[{"volume":7,"language":[{"iso":"eng"}],"file":[{"file_id":"5115","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-790-v1+1_srep41002_1_.pdf","date_created":"2018-12-12T10:14:59Z","creator":"system","file_size":1994139,"date_updated":"2018-12-12T10:14:59Z"}],"publication_status":"published","intvolume":" 7","month":"02","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Characterisation of G protein-coupled receptors (GPCR) relies on the availability of a toolbox of ligands that selectively modulate different functional states of the receptors. To uncover such molecules, we explored a unique strategy for ligand discovery that takes advantage of the evolutionary conservation of the 600-million-year-old oxytocin/vasopressin signalling system. We isolated the insect oxytocin/vasopressin orthologue inotocin from the black garden ant (Lasius niger), identified and cloned its cognate receptor and determined its pharmacological properties on the insect and human oxytocin/vasopressin receptors. Subsequently, we identified a functional dichotomy: inotocin activated the insect inotocin and the human vasopressin V1b receptors, but inhibited the human V1aR. Replacement of Arg8 of inotocin by D-Arg8 led to a potent, stable and competitive V1aR-antagonist ([D-Arg8]-inotocin) with a 3,000-fold binding selectivity for the human V1aR over the other three subtypes, OTR, V1bR and V2R. The Arg8/D-Arg8 ligand-pair was further investigated to gain novel insights into the oxytocin/vasopressin peptide-receptor interaction, which led to the identification of key residues of the receptors that are important for ligand functionality and selectivity. These observations could play an important role for development of oxytocin/vasopressin receptor modulators that would enable clear distinction of the physiological and pathological responses of the individual receptor subtypes."}],"file_date_updated":"2018-12-12T10:14:59Z","ddc":["570","590"],"date_updated":"2023-09-20T11:47:47Z","pubrep_id":"790","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1086","date_created":"2018-12-11T11:50:04Z","doi":"10.1038/srep41002","date_published":"2017-02-01T00:00:00Z","page":"41002","publication":"Scientific Reports","day":"01","year":"2017","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","title":"Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide","article_processing_charge":"No","external_id":{"isi":["000393163800001"]},"author":[{"full_name":"Di Giglio, Maria","last_name":"Di Giglio","first_name":"Maria"},{"full_name":"Muttenthaler, Markus","last_name":"Muttenthaler","first_name":"Markus"},{"full_name":"Harpsøe, Kasper","last_name":"Harpsøe","first_name":"Kasper"},{"full_name":"Liutkeviciute, Zita","last_name":"Liutkeviciute","first_name":"Zita"},{"first_name":"Peter","full_name":"Keov, Peter","last_name":"Keov"},{"first_name":"Thomas","full_name":"Eder, Thomas","last_name":"Eder"},{"last_name":"Rattei","full_name":"Rattei, Thomas","first_name":"Thomas"},{"first_name":"Sarah","last_name":"Arrowsmith","full_name":"Arrowsmith, Sarah"},{"first_name":"Susan","full_name":"Wray, Susan","last_name":"Wray"},{"full_name":"Marek, Ales","last_name":"Marek","first_name":"Ales"},{"first_name":"Tomas","full_name":"Elbert, Tomas","last_name":"Elbert"},{"last_name":"Alewood","full_name":"Alewood, Paul","first_name":"Paul"},{"first_name":"David","full_name":"Gloriam, David","last_name":"Gloriam"},{"last_name":"Gruber","full_name":"Gruber, Christian","first_name":"Christian"}],"publist_id":"6291","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Di Giglio, Maria, Markus Muttenthaler, Kasper Harpsøe, Zita Liutkeviciute, Peter Keov, Thomas Eder, Thomas Rattei, et al. “Development of a Human Vasopressin V1a-Receptor Antagonist from an Evolutionary-Related Insect Neuropeptide.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/srep41002.","ista":"Di Giglio M, Muttenthaler M, Harpsøe K, Liutkeviciute Z, Keov P, Eder T, Rattei T, Arrowsmith S, Wray S, Marek A, Elbert T, Alewood P, Gloriam D, Gruber C. 2017. Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide. Scientific Reports. 7, 41002.","mla":"Di Giglio, Maria, et al. “Development of a Human Vasopressin V1a-Receptor Antagonist from an Evolutionary-Related Insect Neuropeptide.” Scientific Reports, vol. 7, Nature Publishing Group, 2017, p. 41002, doi:10.1038/srep41002.","short":"M. Di Giglio, M. Muttenthaler, K. Harpsøe, Z. Liutkeviciute, P. Keov, T. Eder, T. Rattei, S. Arrowsmith, S. Wray, A. Marek, T. Elbert, P. Alewood, D. Gloriam, C. Gruber, Scientific Reports 7 (2017) 41002.","ieee":"M. Di Giglio et al., “Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide,” Scientific Reports, vol. 7. Nature Publishing Group, p. 41002, 2017.","apa":"Di Giglio, M., Muttenthaler, M., Harpsøe, K., Liutkeviciute, Z., Keov, P., Eder, T., … Gruber, C. (2017). Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep41002","ama":"Di Giglio M, Muttenthaler M, Harpsøe K, et al. Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide. Scientific Reports. 2017;7:41002. doi:10.1038/srep41002"}},{"_id":"1084","type":"journal_article","status":"public","date_updated":"2023-09-20T11:48:43Z","department":[{"_id":"CaGu"}],"abstract":[{"lang":"eng","text":"BceRS and PsdRS are paralogous two-component systems in Bacillus subtilis controlling the response to antimicrobial peptides. In the presence of extracellular bacitracin and nisin, respectively, the two response regulators (RRs) bind their target promoters, PbceA or PpsdA, resulting in a strong up-regulation of target gene expression and ultimately antibiotic resistance. Despite high sequence similarity between the RRs BceR and PsdR and their known binding sites, no cross-regulation has been observed between them. We therefore investigated the specificity determinants of PbceA and PpsdA that ensure the insulation of these two paralogous pathways at the RR–promoter interface. In vivo and in vitro analyses demonstrate that the regulatory regions within these two promoters contain three important elements: in addition to the known (main) binding site, we identified a linker region and a secondary binding site that are crucial for functionality. Initial binding to the high-affinity, low-specificity main binding site is a prerequisite for the subsequent highly specific binding of a second RR dimer to the low-affinity secondary binding site. In addition to this hierarchical cooperative binding, discrimination requires a competition of the two RRs for their respective binding site mediated by only slight differences in binding affinities."}],"oa_version":"None","scopus_import":"1","month":"04","intvolume":" 104","publication_identifier":{"issn":[" 0950382X"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"1","volume":104,"citation":{"mla":"Fang, Chong, et al. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” Molecular Microbiology, vol. 104, no. 1, Wiley-Blackwell, 2017, pp. 16–31, doi:10.1111/mmi.13597.","ieee":"C. Fang et al., “Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis,” Molecular Microbiology, vol. 104, no. 1. Wiley-Blackwell, pp. 16–31, 2017.","short":"C. Fang, A.A. Nagy-Staron, M. Grafe, R. Heermann, K. Jung, S. Gebhard, T. Mascher, Molecular Microbiology 104 (2017) 16–31.","apa":"Fang, C., Nagy-Staron, A. A., Grafe, M., Heermann, R., Jung, K., Gebhard, S., & Mascher, T. (2017). Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. Wiley-Blackwell. https://doi.org/10.1111/mmi.13597","ama":"Fang C, Nagy-Staron AA, Grafe M, et al. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. 2017;104(1):16-31. doi:10.1111/mmi.13597","chicago":"Fang, Chong, Anna A Nagy-Staron, Martin Grafe, Ralf Heermann, Kirsten Jung, Susanne Gebhard, and Thorsten Mascher. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” Molecular Microbiology. Wiley-Blackwell, 2017. https://doi.org/10.1111/mmi.13597.","ista":"Fang C, Nagy-Staron AA, Grafe M, Heermann R, Jung K, Gebhard S, Mascher T. 2017. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. 104(1), 16–31."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Chong","last_name":"Fang","full_name":"Fang, Chong"},{"last_name":"Nagy-Staron","orcid":"0000-0002-1391-8377","full_name":"Nagy-Staron, Anna A","first_name":"Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grafe, Martin","last_name":"Grafe","first_name":"Martin"},{"last_name":"Heermann","full_name":"Heermann, Ralf","first_name":"Ralf"},{"first_name":"Kirsten","last_name":"Jung","full_name":"Jung, Kirsten"},{"full_name":"Gebhard, Susanne","last_name":"Gebhard","first_name":"Susanne"},{"last_name":"Mascher","full_name":"Mascher, Thorsten","first_name":"Thorsten"}],"publist_id":"6294","article_processing_charge":"No","external_id":{"isi":["000398059200002"]},"title":"Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis","publisher":"Wiley-Blackwell","quality_controlled":"1","isi":1,"year":"2017","day":"01","publication":"Molecular Microbiology","page":"16 - 31","date_published":"2017-04-01T00:00:00Z","doi":"10.1111/mmi.13597","date_created":"2018-12-11T11:50:03Z"},{"date_created":"2018-12-11T11:50:02Z","date_published":"2017-06-01T00:00:00Z","doi":"10.1007/s11040-017-9238-0","year":"2017","isi":1,"publication":"Mathematical Physics, Analysis and Geometry","day":"01","oa":1,"quality_controlled":"1","publisher":"Springer","external_id":{"isi":["000401270000004"]},"article_processing_charge":"No","publist_id":"6300","author":[{"full_name":"Nam, Phan","last_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan"},{"first_name":"Hanne","last_name":"Van Den Bosch","full_name":"Van Den Bosch, Hanne"}],"title":"Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges","citation":{"chicago":"Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” Mathematical Physics, Analysis and Geometry. Springer, 2017. https://doi.org/10.1007/s11040-017-9238-0.","ista":"Nam P, Van Den Bosch H. 2017. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. 20(2), 6.","mla":"Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” Mathematical Physics, Analysis and Geometry, vol. 20, no. 2, 6, Springer, 2017, doi:10.1007/s11040-017-9238-0.","ieee":"P. Nam and H. Van Den Bosch, “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges,” Mathematical Physics, Analysis and Geometry, vol. 20, no. 2. Springer, 2017.","short":"P. Nam, H. Van Den Bosch, Mathematical Physics, Analysis and Geometry 20 (2017).","apa":"Nam, P., & Van Den Bosch, H. (2017). Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-017-9238-0","ama":"Nam P, Van Den Bosch H. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. 2017;20(2). doi:10.1007/s11040-017-9238-0"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"article_number":"6","issue":"2","volume":20,"publication_status":"published","publication_identifier":{"issn":["13850172"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1603.07368"}],"scopus_import":"1","intvolume":" 20","month":"06","abstract":[{"text":"We study the ionization problem in the Thomas-Fermi-Dirac-von Weizsäcker theory for atoms and molecules. We prove the nonexistence of minimizers for the energy functional when the number of electrons is large and the total nuclear charge is small. This nonexistence result also applies to external potentials decaying faster than the Coulomb potential. In the case of arbitrary nuclear charges, we obtain the nonexistence of stable minimizers and radial minimizers.","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"RoSe"}],"date_updated":"2023-09-20T11:53:35Z","type":"journal_article","status":"public","_id":"1079"},{"related_material":{"record":[{"status":"public","id":"9864","relation":"research_data"}]},"volume":14,"issue":"126","ec_funded":1,"publication_identifier":{"issn":["17425689"]},"publication_status":"published","file":[{"file_id":"5843","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-01-18T09:14:02Z","file_name":"2017_JRSI_Redondo.pdf","date_updated":"2019-01-18T09:14:02Z","file_size":1092015,"creator":"dernst"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"01","intvolume":" 14","abstract":[{"text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the fX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2019-01-18T09:14:02Z","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"date_updated":"2023-09-20T11:56:34Z","ddc":["570"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"1077","doi":"10.1098/rsif.2016.0139","date_published":"2017-01-04T00:00:00Z","date_created":"2018-12-11T11:50:01Z","has_accepted_license":"1","isi":1,"year":"2017","day":"04","publication":"Journal of the Royal Society Interface","publisher":"Royal Society of London","quality_controlled":"1","oa":1,"publist_id":"6303","author":[{"id":"409D5C96-F248-11E8-B48F-1D18A9856A87","first_name":"Rodrigo A","last_name":"Fernandes Redondo","orcid":"0000-0002-5837-2793","full_name":"Fernandes Redondo, Rodrigo A"},{"orcid":"0000-0002-5985-7653","full_name":"Vladar, Harold","last_name":"Vladar","first_name":"Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tomasz","last_name":"Włodarski","full_name":"Włodarski, Tomasz"},{"first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000393380400001"]},"title":"Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","citation":{"mla":"Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface, vol. 14, no. 126, 20160139, Royal Society of London, 2017, doi:10.1098/rsif.2016.0139.","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 2017;14(126). doi:10.1098/rsif.2016.0139","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. Royal Society of London. https://doi.org/10.1098/rsif.2016.0139","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017).","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family,” Journal of the Royal Society Interface, vol. 14, no. 126. Royal Society of London, 2017.","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface. Royal Society of London, 2017. https://doi.org/10.1098/rsif.2016.0139.","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 14(126), 20160139."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"article_number":"20160139"},{"date_updated":"2023-09-20T12:06:27Z","ddc":["572","597"],"file_date_updated":"2018-12-12T10:10:57Z","department":[{"_id":"CaHe"}],"_id":"1067","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"869","status":"public","publication_status":"published","publication_identifier":{"issn":["15345807"]},"language":[{"iso":"eng"}],"file":[{"file_id":"4849","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2017-869-v1+1_1-s2.0-S1534580717300370-main.pdf","date_created":"2018-12-12T10:10:57Z","file_size":6866187,"date_updated":"2018-12-12T10:10:57Z","creator":"system"}],"ec_funded":1,"volume":40,"issue":"4","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"}],"acknowledged_ssus":[{"_id":"PreCl"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 40","month":"02","citation":{"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.","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","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","short":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, C.-P.J. Heisenberg, Developmental Cell 40 (2017) 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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000395368300007"]},"publist_id":"6320","author":[{"first_name":"Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","full_name":"Morita, Hitoshi","last_name":"Morita"},{"last_name":"Grigolon","full_name":"Grigolon, Silvia","first_name":"Silvia"},{"full_name":"Bock, Martin","last_name":"Bock","first_name":"Martin"},{"first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens"},{"last_name":"Salbreux","full_name":"Salbreux, Guillaume","first_name":"Guillaume"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"title":"The physical basis of coordinated tissue spreading in zebrafish gastrulation","project":[{"call_identifier":"FP7","_id":"2524F500-B435-11E9-9278-68D0E5697425","name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","grant_number":"201439"}],"year":"2017","has_accepted_license":"1","isi":1,"publication":"Developmental Cell","day":"27","page":"354 - 366","date_created":"2018-12-11T11:49:58Z","date_published":"2017-02-27T00:00:00Z","doi":"10.1016/j.devcel.2017.01.010","oa":1,"quality_controlled":"1","publisher":"Cell Press"},{"publisher":"Genetics Society of America","quality_controlled":"1","oa":1,"day":"01","publication":"Genetics","isi":1,"year":"2017","date_published":"2017-03-01T00:00:00Z","doi":"10.1534/genetics.116.196220","date_created":"2018-12-11T11:50:00Z","page":"1335 - 1351","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Ringbauer H, Coop G, Barton NH. 2017. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 205(3), 1335–1351.","chicago":"Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.196220.","ama":"Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 2017;205(3):1335-1351. doi:10.1534/genetics.116.196220","apa":"Ringbauer, H., Coop, G., & Barton, N. H. (2017). Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.196220","ieee":"H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from isolation by distance of long shared sequence blocks,” Genetics, vol. 205, no. 3. Genetics Society of America, pp. 1335–1351, 2017.","short":"H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351.","mla":"Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics, vol. 205, no. 3, Genetics Society of America, 2017, pp. 1335–51, doi:10.1534/genetics.116.196220."},"title":"Inferring recent demography from isolation by distance of long shared sequence blocks","publist_id":"6307","author":[{"last_name":"Ringbauer","orcid":"0000-0002-4884-9682","full_name":"Ringbauer, Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","first_name":"Harald"},{"full_name":"Coop, Graham","last_name":"Coop","first_name":"Graham"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"external_id":{"isi":["000395807200023"]},"article_processing_charge":"No","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These IBD blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulae for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes. We introduce an inference scheme that uses a composite likelihood approach to fit these formulae. We then extensively evaluate our theory and inference method on a range of scenarios using simulated data. We first validate the diffusion approximation by showing that the theoretical results closely match the simulated block sharing patterns. We then demonstrate that our inference scheme can accurately and robustly infer dispersal rate and effective density, as well as bounds on recent dynamics of population density. To demonstrate an application, we use our estimation scheme to explore the fit of a diffusion model to Eastern European samples in the POPRES data set. We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last centuries, combined with accelerating population growth, can explain the observed exponential decay of block sharing with increasing pairwise sample distance."}],"month":"03","intvolume":" 205","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://www.biorxiv.org/content/early/2016/09/23/076810"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00166731"]},"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","id":"200","status":"public"}]},"volume":205,"issue":"3","ec_funded":1,"_id":"1074","status":"public","type":"journal_article","date_updated":"2023-09-20T12:00:56Z","department":[{"_id":"NiBa"}]},{"article_number":"023403","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, C. Keitel, Physical Review A - Atomic, Molecular, and Optical Physics 95 (2017).","ieee":"M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, and C. Keitel, “Strong-field ionization via a high-order Coulomb-corrected strong-field approximation,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 95, no. 2. American Physical Society, 2017.","apa":"Klaiber, M., Daněk, J., Yakaboylu, E., Hatsagortsyan, K., & Keitel, C. (2017). Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.95.023403","ama":"Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. Physical Review A - Atomic, Molecular, and Optical Physics. 2017;95(2). doi:10.1103/PhysRevA.95.023403","mla":"Klaiber, Michael, et al. “Strong-Field Ionization via a High-Order Coulomb-Corrected Strong-Field Approximation.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 95, no. 2, 023403, American Physical Society, 2017, doi:10.1103/PhysRevA.95.023403.","ista":"Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. 2017. Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. Physical Review A - Atomic, Molecular, and Optical Physics. 95(2), 023403.","chicago":"Klaiber, Michael, Jiří Daněk, Enderalp Yakaboylu, Karen Hatsagortsyan, and Christoph Keitel. “Strong-Field Ionization via a High-Order Coulomb-Corrected Strong-Field Approximation.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevA.95.023403."},"title":"Strong-field ionization via a high-order Coulomb-corrected strong-field approximation","author":[{"last_name":"Klaiber","full_name":"Klaiber, Michael","first_name":"Michael"},{"last_name":"Daněk","full_name":"Daněk, Jiří","first_name":"Jiří"},{"orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp","last_name":"Yakaboylu","first_name":"Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hatsagortsyan, Karen","last_name":"Hatsagortsyan","first_name":"Karen"},{"first_name":"Christoph","last_name":"Keitel","full_name":"Keitel, Christoph"}],"publist_id":"6305","article_processing_charge":"No","external_id":{"isi":["000400571700011"]},"publisher":"American Physical Society","quality_controlled":"1","oa":1,"day":"01","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","isi":1,"year":"2017","date_published":"2017-02-01T00:00:00Z","doi":"10.1103/PhysRevA.95.023403","date_created":"2018-12-11T11:50:01Z","_id":"1076","status":"public","type":"journal_article","date_updated":"2023-09-20T11:57:23Z","department":[{"_id":"MiLe"}],"oa_version":"Submitted Version","abstract":[{"text":"Signatures of the Coulomb corrections in the photoelectron momentum distribution during laser-induced ionization of atoms or ions in tunneling and multiphoton regimes are investigated analytically in the case of a one-dimensional problem. A high-order Coulomb-corrected strong-field approximation is applied, where the exact continuum state in the S matrix is approximated by the eikonal Coulomb-Volkov state including the second-order corrections to the eikonal. Although without high-order corrections our theory coincides with the known analytical R-matrix (ARM) theory, we propose a simplified procedure for the matrix element derivation. Rather than matching the eikonal Coulomb-Volkov wave function with the bound state as in the ARM theory to remove the Coulomb singularity, we calculate the matrix element via the saddle-point integration method by time as well as by coordinate, and in this way avoiding the Coulomb singularity. The momentum shift in the photoelectron momentum distribution with respect to the ARM theory due to high-order corrections is analyzed for tunneling and multiphoton regimes. The relation of the quantum corrections to the tunneling delay time is discussed.","lang":"eng"}],"month":"02","intvolume":" 95","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1609.07018"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["24699926"]},"publication_status":"published","volume":95,"issue":"2","ec_funded":1},{"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":369,"issue":"5","oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"intvolume":" 369","month":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1312.1231"}],"scopus_import":"1","date_updated":"2023-09-20T12:05:56Z","department":[{"_id":"HeEd"}],"_id":"1072","status":"public","article_type":"original","type":"journal_article","publication":"Transactions of the American Mathematical Society","day":"01","year":"2017","isi":1,"date_created":"2018-12-11T11:49:59Z","doi":"10.1090/tran/6991","date_published":"2017-05-01T00:00:00Z","page":"3741 - 3762","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”.","oa":1,"publisher":"American Mathematical Society","quality_controlled":"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.","short":"U. Bauer, H. Edelsbrunner, Transactions of the American Mathematical Society 369 (2017) 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.","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","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","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.","ista":"Bauer U, Edelsbrunner H. 2017. The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. 369(5), 3741–3762."},"title":"The Morse theory of Čech and delaunay complexes","external_id":{"isi":["000398030400024"],"arxiv":["1312.1231"]},"article_processing_charge":"No","author":[{"first_name":"Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","full_name":"Bauer, Ulrich","orcid":"0000-0002-9683-0724","last_name":"Bauer"},{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6311","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"318493","name":"Topological Complex Systems"}]},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["01795376"]},"volume":54,"issue":"4","oa_version":"Submitted Version","abstract":[{"text":"Let X and Y be finite simplicial sets (e.g. finite simplicial complexes), both equipped with a free simplicial action of a finite group G. Assuming that Y is d-connected and dimX≤2d, for some d≥1, we provide an algorithm that computes the set of all equivariant homotopy classes of equivariant continuous maps |X|→|Y|; the existence of such a map can be decided even for dimX≤2d+1. This yields the first algorithm for deciding topological embeddability of a k-dimensional finite simplicial complex into Rn under the condition k≤23n−1. More generally, we present an algorithm that, given a lifting-extension problem satisfying an appropriate stability assumption, computes the set of all homotopy classes of solutions. This result is new even in the non-equivariant situation.","lang":"eng"}],"intvolume":" 54","month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1307.6444"}],"scopus_import":"1","date_updated":"2023-09-20T12:01:28Z","department":[{"_id":"UlWa"}],"_id":"1073","status":"public","type":"journal_article","publication":"Discrete & Computational Geometry","day":"01","year":"2017","isi":1,"date_created":"2018-12-11T11:50:00Z","doi":"10.1007/s00454-016-9855-6","date_published":"2017-06-01T00:00:00Z","page":"915 - 965","oa":1,"publisher":"Springer","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"M. Čadek, M. Krcál, and L. Vokřínek, “Algorithmic solvability of the lifting extension problem,” Discrete & Computational Geometry, vol. 54, no. 4. Springer, pp. 915–965, 2017.","short":"M. Čadek, M. Krcál, L. Vokřínek, Discrete & Computational Geometry 54 (2017) 915–965.","ama":"Čadek M, Krcál M, Vokřínek L. Algorithmic solvability of the lifting extension problem. Discrete & Computational Geometry. 2017;54(4):915-965. doi:10.1007/s00454-016-9855-6","apa":"Čadek, M., Krcál, M., & Vokřínek, L. (2017). Algorithmic solvability of the lifting extension problem. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-016-9855-6","mla":"Čadek, Martin, et al. “Algorithmic Solvability of the Lifting Extension Problem.” Discrete & Computational Geometry, vol. 54, no. 4, Springer, 2017, pp. 915–65, doi:10.1007/s00454-016-9855-6.","ista":"Čadek M, Krcál M, Vokřínek L. 2017. Algorithmic solvability of the lifting extension problem. Discrete & Computational Geometry. 54(4), 915–965.","chicago":"Čadek, Martin, Marek Krcál, and Lukáš Vokřínek. “Algorithmic Solvability of the Lifting Extension Problem.” Discrete & Computational Geometry. Springer, 2017. https://doi.org/10.1007/s00454-016-9855-6."},"title":"Algorithmic solvability of the lifting extension problem","article_processing_charge":"No","external_id":{"isi":["000400072700008"]},"author":[{"first_name":"Martin","last_name":"Čadek","full_name":"Čadek, Martin"},{"first_name":"Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87","last_name":"Krcál","full_name":"Krcál, Marek"},{"full_name":"Vokřínek, Lukáš","last_name":"Vokřínek","first_name":"Lukáš"}],"publist_id":"6309"},{"isi":1,"has_accepted_license":"1","year":"2017","day":"23","publication":"Microbial Cell Factories","doi":"10.1186/s12934-017-0645-5","date_published":"2017-02-23T00:00:00Z","date_created":"2018-12-11T11:49:56Z","publisher":"BioMed Central","quality_controlled":"1","oa":1,"citation":{"ista":"Veetil V, Angermayr A, Hellingwerf K. 2017. Ethylene production with engineered Synechocystis sp PCC 6803 strains. Microbial Cell Factories. 16(1), 34.","chicago":"Veetil, Vinod, Andreas Angermayr, and Klaas Hellingwerf. “Ethylene Production with Engineered Synechocystis Sp PCC 6803 Strains.” Microbial Cell Factories. BioMed Central, 2017. https://doi.org/10.1186/s12934-017-0645-5.","ieee":"V. Veetil, A. Angermayr, and K. Hellingwerf, “Ethylene production with engineered Synechocystis sp PCC 6803 strains,” Microbial Cell Factories, vol. 16, no. 1. BioMed Central, 2017.","short":"V. Veetil, A. Angermayr, K. Hellingwerf, Microbial Cell Factories 16 (2017).","apa":"Veetil, V., Angermayr, A., & Hellingwerf, K. (2017). Ethylene production with engineered Synechocystis sp PCC 6803 strains. Microbial Cell Factories. BioMed Central. https://doi.org/10.1186/s12934-017-0645-5","ama":"Veetil V, Angermayr A, Hellingwerf K. Ethylene production with engineered Synechocystis sp PCC 6803 strains. Microbial Cell Factories. 2017;16(1). doi:10.1186/s12934-017-0645-5","mla":"Veetil, Vinod, et al. “Ethylene Production with Engineered Synechocystis Sp PCC 6803 Strains.” Microbial Cell Factories, vol. 16, no. 1, 34, BioMed Central, 2017, doi:10.1186/s12934-017-0645-5."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Veetil, Vinod","last_name":"Veetil","first_name":"Vinod"},{"first_name":"Andreas","id":"4677C796-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8619-2223","full_name":"Angermayr, Andreas","last_name":"Angermayr"},{"full_name":"Hellingwerf, Klaas","last_name":"Hellingwerf","first_name":"Klaas"}],"publist_id":"6325","article_processing_charge":"No","external_id":{"isi":["000397733000001"],"pmid":["28231787"]},"title":"Ethylene production with engineered Synechocystis sp PCC 6803 strains","article_number":"34","publication_identifier":{"issn":["14752859"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5240","file_size":1361313,"date_updated":"2018-12-12T10:16:50Z","creator":"system","file_name":"IST-2017-792-v1+1_s12934-017-0645-5.pdf","date_created":"2018-12-12T10:16:50Z"}],"language":[{"iso":"eng"}],"volume":16,"issue":"1","abstract":[{"text":"Background: Metabolic engineering and synthetic biology of cyanobacteria offer a promising sustainable alternative approach for fossil-based ethylene production, by using sunlight via oxygenic photosynthesis, to convert carbon dioxide directly into ethylene. Towards this, both well-studied cyanobacteria, i.e., Synechocystis sp PCC 6803 and Synechococcus elongatus PCC 7942, have been engineered to produce ethylene by introducing the ethylene-forming enzyme (Efe) from Pseudomonas syringae pv. phaseolicola PK2 (the Kudzu strain), which catalyzes the conversion of the ubiquitous tricarboxylic acid cycle intermediate 2-oxoglutarate into ethylene. Results: This study focuses on Synechocystis sp PCC 6803 and shows stable ethylene production through the integration of a codon-optimized version of the efe gene under control of the Ptrc promoter and the core Shine-Dalgarno sequence (5\\'-AGGAGG-3\\') as the ribosome-binding site (RBS), at the slr0168 neutral site. We have increased ethylene production twofold by RBS screening and further investigated improving ethylene production from a single gene copy of efe, using multiple tandem promoters and by putting our best construct on an RSF1010-based broad-host-self-replicating plasmid, which has a higher copy number than the genome. Moreover, to raise the intracellular amounts of the key Efe substrate, 2-oxoglutarate, from which ethylene is formed, we constructed a glycogen-synthesis knockout mutant (glgC) and introduced the ethylene biosynthetic pathway in it. Under nitrogen limiting conditions, the glycogen knockout strain has increased intracellular 2-oxoglutarate levels; however, surprisingly, ethylene production was lower in this strain than in the wild-type background. Conclusion: Making use of different RBS sequences, production of ethylene ranging over a 20-fold difference has been achieved. However, a further increase of production through multiple tandem promoters and a broad-host plasmid was not achieved speculating that the transcription strength and the gene copy number are not the limiting factors in our system.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"02","intvolume":" 16","date_updated":"2023-09-20T12:09:21Z","extern":"1","ddc":["579"],"file_date_updated":"2018-12-12T10:16:50Z","_id":"1061","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"792"},{"month":"06","intvolume":" 122","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We consider the problem of reachability in pushdown graphs. We study the problem for pushdown graphs with constant treewidth. Even for pushdown graphs with treewidth 1, for the reachability problem we establish the following: (i) the problem is PTIME-complete, and (ii) any subcubic algorithm for the problem would contradict the k-clique conjecture and imply faster combinatorial algorithms for cliques in graphs."}],"volume":122,"ec_funded":1,"file":[{"file_id":"4998","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:13:17Z","file_name":"IST-2018-991-v1+2_2018_Chatterjee_Pushdown_PREPRINT.pdf","date_updated":"2019-10-15T07:44:51Z","file_size":247657,"creator":"system"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00200190"]},"publication_status":"published","status":"public","pubrep_id":"991","type":"journal_article","_id":"1065","department":[{"_id":"KrCh"},{"_id":"HeEd"}],"file_date_updated":"2019-10-15T07:44:51Z","ddc":["000"],"date_updated":"2023-09-20T12:08:18Z","publisher":"Elsevier","quality_controlled":"1","oa":1,"doi":"10.1016/j.ipl.2017.02.003","date_published":"2017-06-01T00:00:00Z","date_created":"2018-12-11T11:49:57Z","page":"25 - 29","day":"01","publication":"Information Processing Letters","has_accepted_license":"1","isi":1,"year":"2017","project":[{"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"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"title":"Pushdown reachability with constant treewidth","publist_id":"6323","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0002-8882-5116","full_name":"Osang, Georg F","last_name":"Osang","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F"}],"external_id":{"isi":["000399506600005"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Chatterjee, Krishnendu, and Georg F Osang. “Pushdown Reachability with Constant Treewidth.” Information Processing Letters. Elsevier, 2017. https://doi.org/10.1016/j.ipl.2017.02.003.","ista":"Chatterjee K, Osang GF. 2017. Pushdown reachability with constant treewidth. Information Processing Letters. 