrier formed by the superposition of both laser and atomic fields. Attosecond-time and angstrom-space resolution of the strong laser-field technique allow to address fundamental questions related to tunneling, which are still open and debated: Which time is spent under the barrier and what momentum is picked up by the particle in the meantime? In this combined experimental and theoretical study we demonstrate that for strong-field ionization the leading quantum mechanical Wigner treatment for the time resolved description of tunneling is valid. We achieve a high sensitivity on the tunneling barrier and unambiguously isolate its effects by performing a differential study of two systems with almost identical tunneling geometry. Moreover, working with a low frequency laser, we essentially limit the non-adiabaticity of the process as a major source of uncertainty. The agreement between experiment and theory implies two substantial corrections with respect to the widely employed quasiclassical treatment: In addition to a non-vanishing longitudinal momentum along the laser field-direction we provide clear evidence for a non-zero tunneling time delay. This addresses also the fundamental question how the transition occurs from the tunnel barrier to free space classical evolution of the ejected electron."}],"publist_id":"7552","alternative_title":["Journal of Physics: Conference Series"],"month":"07","related_material":{"record":[{"status":"public","relation":"later_version","id":"6013"}]},"publication_status":"published","day":"14","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"conference":{"end_date":"2017-08-21","start_date":"2017-08-17","location":"Kazan, Russian Federation","name":"Annual International Laser Physics Workshop LPHYS"},"date_published":"2017-07-14T00:00:00Z","title":"Experimental evidence for Wigner's tunneling time","quality_controlled":"1","ddc":["530"],"date_created":"2018-12-11T11:45:46Z","year":"2017","volume":999,"_id":"313","external_id":{"arxiv":["1611.03701"]},"file_date_updated":"2020-07-14T12:46:00Z","scopus_import":1,"type":"conference","oa_version":"Published Version","date_updated":"2023-02-23T12:36:07Z","department":[{"_id":"MiLe"}],"file":[{"file_size":949321,"content_type":"application/pdf","date_updated":"2020-07-14T12:46:00Z","file_name":"2017_Physics_Camus.pdf","date_created":"2019-01-22T08:34:10Z","file_id":"5871","access_level":"open_access","creator":"dernst","relation":"main_file","checksum":"6e70b525a84f6d5fb175c48e9f5cb59a"}],"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Camus, Nicolas, et al. Experimental Evidence for Wigner’s Tunneling Time. Vol. 999, no. 1, 012004, American Physical Society, 2017, doi:10.1088/1742-6596/999/1/012004.","apa":"Camus, N., Yakaboylu, E., Fechner, L., Klaiber, M., Laux, M., Mi, Y., … Moshammer, R. (2017). Experimental evidence for Wigner’s tunneling time (Vol. 999). Presented at the Annual International Laser Physics Workshop LPHYS, Kazan, Russian Federation: American Physical Society. https://doi.org/10.1088/1742-6596/999/1/012004","ista":"Camus N, Yakaboylu E, Fechner L, Klaiber M, Laux M, Mi Y, Hatsagortsyan K, Pfeifer T, Keitel C, Moshammer R. 2017. Experimental evidence for Wigner’s tunneling time. Annual International Laser Physics Workshop LPHYS, Journal of Physics: Conference Series, vol. 999, 012004.","chicago":"Camus, Nicolas, Enderalp Yakaboylu, Lutz Fechner, Michael Klaiber, Martin Laux, Yonghao Mi, Karen Hatsagortsyan, Thomas Pfeifer, Cristoph Keitel, and Robert Moshammer. “Experimental Evidence for Wigner’s Tunneling Time,” Vol. 999. American Physical Society, 2017. https://doi.org/10.1088/1742-6596/999/1/012004.","ama":"Camus N, Yakaboylu E, Fechner L, et al. Experimental evidence for Wigner’s tunneling time. In: Vol 999. American Physical Society; 2017. doi:10.1088/1742-6596/999/1/012004","short":"N. Camus, E. Yakaboylu, L. Fechner, M. Klaiber, M. Laux, Y. Mi, K. Hatsagortsyan, T. Pfeifer, C. Keitel, R. Moshammer, in:, American Physical Society, 2017.","ieee":"N. Camus et al., “Experimental evidence for Wigner’s tunneling time,” presented at the Annual International Laser Physics Workshop LPHYS, Kazan, Russian Federation, 2017, vol. 999, no. 1."},"author":[{"first_name":"Nicolas","full_name":"Camus, Nicolas","last_name":"Camus"},{"last_name":"Yakaboylu","orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp","first_name":"Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fechner","first_name":"Lutz","full_name":"Fechner, Lutz"},{"first_name":"Michael","full_name":"Klaiber, Michael","last_name":"Klaiber"},{"last_name":"Laux","first_name":"Martin","full_name":"Laux, Martin"},{"last_name":"Mi","full_name":"Mi, Yonghao","first_name":"Yonghao"},{"last_name":"Hatsagortsyan","full_name":"Hatsagortsyan, Karen","first_name":"Karen"},{"first_name":"Thomas","full_name":"Pfeifer, Thomas","last_name":"Pfeifer"},{"last_name":"Keitel","full_name":"Keitel, Cristoph","first_name":"Cristoph"},{"last_name":"Moshammer","first_name":"Robert","full_name":"Moshammer, Robert"}],"oa":1},{"publisher":"Elsevier","language":[{"iso":"eng"}],"intvolume":" 254","page":"143 - 166","issue":"2","doi":"10.1016/j.ic.2016.10.006","abstract":[{"text":"Simulation is an attractive alternative to language inclusion for automata as it is an under-approximation of language inclusion, but usually has much lower complexity. Simulation has also been extended in two orthogonal directions, namely, (1) fair simulation, for simulation over specified set of infinite runs; and (2) quantitative simulation, for simulation between weighted automata. While fair trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial time. For weighted automata, the (quantitative) language inclusion problem is undecidable in general, whereas the (quantitative) simulation reduces to quantitative games, which admit pseudo-polynomial time algorithms.