122, 25–29.","mla":"Chatterjee, Krishnendu, and Georg F. Osang. “Pushdown Reachability with Constant Treewidth.” Information Processing Letters, vol. 122, Elsevier, 2017, pp. 25–29, doi:10.1016/j.ipl.2017.02.003.","short":"K. Chatterjee, G.F. Osang, Information Processing Letters 122 (2017) 25–29.","ieee":"K. Chatterjee and G. F. Osang, “Pushdown reachability with constant treewidth,” Information Processing Letters, vol. 122. Elsevier, pp. 25–29, 2017.","apa":"Chatterjee, K., & Osang, G. F. (2017). Pushdown reachability with constant treewidth. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2017.02.003","ama":"Chatterjee K, Osang GF. Pushdown reachability with constant treewidth. Information Processing Letters. 2017;122:25-29. doi:10.1016/j.ipl.2017.02.003"}},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","extern":"1","citation":{"ista":"Guarina L, Vandael DH, Carabelli V, Carbone E. 2017. Low pH inf o boosts burst firing and catecholamine release by blocking TASK-1 and BK channels while preserving Cav1 channels in mouse chromaffin cells. Journal of Physiology. 595(8), 2587–2609.","chicago":"Guarina, Laura, David H Vandael, Valentina Carabelli, and Emilio Carbone. “Low PH Inf o Boosts Burst Firing and Catecholamine Release by Blocking TASK-1 and BK Channels While Preserving Cav1 Channels in Mouse Chromaffin Cells.” Journal of Physiology. Wiley-Blackwell, 2017. https://doi.org/10.1113/JP273735.","apa":"Guarina, L., Vandael, D. H., Carabelli, V., & Carbone, E. (2017). Low pH inf o boosts burst firing and catecholamine release by blocking TASK-1 and BK channels while preserving Cav1 channels in mouse chromaffin cells. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/JP273735","ama":"Guarina L, Vandael DH, Carabelli V, Carbone E. Low pH inf o boosts burst firing and catecholamine release by blocking TASK-1 and BK channels while preserving Cav1 channels in mouse chromaffin cells. Journal of Physiology. 2017;595(8):2587-2609. doi:10.1113/JP273735","ieee":"L. Guarina, D. H. Vandael, V. Carabelli, and E. Carbone, “Low pH inf o boosts burst firing and catecholamine release by blocking TASK-1 and BK channels while preserving Cav1 channels in mouse chromaffin cells,” Journal of Physiology, vol. 595, no. 8. Wiley-Blackwell, pp. 2587–2609, 2017.","short":"L. Guarina, D.H. Vandael, V. Carabelli, E. Carbone, Journal of Physiology 595 (2017) 2587–2609.","mla":"Guarina, Laura, et al. “Low PH Inf o Boosts Burst Firing and Catecholamine Release by Blocking TASK-1 and BK Channels While Preserving Cav1 Channels in Mouse Chromaffin Cells.” Journal of Physiology, vol. 595, no. 8, Wiley-Blackwell, 2017, pp. 2587–609, doi:10.1113/JP273735."},"date_updated":"2023-09-20T12:09:47Z","title":"Low pH inf o boosts burst firing and catecholamine release by blocking TASK-1 and BK channels while preserving Cav1 channels in mouse chromaffin cells","external_id":{"isi":["000399430300022"]},"article_processing_charge":"No","author":[{"first_name":"Laura","last_name":"Guarina","full_name":"Guarina, Laura"},{"first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","last_name":"Vandael"},{"first_name":"Valentina","last_name":"Carabelli","full_name":"Carabelli, Valentina"},{"last_name":"Carbone","full_name":"Carbone, Emilio","first_name":"Emilio"}],"publist_id":"6326","_id":"1062","status":"public","type":"journal_article","publication":"Journal of Physiology","language":[{"iso":"eng"}],"day":"15","publication_status":"published","year":"2017","isi":1,"date_created":"2018-12-11T11:49:56Z","date_published":"2017-04-15T00:00:00Z","volume":595,"doi":"10.1113/JP273735","issue":"8","page":"2587 - 2609 ","oa_version":"None","abstract":[{"lang":"eng","text":"Mouse chromaffin cells (MCCs) generate action potential (AP) firing that regulates the Ca2+‐dependent release of catecholamines (CAs). Recent findings indicate that MCCs possess a variety of spontaneous firing modes that span from the common ‘tonic‐irregular’ to the less frequent ‘burst’ firing. This latter is evident in a small fraction of MCCs but occurs regularly when Nav1.3/1.7 channels are made less available or when the Slo1β2‐subunit responsible for BK channel inactivation is deleted. Burst firing causes large increases of Ca2+‐entry and potentiates CA release by ∼3.5‐fold and thus may be a key mechanism for regulating MCC function. With the aim to uncover a physiological role for burst‐firing we investigated the effects of acidosis on MCC activity. Lowering the extracellular pH (pHo) from 7.4 to 7.0 and 6.6 induces cell depolarizations of 10–15 mV that generate repeated bursts. Bursts at pHo 6.6 lasted ∼330 ms, occurred at 1–2 Hz and caused an ∼7‐fold increase of CA cumulative release. Burst firing originates from the inhibition of the pH‐sensitive TASK‐1/TASK‐3 channels and from a 40% BK channel conductance reduction at pHo 7.0. The same pHo had little or no effect on Nav, Cav, Kv and SK channels that support AP firing in MCCs. Burst firing of pHo 6.6 could be mimicked by mixtures of the TASK‐1 blocker A1899 (300 nm) and BK blocker paxilline (300 nm) and could be prevented by blocking L‐type channels by adding 3 μm nifedipine. Mixtures of the two blockers raised cumulative CA‐secretion even more than low pHo (∼12‐fold), showing that the action of protons on vesicle release is mainly a result of the ionic conductance changes that increase Ca2+‐entry during bursts. Our data provide direct evidence suggesting that MCCs respond to low pHo with sustained depolarization, burst firing and enhanced CA‐secretion, thus mimicking the physiological response of CCs to acute acidosis and hyperkalaemia generated during heavy exercise and muscle fatigue."}],"intvolume":" 595","month":"04","quality_controlled":"1","publisher":"Wiley-Blackwell"},{"title":"Evolutionary rescue in randomly mating, selfing, and clonal populations","external_id":{"isi":["000398545200003"]},"article_processing_charge":"No","publist_id":"6327","author":[{"first_name":"Hildegard","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9435-2813","full_name":"Uecker, Hildegard","last_name":"Uecker"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution, vol. 71, no. 4, Wiley-Blackwell, 2017, pp. 845–58, doi:10.1111/evo.13191.","ieee":"H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,” Evolution, vol. 71, no. 4. Wiley-Blackwell, pp. 845–858, 2017.","short":"H. Uecker, Evolution 71 (2017) 845–858.","apa":"Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13191","ama":"Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 2017;71(4):845-858. doi:10.1111/evo.13191","chicago":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13191.","ista":"Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 71(4), 845–858."},"project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"date_created":"2018-12-11T11:49:57Z","date_published":"2017-04-01T00:00:00Z","doi":"10.1111/evo.13191","page":"845 - 858","publication":"Evolution","day":"01","year":"2017","isi":1,"oa":1,"quality_controlled":"1","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"date_updated":"2023-09-20T12:10:32Z","status":"public","type":"journal_article","_id":"1063","ec_funded":1,"issue":"4","volume":71,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00143820"]},"intvolume":" 71","month":"04","main_file_link":[{"open_access":"1","url":"http://biorxiv.org/content/early/2016/10/14/081042"}],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"Severe environmental change can drive a population extinct unless the population adapts in time to the new conditions (“evolutionary rescue”). How does biparental sexual reproduction influence the chances of population persistence compared to clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele model for adaptation in diploid species, where rescue is contingent on the establishment of the mutant homozygote. Reproduction can occur by random mating, selfing, or clonally. Random mating generates and destroys the rescue mutant; selfing is efficient at generating it but at the same time depletes the heterozygote, which can lead to a low mutant frequency in the standing genetic variation. Due to these (and other) antagonistic effects, we find a nontrivial dependence of population survival on the rate of sex/selfing, which is strongly influenced by the dominance coefficient of the mutation before and after the environmental change. Importantly, since mating with the wild‐type breaks the mutant homozygote up, a slow decay of the wild‐type population size can impede rescue in randomly mating populations.","lang":"eng"}]},{"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"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"title":"Quantitative fair simulation games","publist_id":"6322","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"full_name":"Otop, Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"last_name":"Velner","full_name":"Velner, Yaron","first_name":"Yaron"}],"external_id":{"isi":["000402025600002"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Chatterjee K, Henzinger TA, Otop J, Velner Y. 2017. Quantitative fair simulation games. Information and Computation. 254(2), 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.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Information and Computation 254 (2017) 143–166.","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","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."},"publisher":"Elsevier","quality_controlled":"1","date_published":"2017-06-01T00:00:00Z","doi":"10.1016/j.ic.2016.10.006","date_created":"2018-12-11T11:49:58Z","page":"143 - 166","day":"01","publication":"Information and Computation","isi":1,"year":"2017","status":"public","type":"journal_article","_id":"1066","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2023-09-20T12:07:48Z","month":"06","intvolume":" 254","scopus_import":"1","oa_version":"None","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"}],"related_material":{"record":[{"status":"public","id":"5428","relation":"earlier_version"}]},"volume":254,"issue":"2","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published"},{"volume":22,"publication_identifier":{"issn":["10836489"]},"publication_status":"published","file":[{"date_updated":"2018-12-12T10:15:29Z","file_size":742275,"creator":"system","date_created":"2018-12-12T10:15:29Z","file_name":"IST-2017-802-v1+1_euclid.ejp.1487991681.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5149"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"02","intvolume":" 22","abstract":[{"text":"We consider products of independent square non-Hermitian random matrices. More precisely, let X1,…, Xn be independent N × N random matrices with independent entries (real or complex with independent real and imaginary parts) with zero mean and variance 1/N. Soshnikov-O’Rourke [19] and Götze-Tikhomirov [15] showed that the empirical spectral distribution of the product of n random matrices with iid entries converges to (equation found). We prove that if the entries of the matrices X1,…, Xn are independent (but not necessarily identically distributed) and satisfy uniform subexponential decay condition, then in the bulk the convergence of the ESD of X1,…, Xn to (0.1) holds up to the scale N–1/2+ε.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"LaEr"}],"file_date_updated":"2018-12-12T10:15:29Z","date_updated":"2023-09-22T09:27:51Z","ddc":["510"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"802","_id":"1023","doi":"10.1214/17-EJP38","date_published":"2017-02-06T00:00:00Z","date_created":"2018-12-11T11:49:44Z","isi":1,"has_accepted_license":"1","year":"2017","day":"06","publication":"Electronic Journal of Probability","quality_controlled":"1","publisher":"Institute of Mathematical Statistics","oa":1,"publist_id":"6370","author":[{"orcid":"0000-0002-7327-856X","full_name":"Nemish, Yuriy","last_name":"Nemish","first_name":"Yuriy","id":"4D902E6A-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000396611900022"]},"article_processing_charge":"No","title":"Local law for the product of independent non-Hermitian random matrices with independent entries","citation":{"mla":"Nemish, Yuriy. “Local Law for the Product of Independent Non-Hermitian Random Matrices with Independent Entries.” Electronic Journal of Probability, vol. 22, 22, Institute of Mathematical Statistics, 2017, doi:10.1214/17-EJP38.","short":"Y. Nemish, Electronic Journal of Probability 22 (2017).","ieee":"Y. Nemish, “Local law for the product of independent non-Hermitian random matrices with independent entries,” Electronic Journal of Probability, vol. 22. Institute of Mathematical Statistics, 2017.","ama":"Nemish Y. Local law for the product of independent non-Hermitian random matrices with independent entries. Electronic Journal of Probability. 2017;22. doi:10.1214/17-EJP38","apa":"Nemish, Y. (2017). Local law for the product of independent non-Hermitian random matrices with independent entries. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/17-EJP38","chicago":"Nemish, Yuriy. “Local Law for the Product of Independent Non-Hermitian Random Matrices with Independent Entries.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/17-EJP38.","ista":"Nemish Y. 2017. Local law for the product of independent non-Hermitian random matrices with independent entries. Electronic Journal of Probability. 22, 22."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"22"},{"page":"4281 - 4310","doi":"10.1093/mnras/stw2862","date_published":"2017-01-01T00:00:00Z","date_created":"2018-12-11T11:49:44Z","isi":1,"year":"2017","day":"01","publication":"Monthly Notices of the Royal Astronomical Society","quality_controlled":"1","publisher":"Oxford University Press","oa":1,"acknowledgement":"Part of this work has been supported by the 7th Framework Programme for Research of the European Commission, under FETOpen grant number 255827 (CGL Computational Geometry Learning) and ERC advanced grant, URSAT (Understanding Random Systems via Algebraic Topology) number 320422.","author":[{"last_name":"Pranav","full_name":"Pranav, Pratyush","first_name":"Pratyush"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"full_name":"Van De Weygaert, Rien","last_name":"Van De Weygaert","first_name":"Rien"},{"first_name":"Gert","last_name":"Vegter","full_name":"Vegter, Gert"},{"first_name":"Michael","last_name":"Kerber","full_name":"Kerber, Michael"},{"first_name":"Bernard","last_name":"Jones","full_name":"Jones, Bernard"},{"id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","first_name":"Mathijs","orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken"}],"publist_id":"6373","external_id":{"isi":["000395170200039"]},"article_processing_charge":"No","title":"The topology of the cosmic web in terms of persistent Betti numbers","citation":{"chicago":"Pranav, Pratyush, Herbert Edelsbrunner, Rien Van De Weygaert, Gert Vegter, Michael Kerber, Bernard Jones, and Mathijs Wintraecken. “The Topology of the Cosmic Web in Terms of Persistent Betti Numbers.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stw2862.","ista":"Pranav P, Edelsbrunner H, Van De Weygaert R, Vegter G, Kerber M, Jones B, Wintraecken M. 2017. The topology of the cosmic web in terms of persistent Betti numbers. Monthly Notices of the Royal Astronomical Society. 465(4), 4281–4310.","mla":"Pranav, Pratyush, et al. “The Topology of the Cosmic Web in Terms of Persistent Betti Numbers.” Monthly Notices of the Royal Astronomical Society, vol. 465, no. 4, Oxford University Press, 2017, pp. 4281–310, doi:10.1093/mnras/stw2862.","apa":"Pranav, P., Edelsbrunner, H., Van De Weygaert, R., Vegter, G., Kerber, M., Jones, B., & Wintraecken, M. (2017). The topology of the cosmic web in terms of persistent Betti numbers. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stw2862","ama":"Pranav P, Edelsbrunner H, Van De Weygaert R, et al. The topology of the cosmic web in terms of persistent Betti numbers. Monthly Notices of the Royal Astronomical Society. 2017;465(4):4281-4310. doi:10.1093/mnras/stw2862","short":"P. Pranav, H. Edelsbrunner, R. Van De Weygaert, G. Vegter, M. Kerber, B. Jones, M. Wintraecken, Monthly Notices of the Royal Astronomical Society 465 (2017) 4281–4310.","ieee":"P. Pranav et al., “The topology of the cosmic web in terms of persistent Betti numbers,” Monthly Notices of the Royal Astronomical Society, vol. 465, no. 4. Oxford University Press, pp. 4281–4310, 2017."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":465,"issue":"4","publication_identifier":{"issn":["00358711"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1608.04519","open_access":"1"}],"month":"01","intvolume":" 465","abstract":[{"text":"We introduce a multiscale topological description of the Megaparsec web-like cosmic matter distribution. Betti numbers and topological persistence offer a powerful means of describing the rich connectivity structure of the cosmic web and of its multiscale arrangement of matter and galaxies. Emanating from algebraic topology and Morse theory, Betti numbers and persistence diagrams represent an extension and deepening of the cosmologically familiar topological genus measure and the related geometric Minkowski functionals. In addition to a description of the mathematical background, this study presents the computational procedure for computing Betti numbers and persistence diagrams for density field filtrations. The field may be computed starting from a discrete spatial distribution of galaxies or simulation particles. The main emphasis of this study concerns an extensive and systematic exploration of the imprint of different web-like morphologies and different levels of multiscale clustering in the corresponding computed Betti numbers and persistence diagrams. To this end, we use Voronoi clustering models as templates for a rich variety of web-like configurations and the fractal-like Soneira-Peebles models exemplify a range of multiscale configurations. We have identified the clear imprint of cluster nodes, filaments, walls, and voids in persistence diagrams, along with that of the nested hierarchy of structures in multiscale point distributions. We conclude by outlining the potential of persistent topology for understanding the connectivity structure of the cosmic web, in large simulations of cosmic structure formation and in the challenging context of the observed galaxy distribution in large galaxy surveys.","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"HeEd"}],"date_updated":"2023-09-22T09:40:55Z","type":"journal_article","status":"public","_id":"1022"},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["09581669"]},"publication_status":"published","volume":48,"ec_funded":1,"oa_version":"None","abstract":[{"text":"The optogenetic revolution enabled spatially-precise and temporally-precise control over protein function, signaling pathway activation, and animal behavior with tremendous success in the dissection of signaling networks and neural circuits. Very recently, optogenetic methods have been paired with optical reporters in novel drug screening platforms. In these all-optical platforms, light remotely activated ion channels and kinases thereby obviating the use of electrophysiology or reagents. Consequences were remarkable operational simplicity, throughput, and cost-effectiveness that culminated in the identification of new drug candidates. These blueprints for all-optical assays also revealed potential pitfalls and inspire all-optical variants of other screens, such as those that aim at better understanding dynamic drug action or orphan protein function.","lang":"eng"}],"month":"12","intvolume":" 48","scopus_import":"1","date_updated":"2023-09-22T09:26:06Z","department":[{"_id":"HaJa"}],"_id":"1026","status":"public","article_type":"original","type":"journal_article","day":"01","publication":"Current Opinion in Biotechnology","isi":1,"year":"2017","doi":"10.1016/j.copbio.2017.02.006","date_published":"2017-12-01T00:00:00Z","date_created":"2018-12-11T11:49:45Z","page":"8 - 14","acknowledgement":"This work was supported by grants of the European Union Seventh Framework Programme (CIG-303564), the Human Frontier Science Program (RGY0084_2012), and the Austrian Science Fund FWF (W1232 MolecularDrugTargets).","publisher":"Elsevier","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Agus V, Janovjak HL. Optogenetic methods in drug screening: Technologies and applications. Current Opinion in Biotechnology. 2017;48:8-14. doi:10.1016/j.copbio.2017.02.006","apa":"Agus, V., & Janovjak, H. L. (2017). Optogenetic methods in drug screening: Technologies and applications. Current Opinion in Biotechnology. Elsevier. https://doi.org/10.1016/j.copbio.2017.02.006","ieee":"V. Agus and H. L. Janovjak, “Optogenetic methods in drug screening: Technologies and applications,” Current Opinion in Biotechnology, vol. 48. Elsevier, pp. 8–14, 2017.","short":"V. Agus, H.L. Janovjak, Current Opinion in Biotechnology 48 (2017) 8–14.","mla":"Agus, Viviana, and Harald L. Janovjak. “Optogenetic Methods in Drug Screening: Technologies and Applications.” Current Opinion in Biotechnology, vol. 48, Elsevier, 2017, pp. 8–14, doi:10.1016/j.copbio.2017.02.006.","ista":"Agus V, Janovjak HL. 2017. Optogenetic methods in drug screening: Technologies and applications. Current Opinion in Biotechnology. 48, 8–14.","chicago":"Agus, Viviana, and Harald L Janovjak. “Optogenetic Methods in Drug Screening: Technologies and Applications.” Current Opinion in Biotechnology. Elsevier, 2017. https://doi.org/10.1016/j.copbio.2017.02.006."},"title":"Optogenetic methods in drug screening: Technologies and applications","publist_id":"6365","author":[{"first_name":"Viviana","full_name":"Agus, Viviana","last_name":"Agus"},{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak"}],"article_processing_charge":"No","external_id":{"isi":["000418313200003"]},"project":[{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)"},{"call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"255A6082-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}]},{"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1702.01415","open_access":"1"}],"month":"03","intvolume":" 9","abstract":[{"text":"Cellulose is the most abundant biopolymer on Earth. Cellulose fibers, such as the one extracted form cotton or woodpulp, have been used by humankind for hundreds of years to make textiles and paper. Here we show how, by engineering light-matter interaction, we can optimize light scattering using exclusively cellulose nanocrystals. The produced material is sustainable, biocompatible, and when compared to ordinary microfiber-based paper, it shows enhanced scattering strength (×4), yielding a transport mean free path as low as 3.5 μm in the visible light range. The experimental results are in a good agreement with the theoretical predictions obtained with a diffusive model for light propagation.","lang":"eng"}],"oa_version":"Submitted Version","issue":"9","volume":9,"publication_identifier":{"issn":["19448244"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1020","department":[{"_id":"JoFi"}],"date_updated":"2023-09-22T09:40:14Z","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"acknowledgement":"This research was funded by the EPSRC (EP/M027961/1), the Leverhulme Trust (RPG-2014-238), Royal Society (RG140457), the BBSRC David Phillips fellowship (BB/K014617/1), and the European Research Council (ERC-2014-STG H2020 639088). All data created during this research are provided in full in the results section and Supporting Information. They are openly available from figshare and can be accessed at ref 30.","page":"7885 - 7890","date_published":"2017-03-08T00:00:00Z","doi":"10.1021/acsami.6b15986","date_created":"2018-12-11T11:49:44Z","isi":1,"year":"2017","day":"08","publication":"ACS Applied Materials and Interfaces","author":[{"last_name":"Caixeiro","full_name":"Caixeiro, Soraya","first_name":"Soraya"},{"full_name":"Peruzzo, Matilda","orcid":"0000-0002-3415-4628","last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda"},{"first_name":"Olimpia","full_name":"Onelli, Olimpia","last_name":"Onelli"},{"first_name":"Silvia","last_name":"Vignolini","full_name":"Vignolini, Silvia"},{"first_name":"Riccardo","last_name":"Sapienza","full_name":"Sapienza, Riccardo"}],"publist_id":"6372","external_id":{"isi":["000396186000002"]},"article_processing_charge":"No","title":"Disordered cellulose based nanostructures for enhanced light scattering","citation":{"chicago":"Caixeiro, Soraya, Matilda Peruzzo, Olimpia Onelli, Silvia Vignolini, and Riccardo Sapienza. “Disordered Cellulose Based Nanostructures for Enhanced Light Scattering.” ACS Applied Materials and Interfaces. American Chemical Society, 2017. https://doi.org/10.1021/acsami.6b15986.","ista":"Caixeiro S, Peruzzo M, Onelli O, Vignolini S, Sapienza R. 2017. Disordered cellulose based nanostructures for enhanced light scattering. ACS Applied Materials and Interfaces. 9(9), 7885–7890.","mla":"Caixeiro, Soraya, et al. “Disordered Cellulose Based Nanostructures for Enhanced Light Scattering.” ACS Applied Materials and Interfaces, vol. 9, no. 9, American Chemical Society, 2017, pp. 7885–90, doi:10.1021/acsami.6b15986.","ama":"Caixeiro S, Peruzzo M, Onelli O, Vignolini S, Sapienza R. Disordered cellulose based nanostructures for enhanced light scattering. ACS Applied Materials and Interfaces. 2017;9(9):7885-7890. doi:10.1021/acsami.6b15986","apa":"Caixeiro, S., Peruzzo, M., Onelli, O., Vignolini, S., & Sapienza, R. (2017). Disordered cellulose based nanostructures for enhanced light scattering. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.6b15986","ieee":"S. Caixeiro, M. Peruzzo, O. Onelli, S. Vignolini, and R. Sapienza, “Disordered cellulose based nanostructures for enhanced light scattering,” ACS Applied Materials and Interfaces, vol. 9, no. 9. American Chemical Society, pp. 7885–7890, 2017.","short":"S. Caixeiro, M. Peruzzo, O. Onelli, S. Vignolini, R. Sapienza, ACS Applied Materials and Interfaces 9 (2017) 7885–7890."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"day":"25","publication":"Journal of Fluid Mechanics","isi":1,"year":"2017","date_published":"2017-04-25T00:00:00Z","doi":"10.1017/jfm.2017.109","date_created":"2018-12-11T11:49:44Z","page":"21 - 34","project":[{"_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012","name":"Information processing and computation in fish groups"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Lopez Alonso JM, Avila M. 2017. Boundary layer turbulence in experiments on quasi Keplerian flows. Journal of Fluid Mechanics. 817, 21–34.","chicago":"Lopez Alonso, Jose M, and Marc Avila. “Boundary Layer Turbulence in Experiments on Quasi Keplerian Flows.” Journal of Fluid Mechanics. Cambridge University Press, 2017. https://doi.org/10.1017/jfm.2017.109.","apa":"Lopez Alonso, J. M., & Avila, M. (2017). Boundary layer turbulence in experiments on quasi Keplerian flows. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.109","ama":"Lopez Alonso JM, Avila M. Boundary layer turbulence in experiments on quasi Keplerian flows. Journal of Fluid Mechanics. 2017;817:21-34. doi:10.1017/jfm.2017.109","short":"J.M. Lopez Alonso, M. Avila, Journal of Fluid Mechanics 817 (2017) 21–34.","ieee":"J. M. Lopez Alonso and M. Avila, “Boundary layer turbulence in experiments on quasi Keplerian flows,” Journal of Fluid Mechanics, vol. 817. Cambridge University Press, pp. 21–34, 2017.","mla":"Lopez Alonso, Jose M., and Marc Avila. “Boundary Layer Turbulence in Experiments on Quasi Keplerian Flows.” Journal of Fluid Mechanics, vol. 817, Cambridge University Press, 2017, pp. 21–34, doi:10.1017/jfm.2017.109."},"title":"Boundary layer turbulence in experiments on quasi Keplerian flows","publist_id":"6371","author":[{"full_name":"Lopez Alonso, Jose M","orcid":"0000-0002-0384-2022","last_name":"Lopez Alonso","first_name":"Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Avila","full_name":"Avila, Marc","first_name":"Marc"}],"external_id":{"isi":["000398179100006"]},"article_processing_charge":"No","oa_version":"Submitted Version","abstract":[{"text":"Most flows in nature and engineering are turbulent because of their large velocities and spatial scales. Laboratory experiments on rotating quasi-Keplerian flows, for which the angular velocity decreases radially but the angular momentum increases, are however laminar at Reynolds numbers exceeding one million. This is in apparent contradiction to direct numerical simulations showing that in these experiments turbulence transition is triggered by the axial boundaries. We here show numerically that as the Reynolds number increases, turbulence becomes progressively confined to the boundary layers and the flow in the bulk fully relaminarizes. Our findings support that turbulence is unlikely to occur in isothermal constant-density quasi-Keplerian flows.","lang":"eng"}],"month":"04","intvolume":" 817","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.05527"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00221120"]},"publication_status":"published","volume":817,"_id":"1021","status":"public","type":"journal_article","date_updated":"2023-09-22T09:39:46Z","department":[{"_id":"BjHo"}]},{"publist_id":"6367","author":[{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"article_processing_charge":"No","external_id":{"isi":["000395671500025"]},"title":"Cell biology: Stretched divisions","citation":{"chicago":"Heisenberg, Carl-Philipp J. “Cell Biology: Stretched Divisions.” Nature. Nature Publishing Group, 2017. https://doi.org/10.1038/nature21502.","ista":"Heisenberg C-PJ. 2017. Cell biology: Stretched divisions. Nature. 543(7643), 43–44.","mla":"Heisenberg, Carl-Philipp J. “Cell Biology: Stretched Divisions.” Nature, vol. 543, no. 7643, Nature Publishing Group, 2017, pp. 43–44, doi:10.1038/nature21502.","short":"C.-P.J. Heisenberg, Nature 543 (2017) 43–44.","ieee":"C.-P. J. Heisenberg, “Cell biology: Stretched divisions,” Nature, vol. 543, no. 7643. Nature Publishing Group, pp. 43–44, 2017.","apa":"Heisenberg, C.-P. J. (2017). Cell biology: Stretched divisions. Nature. Nature Publishing Group. https://doi.org/10.1038/nature21502","ama":"Heisenberg C-PJ. Cell biology: Stretched divisions. Nature. 2017;543(7643):43-44. doi:10.1038/nature21502"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"43 - 44","date_published":"2017-03-02T00:00:00Z","doi":"10.1038/nature21502","date_created":"2018-12-11T11:49:45Z","isi":1,"year":"2017","day":"02","publication":"Nature","quality_controlled":"1","publisher":"Nature Publishing Group","department":[{"_id":"CaHe"}],"date_updated":"2023-09-22T09:26:59Z","type":"journal_article","status":"public","_id":"1025","volume":543,"issue":"7643","publication_identifier":{"issn":["00280836"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","month":"03","intvolume":" 543","abstract":[{"lang":"eng","text":"Many organ surfaces are covered by a protective epithelial-cell layer. It emerges that such layers are maintained by cell stretching that triggers cell division mediated by the force-sensitive ion-channel protein Piezo1. See Letter p.118"}],"oa_version":"None"},{"oa":1,"quality_controlled":"1","publisher":"Academic Press","page":"58 - 67","date_created":"2018-12-11T11:49:42Z","date_published":"2017-10-01T00:00:00Z","doi":"10.1016/j.mcn.2017.03.002","year":"2017","isi":1,"has_accepted_license":"1","publication":"Molecular and Cellular Neuroscience","day":"01","article_processing_charge":"No","external_id":{"isi":["000415140700007"]},"publist_id":"6377","author":[{"first_name":"Martin","last_name":"Breuss","full_name":"Breuss, Martin"},{"first_name":"Ines","last_name":"Leca","full_name":"Leca, Ines"},{"last_name":"Gstrein","full_name":"Gstrein, Thomas","first_name":"Thomas"},{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H","last_name":"Hansen","full_name":"Hansen, Andi H"},{"first_name":"David","last_name":"Keays","full_name":"Keays, David"}],"title":"Tubulins and brain development: The origins of functional specification","citation":{"mla":"Breuss, Martin, et al. “Tubulins and Brain Development: The Origins of Functional Specification.” Molecular and Cellular Neuroscience, vol. 84, Academic Press, 2017, pp. 58–67, doi:10.1016/j.mcn.2017.03.002.","ama":"Breuss M, Leca I, Gstrein T, Hansen AH, Keays D. Tubulins and brain development: The origins of functional specification. Molecular and Cellular Neuroscience. 2017;84:58-67. doi:10.1016/j.mcn.2017.03.002","apa":"Breuss, M., Leca, I., Gstrein, T., Hansen, A. H., & Keays, D. (2017). Tubulins and brain development: The origins of functional specification. Molecular and Cellular Neuroscience. Academic Press. https://doi.org/10.1016/j.mcn.2017.03.002","ieee":"M. Breuss, I. Leca, T. Gstrein, A. H. Hansen, and D. Keays, “Tubulins and brain development: The origins of functional specification,” Molecular and Cellular Neuroscience, vol. 84. Academic Press, pp. 58–67, 2017.","short":"M. Breuss, I. Leca, T. Gstrein, A.H. Hansen, D. Keays, Molecular and Cellular Neuroscience 84 (2017) 58–67.","chicago":"Breuss, Martin, Ines Leca, Thomas Gstrein, Andi H Hansen, and David Keays. “Tubulins and Brain Development: The Origins of Functional Specification.” Molecular and Cellular Neuroscience. Academic Press, 2017. https://doi.org/10.1016/j.mcn.2017.03.002.","ista":"Breuss M, Leca I, Gstrein T, Hansen AH, Keays D. 2017. Tubulins and brain development: The origins of functional specification. Molecular and Cellular Neuroscience. 84, 58–67."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","intvolume":" 84","month":"10","abstract":[{"text":"The development of the vertebrate central nervous system is reliant on a complex cascade of biological processes that include mitotic division, relocation of migrating neurons, and the extension of dendritic and axonal processes. Each of these cellular events requires the diverse functional repertoire of the microtubule cytoskeleton for the generation of forces, assembly of macromolecular complexes and transport of molecules and organelles. The tubulins are a multi-gene family that encode for the constituents of microtubules, and have been implicated in a spectrum of neurological disorders. Evidence is building that different tubulins tune the functional properties of the microtubule cytoskeleton dependent on the cell type, developmental profile and subcellular localisation. Here we review of the origins of the functional specification of the tubulin gene family in the developing brain at a transcriptional, translational, and post-transcriptional level. We remind the reader that tubulins are not just loading controls for your average Western blot.","lang":"eng"}],"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","volume":84,"publication_status":"published","publication_identifier":{"issn":["10447431"]},"language":[{"iso":"eng"}],"file":[{"file_id":"4742","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-806-v1+2_1-s2.0-S1044743116302500-main_1_.pdf","date_created":"2018-12-12T10:09:19Z","creator":"system","file_size":1436377,"date_updated":"2018-12-12T10:09:19Z"}],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","pubrep_id":"806","status":"public","_id":"1017","file_date_updated":"2018-12-12T10:09:19Z","department":[{"_id":"SiHi"}],"date_updated":"2023-09-22T09:42:15Z","ddc":["571"]},{"oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","year":"2017","isi":1,"has_accepted_license":"1","publication":"Scientific Reports","day":"04","date_created":"2018-12-11T11:49:42Z","doi":"10.1038/srep45702","date_published":"2017-04-04T00:00:00Z","article_number":"45702","citation":{"chicago":"Bighin, Giacomo, and Luca Salasnich. “Vortices and Antivortices in Two-Dimensional Ultracold Fermi Gases.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/srep45702.","ista":"Bighin G, Salasnich L. 2017. Vortices and antivortices in two-dimensional ultracold Fermi gases. Scientific Reports. 7, 45702.","mla":"Bighin, Giacomo, and Luca Salasnich. “Vortices and Antivortices in Two-Dimensional Ultracold Fermi Gases.” Scientific Reports, vol. 7, 45702, Nature Publishing Group, 2017, doi:10.1038/srep45702.","ama":"Bighin G, Salasnich L. Vortices and antivortices in two-dimensional ultracold Fermi gases. Scientific Reports. 2017;7. doi:10.1038/srep45702","apa":"Bighin, G., & Salasnich, L. (2017). Vortices and antivortices in two-dimensional ultracold Fermi gases. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep45702","short":"G. Bighin, L. Salasnich, Scientific Reports 7 (2017).","ieee":"G. Bighin and L. Salasnich, “Vortices and antivortices in two-dimensional ultracold Fermi gases,” Scientific Reports, vol. 7. Nature Publishing Group, 2017."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000398148100001"]},"publist_id":"6380","author":[{"id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo","last_name":"Bighin","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo"},{"full_name":"Salasnich, Luca","last_name":"Salasnich","first_name":"Luca"}],"title":"Vortices and antivortices in two-dimensional ultracold Fermi gases","abstract":[{"lang":"eng","text":"Vortices are commonly observed in the context of classical hydrodynamics: from whirlpools after stirring the coffee in a cup to a violent atmospheric phenomenon such as a tornado, all classical vortices are characterized by an arbitrary circulation value of the local velocity field. On the other hand the appearance of vortices with quantized circulation represents one of the fundamental signatures of macroscopic quantum phenomena. In two-dimensional superfluids quantized vortices play a key role in determining finite-temperature properties, as the superfluid phase and the normal state are separated by a vortex unbinding transition, the Berezinskii-Kosterlitz-Thouless transition. Very recent experiments with two-dimensional superfluid fermions motivate the present work: we present theoretical results based on the renormalization group showing that the universal jump of the superfluid density and the critical temperature crucially depend on the interaction strength, providing a strong benchmark for forthcoming investigations."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 7","month":"04","publication_status":"published","publication_identifier":{"issn":["20452322"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4950","file_size":478289,"date_updated":"2018-12-12T10:12:32Z","creator":"system","file_name":"IST-2017-809-v1+1_srep45702.pdf","date_created":"2018-12-12T10:12:32Z"}],"volume":7,"_id":"1015","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"809","status":"public","date_updated":"2023-09-22T09:43:10Z","ddc":["539"],"file_date_updated":"2018-12-12T10:12:32Z","department":[{"_id":"MiLe"}]},{"title":"Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability","article_processing_charge":"No","external_id":{"isi":["000397066400002"]},"publist_id":"6379","author":[{"first_name":"Martin","full_name":"Breuss, Martin","last_name":"Breuss"},{"first_name":"Thai","last_name":"Nguyen","full_name":"Nguyen, Thai"},{"full_name":"Srivatsan, Anjana","last_name":"Srivatsan","first_name":"Anjana"},{"first_name":"Ines","last_name":"Leca","full_name":"Leca, Ines"},{"full_name":"Tian, Guoling","last_name":"Tian","first_name":"Guoling"},{"full_name":"Fritz, Tanja","last_name":"Fritz","first_name":"Tanja"},{"first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","last_name":"Hansen","full_name":"Hansen, Andi H"},{"first_name":"Damir","last_name":"Musaev","full_name":"Musaev, Damir"},{"first_name":"Jennifer","full_name":"Mcevoy Venneri, Jennifer","last_name":"Mcevoy Venneri"},{"full_name":"Kiely, James","last_name":"Kiely","first_name":"James"},{"first_name":"Rasim","full_name":"Rosti, Rasim","last_name":"Rosti"},{"full_name":"Scott, Eric","last_name":"Scott","first_name":"Eric"},{"last_name":"Tan","full_name":"Tan, Uner","first_name":"Uner"},{"first_name":"Richard","last_name":"Kolodner","full_name":"Kolodner, Richard"},{"first_name":"Nicholas","full_name":"Cowan, Nicholas","last_name":"Cowan"},{"first_name":"David","last_name":"Keays","full_name":"Keays, David"},{"first_name":"Joseph","last_name":"Gleeson","full_name":"Gleeson, Joseph"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Breuss, Martin, et al. “Uner Tan Syndrome Caused by a Homozygous TUBB2B Mutation Affecting Microtubule Stability.” Human Molecular Genetics, vol. 26, no. 2, Oxford University Press, 2017, pp. 258–69, doi:10.1093/hmg/ddw383.","apa":"Breuss, M., Nguyen, T., Srivatsan, A., Leca, I., Tian, G., Fritz, T., … Gleeson, J. (2017). Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability. Human Molecular Genetics. Oxford University Press. https://doi.org/10.1093/hmg/ddw383","ama":"Breuss M, Nguyen T, Srivatsan A, et al. Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability. Human Molecular Genetics. 2017;26(2):258-269. doi:10.1093/hmg/ddw383","ieee":"M. Breuss et al., “Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability,” Human Molecular Genetics, vol. 26, no. 2. Oxford University Press, pp. 258–269, 2017.","short":"M. Breuss, T. Nguyen, A. Srivatsan, I. Leca, G. Tian, T. Fritz, A.H. Hansen, D. Musaev, J. Mcevoy Venneri, J. Kiely, R. Rosti, E. Scott, U. Tan, R. Kolodner, N. Cowan, D. Keays, J. Gleeson, Human Molecular Genetics 26 (2017) 258–269.","chicago":"Breuss, Martin, Thai Nguyen, Anjana Srivatsan, Ines Leca, Guoling Tian, Tanja Fritz, Andi H Hansen, et al. “Uner Tan Syndrome Caused by a Homozygous TUBB2B Mutation Affecting Microtubule Stability.” Human Molecular Genetics. Oxford University Press, 2017. https://doi.org/10.1093/hmg/ddw383.","ista":"Breuss M, Nguyen T, Srivatsan A, Leca I, Tian G, Fritz T, Hansen AH, Musaev D, Mcevoy Venneri J, Kiely J, Rosti R, Scott E, Tan U, Kolodner R, Cowan N, Keays D, Gleeson J. 2017. Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability. Human Molecular Genetics. 26(2), 258–269."},"publisher":"Oxford University Press","quality_controlled":"1","date_created":"2018-12-11T11:49:42Z","doi":"10.1093/hmg/ddw383","date_published":"2017-01-01T00:00:00Z","page":"258 - 269","publication":"Human Molecular Genetics","day":"01","year":"2017","isi":1,"status":"public","type":"journal_article","_id":"1016","department":[{"_id":"SiHi"}],"date_updated":"2023-09-22T09:42:42Z","intvolume":" 26","month":"01","scopus_import":"1","oa_version":"None","abstract":[{"text":"The integrity and dynamic properties of the microtubule cytoskeleton are indispensable for the development of the mammalian brain. Consequently, mutations in the genes that encode the structural component (the α/β-tubulin heterodimer) can give rise to severe, sporadic neurodevelopmental disorders. These are commonly referred to as the tubulinopathies. Here we report the addition of recessive quadrupedalism, also known as Uner Tan syndrome (UTS), to the growing list of diseases caused by tubulin variants. Analysis of a consanguineous UTS family identified a biallelic TUBB2B mutation, resulting in a p.R390Q amino acid substitution. In addition to the identifying quadrupedal locomotion, all three patients showed severe cerebellar hypoplasia. None, however, displayed the basal ganglia malformations typically associated with TUBB2B mutations. Functional analysis of the R390Q substitution revealed that it did not affect the ability of β-tubulin to fold or become assembled into the α/β-heterodimer, nor did it influence the incorporation of mutant-containing heterodimers into microtubule polymers. The 390Q mutation in S. cerevisiae TUB2 did not affect growth under basal conditions, but did result in increased sensitivity to microtubule-depolymerizing drugs, indicative of a mild impact of this mutation on microtubule function. The TUBB2B mutation described here represents an unusual recessive mode of inheritance for missense-mediated tubulinopathies and reinforces the sensitivity of the developing cerebellum to microtubule defects.","lang":"eng"}],"issue":"2","volume":26,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["09646906"]}},{"quality_controlled":"1","publisher":"American Society of Plant Biologists","isi":1,"year":"2017","day":"17","publication":"Plant Physiology","page":"387 - 404","doi":"10.1104/pp.16.01964","date_published":"2017-05-17T00:00:00Z","date_created":"2018-12-11T11:49:43Z","citation":{"mla":"Dobisova, Tereza, et al. “Light Regulated Expression of Sensor Histidine Kinase CKI1 Controls Cytokinin Related Development.” Plant Physiology, vol. 174, no. 1, American Society of Plant Biologists, 2017, pp. 387–404, doi:10.1104/pp.16.01964.","short":"T. Dobisova, V. Hrdinova, C. Cuesta, S. Michlickova, I. Urbankova, R. Hejatkova, P. Zadnikova, M. Pernisová, E. Benková, J. Hejátko, Plant Physiology 174 (2017) 387–404.","ieee":"T. Dobisova et al., “Light regulated expression of sensor histidine kinase CKI1 controls cytokinin related development,” Plant Physiology, vol. 174, no. 1. American Society of Plant Biologists, pp. 387–404, 2017.","ama":"Dobisova T, Hrdinova V, Cuesta C, et al. Light regulated expression of sensor histidine kinase CKI1 controls cytokinin related development. Plant Physiology. 2017;174(1):387-404. doi:10.1104/pp.16.01964","apa":"Dobisova, T., Hrdinova, V., Cuesta, C., Michlickova, S., Urbankova, I., Hejatkova, R., … Hejátko, J. (2017). Light regulated expression of sensor histidine kinase CKI1 controls cytokinin related development. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.01964","chicago":"Dobisova, Tereza, Vendula Hrdinova, Candela Cuesta, Sarka Michlickova, Ivana Urbankova, Romana Hejatkova, Petra Zadnikova, Markéta Pernisová, Eva Benková, and Jan Hejátko. “Light Regulated Expression of Sensor Histidine Kinase CKI1 Controls Cytokinin Related Development.” Plant Physiology. American Society of Plant Biologists, 2017. https://doi.org/10.1104/pp.16.01964.","ista":"Dobisova T, Hrdinova V, Cuesta C, Michlickova S, Urbankova I, Hejatkova R, Zadnikova P, Pernisová M, Benková E, Hejátko J. 2017. Light regulated expression of sensor histidine kinase CKI1 controls cytokinin related development. Plant Physiology. 174(1), 387–404."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Dobisova, Tereza","last_name":"Dobisova","first_name":"Tereza"},{"last_name":"Hrdinova","full_name":"Hrdinova, Vendula","first_name":"Vendula"},{"last_name":"Cuesta","full_name":"Cuesta, Candela","orcid":"0000-0003-1923-2410","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","first_name":"Candela"},{"last_name":"Michlickova","full_name":"Michlickova, Sarka","first_name":"Sarka"},{"first_name":"Ivana","last_name":"Urbankova","full_name":"Urbankova, Ivana"},{"first_name":"Romana","full_name":"Hejatkova, Romana","last_name":"Hejatkova"},{"first_name":"Petra","full_name":"Zadnikova, Petra","last_name":"Zadnikova"},{"full_name":"Pernisová, Markéta","last_name":"Pernisová","first_name":"Markéta"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková"},{"first_name":"Jan","last_name":"Hejátko","full_name":"Hejátko, Jan"}],"publist_id":"6375","external_id":{"isi":["000402057200028"]},"article_processing_charge":"No","title":"Light regulated expression of sensor histidine kinase CKI1 controls cytokinin related development","abstract":[{"text":"In plants, the multistep phosphorelay (MSP) pathway mediates a range of regulatory processes, including those activated by cytokinins. The crosstalk between cytokinin response and light is known for a long time. However, the molecular mechanism underlying the interactionbetween light and cytokinin signaling remains elusive. In the screen for upstream regulators we identified a LONG PALE HYPOCOTYL (LPH) gene whose activity is indispensable for spatiotemporally correct expression of CYTOKININ INDEPENDENT-1 (CKI1), encoding the constitutively active sensor histidine kinase that activates MSP signaling. lph is a new allele of HEME OXYGENASE 1 (HY1) which encodes the key protein in the biosynthesis of phytochromobilin, a cofactor of photoconvertiblephytochromes. Our analysis confirmed the light-dependent regulation oftheCKI1 expression pattern. We show that CKI1 expression is under the control of phytochrome A (phyA), functioning as a dual (both positive and negative) regulator of CKI1 expression, presumably via the phyA-regulated transcription factors PHYTOCHROME INTERACTING FACTOR 3 (PIF3) and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1). Changes in CKI1 expression observed in lph/hy1-7 and phy mutants correlatewithmisregulation of MSP signaling, changedcytokinin sensitivity and developmental aberrations,previously shown to be associated with cytokinin and/or CKI1 action. Besides that, we demonstrate novel role of phyA-dependent CKI1 expression in the hypocotyl elongation and hook development during skotomorphogenesis. Based on these results, we propose that the light-dependent regulation of CKI1 provides a plausible mechanistic link underlying the well-known interaction between light- and cytokinin-controlled plant development.","lang":"eng"}],"oa_version":"None","scopus_import":"1","month":"05","intvolume":" 174","publication_status":"published","language":[{"iso":"eng"}],"volume":174,"issue":"1","_id":"1018","type":"journal_article","status":"public","date_updated":"2023-09-22T09:41:48Z","department":[{"_id":"EvBe"}]},{"related_material":{"record":[{"relation":"research_data","status":"public","id":"9861"}]},"issue":"1","volume":119,"publication_status":"published","publication_identifier":{"issn":["0018067X"]},"language":[{"iso":"eng"}],"scopus_import":"1","intvolume":" 119","month":"07","abstract":[{"lang":"eng","text":"As a consequence of its difference in copy number between males and females, the X chromosome is subject to unique evolutionary forces and gene regulatory mechanisms. Previous studies of Drosophila melanogaster have shown that the expression of X-linked, testis-specific reporter genes is suppressed in the male germline. However, it is not known whether this phenomenon is restricted to testis-expressed genes or if it is a more general property of genes with tissue-specific expression, which are also underrepresented on the X chromosome. To test this, we compared the expression of three tissue-specific reporter genes (ovary, accessory gland and Malpighian tubule) inserted at various autosomal and X-chromosomal locations. In contrast to testis-specific reporter genes, we found no reduction of X-linked expression in any of the other tissues. In accessory gland and Malpighian tubule, we detected higher expression of the X-linked reporter genes, which suggests that they are at least partially dosage compensated. We found no difference in the tissue-specificity of X-linked and autosomal reporter genes. These findings indicate that, in general, the X chromosome is not a detrimental environment for tissue-specific gene expression and that the suppression of X-linked expression is limited to the male germline."}],"oa_version":"None","department":[{"_id":"BeVi"}],"date_updated":"2023-09-22T09:41:21Z","type":"journal_article","status":"public","_id":"1019","page":"27 - 34","date_created":"2018-12-11T11:49:43Z","doi":"10.1038/hdy.2017.12","date_published":"2017-07-01T00:00:00Z","year":"2017","isi":1,"publication":"Heredity","day":"01","quality_controlled":"1","publisher":"Nature Publishing Group","external_id":{"isi":["000405397800004"]},"article_processing_charge":"No","publist_id":"6374","author":[{"first_name":"Eliza","last_name":"Argyridou","full_name":"Argyridou, Eliza"},{"last_name":"Huylmans","full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Annabella","full_name":"Königer, Annabella","last_name":"Königer"},{"first_name":"John","full_name":"Parsch, John","last_name":"Parsch"}],"title":"X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster","citation":{"ista":"Argyridou E, Huylmans AK, Königer A, Parsch J. 2017. X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. Heredity. 119(1), 27–34.","chicago":"Argyridou, Eliza, Ann K Huylmans, Annabella Königer, and John Parsch. “X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster.” Heredity. Nature Publishing Group, 2017. https://doi.org/10.1038/hdy.2017.12.","apa":"Argyridou, E., Huylmans, A. K., Königer, A., & Parsch, J. (2017). X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2017.12","ama":"Argyridou E, Huylmans AK, Königer A, Parsch J. X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. Heredity. 2017;119(1):27-34. doi:10.1038/hdy.2017.12","short":"E. Argyridou, A.K. Huylmans, A. Königer, J. Parsch, Heredity 119 (2017) 27–34.","ieee":"E. Argyridou, A. K. Huylmans, A. Königer, and J. Parsch, “X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster,” Heredity, vol. 119, no. 1. Nature Publishing Group, pp. 27–34, 2017.","mla":"Argyridou, Eliza, et al. “X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster.” Heredity, vol. 119, no. 1, Nature Publishing Group, 2017, pp. 27–34, doi:10.1038/hdy.2017.12."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"title":"Liouville principles and a large-scale regularity theory for random elliptic operators on the half-space","external_id":{"isi":["000396681800004"]},"article_processing_charge":"No","author":[{"orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Raithel","full_name":"Raithel, Claudia","first_name":"Claudia"}],"publist_id":"6381","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Fischer, Julian L, and Claudia Raithel. “Liouville Principles and a Large-Scale Regularity Theory for Random Elliptic Operators on the Half-Space.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics , 2017. https://doi.org/10.1137/16M1070384.","ista":"Fischer JL, Raithel C. 2017. Liouville principles and a large-scale regularity theory for random elliptic operators on the half-space. SIAM Journal on Mathematical Analysis. 49(1), 82–114.","mla":"Fischer, Julian L., and Claudia Raithel. “Liouville Principles and a Large-Scale Regularity Theory for Random Elliptic Operators on the Half-Space.” SIAM Journal on Mathematical Analysis, vol. 49, no. 1, Society for Industrial and Applied Mathematics , 2017, pp. 82–114, doi:10.1137/16M1070384.","apa":"Fischer, J. L., & Raithel, C. (2017). Liouville principles and a large-scale regularity theory for random elliptic operators on the half-space. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M1070384","ama":"Fischer JL, Raithel C. Liouville principles and a large-scale regularity theory for random elliptic operators on the half-space. SIAM Journal on Mathematical Analysis. 2017;49(1):82-114. doi:10.1137/16M1070384","short":"J.L. Fischer, C. Raithel, SIAM Journal on Mathematical Analysis 49 (2017) 82–114.","ieee":"J. L. Fischer and C. Raithel, “Liouville principles and a large-scale regularity theory for random elliptic operators on the half-space,” SIAM Journal on Mathematical Analysis, vol. 49, no. 1. Society for Industrial and Applied Mathematics , pp. 82–114, 2017."},"oa":1,"quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics ","date_created":"2018-12-11T11:49:41Z","date_published":"2017-01-12T00:00:00Z","doi":"10.1137/16M1070384","page":"82 - 114","publication":"SIAM Journal on Mathematical Analysis","day":"12","year":"2017","isi":1,"status":"public","type":"journal_article","_id":"1014","extern":"1","date_updated":"2023-09-22T09:43:36Z","intvolume":" 49","month":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.04328"}],"oa_version":"Submitted Version","abstract":[{"text":"We consider the large-scale regularity of solutions to second-order linear elliptic equations with random coefficient fields. In contrast to previous works on regularity theory for random elliptic operators, our interest is in the regularity at the boundary: We consider problems posed on the half-space with homogeneous Dirichlet boundary conditions and derive an associated C1,α-type large-scale regularity theory in the form of a corresponding decay estimate for the homogenization-adapted tilt-excess. This regularity theory entails an associated Liouville-type theorem. The results are based on the existence of homogenization correctors adapted to the half-space setting, which we construct-by an entirely deterministic argument-as a modification of the homogenization corrector on the whole space. This adaption procedure is carried out inductively on larger scales, crucially relying on the regularity theory already established on smaller scales.","lang":"eng"}],"issue":"1","volume":49,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00361410"]}},{"publisher":"Dryad","main_file_link":[{"url":"https://doi.org/10.5061/dryad.02f6r","open_access":"1"}],"oa":1,"month":"02","abstract":[{"text":"As a consequence of its difference in copy number between males and females, the X chromosome is subject to unique evolutionary forces and gene regulatory mechanisms. Previous studies of Drosophila melanogaster have shown that the expression of X-linked, testis-specific reporter genes is suppressed in the male germline. However, it is not known whether this phenomenon is restricted to testis-expressed genes or if it is a more general property of genes with tissue-specific expression, which are also underrepresented on the X chromosome. To test this, we compared the expression of three tissue-specific reporter genes (ovary, accessory gland and Malpighian tubule) inserted at various autosomal and X-chromosomal locations. In contrast to testis-specific reporter genes, we found no reduction of X-linked expression in any of the other tissues. In accessory gland and Malpighian tubule, we detected higher expression of the X-linked reporter genes, which suggests that they are at least partially dosage compensated. We found no difference in the tissue-specificity of X-linked and autosomal reporter genes. These findings indicate that, in general, the X chromosome is not a detrimental environment for tissue-specific gene expression and that the suppression of X-linked expression is limited to the male germline.","lang":"eng"}],"oa_version":"Published Version","doi":"10.5061/dryad.02f6r","related_material":{"record":[{"id":"1019","status":"public","relation":"used_in_publication"}]},"date_published":"2017-02-14T00:00:00Z","date_created":"2021-08-10T08:12:52Z","year":"2017","day":"14","type":"research_data_reference","status":"public","_id":"9861","author":[{"full_name":"Argyridou, Eliza","last_name":"Argyridou","first_name":"Eliza"},{"orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K","last_name":"Huylmans","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Königer, Annabella","last_name":"Königer","first_name":"Annabella"},{"full_name":"Parsch, John","last_name":"Parsch","first_name":"John"}],"article_processing_charge":"No","title":"Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster","department":[{"_id":"BeVi"}],"citation":{"mla":"Argyridou, Eliza, et al. Data from: X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster. Dryad, 2017, doi:10.5061/dryad.02f6r.","short":"E. Argyridou, A.K. Huylmans, A. Königer, J. Parsch, (2017).","ieee":"E. Argyridou, A. K. Huylmans, A. Königer, and J. Parsch, “Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster.” Dryad, 2017.","apa":"Argyridou, E., Huylmans, A. K., Königer, A., & Parsch, J. (2017). Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. Dryad. https://doi.org/10.5061/dryad.02f6r","ama":"Argyridou E, Huylmans AK, Königer A, Parsch J. Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. 2017. doi:10.5061/dryad.02f6r","chicago":"Argyridou, Eliza, Ann K Huylmans, Annabella Königer, and John Parsch. “Data from: X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster.” Dryad, 2017. https://doi.org/10.5061/dryad.02f6r.","ista":"Argyridou E, Huylmans AK, Königer A, Parsch J. 2017. Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster, Dryad, 10.5061/dryad.02f6r."},"date_updated":"2023-09-22T09:41:20Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"doi":"10.1186/s12864-017-3705-7","date_published":"2017-04-26T00:00:00Z","date_created":"2018-12-11T11:49:39Z","page":"329","day":"26","publication":"BMC Genomics","isi":1,"has_accepted_license":"1","year":"2017","publisher":"BioMed Central","quality_controlled":"1","oa":1,"title":"Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae","publist_id":"6392","author":[{"full_name":"Greenwood, Jenny","last_name":"Greenwood","first_name":"Jenny"},{"orcid":"0000-0002-8214-4758","full_name":"Milutinovic, Barbara","last_name":"Milutinovic","first_name":"Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert","last_name":"Peuß","full_name":"Peuß, Robert"},{"full_name":"Behrens, Sarah","last_name":"Behrens","first_name":"Sarah"},{"first_name":"Daniela","full_name":"Essar, Daniela","last_name":"Essar"},{"last_name":"Rosenstiel","full_name":"Rosenstiel, Philip","first_name":"Philip"},{"first_name":"Hinrich","last_name":"Schulenburg","full_name":"Schulenburg, Hinrich"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"}],"external_id":{"isi":["000400625200004"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Greenwood, Jenny, Barbara Milutinovic, Robert Peuß, Sarah Behrens, Daniela Essar, Philip Rosenstiel, Hinrich Schulenburg, and Joachim Kurtz. “Oral Immune Priming with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium Castaneum Larvae.” BMC Genomics. BioMed Central, 2017. https://doi.org/10.1186/s12864-017-3705-7.","ista":"Greenwood J, Milutinovic B, Peuß R, Behrens S, Essar D, Rosenstiel P, Schulenburg H, Kurtz J. 2017. Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. BMC Genomics. 18(1), 329.","mla":"Greenwood, Jenny, et al. “Oral Immune Priming with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium Castaneum Larvae.” BMC Genomics, vol. 18, no. 1, BioMed Central, 2017, p. 329, doi:10.1186/s12864-017-3705-7.","ieee":"J. Greenwood et al., “Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae,” BMC Genomics, vol. 18, no. 1. BioMed Central, p. 329, 2017.","short":"J. Greenwood, B. Milutinovic, R. Peuß, S. Behrens, D. Essar, P. Rosenstiel, H. Schulenburg, J. Kurtz, BMC Genomics 18 (2017) 329.","ama":"Greenwood J, Milutinovic B, Peuß R, et al. Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. BMC Genomics. 2017;18(1):329. doi:10.1186/s12864-017-3705-7","apa":"Greenwood, J., Milutinovic, B., Peuß, R., Behrens, S., Essar, D., Rosenstiel, P., … Kurtz, J. (2017). Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-017-3705-7"},"volume":18,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9859"},{"relation":"research_data","id":"9860","status":"public"}]},"issue":"1","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5236","date_updated":"2018-12-12T10:16:46Z","file_size":2379672,"creator":"system","date_created":"2018-12-12T10:16:46Z","file_name":"IST-2017-814-v1+1_s12864-017-3705-7.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["14712164"]},"publication_status":"published","month":"04","intvolume":" 18","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Background: The phenomenon of immune priming, i.e. enhanced protection following a secondary exposure to a pathogen, has now been demonstrated in a wide range of invertebrate species. Despite accumulating phenotypic evidence, knowledge of its mechanistic underpinnings is currently very limited. Here we used the system of the red flour beetle, Tribolium castaneum and the insect pathogen Bacillus thuringiensis (Bt) to further our molecular understanding of the oral immune priming phenomenon. We addressed how ingestion of bacterial cues (derived from spore supernatants) of an orally pathogenic and non-pathogenic Bt strain affects gene expression upon later challenge exposure, using a whole-transcriptome sequencing approach. Results: Whereas gene expression of individuals primed with the orally non-pathogenic strain showed minor changes to controls, we found that priming with the pathogenic strain induced regulation of a large set of distinct genes, many of which are known immune candidates. Intriguingly, the immune repertoire activated upon priming and subsequent challenge qualitatively differed from the one mounted upon infection with Bt without previous priming. Moreover, a large subset of priming-specific genes showed an inverse regulation compared to their regulation upon challenge only. Conclusions: Our data demonstrate that gene expression upon infection is strongly affected by previous immune priming. We hypothesise that this shift in gene expression indicates activation of a more targeted and efficient response towards a previously encountered pathogen, in anticipation of potential secondary encounter.","lang":"eng"}],"department":[{"_id":"SyCr"}],"file_date_updated":"2018-12-12T10:16:46Z","ddc":["570"],"date_updated":"2023-09-22T09:47:44Z","status":"public","pubrep_id":"814","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"1006"},{"quality_controlled":"1","publisher":"Springer","oa":1,"page":"287 - 313","date_published":"2017-03-19T00:00:00Z","doi":"10.1007/978-3-662-54434-1_11","date_created":"2018-12-11T11:49:41Z","isi":1,"year":"2017","day":"19","project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"},{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"publist_id":"6384","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard","last_name":"Kragl","full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117"},{"last_name":"Mishra","full_name":"Mishra, Samarth","first_name":"Samarth"},{"last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000681702400011"]},"article_processing_charge":"No","editor":[{"last_name":"Yang","full_name":"Yang, Hongseok","first_name":"Hongseok"}],"title":"Faster algorithms for weighted recursive state machines","citation":{"mla":"Chatterjee, Krishnendu, et al. Faster Algorithms for Weighted Recursive State Machines. Edited by Hongseok Yang, vol. 10201, Springer, 2017, pp. 287–313, doi:10.1007/978-3-662-54434-1_11.","ama":"Chatterjee K, Kragl B, Mishra S, Pavlogiannis A. Faster algorithms for weighted recursive state machines. In: Yang H, ed. Vol 10201. Springer; 2017:287-313. doi:10.1007/978-3-662-54434-1_11","apa":"Chatterjee, K., Kragl, B., Mishra, S., & Pavlogiannis, A. (2017). Faster algorithms for weighted recursive state machines. In H. Yang (Ed.) (Vol. 10201, pp. 287–313). Presented at the ESOP: European Symposium on Programming, Uppsala, Sweden: Springer. https://doi.org/10.1007/978-3-662-54434-1_11","short":"K. Chatterjee, B. Kragl, S. Mishra, A. Pavlogiannis, in:, H. Yang (Ed.), Springer, 2017, pp. 287–313.","ieee":"K. Chatterjee, B. Kragl, S. Mishra, and A. Pavlogiannis, “Faster algorithms for weighted recursive state machines,” presented at the ESOP: European Symposium on Programming, Uppsala, Sweden, 2017, vol. 10201, pp. 287–313.","chicago":"Chatterjee, Krishnendu, Bernhard Kragl, Samarth Mishra, and Andreas Pavlogiannis. “Faster Algorithms for Weighted Recursive State Machines.” edited by Hongseok Yang, 10201:287–313. Springer, 2017. https://doi.org/10.1007/978-3-662-54434-1_11.","ista":"Chatterjee K, Kragl B, Mishra S, Pavlogiannis A. 2017. Faster algorithms for weighted recursive state machines. ESOP: European Symposium on Programming, LNCS, vol. 10201, 287–313."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1701.04914","open_access":"1"}],"month":"03","intvolume":" 10201","abstract":[{"lang":"eng","text":"Pushdown systems (PDSs) and recursive state machines (RSMs), which are linearly equivalent, are standard models for interprocedural analysis. Yet RSMs are more convenient as they (a) explicitly model function calls and returns, and (b) specify many natural parameters for algorithmic analysis, e.g., the number of entries and exits. We consider a general framework where RSM transitions are labeled from a semiring and path properties are algebraic with semiring operations, which can model, e.g., interprocedural reachability and dataflow analysis problems. Our main contributions are new algorithms for several fundamental problems. As compared to a direct translation of RSMs to PDSs and the best-known existing bounds of PDSs, our analysis algorithm improves the complexity for finite-height semirings (that subsumes reachability and standard dataflow properties). We further consider the problem of extracting distance values from the representation structures computed by our algorithm, and give efficient algorithms that distinguish the complexity of a one-time preprocessing from the complexity of each individual query. Another advantage of our algorithm is that our improvements carry over to the concurrent setting, where we improve the bestknown complexity for the context-bounded analysis of concurrent RSMs. Finally, we provide a prototype implementation that gives a significant speed-up on several benchmarks from the SLAM/SDV project."}],"oa_version":"Submitted Version","volume":10201,"ec_funded":1,"publication_identifier":{"issn":["03029743"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"conference","conference":{"end_date":"2017-04-29","location":"Uppsala, Sweden","start_date":"2017-04-22","name":"ESOP: European Symposium on Programming"},"status":"public","_id":"1011","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2023-09-22T09:44:50Z"},{"oa":1,"quality_controlled":"1","publisher":"Elsevier","page":"82 - 89","date_created":"2018-12-11T11:49:38Z","doi":"10.1016/j.gde.2017.03.010","date_published":"2017-08-01T00:00:00Z","year":"2017","has_accepted_license":"1","isi":1,"publication":"Current Opinion in Genetics & Development","day":"01","project":[{"name":"Hormone cross-talk drives nutrient dependent plant development","grant_number":"I 1774-B16","_id":"2542D156-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_processing_charge":"No","external_id":{"pmid":["28391060"],"isi":["000404880400013"]},"publist_id":"6394","author":[{"last_name":"Ötvös","orcid":"0000-0002-5503-4983","full_name":"Ötvös, Krisztina","first_name":"Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"title":"Spatiotemporal mechanisms of root branching","citation":{"chicago":"Ötvös, Krisztina, and Eva Benková. “Spatiotemporal Mechanisms of Root Branching.” Current Opinion in Genetics & Development. Elsevier, 2017. https://doi.org/10.1016/j.gde.2017.03.010.","ista":"Ötvös K, Benková E. 2017. Spatiotemporal mechanisms of root branching. Current Opinion in Genetics & Development. 45, 82–89.","mla":"Ötvös, Krisztina, and Eva Benková. “Spatiotemporal Mechanisms of Root Branching.” Current Opinion in Genetics & Development, vol. 45, Elsevier, 2017, pp. 82–89, doi:10.1016/j.gde.2017.03.010.","apa":"Ötvös, K., & Benková, E. (2017). Spatiotemporal mechanisms of root branching. Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2017.03.010","ama":"Ötvös K, Benková E. Spatiotemporal mechanisms of root branching. Current Opinion in Genetics & Development. 2017;45:82-89. doi:10.1016/j.gde.2017.03.010","ieee":"K. Ötvös and E. Benková, “Spatiotemporal mechanisms of root branching,” Current Opinion in Genetics & Development, vol. 45. Elsevier, pp. 82–89, 2017.","short":"K. Ötvös, E. Benková, Current Opinion in Genetics & Development 45 (2017) 82–89."