\r\n\r\nIn this work, we study (quantitative) simulation for weighted automata with Büchi acceptance conditions, i.e., we generalize fair simulation from non-weighted automata to weighted automata. We show that imposing Büchi acceptance conditions on weighted automata changes many fundamental properties of the simulation games, yet they still admit pseudo-polynomial time algorithms.","lang":"eng"}],"publist_id":"6322","status":"public","publication_status":"published","day":"01","ec_funded":1,"isi":1,"related_material":{"record":[{"id":"5428","relation":"earlier_version","status":"public"}]},"month":"06","project":[{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"title":"Quantitative fair simulation games","date_published":"2017-06-01T00:00:00Z","quality_controlled":"1","year":"2017","publication":"Information and Computation","article_processing_charge":"No","volume":254,"date_created":"2018-12-11T11:49:58Z","external_id":{"isi":["000402025600002"]},"scopus_import":"1","_id":"1066","date_updated":"2023-09-20T12:07:48Z","oa_version":"None","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"citation":{"ista":"Chatterjee K, Henzinger TA, Otop J, Velner Y. 2017. Quantitative fair simulation games. Information and Computation. 254(2), 143–166.","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., & Velner, Y. (2017). Quantitative fair simulation games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2016.10.006","mla":"Chatterjee, Krishnendu, et al. “Quantitative Fair Simulation Games.” Information and Computation, vol. 254, no. 2, Elsevier, 2017, pp. 143–66, doi:10.1016/j.ic.2016.10.006.","ama":"Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative fair simulation games. Information and Computation. 2017;254(2):143-166. doi:10.1016/j.ic.2016.10.006","short":"K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Information and Computation 254 (2017) 143–166.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner. “Quantitative Fair Simulation Games.” Information and Computation. Elsevier, 2017. https://doi.org/10.1016/j.ic.2016.10.006.","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, “Quantitative fair simulation games,” Information and Computation, vol. 254, no. 2. Elsevier, pp. 143–166, 2017."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"first_name":"Jan","full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","last_name":"Otop"},{"last_name":"Velner","full_name":"Velner, Yaron","first_name":"Yaron"}],"type":"journal_article"},{"type":"journal_article","pubrep_id":"869","author":[{"full_name":"Morita, Hitoshi","first_name":"Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","last_name":"Morita"},{"last_name":"Grigolon","full_name":"Grigolon, Silvia","first_name":"Silvia"},{"last_name":"Bock","full_name":"Bock, Martin","first_name":"Martin"},{"last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","first_name":"Gabriel","orcid":"0000-0003-4761-5996"},{"last_name":"Salbreux","first_name":"Guillaume","full_name":"Salbreux, Guillaume"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"oa":1,"citation":{"apa":"Morita, H., Grigolon, S., Bock, M., Krens, G., Salbreux, G., & Heisenberg, C.-P. J. (2017). The physical basis of coordinated tissue spreading in zebrafish gastrulation. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2017.01.010","mla":"Morita, Hitoshi, et al. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” Developmental Cell, vol. 40, no. 4, Cell Press, 2017, pp. 354–66, doi:10.1016/j.devcel.2017.01.010.","ista":"Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. 2017. The physical basis of coordinated tissue spreading in zebrafish gastrulation. Developmental Cell. 40(4), 354–366.","ieee":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, and C.-P. J. Heisenberg, “The physical basis of coordinated tissue spreading in zebrafish gastrulation,” Developmental Cell, vol. 40, no. 4. Cell Press, pp. 354–366, 2017.","chicago":"Morita, Hitoshi, Silvia Grigolon, Martin Bock, Gabriel Krens, Guillaume Salbreux, and Carl-Philipp J Heisenberg. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” Developmental Cell. Cell Press, 2017. https://doi.org/10.1016/j.devcel.2017.01.010.","ama":"Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. The physical basis of coordinated tissue spreading in zebrafish gastrulation. Developmental Cell. 2017;40(4):354-366. doi:10.1016/j.devcel.2017.01.010","short":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, C.-P.J. Heisenberg, Developmental Cell 40 (2017) 354–366."