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","intvolume":" 45","month":"08","abstract":[{"lang":"eng","text":"The fundamental tasks of the root system are, besides anchoring, mediating interactions between plant and soil and providing the plant with water and nutrients. The architecture of the root system is controlled by endogenous mechanisms that constantly integrate environmental signals, such as availability of nutrients and water. Extremely important for efficient soil exploitation and survival under less favorable conditions is the developmental flexibility of the root system that is largely determined by its postembryonic branching capacity. Modulation of initiation and outgrowth of lateral roots provides roots with an exceptional plasticity, allows optimal adjustment to underground heterogeneity, and enables effective soil exploitation and use of resources. Here we discuss recent advances in understanding the molecular mechanisms that shape the plant root system and integrate external cues to adapt to the changing environment."}],"pmid":1,"oa_version":"Submitted Version","volume":45,"publication_status":"published","publication_identifier":{"issn":["0959437X"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":364133,"date_updated":"2019-04-17T08:00:36Z","file_name":"Otvos_Benkova_CurOpDevBiol_2017.pdf","date_created":"2019-04-17T08:00:36Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"6336"}],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","pubrep_id":"1017","status":"public","_id":"1004","file_date_updated":"2019-04-17T08:00:36Z","department":[{"_id":"EvBe"}],"date_updated":"2023-09-22T09:48:15Z","ddc":["575"]},{"_id":"1010","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"807","status":"public","date_updated":"2023-09-22T09:45:23Z","ddc":["510","539"],"department":[{"_id":"LaEr"}],"file_date_updated":"2018-12-12T10:13:39Z","abstract":[{"text":"We prove a local law in the bulk of the spectrum for random Gram matrices XX∗, a generalization of sample covariance matrices, where X is a large matrix with independent, centered entries with arbitrary variances. The limiting eigenvalue density that generalizes the Marchenko-Pastur law is determined by solving a system of nonlinear equations. Our entrywise and averaged local laws are on the optimal scale with the optimal error bounds. They hold both in the square case (hard edge) and in the properly rectangular case (soft edge). In the latter case we also establish a macroscopic gap away from zero in the spectrum of XX∗. ","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 22","month":"03","publication_status":"published","publication_identifier":{"issn":["10836489"]},"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2017-807-v1+1_euclid.ejp.1488942016.pdf","date_created":"2018-12-12T10:13:39Z","creator":"system","file_size":639384,"date_updated":"2018-12-12T10:13:39Z","file_id":"5024","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"ec_funded":1,"volume":22,"related_material":{"record":[{"status":"public","id":"149","relation":"dissertation_contains"}]},"article_number":"25","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"citation":{"mla":"Alt, Johannes, et al. “Local Law for Random Gram Matrices.” Electronic Journal of Probability, vol. 22, 25, Institute of Mathematical Statistics, 2017, doi:10.1214/17-EJP42.","ama":"Alt J, Erdös L, Krüger TH. Local law for random Gram matrices. Electronic Journal of Probability. 2017;22. doi:10.1214/17-EJP42","apa":"Alt, J., Erdös, L., & Krüger, T. H. (2017). Local law for random Gram matrices. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/17-EJP42","short":"J. Alt, L. Erdös, T.H. Krüger, Electronic Journal of Probability 22 (2017).","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “Local law for random Gram matrices,” Electronic Journal of Probability, vol. 22. Institute of Mathematical Statistics, 2017.","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “Local Law for Random Gram Matrices.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/17-EJP42.","ista":"Alt J, Erdös L, Krüger TH. 2017. Local law for random Gram matrices. Electronic Journal of Probability. 22, 25."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000396611900025"],"arxiv":["1606.07353"]},"author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","full_name":"Alt, Johannes","last_name":"Alt"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös"},{"id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H","last_name":"Krüger","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297"}],"publist_id":"6386","title":"Local law for random Gram matrices","oa":1,"publisher":"Institute of Mathematical Statistics","quality_controlled":"1","year":"2017","has_accepted_license":"1","isi":1,"publication":"Electronic Journal of Probability","day":"08","date_created":"2018-12-11T11:49:40Z","doi":"10.1214/17-EJP42","date_published":"2017-03-08T00:00:00Z"},{"type":"conference","conference":{"start_date":"2017-02-04","end_date":"2017-02-10","location":"San Francisco, CA, United States","name":"AAAI: Conference on Artificial Intelligence"},"status":"public","_id":"1009","department":[{"_id":"KrCh"}],"date_updated":"2023-09-22T09:46:41Z","scopus_import":"1","main_file_link":[{"url":"http://www.aaai.org/ocs/index.php/AAAI/AAAI17/paper/download/14354/14092","open_access":"1"}],"month":"01","intvolume":" 5","abstract":[{"text":"A standard objective in partially-observable Markov decision processes (POMDPs) is to find a policy that maximizes the expected discounted-sum payoff. However, such policies may still permit unlikely but highly undesirable outcomes, which is problematic especially in safety-critical applications. Recently, there has been a surge of interest in POMDPs where the goal is to maximize the probability to ensure that the payoff is at least a given threshold, but these approaches do not consider any optimization beyond satisfying this threshold constraint. In this work we go beyond both the “expectation” and “threshold” approaches and consider a “guaranteed payoff optimization (GPO)” problem for POMDPs, where we are given a threshold t and the objective is to find a policy σ such that a) each possible outcome of σ yields a discounted-sum payoff of at least t, and b) the expected discounted-sum payoff of σ is optimal (or near-optimal) among all policies satisfying a). We present a practical approach to tackle the GPO problem and evaluate it on standard POMDP benchmarks.","lang":"eng"}],"oa_version":"Submitted Version","volume":5,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"}],"publist_id":"6387","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","full_name":"Novotny, Petr","last_name":"Novotny"},{"last_name":"Pérez","full_name":"Pérez, Guillermo","first_name":"Guillermo"},{"last_name":"Raskin","full_name":"Raskin, Jean","first_name":"Jean"},{"last_name":"Zikelic","full_name":"Zikelic, Djordje","first_name":"Djordje"}],"article_processing_charge":"No","external_id":{"isi":["000485630703107"]},"title":"Optimizing expectation with guarantees in POMDPs","citation":{"mla":"Chatterjee, Krishnendu, et al. “Optimizing Expectation with Guarantees in POMDPs.” Proceedings of the 31st AAAI Conference on Artificial Intelligence, vol. 5, AAAI Press, 2017, pp. 3725–32.","short":"K. Chatterjee, P. Novotný, G. Pérez, J. Raskin, D. Zikelic, in:, Proceedings of the 31st AAAI Conference on Artificial Intelligence, AAAI Press, 2017, pp. 3725–3732.","ieee":"K. Chatterjee, P. Novotný, G. Pérez, J. Raskin, and D. Zikelic, “Optimizing expectation with guarantees in POMDPs,” in Proceedings of the 31st AAAI Conference on Artificial Intelligence, San Francisco, CA, United States, 2017, vol. 5, pp. 3725–3732.","apa":"Chatterjee, K., Novotný, P., Pérez, G., Raskin, J., & Zikelic, D. (2017). Optimizing expectation with guarantees in POMDPs. In Proceedings of the 31st AAAI Conference on Artificial Intelligence (Vol. 5, pp. 3725–3732). San Francisco, CA, United States: AAAI Press.","ama":"Chatterjee K, Novotný P, Pérez G, Raskin J, Zikelic D. Optimizing expectation with guarantees in POMDPs. In: Proceedings of the 31st AAAI Conference on Artificial Intelligence. Vol 5. AAAI Press; 2017:3725-3732.","chicago":"Chatterjee, Krishnendu, Petr Novotný, Guillermo Pérez, Jean Raskin, and Djordje Zikelic. “Optimizing Expectation with Guarantees in POMDPs.” In Proceedings of the 31st AAAI Conference on Artificial Intelligence, 5:3725–32. AAAI Press, 2017.","ista":"Chatterjee K, Novotný P, Pérez G, Raskin J, Zikelic D. 2017. Optimizing expectation with guarantees in POMDPs. Proceedings of the 31st AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 5, 3725–3732."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"AAAI Press","quality_controlled":"1","oa":1,"acknowledgement":"he research leading to these results was supported by the Austrian Science Fund (FWF) NFN Grant no. S11407-N23 (RiSE/SHiNE); two ERC Starting grants (279307: Graph Games, 279499: inVEST); the Vienna Science and Tech- nology Fund (WWTF) through project ICT15-003; and the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734].","page":"3725 - 3732","date_published":"2017-01-01T00:00:00Z","date_created":"2018-12-11T11:49:40Z","isi":1,"year":"2017","day":"01","publication":"Proceedings of the 31st AAAI Conference on Artificial Intelligence"},{"status":"public","type":"research_data_reference","_id":"9859","title":"Additional file 1: Table S1. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae","department":[{"_id":"SyCr"}],"author":[{"first_name":"Jenny","last_name":"Greenwood","full_name":"Greenwood, Jenny"},{"full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758","last_name":"Milutinovic","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara"},{"first_name":"Robert","last_name":"Peuß","full_name":"Peuß, Robert"},{"first_name":"Sarah","full_name":"Behrens, Sarah","last_name":"Behrens"},{"full_name":"Essar, Daniela","last_name":"Essar","first_name":"Daniela"},{"first_name":"Philip","last_name":"Rosenstiel","full_name":"Rosenstiel, Philip"},{"full_name":"Schulenburg, Hinrich","last_name":"Schulenburg","first_name":"Hinrich"},{"last_name":"Kurtz","full_name":"Kurtz, Joachim","first_name":"Joachim"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-22T09:47:44Z","citation":{"chicago":"Greenwood, Jenny, Barbara Milutinovic, Robert Peuß, Sarah Behrens, Daniela Essar, Philip Rosenstiel, Hinrich Schulenburg, and Joachim Kurtz. “Additional File 1: Table S1. of Oral Immune Priming with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium Castaneum Larvae.” Springer Nature, 2017. https://doi.org/10.6084/m9.figshare.c.3756974_d1.v1.","ista":"Greenwood J, Milutinovic B, Peuß R, Behrens S, Essar D, Rosenstiel P, Schulenburg H, Kurtz J. 2017. Additional file 1: Table S1. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae, Springer Nature, 10.6084/m9.figshare.c.3756974_d1.v1.","mla":"Greenwood, Jenny, et al. Additional File 1: Table S1. of Oral Immune Priming with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium Castaneum Larvae. Springer Nature, 2017, doi:10.6084/m9.figshare.c.3756974_d1.v1.","ama":"Greenwood J, Milutinovic B, Peuß R, et al. Additional file 1: Table S1. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. 2017. doi:10.6084/m9.figshare.c.3756974_d1.v1","apa":"Greenwood, J., Milutinovic, B., Peuß, R., Behrens, S., Essar, D., Rosenstiel, P., … Kurtz, J. (2017). Additional file 1: Table S1. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. Springer Nature. https://doi.org/10.6084/m9.figshare.c.3756974_d1.v1","short":"J. Greenwood, B. Milutinovic, R. Peuß, S. Behrens, D. Essar, P. Rosenstiel, H. Schulenburg, J. Kurtz, (2017).","ieee":"J. Greenwood et al., “Additional file 1: Table S1. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae.” Springer Nature, 2017."},"month":"04","publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.c.3756974_d1.v1"}],"oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Lists of all differentially expressed genes in the different priming-challenge treatments (compared to the fully naïve control; xlsx file). Relevant columns include the following: sample_1 and sample_2 – treatment groups being compared; Normalised FPKM sample_1 and sample_2 – FPKM of samples being compared; log2(fold_change) – log2(FPKM sample 2/FPKM sample 1), i.e. negative means sample 1 upregulated compared with sample 2, positive means sample 2 upregulated compared with sample 1; cuffdiff test_statistic – test statistic of differential expression test; p_value – p-value of differential expression test; q_value (FDR correction) – adjusted P-value of differential expression test. (XLSX 598 kb)"}],"related_material":{"record":[{"id":"1006","status":"public","relation":"used_in_publication"}]},"date_published":"2017-04-26T00:00:00Z","doi":"10.6084/m9.figshare.c.3756974_d1.v1","date_created":"2021-08-10T07:59:02Z","day":"26","year":"2017"},{"type":"research_data_reference","status":"public","_id":"9860","author":[{"first_name":"Jenny","last_name":"Greenwood","full_name":"Greenwood, Jenny"},{"first_name":"Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8214-4758","full_name":"Milutinovic, Barbara","last_name":"Milutinovic"},{"last_name":"Peuß","full_name":"Peuß, Robert","first_name":"Robert"},{"first_name":"Sarah","last_name":"Behrens","full_name":"Behrens, Sarah"},{"first_name":"Daniela","last_name":"Essar","full_name":"Essar, Daniela"},{"first_name":"Philip","last_name":"Rosenstiel","full_name":"Rosenstiel, Philip"},{"last_name":"Schulenburg","full_name":"Schulenburg, Hinrich","first_name":"Hinrich"},{"last_name":"Kurtz","full_name":"Kurtz, Joachim","first_name":"Joachim"}],"article_processing_charge":"No","department":[{"_id":"SyCr"}],"title":"Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae","citation":{"mla":"Greenwood, Jenny, et al. Additional File 5: Table S3. of Oral Immune Priming with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium Castaneum Larvae. Springer Nature, 2017, doi:10.6084/m9.figshare.c.3756974_d5.v1.","ieee":"J. Greenwood et al., “Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae.” Springer Nature, 2017.","short":"J. Greenwood, B. Milutinovic, R. Peuß, S. Behrens, D. Essar, P. Rosenstiel, H. Schulenburg, J. Kurtz, (2017).","apa":"Greenwood, J., Milutinovic, B., Peuß, R., Behrens, S., Essar, D., Rosenstiel, P., … Kurtz, J. (2017). Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. Springer Nature. https://doi.org/10.6084/m9.figshare.c.3756974_d5.v1","ama":"Greenwood J, Milutinovic B, Peuß R, et al. Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. 2017. doi:10.6084/m9.figshare.c.3756974_d5.v1","chicago":"Greenwood, Jenny, Barbara Milutinovic, Robert Peuß, Sarah Behrens, Daniela Essar, Philip Rosenstiel, Hinrich Schulenburg, and Joachim Kurtz. “Additional File 5: Table S3. of Oral Immune Priming with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium Castaneum Larvae.” Springer Nature, 2017. https://doi.org/10.6084/m9.figshare.c.3756974_d5.v1.","ista":"Greenwood J, Milutinovic B, Peuß R, Behrens S, Essar D, Rosenstiel P, Schulenburg H, Kurtz J. 2017. Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae, Springer Nature, 10.6084/m9.figshare.c.3756974_d5.v1."},"date_updated":"2023-09-22T09:47:44Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Springer Nature","oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.c.3756974_d5.v1","open_access":"1"}],"month":"04","oa_version":"Published Version","date_published":"2017-04-26T00:00:00Z","doi":"10.6084/m9.figshare.c.3756974_d5.v1","related_material":{"record":[{"status":"public","id":"1006","relation":"used_in_publication"}]},"date_created":"2021-08-10T08:07:12Z","year":"2017","day":"26"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Zhang, Ran, Thomas Auzinger, Duygu Ceylan, Wilmot Li, and Bernd Bickel. “Functionality-Aware Retargeting of Mechanisms to 3D Shapes,” Vol. 36. ACM, 2017. https://doi.org/10.1145/3072959.3073710.","ista":"Zhang R, Auzinger T, Ceylan D, Li W, Bickel B. 2017. Functionality-aware retargeting of mechanisms to 3D shapes. SIGGRAPH: Computer Graphics and Interactive Techniques, ACM Transactions on Graphics, vol. 36, 81.","mla":"Zhang, Ran, et al. Functionality-Aware Retargeting of Mechanisms to 3D Shapes. Vol. 36, no. 4, 81, ACM, 2017, doi:10.1145/3072959.3073710.","ieee":"R. Zhang, T. Auzinger, D. Ceylan, W. Li, and B. Bickel, “Functionality-aware retargeting of mechanisms to 3D shapes,” presented at the SIGGRAPH: Computer Graphics and Interactive Techniques, Los Angeles, CA, United States , 2017, vol. 36, no. 4.","short":"R. Zhang, T. Auzinger, D. Ceylan, W. Li, B. Bickel, in:, ACM, 2017.","ama":"Zhang R, Auzinger T, Ceylan D, Li W, Bickel B. Functionality-aware retargeting of mechanisms to 3D shapes. In: Vol 36. ACM; 2017. doi:10.1145/3072959.3073710","apa":"Zhang, R., Auzinger, T., Ceylan, D., Li, W., & Bickel, B. (2017). Functionality-aware retargeting of mechanisms to 3D shapes (Vol. 36). Presented at the SIGGRAPH: Computer Graphics and Interactive Techniques, Los Angeles, CA, United States : ACM. https://doi.org/10.1145/3072959.3073710"},"title":"Functionality-aware retargeting of mechanisms to 3D shapes","author":[{"id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","first_name":"Ran","last_name":"Zhang","orcid":"0000-0002-3808-281X","full_name":"Zhang, Ran"},{"last_name":"Auzinger","full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265","id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"last_name":"Ceylan","full_name":"Ceylan, Duygu","first_name":"Duygu"},{"first_name":"Wilmot","full_name":"Li, Wilmot","last_name":"Li"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel"}],"publist_id":"6396","article_processing_charge":"No","external_id":{"isi":["000406432100049"]},"article_number":"81","project":[{"name":"Distributed 3D Object Design","grant_number":"642841","call_identifier":"H2020","_id":"2508E324-B435-11E9-9278-68D0E5697425"},{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"day":"01","has_accepted_license":"1","isi":1,"year":"2017","doi":"10.1145/3072959.3073710","date_published":"2017-06-01T00:00:00Z","date_created":"2018-12-11T11:49:38Z","quality_controlled":"1","publisher":"ACM","oa":1,"ddc":["003","004"],"date_updated":"2023-09-22T09:49:31Z","department":[{"_id":"BeBi"}],"file_date_updated":"2018-12-12T10:09:05Z","_id":"1002","status":"public","pubrep_id":"1050","type":"conference","conference":{"end_date":"2017-08-03","location":"Los Angeles, CA, United States ","start_date":"2017-07-30","name":"SIGGRAPH: Computer Graphics and Interactive Techniques"},"file":[{"file_size":25463895,"date_updated":"2018-12-12T10:09:05Z","creator":"system","file_name":"IST-2018-1050-v1+1_MechRet.pdf","date_created":"2018-12-12T10:09:05Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4728"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["07300301"]},"publication_status":"published","volume":36,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8386"}]},"issue":"4","ec_funded":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":" We present an interactive design system to create functional mechanical objects. Our computational approach allows novice users to retarget an existing mechanical template to a user-specified input shape. Our proposed representation for a mechanical template encodes a parameterized mechanism, mechanical constraints that ensure a physically valid configuration, spatial relationships of mechanical parts to the user-provided shape, and functional constraints that specify an intended functionality. We provide an intuitive interface and optimization-in-the-loop approach for finding a valid configuration of the mechanism and the shape to ensure that higher-level functional goals are met. Our algorithm interactively optimizes the mechanism while the user manipulates the placement of mechanical components and the shape. Our system allows users to efficiently explore various design choices and to synthesize customized mechanical objects that can be fabricated with rapid prototyping technologies. We demonstrate the efficacy of our approach by retargeting various mechanical templates to different shapes and fabricating the resulting functional mechanical objects.\r\n"}],"month":"06","intvolume":" 36","alternative_title":["ACM Transactions on Graphics"],"scopus_import":"1"},{"citation":{"mla":"Guseinov, Ruslan, et al. CurveUps: Shaping Objects from Flat Plates with Tension-Actuated Curvature. Vol. 36, no. 4, 64, ACM, 2017, doi:10.1145/3072959.3073709.","apa":"Guseinov, R., Miguel, E., & Bickel, B. (2017). CurveUps: Shaping objects from flat plates with tension-actuated curvature (Vol. 36). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/3072959.3073709","ama":"Guseinov R, Miguel E, Bickel B. CurveUps: Shaping objects from flat plates with tension-actuated curvature. In: Vol 36. ACM; 2017. doi:10.1145/3072959.3073709","short":"R. Guseinov, E. Miguel, B. Bickel, in:, ACM, 2017.","ieee":"R. Guseinov, E. Miguel, and B. Bickel, “CurveUps: Shaping objects from flat plates with tension-actuated curvature,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2017, vol. 36, no. 4.","chicago":"Guseinov, Ruslan, Eder Miguel, and Bernd Bickel. “CurveUps: Shaping Objects from Flat Plates with Tension-Actuated Curvature,” Vol. 36. ACM, 2017. https://doi.org/10.1145/3072959.3073709.","ista":"Guseinov R, Miguel E, Bickel B. 2017. CurveUps: Shaping objects from flat plates with tension-actuated curvature. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, ACM Transactions on Graphics, vol. 36, 64."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6397","author":[{"last_name":"Guseinov","full_name":"Guseinov, Ruslan","orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ruslan"},{"first_name":"Eder","full_name":"Miguel, Eder","last_name":"Miguel"},{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"article_processing_charge":"No","external_id":{"isi":["000406432100032"]},"title":"CurveUps: Shaping objects from flat plates with tension-actuated curvature","article_number":"64","project":[{"grant_number":"645599","name":"Soft-bodied intelligence for Manipulation","_id":"25082902-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"has_accepted_license":"1","isi":1,"year":"2017","day":"01","date_published":"2017-01-01T00:00:00Z","doi":"10.1145/3072959.3073709","date_created":"2018-12-11T11:49:38Z","quality_controlled":"1","publisher":"ACM","oa":1,"date_updated":"2023-09-22T09:49:58Z","ddc":["003","004"],"file_date_updated":"2018-12-12T10:10:24Z","department":[{"_id":"BeBi"}],"_id":"1001","type":"conference","conference":{"location":"Los Angeles, CA, United States","end_date":"2017-08-25","start_date":"2017-08-19","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"status":"public","pubrep_id":"1053","publication_status":"published","file":[{"date_created":"2018-12-12T10:10:24Z","file_name":"IST-2018-1053-v1+1_CurveUp.pdf","creator":"system","date_updated":"2018-12-12T10:10:24Z","file_size":36159696,"file_id":"4811","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"issue":"4","related_material":{"record":[{"relation":"dissertation_contains","id":"8366","status":"public"}]},"volume":36,"ec_funded":1,"abstract":[{"text":"We present a computational approach for designing CurveUps, curvy shells that form from an initially flat state. They consist of small rigid tiles that are tightly held together by two pre-stretched elastic sheets attached to them. Our method allows the realization of smooth, doubly curved surfaces that can be fabricated as a flat piece. Once released, the restoring forces of the pre-stretched sheets support the object to take shape in 3D. CurveUps are structurally stable in their target configuration. The design process starts with a target surface. Our method generates a tile layout in 2D and optimizes the distribution, shape, and attachment areas of the tiles to obtain a configuration that is fabricable and in which the curved up state closely matches the target. Our approach is based on an efficient approximate model and a local optimization strategy for an otherwise intractable nonlinear optimization problem. We demonstrate the effectiveness of our approach for a wide range of shapes, all realized as physical prototypes.","lang":"eng"}],"oa_version":"Submitted Version","alternative_title":["ACM Transactions on Graphics"],"month":"01","intvolume":" 36"},{"article_processing_charge":"No","external_id":{"isi":["000764137500011"]},"author":[{"first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy"},{"last_name":"Guha","full_name":"Guha, Shibashis","first_name":"Shibashis"},{"first_name":"Orna","full_name":"Kupferman, Orna","last_name":"Kupferman"}],"publist_id":"6395","title":"An abstraction-refinement methodology for reasoning about network games","citation":{"mla":"Avni, Guy, et al. An Abstraction-Refinement Methodology for Reasoning about Network Games. AAAI Press, 2017, pp. 70–76, doi:10.24963/ijcai.2017/11.","ama":"Avni G, Guha S, Kupferman O. An abstraction-refinement methodology for reasoning about network games. In: AAAI Press; 2017:70-76. doi:10.24963/ijcai.2017/11","apa":"Avni, G., Guha, S., & Kupferman, O. (2017). An abstraction-refinement methodology for reasoning about network games (pp. 70–76). Presented at the IJCAI: International Joint Conference on Artificial Intelligence , Melbourne, Australia: AAAI Press. https://doi.org/10.24963/ijcai.2017/11","short":"G. Avni, S. Guha, O. Kupferman, in:, AAAI Press, 2017, pp. 70–76.","ieee":"G. Avni, S. Guha, and O. Kupferman, “An abstraction-refinement methodology for reasoning about network games,” presented at the IJCAI: International Joint Conference on Artificial Intelligence , Melbourne, Australia, 2017, pp. 70–76.","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “An Abstraction-Refinement Methodology for Reasoning about Network Games,” 70–76. AAAI Press, 2017. https://doi.org/10.24963/ijcai.2017/11.","ista":"Avni G, Guha S, Kupferman O. 2017. An abstraction-refinement methodology for reasoning about network games. IJCAI: International Joint Conference on Artificial Intelligence , 70–76."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"page":"70 - 76","date_created":"2018-12-11T11:49:38Z","date_published":"2017-05-30T00:00:00Z","doi":"10.24963/ijcai.2017/11","year":"2017","has_accepted_license":"1","isi":1,"day":"30","oa":1,"publisher":"AAAI Press","quality_controlled":"1","department":[{"_id":"ToHe"}],"file_date_updated":"2018-12-12T10:16:58Z","date_updated":"2023-09-22T09:49:00Z","ddc":["004"],"conference":{"location":"Melbourne, Australia","end_date":"2017-08-25","start_date":"2017-08-19","name":"IJCAI: International Joint Conference on Artificial Intelligence "},"type":"conference","pubrep_id":"818","status":"public","_id":"1003","related_material":{"record":[{"status":"public","id":"6006","relation":"later_version"}]},"publication_status":"published","publication_identifier":{"issn":["10450823"]},"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2017-818-v1+1_allIJCAI_CR.pdf","date_created":"2018-12-12T10:16:58Z","creator":"system","file_size":365172,"date_updated":"2018-12-12T10:16:58Z","file_id":"5249","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"scopus_import":"1","month":"05","abstract":[{"lang":"eng","text":"Network games (NGs) are played on directed graphs and are extensively used in network design and analysis. Search problems for NGs include finding special strategy profiles such as a Nash equilibrium and a globally optimal solution. The networks modeled by NGs may be huge. In formal verification, abstraction has proven to be an extremely effective technique for reasoning about systems with big and even infinite state spaces. We describe an abstraction-refinement methodology for reasoning about NGs. Our methodology is based on an abstraction function that maps the state space of an NG to a much smaller state space. We search for a global optimum and a Nash equilibrium by reasoning on an under- and an overapproximation defined on top of this smaller state space. When the approximations are too coarse to find such profiles, we refine the abstraction function. Our experimental results demonstrate the efficiency of the methodology."}],"oa_version":"Submitted Version"},{"acknowledgement":"We thank Tim Salimans for spotting a mistake in our preliminary arXiv manuscript. This work was funded by the European Research Council under the European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 308036.","oa":1,"quality_controlled":"1","publisher":"JMLR","publication":"34th International Conference on Machine Learning","day":"01","year":"2017","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:49:37Z","date_published":"2017-08-01T00:00:00Z","page":"1905 - 1914","project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Kolesnikov, Alexander, and Christoph Lampert. “PixelCNN Models with Auxiliary Variables for Natural Image Modeling.” 34th International Conference on Machine Learning, vol. 70, JMLR, 2017, pp. 1905–14.","apa":"Kolesnikov, A., & Lampert, C. (2017). PixelCNN models with auxiliary variables for natural image modeling. In 34th International Conference on Machine Learning (Vol. 70, pp. 1905–1914). Sydney, Australia: JMLR.","ama":"Kolesnikov A, Lampert C. PixelCNN models with auxiliary variables for natural image modeling. In: 34th International Conference on Machine Learning. Vol 70. JMLR; 2017:1905-1914.","ieee":"A. Kolesnikov and C. Lampert, “PixelCNN models with auxiliary variables for natural image modeling,” in 34th International Conference on Machine Learning, Sydney, Australia, 2017, vol. 70, pp. 1905–1914.","short":"A. Kolesnikov, C. Lampert, in:, 34th International Conference on Machine Learning, JMLR, 2017, pp. 1905–1914.","chicago":"Kolesnikov, Alexander, and Christoph Lampert. “PixelCNN Models with Auxiliary Variables for Natural Image Modeling.” In 34th International Conference on Machine Learning, 70:1905–14. JMLR, 2017.","ista":"Kolesnikov A, Lampert C. 2017. PixelCNN models with auxiliary variables for natural image modeling. 34th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 70, 1905–1914."},"title":"PixelCNN models with auxiliary variables for natural image modeling","article_processing_charge":"No","external_id":{"arxiv":["1612.08185"],"isi":["000683309501102"]},"publist_id":"6398","author":[{"full_name":"Kolesnikov, Alexander","last_name":"Kolesnikov","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We study probabilistic models of natural images and extend the autoregressive family of PixelCNN models by incorporating latent variables. Subsequently, we describe two new generative image models that exploit different image transformations as latent variables: a quantized grayscale view of the image or a multi-resolution image pyramid. The proposed models tackle two known shortcomings of existing PixelCNN models: 1) their tendency to focus on low-level image details, while largely ignoring high-level image information, such as object shapes, and 2) their computationally costly procedure for image sampling. We experimentally demonstrate benefits of our LatentPixelCNN models, in particular showing that they produce much more realistically looking image samples than previous state-of-the-art probabilistic models. "}],"intvolume":" 70","month":"08","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1612.08185"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-151085514-4"]},"ec_funded":1,"volume":70,"_id":"1000","status":"public","conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2017-08-06","end_date":"2017-08-11","location":"Sydney, Australia"},"type":"conference","date_updated":"2023-09-22T09:50:41Z","department":[{"_id":"ChLa"}]},{"department":[{"_id":"ChLa"},{"_id":"ChWo"}],"date_updated":"2023-09-22T09:51:58Z","status":"public","type":"conference","conference":{"end_date":"2017-07-26","location":"Honolulu, HA, United States","start_date":"2017-07-21","name":"CVPR: Computer Vision and Pattern Recognition"},"_id":"998","volume":2017,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-153860457-1"]},"publication_status":"published","month":"04","intvolume":" 2017","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1611.07725","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"A major open problem on the road to artificial intelligence is the development of incrementally learning systems that learn about more and more concepts over time from a stream of data. In this work, we introduce a new training strategy, iCaRL, that allows learning in such a class-incremental way: only the training data for a small number of classes has to be present at the same time and new classes can be added progressively. iCaRL learns strong classifiers and a data representation simultaneously. This distinguishes it from earlier works that were fundamentally limited to fixed data representations and therefore incompatible with deep learning architectures. We show by experiments on CIFAR-100 and ImageNet ILSVRC 2012 data that iCaRL can learn many classes incrementally over a long period of time where other strategies quickly fail. "}],"title":"iCaRL: Incremental classifier and representation learning","publist_id":"6400","author":[{"first_name":"Sylvestre Alvise","last_name":"Rebuffi","full_name":"Rebuffi, Sylvestre Alvise"},{"first_name":"Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov","full_name":"Kolesnikov, Alexander"},{"first_name":"Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","full_name":"Sperl, Georg","last_name":"Sperl"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert"}],"article_processing_charge":"No","external_id":{"isi":["000418371405066"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Rebuffi, Sylvestre Alvise, Alexander Kolesnikov, Georg Sperl, and Christoph Lampert. “ICaRL: Incremental Classifier and Representation Learning,” 2017:5533–42. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.587.","ista":"Rebuffi SA, Kolesnikov A, Sperl G, Lampert C. 2017. iCaRL: Incremental classifier and representation learning. CVPR: Computer Vision and Pattern Recognition vol. 2017, 5533–5542.","mla":"Rebuffi, Sylvestre Alvise, et al. ICaRL: Incremental Classifier and Representation Learning. Vol. 2017, IEEE, 2017, pp. 5533–42, doi:10.1109/CVPR.2017.587.","apa":"Rebuffi, S. A., Kolesnikov, A., Sperl, G., & Lampert, C. (2017). iCaRL: Incremental classifier and representation learning (Vol. 2017, pp. 5533–5542). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.587","ama":"Rebuffi SA, Kolesnikov A, Sperl G, Lampert C. iCaRL: Incremental classifier and representation learning. In: Vol 2017. IEEE; 2017:5533-5542. doi:10.1109/CVPR.2017.587","short":"S.A. Rebuffi, A. Kolesnikov, G. Sperl, C. Lampert, in:, IEEE, 2017, pp. 5533–5542.","ieee":"S. A. Rebuffi, A. Kolesnikov, G. Sperl, and C. Lampert, “iCaRL: Incremental classifier and representation learning,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 5533–5542."},"project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"doi":"10.1109/CVPR.2017.587","date_published":"2017-04-14T00:00:00Z","date_created":"2018-12-11T11:49:37Z","page":"5533 - 5542","day":"14","isi":1,"year":"2017","publisher":"IEEE","quality_controlled":"1","oa":1},{"_id":"990","type":"journal_article","pubrep_id":"977","status":"public","date_updated":"2023-09-22T09:55:13Z","ddc":["576"],"file_date_updated":"2020-07-14T12:48:18Z","department":[{"_id":"NiBa"}],"abstract":[{"text":"Assortative mating is an important driver of speciation in populations with gene flow and is predicted to evolve under certain conditions in few-locus models. However, the evolution of assortment is less understood for mating based on quantitative traits, which are often characterized by high genetic variability and extensive linkage disequilibrium between trait loci. We explore this scenario for a two-deme model with migration, by considering a single polygenic trait subject to divergent viability selection across demes, as well as assortative mating and sexual selection within demes, and investigate how trait divergence is shaped by various evolutionary forces. Our analysis reveals the existence of sharp thresholds of assortment strength, at which divergence increases dramatically. We also study the evolution of assortment via invasion of modifiers of mate discrimination and show that the ES assortment strength has an intermediate value under a range of migration-selection parameters, even in diverged populations, due to subtle effects which depend sensitively on the extent of phenotypic variation within these populations. The evolutionary dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal models. We further investigate the sensitivity of our results to the assumptions of the hypergeometric model, using individual-based simulations.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"scopus_import":"1","intvolume":" 71","month":"06","publication_status":"published","publication_identifier":{"issn":["00143820"]},"language":[{"iso":"eng"}],"file":[{"checksum":"6d4c38cb1347fd43620d1736c6df5c79","file_id":"6329","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-04-17T07:37:04Z","file_name":"2017_Evolution_Sachdeva_supplement.pdf","date_updated":"2020-07-14T12:48:18Z","file_size":625260,"creator":"dernst"},{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"f1d90dd8831b44baf49b4dd176f263af","file_id":"6330","creator":"dernst","date_updated":"2020-07-14T12:48:18Z","file_size":520110,"date_created":"2019-04-17T07:37:04Z","file_name":"2017_Evolution_Sachdeva_article.pdf"}],"ec_funded":1,"volume":71,"issue":"6","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"ista":"Sachdeva H, Barton NH. 2017. Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. Evolution; International Journal of Organic Evolution. 71(6), 1478–1493.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Divergence and Evolution of Assortative Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution; International Journal of Organic Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13252.","short":"H. Sachdeva, N.H. Barton, Evolution; International Journal of Organic Evolution 71 (2017) 1478–1493.","ieee":"H. Sachdeva and N. H. Barton, “Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow,” Evolution; International Journal of Organic Evolution, vol. 71, no. 6. Wiley-Blackwell, pp. 1478–1493, 2017.","ama":"Sachdeva H, Barton NH. Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. Evolution; International Journal of Organic Evolution. 2017;71(6):1478-1493. doi:10.1111/evo.13252","apa":"Sachdeva, H., & Barton, N. H. (2017). Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. Evolution; International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13252","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Divergence and Evolution of Assortative Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution; International Journal of Organic Evolution, vol. 71, no. 6, Wiley-Blackwell, 2017, pp. 1478–93, doi:10.1111/evo.13252."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"pmid":["28419447"],"isi":["000403014800005"]},"article_processing_charge":"No","author":[{"first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani","last_name":"Sachdeva"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"publist_id":"6409","title":"Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow","oa":1,"quality_controlled":"1","publisher":"Wiley-Blackwell","year":"2017","isi":1,"has_accepted_license":"1","publication":"Evolution; International Journal of Organic Evolution","day":"01","page":"1478 - 1493 ","date_created":"2018-12-11T11:49:34Z","doi":"10.1111/evo.13252","date_published":"2017-06-01T00:00:00Z"},{"volume":17,"issue":"6","publication_status":"published","publication_identifier":{"issn":["15306984"]},"language":[{"iso":"eng"}],"file":[{"checksum":"22021daa90cf13b01becd776838acb7b","file_id":"5037","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2017-826-v1+1_2017_Aguilera-Servin_Current.pdf","date_created":"2018-12-12T10:13:50Z","file_size":508638,"date_updated":"2020-07-14T12:48:18Z","creator":"system"}],"scopus_import":"1","intvolume":" 17","month":"05","abstract":[{"lang":"eng","text":"The current-phase relation (CPR) of a Josephson junction (JJ) determines how the supercurrent evolves with the superconducting phase difference across the junction. Knowledge of the CPR is essential in order to understand the response of a JJ to various external parameters. Despite the rising interest in ultraclean encapsulated graphene JJs, the CPR of such junctions remains unknown. Here, we use a fully gate-tunable graphene superconducting quantum intereference device (SQUID) to determine the CPR of ballistic graphene JJs. Each of the two JJs in the SQUID is made with graphene encapsulated in hexagonal boron nitride. By independently controlling the critical current of the JJs, we can operate the SQUID either in a symmetric or asymmetric configuration. The highly asymmetric SQUID allows us to phase-bias one of the JJs and thereby directly obtain its CPR. The CPR is found to be skewed, deviating significantly from a sinusoidal form. The skewness can be tuned with the gate voltage and oscillates in antiphase with Fabry-Pérot resistance oscillations of the ballistic graphene cavity. We compare our experiments with tight-binding calculations that include realistic graphene-superconductor interfaces and find a good qualitative agreement."}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:18Z","department":[{"_id":"NanoFab"}],"date_updated":"2023-09-22T09:56:21Z","ddc":["621"],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","pubrep_id":"826","status":"public","_id":"988","page":"3396 - 3401","date_created":"2018-12-11T11:49:33Z","date_published":"2017-05-05T00:00:00Z","doi":"10.1021/acs.nanolett.7b00097","year":"2017","isi":1,"has_accepted_license":"1","publication":"Nano Letters","day":"05","oa":1,"quality_controlled":"1","publisher":"American Chemical Society","external_id":{"isi":["000403631600011"]},"article_processing_charge":"No","author":[{"first_name":"Gaurav","full_name":"Nanda, Gaurav","last_name":"Nanda"},{"first_name":"Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","full_name":"Aguilera Servin, Juan L","orcid":"0000-0002-2862-8372","last_name":"Aguilera Servin"},{"first_name":"Péter","last_name":"Rakyta","full_name":"Rakyta, Péter"},{"full_name":"Kormányos, Andor","last_name":"Kormányos","first_name":"Andor"},{"full_name":"Kleiner, Reinhold","last_name":"Kleiner","first_name":"Reinhold"},{"full_name":"Koelle, Dieter","last_name":"Koelle","first_name":"Dieter"},{"first_name":"Kazuo","full_name":"Watanabe, Kazuo","last_name":"Watanabe"},{"first_name":"Takashi","full_name":"Taniguchi, Takashi","last_name":"Taniguchi"},{"first_name":"Lieven","full_name":"Vandersypen, Lieven","last_name":"Vandersypen"},{"first_name":"Srijit","full_name":"Goswami, Srijit","last_name":"Goswami"}],"publist_id":"6412","title":"Current-phase relation of ballistic graphene Josephson junctions","citation":{"chicago":"Nanda, Gaurav, Juan L Aguilera Servin, Péter Rakyta, Andor Kormányos, Reinhold Kleiner, Dieter Koelle, Kazuo Watanabe, Takashi Taniguchi, Lieven Vandersypen, and Srijit Goswami. “Current-Phase Relation of Ballistic Graphene Josephson Junctions.” Nano Letters. American Chemical Society, 2017. https://doi.org/10.1021/acs.nanolett.7b00097.","ista":"Nanda G, Aguilera Servin JL, Rakyta P, Kormányos A, Kleiner R, Koelle D, Watanabe K, Taniguchi T, Vandersypen L, Goswami S. 2017. Current-phase relation of ballistic graphene Josephson junctions. Nano Letters. 17(6), 3396–3401.","mla":"Nanda, Gaurav, et al. “Current-Phase Relation of Ballistic Graphene Josephson Junctions.” Nano Letters, vol. 17, no. 6, American Chemical Society, 2017, pp. 3396–401, doi:10.1021/acs.nanolett.7b00097.","short":"G. Nanda, J.L. Aguilera Servin, P. Rakyta, A. Kormányos, R. Kleiner, D. Koelle, K. Watanabe, T. Taniguchi, L. Vandersypen, S. Goswami, Nano Letters 17 (2017) 3396–3401.","ieee":"G. Nanda et al., “Current-phase relation of ballistic graphene Josephson junctions,” Nano Letters, vol. 17, no. 6. American Chemical Society, pp. 3396–3401, 2017.","apa":"Nanda, G., Aguilera Servin, J. L., Rakyta, P., Kormányos, A., Kleiner, R., Koelle, D., … Goswami, S. (2017). Current-phase relation of ballistic graphene Josephson junctions. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b00097","ama":"Nanda G, Aguilera Servin JL, Rakyta P, et al. Current-phase relation of ballistic graphene Josephson junctions. Nano Letters. 2017;17(6):3396-3401. doi:10.1021/acs.nanolett.7b00097"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"date_created":"2018-12-11T11:49:35Z","doi":"10.1038/ncomms15140","date_published":"2017-05-04T00:00:00Z","year":"2017","has_accepted_license":"1","isi":1,"publication":"Nature Communications","day":"04","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000400560700001"]},"publist_id":"6406","author":[{"first_name":"Anna","id":"35AF8020-F248-11E8-B48F-1D18A9856A87","full_name":"Levina (Martius), Anna","last_name":"Levina (Martius)"},{"last_name":"Priesemann","full_name":"Priesemann, Viola","first_name":"Viola"}],"title":"Subsampling scaling","citation":{"mla":"Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” Nature Communications, vol. 8, 15140, Nature Publishing Group, 2017, doi:10.1038/ncomms15140.","ama":"Levina (Martius) A, Priesemann V. Subsampling scaling. Nature Communications. 2017;8. doi:10.1038/ncomms15140","apa":"Levina (Martius), A., & Priesemann, V. (2017). Subsampling scaling. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms15140","short":"A. Levina (Martius), V. Priesemann, Nature Communications 8 (2017).","ieee":"A. Levina (Martius) and V. Priesemann, “Subsampling scaling,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","chicago":"Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms15140.","ista":"Levina (Martius) A, Priesemann V. 2017. Subsampling scaling. Nature Communications. 8, 15140."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"article_number":"15140","ec_funded":1,"volume":8,"publication_status":"published","publication_identifier":{"issn":["20411723"]},"language":[{"iso":"eng"}],"file":[{"checksum":"9880212f8c4c53404c7c6fbf9023c53a","file_id":"5122","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-819-v1+1_2017_Levina_SubsamplingScaling.pdf","date_created":"2018-12-12T10:15:05Z","creator":"system","file_size":746224,"date_updated":"2020-07-14T12:48:19Z"}],"scopus_import":"1","intvolume":" 8","month":"05","abstract":[{"lang":"eng","text":"In real-world applications, observations are often constrained to a small fraction of a system. Such spatial subsampling can be caused by the inaccessibility or the sheer size of the system, and cannot be overcome by longer sampling. Spatial subsampling can strongly bias inferences about a system’s aggregated properties. To overcome the bias, we derive analytically a subsampling scaling framework that is applicable to different observables, including distributions of neuronal avalanches, of number of people infected during an epidemic outbreak, and of node degrees. We demonstrate how to infer the correct distributions of the underlying full system, how to apply it to distinguish critical from subcritical systems, and how to disentangle subsampling and finite size effects. Lastly, we apply subsampling scaling to neuronal avalanche models and to recordings from developing neural networks. We show that only mature, but not young networks follow power-law scaling, indicating self-organization to criticality during development."}],"oa_version":"Published Version","department":[{"_id":"GaTk"},{"_id":"JoCs"}],"file_date_updated":"2020-07-14T12:48:19Z","date_updated":"2023-09-22T09:54:07Z","ddc":["005","571"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"819","status":"public","_id":"993"},{"date_updated":"2023-09-22T09:53:17Z","department":[{"_id":"MiLe"}],"_id":"995","type":"journal_article","status":"public","publication_identifier":{"issn":["24699950"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":96,"issue":"8","abstract":[{"lang":"eng","text":"Recently it was shown that an impurity exchanging orbital angular momentum with a surrounding bath can be described in terms of the angulon quasiparticle [Phys. Rev. Lett. 118, 095301 (2017)]. The angulon consists of a quantum rotor dressed by a many-particle field of boson excitations, and can be formed out of, for example, a molecule or a nonspherical atom in superfluid helium, or out of an electron coupled to lattice phonons or a Bose condensate. Here we develop an approach to the angulon based on the path-integral formalism, which sets the ground for a systematic, perturbative treatment of the angulon problem. The resulting perturbation series can be interpreted in terms of Feynman diagrams, from which, in turn, one can derive a set of diagrammatic rules. These rules extend the machinery of the graphical theory of angular momentum - well known from theoretical atomic spectroscopy - to the case where an environment with an infinite number of degrees of freedom is present. In particular, we show that each diagram can be interpreted as a 'skeleton', which enforces angular momentum conservation, dressed by an additional many-body contribution. This connection between the angulon theory and the graphical theory of angular momentum is particularly important as it allows to systematically and substantially simplify the analytical representation of each diagram. In order to exemplify the technique, we calculate the 1- and 2-loop contributions to the angulon self-energy, the spectral function, and the quasiparticle weight. The diagrammatic theory we develop paves the way to investigate next-to-leading order quantities in a more compact way compared to the variational approaches."}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1704.02616","open_access":"1"}],"month":"08","intvolume":" 96","citation":{"ieee":"G. Bighin and M. Lemeshko, “Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment,” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 8. American Physical Society, 2017.","short":"G. Bighin, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 96 (2017).","apa":"Bighin, G., & Lemeshko, M. (2017). Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.96.085410","ama":"Bighin G, Lemeshko M. Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment. Physical Review B - Condensed Matter and Materials Physics. 2017;96(8). doi:10.1103/PhysRevB.96.085410","mla":"Bighin, Giacomo, and Mikhail Lemeshko. “Diagrammatic Approach to Orbital Quantum Impurities Interacting with a Many-Particle Environment.” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 8, 085410, American Physical Society, 2017, doi:10.1103/PhysRevB.96.085410.","ista":"Bighin G, Lemeshko M. 2017. Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment. Physical Review B - Condensed Matter and Materials Physics. 96(8), 085410.","chicago":"Bighin, Giacomo, and Mikhail Lemeshko. “Diagrammatic Approach to Orbital Quantum Impurities Interacting with a Many-Particle Environment.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.085410."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6404","author":[{"orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo","last_name":"Bighin","first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}],"external_id":{"isi":["000407017100009"]},"article_processing_charge":"No","title":"Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment","article_number":"085410","project":[{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"isi":1,"year":"2017","day":"07","publication":"Physical Review B - Condensed Matter and Materials Physics","doi":"10.1103/PhysRevB.96.085410","date_published":"2017-08-07T00:00:00Z","date_created":"2018-12-11T11:49:36Z","quality_controlled":"1","publisher":"American Physical Society","oa":1},{"title":"Transport based image morphing with intensity modulation","editor":[{"full_name":"Lauze, François","last_name":"Lauze","first_name":"François"},{"first_name":"Yiqiu","full_name":"Dong, Yiqiu","last_name":"Dong"},{"first_name":"Anders","last_name":"Bjorholm Dahl","full_name":"Bjorholm Dahl, Anders"}],"external_id":{"isi":["000432210900045"]},"article_processing_charge":"No","publist_id":"6410","author":[{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas"},{"full_name":"Rumpf, Martin","last_name":"Rumpf","first_name":"Martin"},{"first_name":"Stefan","last_name":"Simon","full_name":"Simon, Stefan"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Maas, J., Rumpf, M., & Simon, S. (2017). Transport based image morphing with intensity modulation. In F. Lauze, Y. Dong, & A. Bjorholm Dahl (Eds.) (Vol. 10302, pp. 563–577). Presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark: Springer. https://doi.org/10.1007/978-3-319-58771-4_45","ama":"Maas J, Rumpf M, Simon S. Transport based image morphing with intensity modulation. In: Lauze F, Dong Y, Bjorholm Dahl A, eds. Vol 10302. Springer; 2017:563-577. doi:10.1007/978-3-319-58771-4_45","ieee":"J. Maas, M. Rumpf, and S. Simon, “Transport based image morphing with intensity modulation,” presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark, 2017, vol. 10302, pp. 563–577.","short":"J. Maas, M. Rumpf, S. Simon, in:, F. Lauze, Y. Dong, A. Bjorholm Dahl (Eds.), Springer, 2017, pp. 563–577.","mla":"Maas, Jan, et al. Transport Based Image Morphing with Intensity Modulation. Edited by François Lauze et al., vol. 10302, Springer, 2017, pp. 563–77, doi:10.1007/978-3-319-58771-4_45.","ista":"Maas J, Rumpf M, Simon S. 2017. Transport based image morphing with intensity modulation. SSVM: Scale Space and Variational Methods in Computer Vision, LNCS, vol. 10302, 563–577.","chicago":"Maas, Jan, Martin Rumpf, and Stefan Simon. “Transport Based Image Morphing with Intensity Modulation.” edited by François Lauze, Yiqiu Dong, and Anders Bjorholm Dahl, 10302:563–77. Springer, 2017. https://doi.org/10.1007/978-3-319-58771-4_45."},"date_created":"2018-12-11T11:49:34Z","doi":"10.1007/978-3-319-58771-4_45","date_published":"2017-05-18T00:00:00Z","page":"563 - 577","day":"18","year":"2017","isi":1,"publisher":"Springer","quality_controlled":"1","department":[{"_id":"JaMa"}],"date_updated":"2023-09-22T09:55:50Z","status":"public","conference":{"location":"Kolding, Denmark","end_date":"2017-06-08","start_date":"2017-06-04","name":"SSVM: Scale Space and Variational Methods in Computer Vision"},"type":"conference","_id":"989","volume":10302,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["03029743"]},"intvolume":" 10302","month":"05","alternative_title":["LNCS"],"scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"We present a generalized optimal transport model in which the mass-preserving constraint for the L2-Wasserstein distance is relaxed by introducing a source term in the continuity equation. The source term is also incorporated in the path energy by means of its squared L2-norm in time of a functional with linear growth in space. This extension of the original transport model enables local density modulations, which is a desirable feature in applications such as image warping and blending. A key advantage of the use of a functional with linear growth in space is that it allows for singular sources and sinks, which can be supported on points or lines. On a technical level, the L2-norm in time ensures a disintegration of the source in time, which we use to obtain the well-posedness of the model and the existence of geodesic paths. The numerical discretization is based on the proximal splitting approach [18] and selected numerical test cases show the potential of the proposed approach. Furthermore, the approach is applied to the warping and blending of textures."}]},{"title":"Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules","publist_id":"6405","author":[{"id":"339C7E5A-F248-11E8-B48F-1D18A9856A87","first_name":"Igor","last_name":"Cherepanov","full_name":"Cherepanov, Igor"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000416564000004"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Cherepanov I, Lemeshko M. 2017. Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules. Physical Review Materials. 1(3).","chicago":"Cherepanov, Igor, and Mikhail Lemeshko. “Fingerprints of Angulon Instabilities in the Spectra of Matrix-Isolated Molecules.” Physical Review Materials. American Physical Society, 2017. https://doi.org/10.1103/PhysRevMaterials.1.035602.","apa":"Cherepanov, I., & Lemeshko, M. (2017). Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules. Physical Review Materials. American Physical Society. https://doi.org/10.1103/PhysRevMaterials.1.035602","ama":"Cherepanov I, Lemeshko M. Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules. Physical Review Materials. 2017;1(3). doi:10.1103/PhysRevMaterials.1.035602","ieee":"I. Cherepanov and M. Lemeshko, “Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules,” Physical Review Materials, vol. 1, no. 3. American Physical Society, 2017.","short":"I. Cherepanov, M. Lemeshko, Physical Review Materials 1 (2017).","mla":"Cherepanov, Igor, and Mikhail Lemeshko. “Fingerprints of Angulon Instabilities in the Spectra of Matrix-Isolated Molecules.” Physical Review Materials, vol. 1, no. 3, American Physical Society, 2017, doi:10.1103/PhysRevMaterials.1.035602."},"project":[{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"date_published":"2017-08-08T00:00:00Z","doi":"10.1103/PhysRevMaterials.1.035602","date_created":"2018-12-11T11:49:35Z","day":"08","publication":"Physical Review Materials","isi":1,"year":"2017","publisher":"American Physical Society","quality_controlled":"1","oa":1,"department":[{"_id":"MiLe"}],"date_updated":"2023-09-22T09:53:42Z","status":"public","type":"journal_article","_id":"994","issue":"3","volume":1,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"08","intvolume":" 1","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1705.09220","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"text":"The formation of vortices is usually considered to be the main mechanism of angular momentum disposal in superfluids. Recently, it was predicted that a superfluid can acquire angular momentum via an alternative, microscopic route -- namely, through interaction with rotating impurities, forming so-called `angulon quasiparticles' [Phys. Rev. Lett. 114, 203001 (2015)]. The angulon instabilities correspond to transfer of a small number of angular momentum quanta from the impurity to the superfluid, as opposed to vortex instabilities, where angular momentum is quantized in units of ℏ per atom. Furthermore, since conventional impurities (such as molecules) represent three-dimensional (3D) rotors, the angular momentum transferred is intrinsically 3D as well, as opposed to a merely planar rotation which is inherent to vortices. Herein we show that the angulon theory can explain the anomalous broadening of the spectroscopic lines observed for CH 3 and NH 3 molecules in superfluid helium nanodroplets, thereby providing a fingerprint of the emerging angulon instabilities in experiment.","lang":"eng"}]},{"volume":94,"issue":"4","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["08966273"]},"intvolume":" 94","month":"05","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"Synaptotagmin 7 (Syt7) was originally identified as a slow Ca2+ sensor for lysosome fusion, but its function at fast synapses is controversial. The paper by Luo and Südhof (2017) in this issue of Neuron shows that at the calyx of Held in the auditory brainstem Syt7 triggers asynchronous release during stimulus trains, resulting in reliable and temporally precise high-frequency transmission. Thus, a slow Ca2+ sensor contributes to the fast signaling properties of the calyx synapse."}],"department":[{"_id":"PeJo"}],"date_updated":"2023-09-22T09:54:37Z","status":"public","type":"journal_article","_id":"991","date_created":"2018-12-11T11:49:34Z","date_published":"2017-05-17T00:00:00Z","doi":"10.1016/j.neuron.2017.05.011","page":"694 - 696","publication":"Neuron","day":"17","year":"2017","isi":1,"publisher":"Elsevier","quality_controlled":"1","title":"Synaptotagmins: That’s why so many","external_id":{"isi":["000401415100002"]},"article_processing_charge":"No","author":[{"first_name":"Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","full_name":"Chen, Chong"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas"}],"publist_id":"6408","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Chen C, Jonas PM. 2017. Synaptotagmins: That’s why so many. Neuron. 94(4), 694–696.","chicago":"Chen, Chong, and Peter M Jonas. “Synaptotagmins: That’s Why so Many.” Neuron. Elsevier, 2017. https://doi.org/10.1016/j.neuron.2017.05.011.","ieee":"C. Chen and P. M. Jonas, “Synaptotagmins: That’s why so many,” Neuron, vol. 94, no. 4. Elsevier, pp. 694–696, 2017.","short":"C. Chen, P.M. Jonas, Neuron 94 (2017) 694–696.","apa":"Chen, C., & Jonas, P. M. (2017). Synaptotagmins: That’s why so many. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2017.05.011","ama":"Chen C, Jonas PM. Synaptotagmins: That’s why so many. Neuron. 2017;94(4):694-696. doi:10.1016/j.neuron.2017.05.011","mla":"Chen, Chong, and Peter M. Jonas. “Synaptotagmins: That’s Why so Many.” Neuron, vol. 94, no. 4, Elsevier, 2017, pp. 694–96, doi:10.1016/j.neuron.2017.05.011."}},{"project":[{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"article_number":"e25192","author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato","full_name":"Lagator, Mato","last_name":"Lagator"},{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"last_name":"Bollback","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"publist_id":"6460","external_id":{"isi":["000404024800001"]},"article_processing_charge":"Yes","title":"On the mechanistic nature of epistasis in a canonical cis-regulatory element","citation":{"chicago":"Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25192.","ista":"Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 6, e25192.","mla":"Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife, vol. 6, e25192, eLife Sciences Publications, 2017, doi:10.7554/eLife.25192.","ama":"Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192","apa":"Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., & Guet, C. C. (2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25192","ieee":"M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the mechanistic nature of epistasis in a canonical cis-regulatory element,” eLife, vol. 6. eLife Sciences Publications, 2017.","short":"M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"doi":"10.7554/eLife.25192","date_published":"2017-05-18T00:00:00Z","date_created":"2018-12-11T11:49:23Z","isi":1,"has_accepted_license":"1","year":"2017","day":"18","publication":"eLife","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"841","_id":"954","department":[{"_id":"CaGu"},{"_id":"NiBa"},{"_id":"JoBo"}],"file_date_updated":"2020-07-14T12:48:16Z","date_updated":"2023-09-22T10:01:17Z","ddc":["576"],"scopus_import":"1","month":"05","intvolume":" 6","abstract":[{"lang":"eng","text":"Understanding the relation between genotype and phenotype remains a major challenge. The difficulty of predicting individual mutation effects, and particularly the interactions between them, has prevented the development of a comprehensive theory that links genotypic changes to their phenotypic effects. We show that a general thermodynamic framework for gene regulation, based on a biophysical understanding of protein-DNA binding, accurately predicts the sign of epistasis in a canonical cis-regulatory element consisting of overlapping RNA polymerase and repressor binding sites. Sign and magnitude of individual mutation effects are sufficient to predict the sign of epistasis and its environmental dependence. Thus, the thermodynamic model offers the correct null prediction for epistasis between mutations across DNA-binding sites. Our results indicate that a predictive theory for the effects of cis-regulatory mutations is possible from first principles, as long as the essential molecular mechanisms and the constraints these impose on a biological system are accounted for."}],"oa_version":"Published Version","volume":6,"ec_funded":1,"publication_identifier":{"issn":["2050084X"]},"publication_status":"published","file":[{"file_name":"IST-2017-841-v1+1_elife-25192-v2.pdf","date_created":"2018-12-12T10:17:49Z","creator":"system","file_size":2441529,"date_updated":"2020-07-14T12:48:16Z","checksum":"59cdd4400fb41280122d414fea971546","file_id":"5306","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"checksum":"b69024880558b858eb8c5d47a92b6377","file_id":"5307","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-841-v1+2_elife-25192-figures-v2.pdf","date_created":"2018-12-12T10:17:50Z","creator":"system","file_size":3752660,"date_updated":"2020-07-14T12:48:16Z"}],"language":[{"iso":"eng"}]},{"oa_version":"Published Version","abstract":[{"text":"Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components.","lang":"eng"}],"month":"08","intvolume":" 8","scopus_import":"1","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5064","checksum":"29a1b5db458048d3bd5c67e0e2a56818","date_updated":"2020-07-14T12:48:16Z","file_size":998157,"creator":"system","date_created":"2018-12-12T10:14:14Z","file_name":"IST-2017-864-v1+1_s41467-017-00238-8.pdf"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"7b78401e52a576cf3e6bbf8d0abadc17","file_id":"5065","file_size":9715993,"date_updated":"2020-07-14T12:48:16Z","creator":"system","file_name":"IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf","date_created":"2018-12-12T10:14:15Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["20411723"]},"publication_status":"published","volume":8,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6071"}]},"issue":"1","ec_funded":1,"_id":"955","status":"public","pubrep_id":"864","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["539","576"],"date_updated":"2023-09-22T10:00:49Z","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:48:16Z","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"day":"09","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2017","doi":"10.1038/s41467-017-00238-8","date_published":"2017-08-09T00:00:00Z","date_created":"2018-12-11T11:49:23Z","article_number":"216","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"},{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Friedlander, T., Prizak, R., Barton, N. H., & Tkačik, G. (2017). Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00238-8","ama":"Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-00238-8","ieee":"T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","short":"T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017).","mla":"Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8.","ista":"Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 8(1), 216.","chicago":"Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00238-8."},"title":"Evolution of new regulatory functions on biophysically realistic fitness landscapes","author":[{"first_name":"Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","full_name":"Friedlander, Tamar","last_name":"Friedlander"},{"first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak","full_name":"Prizak, Roshan"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"}],"publist_id":"6459","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000407198800005"]}},{"page":"399 - 418","date_created":"2018-12-11T11:49:26Z","date_published":"2017-01-01T00:00:00Z","doi":"10.1007/978-3-319-63390-9_21","year":"2017","isi":1,"day":"01","quality_controlled":"1","publisher":"Springer","article_processing_charge":"No","external_id":{"isi":["000431900900021"]},"author":[{"first_name":"Minh","last_name":"Trinh","full_name":"Trinh, Minh"},{"last_name":"Chu","full_name":"Chu, Duc Hiep","id":"3598E630-F248-11E8-B48F-1D18A9856A87","first_name":"Duc Hiep"},{"full_name":"Jaffar, Joxan","last_name":"Jaffar","first_name":"Joxan"}],"publist_id":"6443","editor":[{"first_name":"Rupak","last_name":"Majumdar","full_name":"Majumdar, Rupak"},{"first_name":"Viktor","last_name":"Kunčak","full_name":"Kunčak, Viktor"}],"title":"Model counting for recursively-defined strings","citation":{"mla":"Trinh, Minh, et al. Model Counting for Recursively-Defined Strings. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer, 2017, pp. 399–418, doi:10.1007/978-3-319-63390-9_21.","short":"M. Trinh, D.H. Chu, J. Jaffar, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 399–418.","ieee":"M. Trinh, D. H. Chu, and J. Jaffar, “Model counting for recursively-defined strings,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10427, pp. 399–418.","apa":"Trinh, M., Chu, D. H., & Jaffar, J. (2017). Model counting for recursively-defined strings. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10427, pp. 399–418). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63390-9_21","ama":"Trinh M, Chu DH, Jaffar J. Model counting for recursively-defined strings. In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:399-418. doi:10.1007/978-3-319-63390-9_21","chicago":"Trinh, Minh, Duc Hiep Chu, and Joxan Jaffar. “Model Counting for Recursively-Defined Strings.” edited by Rupak Majumdar and Viktor Kunčak, 10427:399–418. Springer, 2017. https://doi.org/10.1007/978-3-319-63390-9_21.","ista":"Trinh M, Chu DH, Jaffar J. 2017. Model counting for recursively-defined strings. CAV: Computer Aided Verification, LNCS, vol. 10427, 399–418."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"volume":10427,"publication_status":"published","publication_identifier":{"issn":["03029743"]},"language":[{"iso":"eng"}],"alternative_title":["LNCS"],"scopus_import":"1","intvolume":" 10427","month":"01","abstract":[{"lang":"eng","text":"We present a new algorithm for model counting of a class of string constraints. In addition to the classic operation of concatenation, our class includes some recursively defined operations such as Kleene closure, and replacement of substrings. Additionally, our class also includes length constraints on the string expressions, which means, by requiring reasoning about numbers, that we face a multi-sorted logic. In the end, our string constraints are motivated by their use in programming for web applications. Our algorithm comprises two novel features: the ability to use a technique of (1) partial derivatives for constraints that are already in a solved form, i.e. a form where its (string) satisfiability is clearly displayed, and (2) non-progression, where cyclic reasoning in the reduction process may be terminated (thus allowing for the algorithm to look elsewhere). Finally, we experimentally compare our model counter with two recent works on model counting of similar constraints, SMC [18] and ABC [5], to demonstrate its superior performance."