},"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_size":6866187,"date_updated":"2018-12-12T10:10:57Z","content_type":"application/pdf","file_name":"IST-2017-869-v1+1_1-s2.0-S1534580717300370-main.pdf","date_created":"2018-12-12T10:10:57Z","file_id":"4849","access_level":"open_access","creator":"system","relation":"main_file"}],"department":[{"_id":"CaHe"}],"date_updated":"2023-09-20T12:06:27Z","oa_version":"Published Version","_id":"1067","scopus_import":"1","file_date_updated":"2018-12-12T10:10:57Z","external_id":{"isi":["000395368300007"]},"date_created":"2018-12-11T11:49:58Z","ddc":["572","597"],"volume":40,"article_processing_charge":"No","publication":"Developmental Cell","year":"2017","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","title":"The physical basis of coordinated tissue spreading in zebrafish gastrulation","date_published":"2017-02-27T00:00:00Z","project":[{"grant_number":"201439","name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","_id":"2524F500-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"month":"02","isi":1,"ec_funded":1,"day":"27","publication_status":"published","publication_identifier":{"issn":["15345807"]},"status":"public","publist_id":"6320","doi":"10.1016/j.devcel.2017.01.010","abstract":[{"text":"Embryo morphogenesis relies on highly coordinated movements of different tissues. However, remarkably little is known about how tissues coordinate their movements to shape the embryo. In zebrafish embryogenesis, coordinated tissue movements first become apparent during “doming,” when the blastoderm begins to spread over the yolk sac, a process involving coordinated epithelial surface cell layer expansion and mesenchymal deep cell intercalations. Here, we find that active surface cell expansion represents the key process coordinating tissue movements during doming. By using a combination of theory and experiments, we show that epithelial surface cells not only trigger blastoderm expansion by reducing tissue surface tension, but also drive blastoderm thinning by inducing tissue contraction through radial deep cell intercalations. Thus, coordinated tissue expansion and thinning during doming relies on surface cells simultaneously controlling tissue surface tension and radial tissue contraction.","lang":"eng"}],"issue":"4","acknowledged_ssus":[{"_id":"PreCl"}],"page":"354 - 366","intvolume":" 40","language":[{"iso":"eng"}],"publisher":"Cell Press"},{"doi":"10.1090/tran/6991","abstract":[{"lang":"eng","text":"Given a finite set of points in Rn and a radius parameter, we study the Čech, Delaunay–Čech, Delaunay (or alpha), and Wrap complexes in the light of generalized discrete Morse theory. Establishing the Čech and Delaunay complexes as sublevel sets of generalized discrete Morse functions, we prove that the four complexes are simple-homotopy equivalent by a sequence of simplicial collapses, which are explicitly described by a single discrete gradient field."}],"publist_id":"6311","issue":"5","status":"public","ec_funded":1,"day":"01","publication_status":"published","acknowledgement":"This research has been supported by the EU project Toposys(FP7-ICT-318493-STREP), by ESF under the ACAT Research Network Programme, by the Russian Government under mega project 11.G34.31.0053, and by the DFG Collaborative Research Center SFB/TRR 109 “Discretization in Geometry and Dynamics”.","month":"05","isi":1,"publisher":"American Mathematical Society","arxiv":1,"language":[{"iso":"eng"}],"article_type":"original","page":"3741 - 3762","intvolume":" 369","scopus_import":"1","external_id":{"isi":["000398030400024"],"arxiv":["1312.1231"]},"_id":"1072","author":[{"last_name":"Bauer","full_name":"Bauer, Ulrich","first_name":"Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9683-0724"},{"orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"}],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” Transactions of the American Mathematical Society, vol. 369, no. 5, American Mathematical Society, 2017, pp. 3741–62, doi:10.1090/tran/6991.","apa":"Bauer, U., & Edelsbrunner, H. (2017). The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/6991","ista":"Bauer U, Edelsbrunner H. 2017. The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. 369(5), 3741–3762.","ieee":"U. Bauer and H. Edelsbrunner, “The Morse theory of Čech and delaunay complexes,” Transactions of the American Mathematical Society, vol. 369, no. 5. American Mathematical Society, pp. 3741–3762, 2017.","chicago":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” Transactions of the American Mathematical Society. American Mathematical Society, 2017. https://doi.org/10.1090/tran/6991.","ama":"Bauer U, Edelsbrunner H. The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. 2017;369(5):3741-3762. doi:10.1090/tran/6991","short":"U. Bauer, H. Edelsbrunner, Transactions of the American Mathematical Society 369 (2017) 3741–3762."},"department":[{"_id":"HeEd"}],"oa_version":"Preprint","date_updated":"2023-09-20T12:05:56Z","type":"journal_article","quality_controlled":"1","title":"The Morse theory of Čech and delaunay complexes","date_published":"2017-05-01T00:00:00Z","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"318493","name":"Topological Complex Systems"}],"article_processing_charge":"No","volume":369,"publication":"Transactions of the American Mathematical Society","year":"2017","main_file_link":[{"url":"https://arxiv.org/abs/1312.1231","open_access":"1"}],"date_created":"2018-12-11T11:49:59Z"}]