}],"oa_version":"None","department":[{"_id":"ToHe"}],"date_updated":"2023-09-22T09:58:02Z","conference":{"name":"CAV: Computer Aided Verification","location":"Heidelberg, Germany","end_date":"2017-07-28","start_date":"2017-07-24"},"type":"conference","status":"public","_id":"962"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Charlesworth, Deborah, Nicholas H Barton, and Brian Charlesworth. “The Sources of Adaptive Evolution.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2017. https://doi.org/10.1098/rspb.2016.2864.","ista":"Charlesworth D, Barton NH, Charlesworth B. 2017. The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. 284(1855), 20162864.","mla":"Charlesworth, Deborah, et al. “The Sources of Adaptive Evolution.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 284, no. 1855, 20162864, Royal Society, The, 2017, doi:10.1098/rspb.2016.2864.","short":"D. Charlesworth, N.H. Barton, B. Charlesworth, Proceedings of the Royal Society of London Series B Biological Sciences 284 (2017).","ieee":"D. Charlesworth, N. H. Barton, and B. Charlesworth, “The sources of adaptive evolution,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 284, no. 1855. Royal Society, The, 2017.","ama":"Charlesworth D, Barton NH, Charlesworth B. The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. 2017;284(1855). doi:10.1098/rspb.2016.2864","apa":"Charlesworth, D., Barton, N. H., & Charlesworth, B. (2017). The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2016.2864"},"title":"The sources of adaptive evolution","publist_id":"6462","author":[{"last_name":"Charlesworth","full_name":"Charlesworth, Deborah","first_name":"Deborah"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"full_name":"Charlesworth, Brian","last_name":"Charlesworth","first_name":"Brian"}],"article_processing_charge":"No","external_id":{"pmid":["28566483"],"isi":["000405148800021"]},"article_number":"20162864","day":"31","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","isi":1,"year":"2017","doi":"10.1098/rspb.2016.2864","date_published":"2017-05-31T00:00:00Z","date_created":"2018-12-11T11:49:23Z","quality_controlled":"1","publisher":"Royal Society, The","oa":1,"date_updated":"2023-09-22T10:01:48Z","department":[{"_id":"NiBa"}],"_id":"953","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","volume":284,"issue":"1855","pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed.","lang":"eng"}],"month":"05","intvolume":" 284","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454256/"}]},{"oa":1,"quality_controlled":"1","publisher":"American Institute of Physics","publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","day":"28","year":"2017","isi":1,"date_created":"2018-12-11T11:49:25Z","doi":"10.1103/PhysRevE.95.062419","date_published":"2017-06-28T00:00:00Z","page":"062419","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 95, no. 6, American Institute of Physics, 2017, p. 062419, doi:10.1103/PhysRevE.95.062419.","ama":"De Martino D. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. Physical Review E Statistical Nonlinear and Soft Matter Physics . 2017;95(6):062419. doi:10.1103/PhysRevE.95.062419","apa":"De Martino, D. (2017). Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.95.062419","short":"D. De Martino, Physical Review E Statistical Nonlinear and Soft Matter Physics 95 (2017) 062419.","ieee":"D. De Martino, “Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics,” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 95, no. 6. American Institute of Physics, p. 062419, 2017.","chicago":"De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.95.062419.","ista":"De Martino D. 2017. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. Physical Review E Statistical Nonlinear and Soft Matter Physics . 95(6), 062419."},"title":"Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics","external_id":{"isi":["000404546400004"]},"article_processing_charge":"No","author":[{"last_name":"De Martino","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele"}],"publist_id":"6446","oa_version":"Submitted Version","abstract":[{"text":"In this work it is shown that scale-free tails in metabolic flux distributions inferred in stationary models are an artifact due to reactions involved in thermodynamically unfeasible cycles, unbounded by physical constraints and in principle able to perform work without expenditure of free energy. After implementing thermodynamic constraints by removing such loops, metabolic flux distributions scale meaningfully with the physical limiting factors, acquiring in turn a richer multimodal structure potentially leading to symmetry breaking while optimizing for objective functions.","lang":"eng"}],"intvolume":" 95","month":"06","main_file_link":[{"url":"https://arxiv.org/pdf/1703.00853.pdf","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["24700045"]},"ec_funded":1,"volume":95,"issue":"6","_id":"959","status":"public","type":"journal_article","date_updated":"2023-09-22T09:59:01Z","department":[{"_id":"GaTk"}]},{"quality_controlled":"1","publisher":"Academic Press","oa":1,"day":"01","publication":"Journal of Functional Analysis","isi":1,"year":"2017","doi":"10.1016/j.jfa.2017.05.003","date_published":"2017-09-01T00:00:00Z","date_created":"2018-12-11T11:49:24Z","page":"1810 - 1869","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum Markov Semigroups with Detailed Balance.” Journal of Functional Analysis. Academic Press, 2017. https://doi.org/10.1016/j.jfa.2017.05.003.","ista":"Carlen E, Maas J. 2017. Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. 273(5), 1810–1869.","mla":"Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum Markov Semigroups with Detailed Balance.” Journal of Functional Analysis, vol. 273, no. 5, Academic Press, 2017, pp. 1810–69, doi:10.1016/j.jfa.2017.05.003.","ama":"Carlen E, Maas J. Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. 2017;273(5):1810-1869. doi:10.1016/j.jfa.2017.05.003","apa":"Carlen, E., & Maas, J. (2017). Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2017.05.003","ieee":"E. Carlen and J. Maas, “Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance,” Journal of Functional Analysis, vol. 273, no. 5. Academic Press, pp. 1810–1869, 2017.","short":"E. Carlen, J. Maas, Journal of Functional Analysis 273 (2017) 1810–1869."},"title":"Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance","publist_id":"6452","author":[{"last_name":"Carlen","full_name":"Carlen, Eric","first_name":"Eric"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Maas","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan"}],"article_processing_charge":"No","external_id":{"isi":["000406082300005"]},"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We study a class of ergodic quantum Markov semigroups on finite-dimensional unital C⁎-algebras. These semigroups have a unique stationary state σ, and we are concerned with those that satisfy a quantum detailed balance condition with respect to σ. We show that the evolution on the set of states that is given by such a quantum Markov semigroup is gradient flow for the relative entropy with respect to σ in a particular Riemannian metric on the set of states. This metric is a non-commutative analog of the 2-Wasserstein metric, and in several interesting cases we are able to show, in analogy with work of Otto on gradient flows with respect to the classical 2-Wasserstein metric, that the relative entropy is strictly and uniformly convex with respect to the Riemannian metric introduced here. As a consequence, we obtain a number of new inequalities for the decay of relative entropy for ergodic quantum Markov semigroups with detailed balance."}],"month":"09","intvolume":" 273","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1609.01254"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00221236"]},"publication_status":"published","issue":"5","volume":273,"_id":"956","status":"public","type":"journal_article","date_updated":"2023-09-22T10:00:18Z","department":[{"_id":"JaMa"}]},{"oa":1,"quality_controlled":"1","publisher":"Elsevier","date_created":"2018-12-11T11:49:22Z","date_published":"2017-06-01T00:00:00Z","doi":"10.1016/j.tpb.2017.03.003","page":"45 - 60","publication":"Theoretical Population Biology","day":"01","year":"2017","has_accepted_license":"1","title":"Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti","article_processing_charge":"No","external_id":{"pmid":["28411063"]},"author":[{"full_name":"Turelli, Michael","last_name":"Turelli","first_name":"Michael"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"publist_id":"6463","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Turelli, Michael, and Nicholas H Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical Population Biology. Elsevier, 2017. https://doi.org/10.1016/j.tpb.2017.03.003.","ista":"Turelli M, Barton NH. 2017. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. 115, 45–60.","mla":"Turelli, Michael, and Nicholas H. Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical Population Biology, vol. 115, Elsevier, 2017, pp. 45–60, doi:10.1016/j.tpb.2017.03.003.","ieee":"M. Turelli and N. H. Barton, “Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti,” Theoretical Population Biology, vol. 115. Elsevier, pp. 45–60, 2017.","short":"M. Turelli, N.H. Barton, Theoretical Population Biology 115 (2017) 45–60.","apa":"Turelli, M., & Barton, N. H. (2017). Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2017.03.003","ama":"Turelli M, Barton NH. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. 2017;115:45-60. doi:10.1016/j.tpb.2017.03.003"},"intvolume":" 115","month":"06","scopus_import":"1","pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"A novel strategy for controlling the spread of arboviral diseases such as dengue, Zika and chikungunya is to transform mosquito populations with virus-suppressing Wolbachia. In general, Wolbachia transinfected into mosquitoes induce fitness costs through lower viability or fecundity. These maternally inherited bacteria also produce a frequency-dependent advantage for infected females by inducing cytoplasmic incompatibility (CI), which kills the embryos produced by uninfected females mated to infected males. These competing effects, a frequency-dependent advantage and frequency-independent costs, produce bistable Wolbachia frequency dynamics. Above a threshold frequency, denoted pˆ, CI drives fitness-decreasing Wolbachia transinfections through local populations; but below pˆ, infection frequencies tend to decline to zero. If pˆ is not too high, CI also drives spatial spread once infections become established over sufficiently large areas. We illustrate how simple models provide testable predictions concerning the spatial and temporal dynamics of Wolbachia introductions, focusing on rate of spatial spread, the shape of spreading waves, and the conditions for initiating spread from local introductions. First, we consider the robustness of diffusion-based predictions to incorporating two important features of wMel-Aedes aegypti biology that may be inconsistent with the diffusion approximations, namely fast local dynamics induced by complete CI (i.e., all embryos produced from incompatible crosses die) and long-tailed, non-Gaussian dispersal. With complete CI, our numerical analyses show that long-tailed dispersal changes wave-width predictions only slightly; but it can significantly reduce wave speed relative to the diffusion prediction; it also allows smaller local introductions to initiate spatial spread. Second, we use approximations for pˆ and dispersal distances to predict the outcome of 2013 releases of wMel-infected Aedes aegypti in Cairns, Australia, Third, we describe new data from Ae. aegypti populations near Cairns, Australia that demonstrate long-distance dispersal and provide an approximate lower bound on pˆ for wMel in northeastern Australia. Finally, we apply our analyses to produce operational guidelines for efficient transformation of vector populations over large areas. We demonstrate that even very slow spatial spread, on the order of 10-20 m/month (as predicted), can produce area-wide population transformation within a few years following initial releases covering about 20-30% of the target area."}],"volume":115,"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"9aeff86fa7de69f7a15cf4fc60d57d01","file_id":"6327","creator":"dernst","file_size":2073856,"date_updated":"2020-07-14T12:48:16Z","file_name":"2017_TheoreticalPopulationBio_Turelli.pdf","date_created":"2019-04-17T06:39:45Z"}],"publication_status":"published","publication_identifier":{"issn":["00405809"]},"pubrep_id":"972","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","_id":"952","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:48:16Z","ddc":["576"],"date_updated":"2023-09-22T10:02:21Z"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"843","status":"public","_id":"951","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:48:16Z","date_updated":"2023-09-22T10:02:52Z","ddc":["576"],"scopus_import":"1","intvolume":" 15","month":"05","abstract":[{"lang":"eng","text":"Dengue-suppressing Wolbachia strains are promising tools for arbovirus control, particularly as they have the potential to self-spread following local introductions. To test this, we followed the frequency of the transinfected Wolbachia strain wMel through Ae. aegypti in Cairns, Australia, following releases at 3 nonisolated locations within the city in early 2013. Spatial spread was analysed graphically using interpolation and by fitting a statistical model describing the position and width of the wave. For the larger 2 of the 3 releases (covering 0.97 km2 and 0.52 km2), we observed slow but steady spatial spread, at about 100–200 m per year, roughly consistent with theoretical predictions. In contrast, the smallest release (0.11 km2) produced erratic temporal and spatial dynamics, with little evidence of spread after 2 years. This is consistent with the prediction concerning fitness-decreasing Wolbachia transinfections that a minimum release area is needed to achieve stable local establishment and spread in continuous habitats. Our graphical and likelihood analyses produced broadly consistent estimates of wave speed and wave width. Spread at all sites was spatially heterogeneous, suggesting that environmental heterogeneity will affect large-scale Wolbachia transformations of urban mosquito populations. The persistence and spread of Wolbachia in release areas meeting minimum area requirements indicates the promise of successful large-scale population transfo"}],"oa_version":"Published Version","volume":15,"related_material":{"record":[{"id":"9856","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"9857"},{"id":"9858","status":"public","relation":"research_data"}]},"issue":"5","publication_status":"published","publication_identifier":{"issn":["15449173"]},"language":[{"iso":"eng"}],"file":[{"checksum":"107d290bd1159ec77b734eb2824b01c8","file_id":"4691","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:08:30Z","file_name":"IST-2017-843-v1+1_journal.pbio.2001894.pdf","creator":"system","date_updated":"2020-07-14T12:48:16Z","file_size":5541206}],"article_number":"e2001894","article_processing_charge":"No","external_id":{"isi":["000402520000012"]},"publist_id":"6464","author":[{"first_name":"Tom","full_name":"Schmidt, Tom","last_name":"Schmidt"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Rasic, Gordana","last_name":"Rasic","first_name":"Gordana"},{"full_name":"Turley, Andrew","last_name":"Turley","first_name":"Andrew"},{"full_name":"Montgomery, Brian","last_name":"Montgomery","first_name":"Brian"},{"first_name":"Inaki","last_name":"Iturbe Ormaetxe","full_name":"Iturbe Ormaetxe, Inaki"},{"first_name":"Peter","full_name":"Cook, Peter","last_name":"Cook"},{"first_name":"Peter","last_name":"Ryan","full_name":"Ryan, Peter"},{"first_name":"Scott","full_name":"Ritchie, Scott","last_name":"Ritchie"},{"first_name":"Ary","full_name":"Hoffmann, Ary","last_name":"Hoffmann"},{"full_name":"O’Neill, Scott","last_name":"O’Neill","first_name":"Scott"},{"first_name":"Michael","full_name":"Turelli, Michael","last_name":"Turelli"}],"title":"Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti","citation":{"ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. 15(5), e2001894.","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” PLoS Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894","ama":"Schmidt T, Barton NH, Rasic G, et al. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. 2017;15(5). doi:10.1371/journal.pbio.2001894","ieee":"T. Schmidt et al., “Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti,” PLoS Biology, vol. 15, no. 5. Public Library of Science, 2017.","short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, PLoS Biology 15 (2017).","mla":"Schmidt, Tom, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” PLoS Biology, vol. 15, no. 5, e2001894, Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","date_created":"2018-12-11T11:49:22Z","doi":"10.1371/journal.pbio.2001894","date_published":"2017-05-30T00:00:00Z","year":"2017","has_accepted_license":"1","isi":1,"publication":"PLoS Biology","day":"30"},{"day":"10","publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","isi":1,"year":"2017","doi":"10.1103/PhysRevE.96.010401","date_published":"2017-07-10T00:00:00Z","date_created":"2018-12-11T11:49:21Z","quality_controlled":"1","publisher":"American Institute of Physics","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"De Martino, Daniele, et al. “Quantifying the Entropic Cost of Cellular Growth Control.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1, 010401, American Institute of Physics, 2017, doi:10.1103/PhysRevE.96.010401.","short":"D. De Martino, F. Capuani, A. De Martino, Physical Review E Statistical Nonlinear and Soft Matter Physics 96 (2017).","ieee":"D. De Martino, F. Capuani, and A. De Martino, “Quantifying the entropic cost of cellular growth control,” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1. American Institute of Physics, 2017.","ama":"De Martino D, Capuani F, De Martino A. Quantifying the entropic cost of cellular growth control. Physical Review E Statistical Nonlinear and Soft Matter Physics . 2017;96(1). doi:10.1103/PhysRevE.96.010401","apa":"De Martino, D., Capuani, F., & De Martino, A. (2017). Quantifying the entropic cost of cellular growth control. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.96.010401","chicago":"De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Quantifying the Entropic Cost of Cellular Growth Control.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.96.010401.","ista":"De Martino D, Capuani F, De Martino A. 2017. Quantifying the entropic cost of cellular growth control. Physical Review E Statistical Nonlinear and Soft Matter Physics . 96(1), 010401."},"title":"Quantifying the entropic cost of cellular growth control","author":[{"first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","last_name":"De Martino"},{"full_name":"Capuani, Fabrizio","last_name":"Capuani","first_name":"Fabrizio"},{"first_name":"Andrea","full_name":"De Martino, Andrea","last_name":"De Martino"}],"publist_id":"6470","article_processing_charge":"No","external_id":{"isi":["000405194200002"]},"article_number":"010401","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["24700045"]},"publication_status":"published","volume":96,"issue":"1","ec_funded":1,"oa_version":"Submitted Version","abstract":[{"text":"Viewing the ways a living cell can organize its metabolism as the phase space of a physical system, regulation can be seen as the ability to reduce the entropy of that space by selecting specific cellular configurations that are, in some sense, optimal. Here we quantify the amount of regulation required to control a cell's growth rate by a maximum-entropy approach to the space of underlying metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern as described by genome-scale models. We link the mean growth rate achieved by a population of cells to the minimal amount of metabolic regulation needed to achieve it through a phase diagram that highlights how growth suppression can be as costly (in regulatory terms) as growth enhancement. Moreover, we provide an interpretation of the inverse temperature β controlling maximum-entropy distributions based on the underlying growth dynamics. Specifically, we show that the asymptotic value of β for a cell population can be expected to depend on (i) the carrying capacity of the environment, (ii) the initial size of the colony, and (iii) the probability distribution from which the inoculum was sampled. Results obtained for E. coli and human cells are found to be remarkably consistent with empirical evidence.","lang":"eng"}],"month":"07","intvolume":" 96","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1703.00219","open_access":"1"}],"date_updated":"2023-09-22T10:03:50Z","department":[{"_id":"GaTk"}],"_id":"947","status":"public","type":"journal_article"},{"year":"2017","day":"30","date_created":"2021-08-10T07:47:07Z","doi":"10.1371/journal.pbio.2001894.s016","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"951"}]},"date_published":"2017-05-30T00:00:00Z","oa_version":"Published Version","publisher":"Public Library of Science","month":"05","date_updated":"2023-09-22T10:02:51Z","citation":{"ama":"Schmidt T, Barton NH, Rasic G, et al. Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics. 2017. doi:10.1371/journal.pbio.2001894.s016","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894.s016","short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017).","ieee":"T. Schmidt et al., “Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics.” Public Library of Science, 2017.","mla":"Schmidt, Tom, et al. Excel File with Data on Mosquito Densities, Wolbachia Infection Status and Housing Characteristics. Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.s016.","ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics, Public Library of Science, 10.1371/journal.pbio.2001894.s016.","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Excel File with Data on Mosquito Densities, Wolbachia Infection Status and Housing Characteristics.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.s016."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"last_name":"Schmidt","full_name":"Schmidt, Tom","first_name":"Tom"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"last_name":"Rasic","full_name":"Rasic, Gordana","first_name":"Gordana"},{"first_name":"Andrew","last_name":"Turley","full_name":"Turley, Andrew"},{"last_name":"Montgomery","full_name":"Montgomery, Brian","first_name":"Brian"},{"last_name":"Iturbe Ormaetxe","full_name":"Iturbe Ormaetxe, Inaki","first_name":"Inaki"},{"first_name":"Peter","last_name":"Cook","full_name":"Cook, Peter"},{"first_name":"Peter","full_name":"Ryan, Peter","last_name":"Ryan"},{"full_name":"Ritchie, Scott","last_name":"Ritchie","first_name":"Scott"},{"last_name":"Hoffmann","full_name":"Hoffmann, Ary","first_name":"Ary"},{"full_name":"O’Neill, Scott","last_name":"O’Neill","first_name":"Scott"},{"first_name":"Michael","last_name":"Turelli","full_name":"Turelli, Michael"}],"title":"Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics","department":[{"_id":"NiBa"}],"_id":"9858","type":"research_data_reference","status":"public"},{"date_created":"2021-08-10T07:41:52Z","date_published":"2017-05-30T00:00:00Z","related_material":{"record":[{"status":"public","id":"951","relation":"used_in_publication"}]},"doi":"10.1371/journal.pbio.2001894.s015","day":"30","year":"2017","month":"05","publisher":"Public Library of Science ","oa_version":"Published Version","department":[{"_id":"NiBa"}],"title":"Supporting information concerning observed wMel frequencies and analyses of habitat variables","article_processing_charge":"No","author":[{"last_name":"Schmidt","full_name":"Schmidt, Tom","first_name":"Tom"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"first_name":"Gordana","full_name":"Rasic, Gordana","last_name":"Rasic"},{"first_name":"Andrew","last_name":"Turley","full_name":"Turley, Andrew"},{"first_name":"Brian","last_name":"Montgomery","full_name":"Montgomery, Brian"},{"last_name":"Iturbe Ormaetxe","full_name":"Iturbe Ormaetxe, Inaki","first_name":"Inaki"},{"last_name":"Cook","full_name":"Cook, Peter","first_name":"Peter"},{"first_name":"Peter","last_name":"Ryan","full_name":"Ryan, Peter"},{"first_name":"Scott","full_name":"Ritchie, Scott","last_name":"Ritchie"},{"first_name":"Ary","full_name":"Hoffmann, Ary","last_name":"Hoffmann"},{"first_name":"Scott","full_name":"O’Neill, Scott","last_name":"O’Neill"},{"last_name":"Turelli","full_name":"Turelli, Michael","first_name":"Michael"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-22T10:02:51Z","citation":{"chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Supporting Information Concerning Observed WMel Frequencies and Analyses of Habitat Variables.” Public Library of Science , 2017. https://doi.org/10.1371/journal.pbio.2001894.s015.","ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Supporting information concerning observed wMel frequencies and analyses of habitat variables, Public Library of Science , 10.1371/journal.pbio.2001894.s015.","mla":"Schmidt, Tom, et al. Supporting Information Concerning Observed WMel Frequencies and Analyses of Habitat Variables. Public Library of Science , 2017, doi:10.1371/journal.pbio.2001894.s015.","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Supporting information concerning observed wMel frequencies and analyses of habitat variables. Public Library of Science . https://doi.org/10.1371/journal.pbio.2001894.s015","ama":"Schmidt T, Barton NH, Rasic G, et al. Supporting information concerning observed wMel frequencies and analyses of habitat variables. 2017. doi:10.1371/journal.pbio.2001894.s015","ieee":"T. Schmidt et al., “Supporting information concerning observed wMel frequencies and analyses of habitat variables.” Public Library of Science , 2017.","short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017)."},"status":"public","type":"research_data_reference","_id":"9857"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-22T10:02:51Z","citation":{"mla":"Schmidt, Tom, et al. Supporting Information Concerning Additional Likelihood Analyses and Results. Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.s014.","ama":"Schmidt T, Barton NH, Rasic G, et al. Supporting Information concerning additional likelihood analyses and results. 2017. doi:10.1371/journal.pbio.2001894.s014","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Supporting Information concerning additional likelihood analyses and results. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894.s014","short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017).","ieee":"T. Schmidt et al., “Supporting Information concerning additional likelihood analyses and results.” Public Library of Science, 2017.","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Supporting Information Concerning Additional Likelihood Analyses and Results.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.s014.","ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Supporting Information concerning additional likelihood analyses and results, Public Library of Science, 10.1371/journal.pbio.2001894.s014."},"title":"Supporting Information concerning additional likelihood analyses and results","department":[{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"full_name":"Schmidt, Tom","last_name":"Schmidt","first_name":"Tom"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"first_name":"Gordana","full_name":"Rasic, Gordana","last_name":"Rasic"},{"full_name":"Turley, Andrew","last_name":"Turley","first_name":"Andrew"},{"full_name":"Montgomery, Brian","last_name":"Montgomery","first_name":"Brian"},{"last_name":"Iturbe Ormaetxe","full_name":"Iturbe Ormaetxe, Inaki","first_name":"Inaki"},{"last_name":"Cook","full_name":"Cook, Peter","first_name":"Peter"},{"full_name":"Ryan, Peter","last_name":"Ryan","first_name":"Peter"},{"first_name":"Scott","last_name":"Ritchie","full_name":"Ritchie, Scott"},{"first_name":"Ary","last_name":"Hoffmann","full_name":"Hoffmann, Ary"},{"first_name":"Scott","full_name":"O’Neill, Scott","last_name":"O’Neill"},{"first_name":"Michael","full_name":"Turelli, Michael","last_name":"Turelli"}],"_id":"9856","status":"public","type":"research_data_reference","day":"30","year":"2017","date_created":"2021-08-10T07:36:04Z","doi":"10.1371/journal.pbio.2001894.s014","date_published":"2017-05-30T00:00:00Z","related_material":{"record":[{"status":"public","id":"951","relation":"used_in_publication"}]},"oa_version":"Published Version","month":"05","publisher":"Public Library of Science"},{"project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22"}],"title":"Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000411814800016"]},"author":[{"last_name":"Huylmans","orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K"},{"last_name":"Macon","full_name":"Macon, Ariana","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6472","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"A.K. Huylmans, A. Macon, B. Vicoso, Molecular Biology and Evolution 34 (2017) 2637–2649.","ieee":"A. K. Huylmans, A. Macon, and B. Vicoso, “Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome,” Molecular Biology and Evolution, vol. 34, no. 10. Oxford University Press, pp. 2637–2649, 2017.","ama":"Huylmans AK, Macon A, Vicoso B. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 2017;34(10):2637-2649. doi:10.1093/molbev/msx190","apa":"Huylmans, A. K., Macon, A., & Vicoso, B. (2017). Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msx190","mla":"Huylmans, Ann K., et al. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” Molecular Biology and Evolution, vol. 34, no. 10, Oxford University Press, 2017, pp. 2637–49, doi:10.1093/molbev/msx190.","ista":"Huylmans AK, Macon A, Vicoso B. 2017. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 34(10), 2637–2649.","chicago":"Huylmans, Ann K, Ariana Macon, and Beatriz Vicoso. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” Molecular Biology and Evolution. Oxford University Press, 2017. https://doi.org/10.1093/molbev/msx190."},"oa":1,"publisher":"Oxford University Press","quality_controlled":"1","date_created":"2018-12-11T11:49:20Z","date_published":"2017-07-06T00:00:00Z","doi":"10.1093/molbev/msx190","page":"2637 - 2649","publication":"Molecular Biology and Evolution","day":"06","year":"2017","has_accepted_license":"1","isi":1,"pubrep_id":"848","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"945","department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:48:15Z","ddc":["570","576"],"date_updated":"2023-09-26T15:36:34Z","intvolume":" 34","month":"07","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"While chromosome-wide dosage compensation of the X chromosome has been found in many species, studies in ZW clades have indicated that compensation of the Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show complete compensation of the Z chromosome, while others lack full equalization, but what drives these inconsistencies is unclear. Here, we compare patterns of male and female gene expression on the Z chromosome of two closely related butterfly species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths species, Plodia interpunctella and Bombyx mori, which were previously found to differ in the extent to which they equalize Z-linked gene expression between the sexes. We find that, while some species and tissues seem to have incomplete dosage compensation, this is in fact due to the accumulation of male-biased genes and the depletion of female-biased genes on the Z chromosome. Once this is accounted for, the Z chromosome is fully compensated in all four species, through the up-regulation of Z expression in females and in some cases additional down-regulation in males. We further find that both sex-biased genes and Z-linked genes have increased rates of expression divergence in this clade, and that this can lead to fast shifts in patterns of gene expression even between closely related species. Taken together, these results show that the uneven distribution of sex-biased genes on sex chromosomes can confound conclusions about dosage compensation and that Z chromosome-wide dosage compensation is not only possible but ubiquitous among Lepidoptera."}],"volume":34,"issue":"10","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"009fd68043211d645ceb9d1de28274f2","file_id":"4810","creator":"system","file_size":462863,"date_updated":"2020-07-14T12:48:15Z","file_name":"IST-2017-848-v1+1_2017_Vicoso_GlobalDosage.pdf","date_created":"2018-12-12T10:10:23Z"}],"publication_status":"published","publication_identifier":{"issn":["07374038"]}},{"date_created":"2018-12-11T11:48:18Z","date_published":"2017-11-09T00:00:00Z","doi":"10.1016/j.cub.2017.10.001","page":"3526 - 3534e.4","publication":"Current Biology","day":"09","year":"2017","isi":1,"has_accepted_license":"1","oa":1,"publisher":"Cell Press","quality_controlled":"1","title":"A moving source of matrix components is essential for De Novo basement membrane formation","external_id":{"isi":["000415815800031"]},"article_processing_charge":"No","publist_id":"6905","author":[{"last_name":"Matsubayashi","full_name":"Matsubayashi, Yutaka","first_name":"Yutaka"},{"last_name":"Louani","full_name":"Louani, Adam","first_name":"Adam"},{"first_name":"Anca","full_name":"Dragu, Anca","last_name":"Dragu"},{"first_name":"Besaiz","last_name":"Sanchez Sanchez","full_name":"Sanchez Sanchez, Besaiz"},{"first_name":"Eduardo","last_name":"Serna Morales","full_name":"Serna Morales, Eduardo"},{"first_name":"Lawrence","full_name":"Yolland, Lawrence","last_name":"Yolland"},{"id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","first_name":"Attila","orcid":"0000-0002-1819-198X","full_name":"György, Attila","last_name":"György"},{"first_name":"Gema","last_name":"Vizcay","full_name":"Vizcay, Gema"},{"first_name":"Roland","last_name":"Fleck","full_name":"Fleck, Roland"},{"full_name":"Heddleston, John","last_name":"Heddleston","first_name":"John"},{"last_name":"Chew","full_name":"Chew, Teng","first_name":"Teng"},{"first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E"},{"first_name":"Brian","last_name":"Stramer","full_name":"Stramer, Brian"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Matsubayashi, Yutaka, Adam Louani, Anca Dragu, Besaiz Sanchez Sanchez, Eduardo Serna Morales, Lawrence Yolland, Attila György, et al. “A Moving Source of Matrix Components Is Essential for De Novo Basement Membrane Formation.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.10.001.","ista":"Matsubayashi Y, Louani A, Dragu A, Sanchez Sanchez B, Serna Morales E, Yolland L, György A, Vizcay G, Fleck R, Heddleston J, Chew T, Siekhaus DE, Stramer B. 2017. A moving source of matrix components is essential for De Novo basement membrane formation. Current Biology. 27(22), 3526–3534e.4.","mla":"Matsubayashi, Yutaka, et al. “A Moving Source of Matrix Components Is Essential for De Novo Basement Membrane Formation.” Current Biology, vol. 27, no. 22, Cell Press, 2017, p. 3526–3534e.4, doi:10.1016/j.cub.2017.10.001.","ieee":"Y. Matsubayashi et al., “A moving source of matrix components is essential for De Novo basement membrane formation,” Current Biology, vol. 27, no. 22. Cell Press, p. 3526–3534e.4, 2017.","short":"Y. Matsubayashi, A. Louani, A. Dragu, B. Sanchez Sanchez, E. Serna Morales, L. Yolland, A. György, G. Vizcay, R. Fleck, J. Heddleston, T. Chew, D.E. Siekhaus, B. Stramer, Current Biology 27 (2017) 3526–3534e.4.","apa":"Matsubayashi, Y., Louani, A., Dragu, A., Sanchez Sanchez, B., Serna Morales, E., Yolland, L., … Stramer, B. (2017). A moving source of matrix components is essential for De Novo basement membrane formation. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.10.001","ama":"Matsubayashi Y, Louani A, Dragu A, et al. A moving source of matrix components is essential for De Novo basement membrane formation. Current Biology. 2017;27(22):3526-3534e.4. doi:10.1016/j.cub.2017.10.001"},"issue":"22","volume":27,"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"264cf6c6c3551486ba5ea786850e000a","file_id":"4770","creator":"system","date_updated":"2020-07-14T12:47:59Z","file_size":4770657,"date_created":"2018-12-12T10:09:45Z","file_name":"IST-2017-875-v1+1_1-s2.0-S0960982217312691-main.pdf"}],"publication_status":"published","publication_identifier":{"issn":["09609822"]},"intvolume":" 27","month":"11","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The basement membrane (BM) is a thin layer of extracellular matrix (ECM) beneath nearly all epithelial cell types that is critical for cellular and tissue function. It is composed of numerous components conserved among all bilaterians [1]; however, it is unknown how all of these components are generated and subsequently constructed to form a fully mature BM in the living animal. Although BM formation is thought to simply involve a process of self-assembly [2], this concept suffers from a number of logistical issues when considering its construction in vivo. First, incorporation of BM components appears to be hierarchical [3-5], yet it is unclear whether their production during embryogenesis must also be regulated in a temporal fashion. Second, many BM proteins are produced not only by the cells residing on the BM but also by surrounding cell types [6-9], and it is unclear how large, possibly insoluble protein complexes [10] are delivered into the matrix. Here we exploit our ability to live image and genetically dissect de novo BM formation during Drosophila development. This reveals that there is a temporal hierarchy of BM protein production that is essential for proper component incorporation. Furthermore, we show that BM components require secretion by migrating macrophages (hemocytes) during their developmental dispersal, which is critical for embryogenesis. Indeed, hemocyte migration is essential to deliver a subset of ECM components evenly throughout the embryo. This reveals that de novo BM construction requires a combination of both production and distribution logistics allowing for the timely delivery of core components."}],"department":[{"_id":"DaSi"}],"file_date_updated":"2020-07-14T12:47:59Z","ddc":["570","576"],"date_updated":"2023-09-27T12:25:31Z","pubrep_id":"875","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"751"},{"_id":"798","pubrep_id":"867","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["539"],"date_updated":"2023-09-27T12:11:28Z","file_date_updated":"2020-07-14T12:48:06Z","department":[{"_id":"JoFi"}],"oa_version":"Published Version","abstract":[{"text":"Nonreciprocal circuit elements form an integral part of modern measurement and communication systems. Mathematically they require breaking of time-reversal symmetry, typically achieved using magnetic materials and more recently using the quantum Hall effect, parametric permittivity modulation or Josephson nonlinearities. Here we demonstrate an on-chip magnetic-free circulator based on reservoir-engineered electromechanic interactions. Directional circulation is achieved with controlled phase-sensitive interference of six distinct electro-mechanical signal conversion paths. The presented circulator is compact, its silicon-on-insulator platform is compatible with both superconducting qubits and silicon photonics, and its noise performance is close to the quantum limit. With a high dynamic range, a tunable bandwidth of up to 30 MHz and an in situ reconfigurability as beam splitter or wavelength converter, it could pave the way for superconducting qubit processors with multiplexed on-chip signal processing and readout.","lang":"eng"}],"intvolume":" 8","month":"10","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:15:25Z","file_name":"IST-2017-867-v1+1_s41467-017-01304-x.pdf","creator":"system","date_updated":"2020-07-14T12:48:06Z","file_size":1467696,"file_id":"5145","checksum":"b68dafa71d1834c23b742cd9987a3d5f","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["20411723"]},"ec_funded":1,"issue":"1","volume":8,"article_number":"1304","project":[{"call_identifier":"H2020","_id":"257EB838-B435-11E9-9278-68D0E5697425","name":"Hybrid Optomechanical Technologies","grant_number":"732894"},{"call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Barzanjeh S, Wulf M, Peruzzo M, Kalaee M, Dieterle P, Painter O, Fink JM. 2017. Mechanical on chip microwave circulator. Nature Communications. 8(1), 1304.","chicago":"Barzanjeh, Shabir, Matthias Wulf, Matilda Peruzzo, Mahmoud Kalaee, Paul Dieterle, Oskar Painter, and Johannes M Fink. “Mechanical on Chip Microwave Circulator.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01304-x.","ieee":"S. Barzanjeh et al., “Mechanical on chip microwave circulator,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","short":"S. Barzanjeh, M. Wulf, M. Peruzzo, M. Kalaee, P. Dieterle, O. Painter, J.M. Fink, Nature Communications 8 (2017).","ama":"Barzanjeh S, Wulf M, Peruzzo M, et al. Mechanical on chip microwave circulator. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01304-x","apa":"Barzanjeh, S., Wulf, M., Peruzzo, M., Kalaee, M., Dieterle, P., Painter, O., & Fink, J. M. (2017). Mechanical on chip microwave circulator. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01304-x","mla":"Barzanjeh, Shabir, et al. “Mechanical on Chip Microwave Circulator.” Nature Communications, vol. 8, no. 1, 1304, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01304-x."},"title":"Mechanical on chip microwave circulator","external_id":{"isi":["000412999700021"]},"article_processing_charge":"Yes (in subscription journal)","publist_id":"6855","author":[{"first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","last_name":"Barzanjeh"},{"id":"45598606-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","full_name":"Wulf, Matthias","orcid":"0000-0001-6613-1378","last_name":"Wulf"},{"last_name":"Peruzzo","full_name":"Peruzzo, Matilda","orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda"},{"first_name":"Mahmoud","full_name":"Kalaee, Mahmoud","last_name":"Kalaee"},{"first_name":"Paul","full_name":"Dieterle, Paul","last_name":"Dieterle"},{"full_name":"Painter, Oskar","last_name":"Painter","first_name":"Oskar"},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","publication":"Nature Communications","day":"16","year":"2017","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:48:33Z","doi":"10.1038/s41467-017-01304-x","date_published":"2017-10-16T00:00:00Z"},{"publication_identifier":{"isbn":["978-145034992-5"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":"Part F129314","abstract":[{"text":"Consider the following random process: we are given n queues, into which elements of increasing labels are inserted uniformly at random. To remove an element, we pick two queues at random, and remove the element of lower label (higher priority) among the two. The cost of a removal is the rank of the label removed, among labels still present in any of the queues, that is, the distance from the optimal choice at each step. Variants of this strategy are prevalent in state-of-the-art concurrent priority queue implementations. Nonetheless, it is not known whether such implementations provide any rank guarantees, even in a sequential model. We answer this question, showing that this strategy provides surprisingly strong guarantees: Although the single-choice process, where we always insert and remove from a single randomly chosen queue, has degrading cost, going to infinity as we increase the number of steps, in the two choice process, the expected rank of a removed element is O(n) while the expected worst-case cost is O(n log n). These bounds are tight, and hold irrespective of the number of steps for which we run the process. The argument is based on a new technical connection between "heavily loaded" balls-into-bins processes and priority scheduling. Our analytic results inspire a new concurrent priority queue implementation, which improves upon the state of the art in terms of practical performance.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1706.04178","open_access":"1"}],"month":"07","date_updated":"2023-09-27T12:17:59Z","department":[{"_id":"DaAl"}],"_id":"791","type":"conference","conference":{"start_date":"2017-07-25","location":"Washington, WA, USA","end_date":"2017-07-27","name":"PODC: Principles of Distributed Computing"},"status":"public","isi":1,"year":"2017","day":"26","publication":"Proceedings of the ACM Symposium on Principles of Distributed Computing","page":"283 - 292","date_published":"2017-07-26T00:00:00Z","doi":"10.1145/3087801.3087810","date_created":"2018-12-11T11:48:31Z","quality_controlled":"1","publisher":"ACM","oa":1,"citation":{"mla":"Alistarh, Dan-Adrian, et al. “The Power of Choice in Priority Scheduling.” Proceedings of the ACM Symposium on Principles of Distributed Computing, vol. Part F129314, ACM, 2017, pp. 283–92, doi:10.1145/3087801.3087810.","ieee":"D.-A. Alistarh, J. Kopinsky, J. Li, and G. Nadiradze, “The power of choice in priority scheduling,” in Proceedings of the ACM Symposium on Principles of Distributed Computing, Washington, WA, USA, 2017, vol. Part F129314, pp. 283–292.","short":"D.-A. Alistarh, J. Kopinsky, J. Li, G. Nadiradze, in:, Proceedings of the ACM Symposium on Principles of Distributed Computing, ACM, 2017, pp. 283–292.","ama":"Alistarh D-A, Kopinsky J, Li J, Nadiradze G. The power of choice in priority scheduling. In: Proceedings of the ACM Symposium on Principles of Distributed Computing. Vol Part F129314. ACM; 2017:283-292. doi:10.1145/3087801.3087810","apa":"Alistarh, D.-A., Kopinsky, J., Li, J., & Nadiradze, G. (2017). The power of choice in priority scheduling. In Proceedings of the ACM Symposium on Principles of Distributed Computing (Vol. Part F129314, pp. 283–292). Washington, WA, USA: ACM. https://doi.org/10.1145/3087801.3087810","chicago":"Alistarh, Dan-Adrian, Justin Kopinsky, Jerry Li, and Giorgi Nadiradze. “The Power of Choice in Priority Scheduling.” In Proceedings of the ACM Symposium on Principles of Distributed Computing, Part F129314:283–92. ACM, 2017. https://doi.org/10.1145/3087801.3087810.","ista":"Alistarh D-A, Kopinsky J, Li J, Nadiradze G. 2017. The power of choice in priority scheduling. Proceedings of the ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing vol. Part F129314, 283–292."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6864","author":[{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"full_name":"Kopinsky, Justin","last_name":"Kopinsky","first_name":"Justin"},{"first_name":"Jerry","full_name":"Li, Jerry","last_name":"Li"},{"last_name":"Nadiradze","full_name":"Nadiradze, Giorgi","orcid":"0000-0001-5634-0731","first_name":"Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000462995000035"]},"title":"The power of choice in priority scheduling"},{"date_created":"2018-12-11T11:48:32Z","doi":"10.1017/jfm.2017.699","date_published":"2017-12-25T00:00:00Z","page":"274 - 301","publication":"Journal of Fluid Mechanics","day":"25","year":"2017","isi":1,"oa":1,"quality_controlled":"1","publisher":"Cambridge University Press","title":"Relative periodic orbits form the backbone of turbulent pipe flow","article_processing_charge":"No","external_id":{"isi":["000414641700001"]},"author":[{"full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur","first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kimberly","last_name":"Short","full_name":"Short, Kimberly"},{"first_name":"Mohammad","full_name":"Farazmand, Mohammad","last_name":"Farazmand"},{"full_name":"Willis, Ashley","last_name":"Willis","first_name":"Ashley"},{"first_name":"Predrag","full_name":"Cvitanović, Predrag","last_name":"Cvitanović"}],"publist_id":"6862","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Budanur, Nazmi B., et al. “Relative Periodic Orbits Form the Backbone of Turbulent Pipe Flow.” Journal of Fluid Mechanics, vol. 833, Cambridge University Press, 2017, pp. 274–301, doi:10.1017/jfm.2017.699.","apa":"Budanur, N. B., Short, K., Farazmand, M., Willis, A., & Cvitanović, P. (2017). Relative periodic orbits form the backbone of turbulent pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.699","ama":"Budanur NB, Short K, Farazmand M, Willis A, Cvitanović P. Relative periodic orbits form the backbone of turbulent pipe flow. Journal of Fluid Mechanics. 2017;833:274-301. doi:10.1017/jfm.2017.699","short":"N.B. Budanur, K. Short, M. Farazmand, A. Willis, P. Cvitanović, Journal of Fluid Mechanics 833 (2017) 274–301.","ieee":"N. B. Budanur, K. Short, M. Farazmand, A. Willis, and P. Cvitanović, “Relative periodic orbits form the backbone of turbulent pipe flow,” Journal of Fluid Mechanics, vol. 833. Cambridge University Press, pp. 274–301, 2017.","chicago":"Budanur, Nazmi B, Kimberly Short, Mohammad Farazmand, Ashley Willis, and Predrag Cvitanović. “Relative Periodic Orbits Form the Backbone of Turbulent Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2017. https://doi.org/10.1017/jfm.2017.699.","ista":"Budanur NB, Short K, Farazmand M, Willis A, Cvitanović P. 2017. Relative periodic orbits form the backbone of turbulent pipe flow. Journal of Fluid Mechanics. 833, 274–301."},"project":[{"_id":"25636330-B435-11E9-9278-68D0E5697425","name":"ROOTS Genome-wide Analysis of Root Traits","grant_number":"11-NSF-1070"}],"volume":833,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00221120"]},"intvolume":" 833","month":"12","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.03720"}],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"The chaotic dynamics of low-dimensional systems, such as Lorenz or Rössler flows, is guided by the infinity of periodic orbits embedded in their strange attractors. Whether this is also the case for the infinite-dimensional dynamics of Navier–Stokes equations has long been speculated, and is a topic of ongoing study. Periodic and relative periodic solutions have been shown to be involved in transitions to turbulence. Their relevance to turbulent dynamics – specifically, whether periodic orbits play the same role in high-dimensional nonlinear systems like the Navier–Stokes equations as they do in lower-dimensional systems – is the focus of the present investigation. We perform here a detailed study of pipe flow relative periodic orbits with energies and mean dissipations close to turbulent values. We outline several approaches to reduction of the translational symmetry of the system. We study pipe flow in a minimal computational cell at Re=2500, and report a library of invariant solutions found with the aid of the method of slices. Detailed study of the unstable manifolds of a sample of these solutions is consistent with the picture that relative periodic orbits are embedded in the chaotic saddle and that they guide the turbulent dynamics.","lang":"eng"}],"department":[{"_id":"BjHo"}],"date_updated":"2023-09-27T12:17:35Z","status":"public","type":"journal_article","_id":"792"},{"date_created":"2018-12-11T11:48:33Z","doi":"10.1063/1.4994661","date_published":"2017-07-01T00:00:00Z","publication":"Applied Physics Letters","day":"01","year":"2017","isi":1,"oa":1,"publisher":"American Institute of Physics","quality_controlled":"1","acknowledgement":"This work was supported by the AFOSR MURI Quantum Photonic Matter (Grant No. 16RT0696), the AFOSR MURI Wiring Quantum Networks with Mechanical Transducers (Grant No. FA9550-15-1-0015), the Institute for Quantum Information and Matter, an NSF Physics Frontiers Center (Grant No. PHY-1125565) with the support of the Gordon and Betty Moore Foundation, and the Kavli Nanoscience Institute at Caltech. A.J.K. acknowledges the IQIM Postdoctoral Fellowship.","title":"Al transmon qubits on silicon on insulator for quantum device integration","external_id":{"isi":["000406779700031"]},"article_processing_charge":"No","publist_id":"6857","author":[{"first_name":"Andrew J","full_name":"Keller, Andrew J","last_name":"Keller"},{"first_name":"Paul","full_name":"Dieterle, Paul","last_name":"Dieterle"},{"full_name":"Fang, Michael","last_name":"Fang","first_name":"Michael"},{"full_name":"Berger, Brett","last_name":"Berger","first_name":"Brett"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink"},{"first_name":"Oskar","full_name":"Painter, Oskar","last_name":"Painter"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Keller, Andrew J., et al. “Al Transmon Qubits on Silicon on Insulator for Quantum Device Integration.” Applied Physics Letters, vol. 111, no. 4, 042603, American Institute of Physics, 2017, doi:10.1063/1.4994661.","ieee":"A. J. Keller, P. Dieterle, M. Fang, B. Berger, J. M. Fink, and O. Painter, “Al transmon qubits on silicon on insulator for quantum device integration,” Applied Physics Letters, vol. 111, no. 4. American Institute of Physics, 2017.","short":"A.J. Keller, P. Dieterle, M. Fang, B. Berger, J.M. Fink, O. Painter, Applied Physics Letters 111 (2017).","apa":"Keller, A. J., Dieterle, P., Fang, M., Berger, B., Fink, J. M., & Painter, O. (2017). Al transmon qubits on silicon on insulator for quantum device integration. Applied Physics Letters. American Institute of Physics. https://doi.org/10.1063/1.4994661","ama":"Keller AJ, Dieterle P, Fang M, Berger B, Fink JM, Painter O. Al transmon qubits on silicon on insulator for quantum device integration. Applied Physics Letters. 2017;111(4). doi:10.1063/1.4994661","chicago":"Keller, Andrew J, Paul Dieterle, Michael Fang, Brett Berger, Johannes M Fink, and Oskar Painter. “Al Transmon Qubits on Silicon on Insulator for Quantum Device Integration.” Applied Physics Letters. American Institute of Physics, 2017. https://doi.org/10.1063/1.4994661.","ista":"Keller AJ, Dieterle P, Fang M, Berger B, Fink JM, Painter O. 2017. Al transmon qubits on silicon on insulator for quantum device integration. Applied Physics Letters. 111(4), 042603."},"article_number":"042603","volume":111,"issue":"4","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00036951"]},"intvolume":" 111","month":"07","main_file_link":[{"url":"https://arxiv.org/abs/1703.10195","open_access":"1"}],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We present the fabrication and characterization of an aluminum transmon qubit on a silicon-on-insulator substrate. Key to the qubit fabrication is the use of an anhydrous hydrofluoric vapor process which selectively removes the lossy silicon oxide buried underneath the silicon device layer. For a 5.6 GHz qubit measured dispersively by a 7.1 GHz resonator, we find T1 = 3.5 μs and T∗2 = 2.2 μs. This process in principle permits the co-fabrication of silicon photonic and mechanical elements, providing a route towards chip-scale integration of electro-opto-mechanical transducers for quantum networking of superconducting microwave quantum circuits. The additional processing steps are compatible with established fabrication techniques for aluminum transmon qubits on silicon."}],"department":[{"_id":"JoFi"}],"date_updated":"2023-09-27T12:13:36Z","status":"public","type":"journal_article","_id":"796"},{"date_updated":"2023-09-27T12:15:16Z","department":[{"_id":"UlWa"}],"_id":"793","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["09257721"]},"publication_status":"published","volume":66,"ec_funded":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Let P be a finite point set in the plane. A cordinary triangle in P is a subset of P consisting of three non-collinear points such that each of the three lines determined by the three points contains at most c points of P . Motivated by a question of Erdös, and answering a question of de Zeeuw, we prove that there exists a constant c > 0such that P contains a c-ordinary triangle, provided that P is not contained in the union of two lines. Furthermore, the number of c-ordinary triangles in P is Ω(| P |). "}],"month":"01","intvolume":" 66","main_file_link":[{"url":"https://arxiv.org/abs/1701.08183","open_access":"1"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Fulek R, Mojarrad H, Naszódi M, Solymosi J, Stich S, Szedlák M. 2017. On the existence of ordinary triangles. Computational Geometry: Theory and Applications. 66, 28–31.","chicago":"Fulek, Radoslav, Hossein Mojarrad, Márton Naszódi, József Solymosi, Sebastian Stich, and May Szedlák. “On the Existence of Ordinary Triangles.” Computational Geometry: Theory and Applications. Elsevier, 2017. https://doi.org/10.1016/j.comgeo.2017.07.002.","ama":"Fulek R, Mojarrad H, Naszódi M, Solymosi J, Stich S, Szedlák M. On the existence of ordinary triangles. Computational Geometry: Theory and Applications. 2017;66:28-31. doi:10.1016/j.comgeo.2017.07.002","apa":"Fulek, R., Mojarrad, H., Naszódi, M., Solymosi, J., Stich, S., & Szedlák, M. (2017). On the existence of ordinary triangles. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2017.07.002","short":"R. Fulek, H. Mojarrad, M. Naszódi, J. Solymosi, S. Stich, M. Szedlák, Computational Geometry: Theory and Applications 66 (2017) 28–31.","ieee":"R. Fulek, H. Mojarrad, M. Naszódi, J. Solymosi, S. Stich, and M. Szedlák, “On the existence of ordinary triangles,” Computational Geometry: Theory and Applications, vol. 66. Elsevier, pp. 28–31, 2017.","mla":"Fulek, Radoslav, et al. “On the Existence of Ordinary Triangles.” Computational Geometry: Theory and Applications, vol. 66, Elsevier, 2017, pp. 28–31, doi:10.1016/j.comgeo.2017.07.002."},"title":"On the existence of ordinary triangles","publist_id":"6861","author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek"},{"first_name":"Hossein","full_name":"Mojarrad, Hossein","last_name":"Mojarrad"},{"first_name":"Márton","last_name":"Naszódi","full_name":"Naszódi, Márton"},{"full_name":"Solymosi, József","last_name":"Solymosi","first_name":"József"},{"first_name":"Sebastian","full_name":"Stich, Sebastian","last_name":"Stich"},{"full_name":"Szedlák, May","last_name":"Szedlák","first_name":"May"}],"article_processing_charge":"No","external_id":{"isi":["000412039700003"]},"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"day":"01","publication":"Computational Geometry: Theory and Applications","isi":1,"year":"2017","doi":"10.1016/j.comgeo.2017.07.002","date_published":"2017-01-01T00:00:00Z","date_created":"2018-12-11T11:48:32Z","page":"28 - 31","publisher":"Elsevier","quality_controlled":"1","oa":1},{"department":[{"_id":"UlWa"}],"date_updated":"2023-09-27T12:14:49Z","status":"public","type":"journal_article","_id":"794","volume":66,"related_material":{"record":[{"id":"1165","status":"public","relation":"earlier_version"}]},"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 66","month":"12","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.01346"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"We show that c-planarity is solvable in quadratic time for flat clustered graphs with three clusters if the combinatorial embedding of the underlying graph is fixed. In simpler graph-theoretical terms our result can be viewed as follows. Given a graph G with the vertex set partitioned into three parts embedded on a 2-sphere, our algorithm decides if we can augment G by adding edges without creating an edge-crossing so that in the resulting spherical graph the vertices of each part induce a connected sub-graph. We proceed by a reduction to the problem of testing the existence of a perfect matching in planar bipartite graphs. We formulate our result in a slightly more general setting of cyclic clustered graphs, i.e., the simple graph obtained by contracting each cluster, where we disregard loops and multi-edges, is a cycle.","lang":"eng"}],"title":"C-planarity of embedded cyclic c-graphs","external_id":{"isi":["000412039700001"]},"article_processing_charge":"No","publist_id":"6860","author":[{"full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","last_name":"Fulek","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs.” Computational Geometry: Theory and Applications, vol. 66, Elsevier, 2017, pp. 1–13, doi:10.1016/j.comgeo.2017.06.016.","ama":"Fulek R. C-planarity of embedded cyclic c-graphs. Computational Geometry: Theory and Applications. 2017;66:1-13. doi:10.1016/j.comgeo.2017.06.016","apa":"Fulek, R. (2017). C-planarity of embedded cyclic c-graphs. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2017.06.016","short":"R. Fulek, Computational Geometry: Theory and Applications 66 (2017) 1–13.","ieee":"R. Fulek, “C-planarity of embedded cyclic c-graphs,” Computational Geometry: Theory and Applications, vol. 66. Elsevier, pp. 1–13, 2017.","chicago":"Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs.” Computational Geometry: Theory and Applications. Elsevier, 2017. https://doi.org/10.1016/j.comgeo.2017.06.016.","ista":"Fulek R. 2017. C-planarity of embedded cyclic c-graphs. Computational Geometry: Theory and Applications. 66, 1–13."},"date_created":"2018-12-11T11:48:32Z","date_published":"2017-12-01T00:00:00Z","doi":"10.1016/j.comgeo.2017.06.016","page":"1 - 13","publication":"Computational Geometry: Theory and Applications","day":"01","year":"2017","isi":1,"oa":1,"quality_controlled":"1","publisher":"Elsevier","acknowledgement":"I would like to thank Jan Kynčl, Dömötör Pálvölgyi and anonymous referees for many comments and suggestions that helped to improve the presentation of the result."},{"date_updated":"2023-09-27T14:14:51Z","ddc":["571"],"file_date_updated":"2020-07-14T12:47:56Z","department":[{"_id":"RySh"}],"_id":"736","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"881","publication_identifier":{"issn":["18632653"]},"publication_status":"published","file":[{"date_updated":"2020-07-14T12:47:56Z","file_size":4011126,"creator":"system","date_created":"2018-12-12T10:10:20Z","file_name":"IST-2017-881-v1+1_s00429-017-1408-0.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"4806","checksum":"73787a22507de8fb585bb598e1418ca7"}],"language":[{"iso":"eng"}],"issue":"8","volume":222,"abstract":[{"text":"The neurotransmitter receptor subtype, number, density, and distribution relative to the location of transmitter release sites are key determinants of signal transmission. AMPA-type ionotropic glutamate receptors (AMPARs) containing GluA3 and GluA4 subunits are prominently expressed in subsets of neurons capable of firing action potentials at high frequencies, such as auditory relay neurons. The auditory nerve (AN) forms glutamatergic synapses on two types of relay neurons, bushy cells (BCs) and fusiform cells (FCs) of the cochlear nucleus. AN-BC and AN-FC synapses have distinct kinetics; thus, we investigated whether the number, density, and localization of GluA3 and GluA4 subunits in these synapses are differentially organized using quantitative freeze-fracture replica immunogold labeling. We identify a positive correlation between the number of AMPARs and the size of AN-BC and AN-FC synapses. Both types of AN synapses have similar numbers of AMPARs; however, the AN-BC have a higher density of AMPARs than AN-FC synapses, because the AN-BC synapses are smaller. A higher number and density of GluA3 subunits are observed at AN-BC synapses, whereas a higher number and density of GluA4 subunits are observed at AN-FC synapses. The intrasynaptic distribution of immunogold labeling revealed that AMPAR subunits, particularly GluA3, are concentrated at the center of the AN-BC synapses. The central distribution of AMPARs is absent in GluA3-knockout mice, and gold particles are evenly distributed along the postsynaptic density. GluA4 gold labeling was homogenously distributed along both synapse types. Thus, GluA3 and GluA4 subunits are distributed at AN synapses in a target-cell-dependent manner.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"11","intvolume":" 222","citation":{"mla":"Rubio, María, et al. “The Number and Distribution of AMPA Receptor Channels Containing Fast Kinetic GluA3 and GluA4 Subunits at Auditory Nerve Synapses Depend on the Target Cells.” Brain Structure and Function, vol. 222, no. 8, Springer, 2017, pp. 3375–93, doi:10.1007/s00429-017-1408-0.","short":"M. Rubio, K. Matsui, Y. Fukazawa, N. Kamasawa, H. Harada, M. Itakura, E. Molnár, M. Abe, K. Sakimura, R. Shigemoto, Brain Structure and Function 222 (2017) 3375–3393.","ieee":"M. Rubio et al., “The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells,” Brain Structure and Function, vol. 222, no. 8. Springer, pp. 3375–3393, 2017.","ama":"Rubio M, Matsui K, Fukazawa Y, et al. The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells. Brain Structure and Function. 2017;222(8):3375-3393. doi:10.1007/s00429-017-1408-0","apa":"Rubio, M., Matsui, K., Fukazawa, Y., Kamasawa, N., Harada, H., Itakura, M., … Shigemoto, R. (2017). The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells. Brain Structure and Function. Springer. https://doi.org/10.1007/s00429-017-1408-0","chicago":"Rubio, María, Ko Matsui, Yugo Fukazawa, Naomi Kamasawa, Harumi Harada, Makoto Itakura, Elek Molnár, Manabu Abe, Kenji Sakimura, and Ryuichi Shigemoto. “The Number and Distribution of AMPA Receptor Channels Containing Fast Kinetic GluA3 and GluA4 Subunits at Auditory Nerve Synapses Depend on the Target Cells.” Brain Structure and Function. Springer, 2017. https://doi.org/10.1007/s00429-017-1408-0.","ista":"Rubio M, Matsui K, Fukazawa Y, Kamasawa N, Harada H, Itakura M, Molnár E, Abe M, Sakimura K, Shigemoto R. 2017. The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells. Brain Structure and Function. 222(8), 3375–3393."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Rubio, María","last_name":"Rubio","first_name":"María"},{"full_name":"Matsui, Ko","last_name":"Matsui","first_name":"Ko"},{"first_name":"Yugo","last_name":"Fukazawa","full_name":"Fukazawa, Yugo"},{"last_name":"Kamasawa","full_name":"Kamasawa, Naomi","first_name":"Naomi"},{"first_name":"Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Harada","orcid":"0000-0001-7429-7896","full_name":"Harada, Harumi"},{"last_name":"Itakura","full_name":"Itakura, Makoto","first_name":"Makoto"},{"first_name":"Elek","full_name":"Molnár, Elek","last_name":"Molnár"},{"first_name":"Manabu","last_name":"Abe","full_name":"Abe, Manabu"},{"last_name":"Sakimura","full_name":"Sakimura, Kenji","first_name":"Kenji"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6932","external_id":{"isi":["000414761700002"]},"article_processing_charge":"No","title":"The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells","has_accepted_license":"1","isi":1,"year":"2017","day":"01","publication":"Brain Structure and Function","page":"3375 - 3393","date_published":"2017-11-01T00:00:00Z","doi":"10.1007/s00429-017-1408-0","date_created":"2018-12-11T11:48:14Z","quality_controlled":"1","publisher":"Springer","oa":1},{"year":"2017","isi":1,"has_accepted_license":"1","publication":"WIREs Developmental Biology","day":"11","date_created":"2018-12-11T11:48:15Z","doi":"10.1002/wdev.288","date_published":"2017-08-11T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Wiley-Blackwell","citation":{"chicago":"Shigemoto, Ryuichi, and Maximilian A Jösch. “The Genetic Encoded Toolbox for Electron Microscopy and Connectomics.” WIREs Developmental Biology. Wiley-Blackwell, 2017. https://doi.org/10.1002/wdev.288.","ista":"Shigemoto R, Jösch MA. 2017. The genetic encoded toolbox for electron microscopy and connectomics. WIREs Developmental Biology. 6(6), e288.","mla":"Shigemoto, Ryuichi, and Maximilian A. Jösch. “The Genetic Encoded Toolbox for Electron Microscopy and Connectomics.” WIREs Developmental Biology, vol. 6, no. 6, e288, Wiley-Blackwell, 2017, doi:10.1002/wdev.288.","apa":"Shigemoto, R., & Jösch, M. A. (2017). The genetic encoded toolbox for electron microscopy and connectomics. WIREs Developmental Biology. Wiley-Blackwell. https://doi.org/10.1002/wdev.288","ama":"Shigemoto R, Jösch MA. The genetic encoded toolbox for electron microscopy and connectomics. WIREs Developmental Biology. 2017;6(6). doi:10.1002/wdev.288","short":"R. Shigemoto, M.A. Jösch, WIREs Developmental Biology 6 (2017).","ieee":"R. Shigemoto and M. A. Jösch, “The genetic encoded toolbox for electron microscopy and connectomics,” WIREs Developmental Biology, vol. 6, no. 6. Wiley-Blackwell, 2017."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000412827400005"],"pmid":["28800674"]},"article_processing_charge":"No","publist_id":"6927","author":[{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"last_name":"Jösch","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"title":"The genetic encoded toolbox for electron microscopy and connectomics","article_number":"e288","publication_status":"published","publication_identifier":{"issn":["17597684"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2017_WIREs_Shigemoto.pdf","date_created":"2019-11-19T07:36:18Z","creator":"dernst","file_size":1647787,"date_updated":"2020-07-14T12:47:57Z","checksum":"a9370f27b1591773b7a0de299bc81c8c","file_id":"7045","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","issue":"6","volume":6,"abstract":[{"text":"Developments in bioengineering and molecular biology have introduced a palette of genetically encoded probes for identification of specific cell populations in electron microscopy. These probes can be targeted to distinct cellular compartments, rendering them electron dense through a subsequent chemical reaction. These electron densities strongly increase the local contrast in samples prepared for electron microscopy, allowing three major advances in ultrastructural mapping of circuits: genetic identification of circuit components, targeted imaging of regions of interest and automated analysis of the tagged circuits. Together, the gains from these advances can decrease the time required for the analysis of targeted circuit motifs by over two orders of magnitude. These genetic encoded tags for electron microscopy promise to simplify the analysis of circuit motifs and become a central tool for structure‐function studies of synaptic connections in the brain. We review the current state‐of‐the‐art with an emphasis on connectomics, the quantitative analysis of neuronal structures and motifs.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"scopus_import":"1","intvolume":" 6","month":"08","date_updated":"2023-09-27T12:51:41Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:57Z","department":[{"_id":"RySh"},{"_id":"MaJö"}],"_id":"740","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","article_type":"original","status":"public"},{"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"},{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"title":"Stability of a fermionic N+1 particle system with point interactions","author":[{"first_name":"Thomas","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","last_name":"Moser","full_name":"Moser, Thomas"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"publist_id":"6926","external_id":{"isi":["000409821300010"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Moser, Thomas, and Robert Seiringer. “Stability of a Fermionic N+1 Particle System with Point Interactions.” Communications in Mathematical Physics. Springer, 2017. https://doi.org/10.1007/s00220-017-2980-0.","ista":"Moser T, Seiringer R. 2017. Stability of a fermionic N+1 particle system with point interactions. Communications in Mathematical Physics. 356(1), 329–355.","mla":"Moser, Thomas, and Robert Seiringer. “Stability of a Fermionic N+1 Particle System with Point Interactions.” Communications in Mathematical Physics, vol. 356, no. 1, Springer, 2017, pp. 329–55, doi:10.1007/s00220-017-2980-0.","short":"T. Moser, R. Seiringer, Communications in Mathematical Physics 356 (2017) 329–355.","ieee":"T. Moser and R. Seiringer, “Stability of a fermionic N+1 particle system with point interactions,” Communications in Mathematical Physics, vol. 356, no. 1. Springer, pp. 329–355, 2017.","apa":"Moser, T., & Seiringer, R. (2017). Stability of a fermionic N+1 particle system with point interactions. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-017-2980-0","ama":"Moser T, Seiringer R. Stability of a fermionic N+1 particle system with point interactions. Communications in Mathematical Physics. 2017;356(1):329-355. doi:10.1007/s00220-017-2980-0"},"quality_controlled":"1","publisher":"Springer","oa":1,"doi":"10.1007/s00220-017-2980-0","date_published":"2017-11-01T00:00:00Z","date_created":"2018-12-11T11:48:15Z","page":"329 - 355","day":"01","publication":"Communications in Mathematical Physics","has_accepted_license":"1","isi":1,"year":"2017","status":"public","pubrep_id":"880","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"741","file_date_updated":"2020-07-14T12:47:57Z","department":[{"_id":"RoSe"}],"ddc":["539"],"date_updated":"2023-09-27T12:34:15Z","month":"11","intvolume":" 356","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We prove that a system of N fermions interacting with an additional particle via point interactions is stable if the ratio of the mass of the additional particle to the one of the fermions is larger than some critical m*. The value of m* is independent of N and turns out to be less than 1. This fact has important implications for the stability of the unitary Fermi gas. We also characterize the domain of the Hamiltonian of this model, and establish the validity of the Tan relations for all wave functions in the domain."}],"volume":356,"issue":"1","related_material":{"record":[{"status":"public","id":"52","relation":"dissertation_contains"}]},"ec_funded":1,"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4841","checksum":"0fd9435400f91e9b3c5346319a2d24e3","creator":"system","date_updated":"2020-07-14T12:47:57Z","file_size":952639,"date_created":"2018-12-12T10:10:50Z","file_name":"IST-2017-880-v1+1_s00220-017-2980-0.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00103616"]},"publication_status":"published"},{"date_updated":"2023-09-27T12:52:07Z","department":[{"_id":"RoSe"}],"_id":"739","type":"journal_article","status":"public","publication_identifier":{"issn":["00217824"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":108,"issue":"5","abstract":[{"text":"We study the norm approximation to the Schrödinger dynamics of N bosons in with an interaction potential of the form . Assuming that in the initial state the particles outside of the condensate form a quasi-free state with finite kinetic energy, we show that in the large N limit, the fluctuations around the condensate can be effectively described using Bogoliubov approximation for all . The range of β is expected to be optimal for this large class of initial states.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.05240"}],"month":"11","intvolume":" 108","citation":{"mla":"Nam, Phan, and Marcin M. Napiórkowski. “A Note on the Validity of Bogoliubov Correction to Mean Field Dynamics.” Journal de Mathématiques Pures et Appliquées, vol. 108, no. 5, Elsevier, 2017, pp. 662–88, doi:10.1016/j.matpur.2017.05.013.","short":"P. Nam, M.M. Napiórkowski, Journal de Mathématiques Pures et Appliquées 108 (2017) 662–688.","ieee":"P. Nam and M. M. Napiórkowski, “A note on the validity of Bogoliubov correction to mean field dynamics,” Journal de Mathématiques Pures et Appliquées, vol. 108, no. 5. Elsevier, pp. 662–688, 2017.","apa":"Nam, P., & Napiórkowski, M. M. (2017). A note on the validity of Bogoliubov correction to mean field dynamics. Journal de Mathématiques Pures et Appliquées. Elsevier. https://doi.org/10.1016/j.matpur.2017.05.013","ama":"Nam P, Napiórkowski MM. A note on the validity of Bogoliubov correction to mean field dynamics. Journal de Mathématiques Pures et Appliquées. 2017;108(5):662-688. doi:10.1016/j.matpur.2017.05.013","chicago":"Nam, Phan, and Marcin M Napiórkowski. “A Note on the Validity of Bogoliubov Correction to Mean Field Dynamics.” Journal de Mathématiques Pures et Appliquées. Elsevier, 2017. https://doi.org/10.1016/j.matpur.2017.05.013.","ista":"Nam P, Napiórkowski MM. 2017. A note on the validity of Bogoliubov correction to mean field dynamics. Journal de Mathématiques Pures et Appliquées. 108(5), 662–688."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6928","author":[{"id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan","last_name":"Nam","full_name":"Nam, Phan"},{"last_name":"Napiórkowski","full_name":"Napiórkowski, Marcin M","first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000414113600003"]},"article_processing_charge":"No","title":"A note on the validity of Bogoliubov correction to mean field dynamics","project":[{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"isi":1,"year":"2017","day":"01","publication":"Journal de Mathématiques Pures et Appliquées","page":"662 - 688","date_published":"2017-11-01T00:00:00Z","doi":"10.1016/j.matpur.2017.05.013","date_created":"2018-12-11T11:48:15Z","quality_controlled":"1","publisher":"Elsevier","oa":1},{"_id":"737","status":"public","type":"journal_article","date_updated":"2023-09-27T12:53:01Z","department":[{"_id":"HeEd"}],"oa_version":"None","abstract":[{"lang":"eng","text":"We generalize Brazas’ topology on the fundamental group to the whole universal path space X˜ i.e., to the set of homotopy classes of all based paths. We develop basic properties of the new notion and provide a complete comparison of the obtained topology with the established topologies, in particular with the Lasso topology and the CO topology, i.e., the topology that is induced by the compact-open topology. It turns out that the new topology is the finest topology contained in the CO topology, for which the action of the fundamental group on the universal path space is a continuous group action."}],"intvolume":" 231","month":"11","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["01668641"]},"volume":231,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"Z. Virk, A. Zastrow, Topology and Its Applications 231 (2017) 186–196.","ieee":"Z. Virk and A. Zastrow, “A new topology on the universal path space,” Topology and its Applications, vol. 231. Elsevier, pp. 186–196, 2017.","ama":"Virk Z, Zastrow A. A new topology on the universal path space. Topology and its Applications. 2017;231:186-196. doi:10.1016/j.topol.2017.09.015","apa":"Virk, Z., & Zastrow, A. (2017). A new topology on the universal path space. Topology and Its Applications. Elsevier. https://doi.org/10.1016/j.topol.2017.09.015","mla":"Virk, Ziga, and Andreas Zastrow. “A New Topology on the Universal Path Space.” Topology and Its Applications, vol. 231, Elsevier, 2017, pp. 186–96, doi:10.1016/j.topol.2017.09.015.","ista":"Virk Z, Zastrow A. 2017. A new topology on the universal path space. Topology and its Applications. 231, 186–196.","chicago":"Virk, Ziga, and Andreas Zastrow. “A New Topology on the Universal Path Space.” Topology and Its Applications. Elsevier, 2017. https://doi.org/10.1016/j.topol.2017.09.015."},"title":"A new topology on the universal path space","article_processing_charge":"No","external_id":{"isi":["000413889100012"]},"publist_id":"6930","author":[{"first_name":"Ziga","id":"2E36B656-F248-11E8-B48F-1D18A9856A87","full_name":"Virk, Ziga","last_name":"Virk"},{"first_name":"Andreas","full_name":"Zastrow, Andreas","last_name":"Zastrow"}],"quality_controlled":"1","publisher":"Elsevier","publication":"Topology and its Applications","day":"01","year":"2017","isi":1,"date_created":"2018-12-11T11:48:14Z","date_published":"2017-11-01T00:00:00Z","doi":"10.1016/j.topol.2017.09.015","page":"186 - 196"},{"month":"10","intvolume":" 319","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1606.03076","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Let A and B be two N by N deterministic Hermitian matrices and let U be an N by N Haar distributed unitary matrix. It is well known that the spectral distribution of the sum H = A + UBU∗ converges weakly to the free additive convolution of the spectral distributions of A and B, as N tends to infinity. We establish the optimal convergence rate in the bulk of the spectrum."}],"volume":319,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"733","department":[{"_id":"LaEr"}],"date_updated":"2023-09-28T11:30:42Z","quality_controlled":"1","publisher":"Academic Press","oa":1,"acknowledgement":"Partially supported by ERC Advanced Grant RANMAT No. 338804, Hong Kong RGC grant ECS 26301517, and the Göran Gustafsson Foundation","doi":"10.1016/j.aim.2017.08.028","date_published":"2017-10-15T00:00:00Z","date_created":"2018-12-11T11:48:13Z","page":"251 - 291","day":"15","publication":"Advances in Mathematics","isi":1,"year":"2017","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"title":"Convergence rate for spectral distribution of addition of random matrices","author":[{"full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475","last_name":"Bao","first_name":"Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"last_name":"Schnelli","orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","first_name":"Kevin"}],"publist_id":"6935","article_processing_charge":"No","external_id":{"isi":["000412150400010"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Convergence Rate for Spectral Distribution of Addition of Random Matrices.” Advances in Mathematics. Academic Press, 2017. https://doi.org/10.1016/j.aim.2017.08.028.","ista":"Bao Z, Erdös L, Schnelli K. 2017. Convergence rate for spectral distribution of addition of random matrices. Advances in Mathematics. 319, 251–291.","mla":"Bao, Zhigang, et al. “Convergence Rate for Spectral Distribution of Addition of Random Matrices.” Advances in Mathematics, vol. 319, Academic Press, 2017, pp. 251–91, doi:10.1016/j.aim.2017.08.028.","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Convergence rate for spectral distribution of addition of random matrices,” Advances in Mathematics, vol. 319. Academic Press, pp. 251–291, 2017.","short":"Z. Bao, L. Erdös, K. Schnelli, Advances in Mathematics 319 (2017) 251–291.","apa":"Bao, Z., Erdös, L., & Schnelli, K. (2017). Convergence rate for spectral distribution of addition of random matrices. Advances in Mathematics. Academic Press. https://doi.org/10.1016/j.aim.2017.08.028","ama":"Bao Z, Erdös L, Schnelli K. Convergence rate for spectral distribution of addition of random matrices. Advances in Mathematics. 2017;319:251-291. doi:10.1016/j.aim.2017.08.028"}},{"ddc":["539"],"date_updated":"2023-09-26T15:50:22Z","file_date_updated":"2020-07-14T12:48:13Z","department":[{"_id":"GeKa"}],"_id":"840","status":"public","pubrep_id":"865","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"761371a0129b2aa442424b9561450ece","file_id":"4951","file_size":2449546,"date_updated":"2020-07-14T12:48:13Z","creator":"system","file_name":"IST-2017-865-v1+1_acs.nanolett.7b02627.pdf","date_created":"2018-12-12T10:12:33Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["15306984"]},"publication_status":"published","issue":"9","volume":17,"related_material":{"record":[{"relation":"popular_science","id":"7977"},{"id":"69","status":"public","relation":"dissertation_contains"},{"status":"public","id":"7996","relation":"dissertation_contains"}]},"ec_funded":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"M-Shop"}],"abstract":[{"lang":"eng","text":"Heavy holes confined in quantum dots are predicted to be promising candidates for the realization of spin qubits with long coherence times. Here we focus on such heavy-hole states confined in germanium hut wires. By tuning the growth density of the latter we can realize a T-like structure between two neighboring wires. Such a structure allows the realization of a charge sensor, which is electrostatically and tunnel coupled to a quantum dot, with charge-transfer signals as high as 0.3 e. By integrating the T-like structure into a radiofrequency reflectometry setup, single-shot measurements allowing the extraction of hole tunneling times are performed. The extracted tunneling times of less than 10 μs are attributed to the small effective mass of Ge heavy-hole states and pave the way toward projective spin readout measurements."}],"month":"08","intvolume":" 17","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Vukušić, Lada, Josip Kukucka, Hannes Watzinger, and Georgios Katsaros. “Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.” Nano Letters. American Chemical Society, 2017. https://doi.org/10.1021/acs.nanolett.7b02627.","ista":"Vukušić L, Kukucka J, Watzinger H, Katsaros G. 2017. Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. Nano Letters. 17(9), 5706–5710.","mla":"Vukušić, Lada, et al. “Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.” Nano Letters, vol. 17, no. 9, American Chemical Society, 2017, pp. 5706–10, doi:10.1021/acs.nanolett.7b02627.","ama":"Vukušić L, Kukucka J, Watzinger H, Katsaros G. Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. Nano Letters. 2017;17(9):5706-5710. doi:10.1021/acs.nanolett.7b02627","apa":"Vukušić, L., Kukucka, J., Watzinger, H., & Katsaros, G. (2017). Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b02627","short":"L. Vukušić, J. Kukucka, H. Watzinger, G. Katsaros, Nano Letters 17 (2017) 5706–5710.","ieee":"L. Vukušić, J. Kukucka, H. Watzinger, and G. Katsaros, “Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry,” Nano Letters, vol. 17, no. 9. American Chemical Society, pp. 5706–5710, 2017."},"title":"Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry","publist_id":"6808","author":[{"id":"31E9F056-F248-11E8-B48F-1D18A9856A87","first_name":"Lada","last_name":"Vukusic","full_name":"Vukusic, Lada","orcid":"0000-0003-2424-8636"},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip","last_name":"Kukucka","full_name":"Kukucka, Josip"},{"full_name":"Watzinger, Hannes","last_name":"Watzinger","first_name":"Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000411043500078"]},"project":[{"name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","grant_number":"335497","call_identifier":"FP7","_id":"25517E86-B435-11E9-9278-68D0E5697425"}],"day":"10","publication":"Nano Letters","has_accepted_license":"1","isi":1,"year":"2017","date_published":"2017-08-10T00:00:00Z","doi":"10.1021/acs.nanolett.7b02627","date_created":"2018-12-11T11:48:47Z","page":"5706 - 5710","publisher":"American Chemical Society","quality_controlled":"1","oa":1},{"doi":"10.1098/rsos.170547","date_published":"2017-07-05T00:00:00Z","date_created":"2018-12-11T11:49:10Z","has_accepted_license":"1","isi":1,"year":"2017","day":"05","publication":"Royal Society Open Science","quality_controlled":"1","publisher":"Royal Society, The","oa":1,"acknowledgement":"We thank two anonymous reviewers for helpful suggestions on the manuscript.","author":[{"first_name":"Julia","full_name":"Giehr, Julia","last_name":"Giehr"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse","full_name":"Grasse, Anna V"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"},{"full_name":"Heinze, Jürgen","last_name":"Heinze","first_name":"Jürgen"},{"last_name":"Schrempf","full_name":"Schrempf, Alexandra","first_name":"Alexandra"}],"publist_id":"6527","external_id":{"isi":["000406670000025"]},"article_processing_charge":"No","title":"Ant queens increase their reproductive efforts after pathogen infection","citation":{"ama":"Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. Ant queens increase their reproductive efforts after pathogen infection. Royal Society Open Science. 2017;4(7). doi:10.1098/rsos.170547","apa":"Giehr, J., Grasse, A. V., Cremer, S., Heinze, J., & Schrempf, A. (2017). Ant queens increase their reproductive efforts after pathogen infection. Royal Society Open Science. Royal Society, The. https://doi.org/10.1098/rsos.170547","short":"J. Giehr, A.V. Grasse, S. Cremer, J. Heinze, A. Schrempf, Royal Society Open Science 4 (2017).","ieee":"J. Giehr, A. V. Grasse, S. Cremer, J. Heinze, and A. Schrempf, “Ant queens increase their reproductive efforts after pathogen infection,” Royal Society Open Science, vol. 4, no. 7. Royal Society, The, 2017.","mla":"Giehr, Julia, et al. “Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” Royal Society Open Science, vol. 4, no. 7, 170547, Royal Society, The, 2017, doi:10.1098/rsos.170547.","ista":"Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. 2017. Ant queens increase their reproductive efforts after pathogen infection. Royal Society Open Science. 4(7), 170547.","chicago":"Giehr, Julia, Anna V Grasse, Sylvia Cremer, Jürgen Heinze, and Alexandra Schrempf. “Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” Royal Society Open Science. Royal Society, The, 2017. https://doi.org/10.1098/rsos.170547."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"170547","related_material":{"record":[{"relation":"research_data","status":"public","id":"9853"}]},"issue":"7","volume":4,"publication_identifier":{"issn":["20545703"]},"publication_status":"published","file":[{"file_size":530412,"date_updated":"2020-07-14T12:48:15Z","creator":"system","file_name":"IST-2017-849-v1+1_2017_Grasse_Cremer_AntQueens.pdf","date_created":"2018-12-12T10:08:24Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"351ae5e7a37e6e7d9295cd41146c4190","file_id":"4684"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"07","intvolume":" 4","abstract":[{"text":"Infections with potentially lethal pathogens may negatively affect an individual’s lifespan and decrease its reproductive value. The terminal investment hypothesis predicts that individuals faced with a reduced survival should invest more into reproduction instead of maintenance and growth. Several studies suggest that individuals are indeed able to estimate their body condition and to increase their reproductive effort with approaching death, while other studies gave ambiguous results. We investigate whether queens of a perennial social insect (ant) are able to boost their reproduction following infection with an obligate killing pathogen. Social insect queens are special with regard to reproduction and aging, as they outlive conspecific non-reproductive workers. Moreover, in the ant Cardiocondyla obscurior, fecundity increases with queen age. However, it remained unclear whether this reflects negative reproductive senescence or terminal investment in response to approaching death. Here, we test whether queens of C. obscurior react to infection with the entomopathogenic fungus Metarhizium brunneum by an increased egg-laying rate. We show that a fungal infection triggers a reinforced investment in reproduction in queens. This adjustment of the reproductive rate by ant queens is consistent with predictions of the terminal investment hypothesis and is reported for the first time in a social insect.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:15Z","department":[{"_id":"SyCr"}],"date_updated":"2023-09-26T15:45:47Z","ddc":["576","592"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"849","_id":"914"},{"date_updated":"2023-09-26T15:49:15Z","ddc":["576"],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:48:15Z","_id":"910","type":"journal_article","pubrep_id":"974","status":"public","publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5264","checksum":"f7c32dabf52e6d9e709d9203761e39fd","date_updated":"2020-07-14T12:48:15Z","file_size":494268,"creator":"system","date_created":"2018-12-12T10:17:12Z","file_name":"IST-2018-974-v1+1_manuscript.pdf"}],"ec_funded":1,"issue":"2","volume":207,"abstract":[{"lang":"eng","text":"Frequency-independent selection is generally considered as a force that acts to reduce the genetic variation in evolving populations, yet rigorous arguments for this idea are scarce. When selection fluctuates in time, it is unclear whether frequency-independent selection may maintain genetic polymorphism without invoking additional mechanisms. We show that constant frequency-independent selection with arbitrary epistasis on a well-mixed haploid population eliminates genetic variation if we assume linkage equilibrium between alleles. To this end, we introduce the notion of frequency-independent selection at the level of alleles, which is sufficient to prove our claim and contains the notion of frequency-independent selection on haploids. When selection and recombination are weak but of the same order, there may be strong linkage disequilibrium; numerical calculations show that stable equilibria are highly unlikely. Using the example of a diallelic two-locus model, we then demonstrate that frequency-independent selection that fluctuates in time can maintain stable polymorphism if linkage disequilibrium changes its sign periodically. We put our findings in the context of results from the existing literature and point out those scenarios in which the possible role of frequency-independent selection in maintaining genetic variation remains unclear.\r\n"}],"oa_version":"Submitted Version","scopus_import":"1","intvolume":" 207","month":"10","citation":{"mla":"Novak, Sebastian, and Nicholas H. Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” Genetics, vol. 207, no. 2, Genetics Society of America, 2017, pp. 653–68, doi:10.1534/genetics.117.300129.","ama":"Novak S, Barton NH. When does frequency-independent selection maintain genetic variation? Genetics. 2017;207(2):653-668. doi:10.1534/genetics.117.300129","apa":"Novak, S., & Barton, N. H. (2017). When does frequency-independent selection maintain genetic variation? Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300129","short":"S. Novak, N.H. Barton, Genetics 207 (2017) 653–668.","ieee":"S. Novak and N. H. Barton, “When does frequency-independent selection maintain genetic variation?,” Genetics, vol. 207, no. 2. Genetics Society of America, pp. 653–668, 2017.","chicago":"Novak, Sebastian, and Nicholas H Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.117.300129.","ista":"Novak S, Barton NH. 2017. When does frequency-independent selection maintain genetic variation? Genetics. 207(2), 653–668."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000412232600019"]},"author":[{"last_name":"Novak","orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6533","title":"When does frequency-independent selection maintain genetic variation?","project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"year":"2017","has_accepted_license":"1","isi":1,"publication":"Genetics","day":"01","page":"653 - 668","date_created":"2018-12-11T11:49:09Z","doi":"10.1534/genetics.117.300129","date_published":"2017-10-01T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Genetics Society of America"},{"intvolume":" 8","month":"07","oa_version":"Published Version","abstract":[{"text":"An outstanding question in animal development, tissue homeostasis and disease is how cell populations adapt to sensory inputs. During Drosophila larval development, hematopoietic sites are in direct contact with sensory neuron clusters of the peripheral nervous system (PNS), and blood cells (hemocytes) require the PNS for their survival and recruitment to these microenvironments, known as Hematopoietic Pockets. Here we report that Activin-β, a TGF-β family ligand, is expressed by sensory neurons of the PNS and regulates the proliferation and adhesion of hemocytes. These hemocyte responses depend on PNS activity, as shown by agonist treatment and transient silencing of sensory neurons. Activin-β has a key role in this regulation, which is apparent from reporter expression and mutant analyses. This mechanism of local sensory neurons controlling blood cell adaptation invites evolutionary parallels with vertebrate hematopoietic progenitors and the independent myeloid system of tissue macrophages, whose regulation by local microenvironments remain undefined.","lang":"eng"}],"volume":8,"language":[{"iso":"eng"}],"file":[{"file_size":3027104,"date_updated":"2020-07-14T12:48:12Z","creator":"system","file_name":"IST-2017-859-v1+1_ncomms15990.pdf","date_created":"2018-12-12T10:15:32Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"99a3d63308d4250eda0a35341171f80e","file_id":"5153"}],"publication_status":"published","publication_identifier":{"issn":["20411723"]},"pubrep_id":"859","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"835","file_date_updated":"2020-07-14T12:48:12Z","ddc":["570","576","616"],"extern":"1","date_updated":"2023-09-26T15:51:28Z","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","date_created":"2018-12-11T11:48:45Z","date_published":"2017-07-27T00:00:00Z","doi":"10.1038/ncomms15990","publication":"Nature Communications","day":"27","year":"2017","isi":1,"has_accepted_license":"1","article_number":"15990","title":"Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons","article_processing_charge":"No","external_id":{"isi":["000406360100001"]},"author":[{"first_name":"Kalpana","full_name":"Makhijani, Kalpana","last_name":"Makhijani"},{"full_name":"Alexander, Brandy","last_name":"Alexander","first_name":"Brandy"},{"full_name":"Rao, Deepti","last_name":"Rao","first_name":"Deepti"},{"full_name":"Petraki, Sophia","last_name":"Petraki","first_name":"Sophia"},{"first_name":"Leire","last_name":"Herboso","full_name":"Herboso, Leire"},{"last_name":"Kukar","full_name":"Kukar, Katelyn","first_name":"Katelyn"},{"full_name":"Batool, Itrat","last_name":"Batool","first_name":"Itrat"},{"full_name":"Wachner, Stephanie","last_name":"Wachner","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie"},{"first_name":"Katrina","full_name":"Gold, Katrina","last_name":"Gold"},{"first_name":"Corinna","full_name":"Wong, Corinna","last_name":"Wong"},{"last_name":"O'Connor","full_name":"O'Connor, Michael","first_name":"Michael"},{"last_name":"Brückner","full_name":"Brückner, Katja","first_name":"Katja"}],"publist_id":"6813","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"K. Makhijani et al., “Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","short":"K. Makhijani, B. Alexander, D. Rao, S. Petraki, L. Herboso, K. Kukar, I. Batool, S. Wachner, K. Gold, C. Wong, M. O’Connor, K. Brückner, Nature Communications 8 (2017).","apa":"Makhijani, K., Alexander, B., Rao, D., Petraki, S., Herboso, L., Kukar, K., … Brückner, K. (2017). Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms15990","ama":"Makhijani K, Alexander B, Rao D, et al. Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons. Nature Communications. 2017;8. doi:10.1038/ncomms15990","mla":"Makhijani, Kalpana, et al. “Regulation of Drosophila Hematopoietic Sites by Activin-β from Active Sensory Neurons.” Nature Communications, vol. 8, 15990, Nature Publishing Group, 2017, doi:10.1038/ncomms15990.","ista":"Makhijani K, Alexander B, Rao D, Petraki S, Herboso L, Kukar K, Batool I, Wachner S, Gold K, Wong C, O’Connor M, Brückner K. 2017. Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons. Nature Communications. 8, 15990.","chicago":"Makhijani, Kalpana, Brandy Alexander, Deepti Rao, Sophia Petraki, Leire Herboso, Katelyn Kukar, Itrat Batool, et al. “Regulation of Drosophila Hematopoietic Sites by Activin-β from Active Sensory Neurons.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms15990."}},{"publisher":"Springer","quality_controlled":"1","date_created":"2018-12-11T11:48:46Z","date_published":"2017-07-27T00:00:00Z","doi":"10.1007/978-3-319-56932-1_8","page":"119 - 136","publication":"Special Sessions in Applications of Computer Algebra","day":"27","year":"2017","isi":1,"project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"318493","name":"Topological Complex Systems"}],"title":"Finding eigenvalues of self-maps with the Kronecker canonical form","article_processing_charge":"No","external_id":{"isi":["000434088200008"]},"publist_id":"6812","author":[{"first_name":"Marc","full_name":"Ethier, Marc","last_name":"Ethier"},{"orcid":"0000-0002-3536-9866","full_name":"Jablonski, Grzegorz","last_name":"Jablonski","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","first_name":"Grzegorz"},{"first_name":"Marian","last_name":"Mrozek","full_name":"Mrozek, Marian"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Ethier, M., Jablonski, G., & Mrozek, M. (2017). Finding eigenvalues of self-maps with the Kronecker canonical form. In Special Sessions in Applications of Computer Algebra (Vol. 198, pp. 119–136). Kalamata, Greece: Springer. https://doi.org/10.1007/978-3-319-56932-1_8","ama":"Ethier M, Jablonski G, Mrozek M. Finding eigenvalues of self-maps with the Kronecker canonical form. In: Special Sessions in Applications of Computer Algebra. Vol 198. Springer; 2017:119-136. doi:10.1007/978-3-319-56932-1_8","ieee":"M. Ethier, G. Jablonski, and M. Mrozek, “Finding eigenvalues of self-maps with the Kronecker canonical form,” in Special Sessions in Applications of Computer Algebra, Kalamata, Greece, 2017, vol. 198, pp. 119–136.","short":"M. Ethier, G. Jablonski, M. Mrozek, in:, Special Sessions in Applications of Computer Algebra, Springer, 2017, pp. 119–136.","mla":"Ethier, Marc, et al. “Finding Eigenvalues of Self-Maps with the Kronecker Canonical Form.” Special Sessions in Applications of Computer Algebra, vol. 198, Springer, 2017, pp. 119–36, doi:10.1007/978-3-319-56932-1_8.","ista":"Ethier M, Jablonski G, Mrozek M. 2017. Finding eigenvalues of self-maps with the Kronecker canonical form. Special Sessions in Applications of Computer Algebra. ACA: Applications of Computer Algebra, PROMS, vol. 198, 119–136.","chicago":"Ethier, Marc, Grzegorz Jablonski, and Marian Mrozek. “Finding Eigenvalues of Self-Maps with the Kronecker Canonical Form.” In Special Sessions in Applications of Computer Algebra, 198:119–36. Springer, 2017. https://doi.org/10.1007/978-3-319-56932-1_8."},"intvolume":" 198","month":"07","alternative_title":["PROMS"],"scopus_import":"1","oa_version":"None","abstract":[{"text":"Recent research has examined how to study the topological features of a continuous self-map by means of the persistence of the eigenspaces, for given eigenvalues, of the endomorphism induced in homology over a field. This raised the question of how to select dynamically significant eigenvalues. The present paper aims to answer this question, giving an algorithm that computes the persistence of eigenspaces for every eigenvalue simultaneously, also expressing said eigenspaces as direct sums of “finite” and “singular” subspaces.","lang":"eng"}],"ec_funded":1,"volume":198,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-331956930-7"]},"status":"public","conference":{"end_date":"2015-07-23","location":"Kalamata, Greece","start_date":"2015-07-20","name":"ACA: Applications of Computer Algebra"},"type":"conference","_id":"836","department":[{"_id":"HeEd"}],"date_updated":"2023-09-26T15:50:52Z"},{"status":"public","type":"conference","conference":{"end_date":"2017-07-26","location":"Honolulu, HA, United States","start_date":"2017-07-21","name":"CVPR: Computer Vision and Pattern Recognition"},"_id":"916","department":[{"_id":"VlKo"}],"file_date_updated":"2020-07-14T12:48:15Z","ddc":["000"],"date_updated":"2023-09-26T15:41:40Z","month":"01","intvolume":" 2017","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"We study the quadratic assignment problem, in computer vision also known as graph matching. Two leading solvers for this problem optimize the Lagrange decomposition duals with sub-gradient and dual ascent (also known as message passing) updates. We explore this direction further and propose several additional Lagrangean relaxations of the graph matching problem along with corresponding algorithms, which are all based on a common dual ascent framework. Our extensive empirical evaluation gives several theoretical insights and suggests a new state-of-the-art anytime solver for the considered problem. Our improvement over state-of-the-art is particularly visible on a new dataset with large-scale sparse problem instances containing more than 500 graph nodes each.","lang":"eng"}],"volume":2017,"ec_funded":1,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5848","checksum":"e38a2740daad1ea178465843b5072906","creator":"dernst","file_size":944332,"date_updated":"2020-07-14T12:48:15Z","file_name":"2017_CVPR_Swoboda2.pdf","date_created":"2019-01-18T12:49:38Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-153860457-1"]},"publication_status":"published","project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"title":"A study of lagrangean decompositions and dual ascent solvers for graph matching","publist_id":"6525","author":[{"first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","full_name":"Swoboda, Paul"},{"first_name":"Carsten","last_name":"Rother","full_name":"Rother, Carsten"},{"first_name":"Carsten","last_name":"Abu Alhaija","full_name":"Abu Alhaija, Carsten"},{"first_name":"Dagmar","full_name":"Kainmueller, Dagmar","last_name":"Kainmueller"},{"first_name":"Bogdan","last_name":"Savchynskyy","full_name":"Savchynskyy, Bogdan"}],"article_processing_charge":"No","external_id":{"isi":["000418371407018"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Swoboda, Paul, et al. A Study of Lagrangean Decompositions and Dual Ascent Solvers for Graph Matching. Vol. 2017, IEEE, 2017, pp. 7062–71, doi:10.1109/CVPR.2017.747.","short":"P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, B. Savchynskyy, in:, IEEE, 2017, pp. 7062–7071.","ieee":"P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, and B. Savchynskyy, “A study of lagrangean decompositions and dual ascent solvers for graph matching,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 7062–7071.","apa":"Swoboda, P., Rother, C., Abu Alhaija, C., Kainmueller, D., & Savchynskyy, B. (2017). A study of lagrangean decompositions and dual ascent solvers for graph matching (Vol. 2017, pp. 7062–7071). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.747","ama":"Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. A study of lagrangean decompositions and dual ascent solvers for graph matching. In: Vol 2017. IEEE; 2017:7062-7071. doi:10.1109/CVPR.2017.747","chicago":"Swoboda, Paul, Carsten Rother, Carsten Abu Alhaija, Dagmar Kainmueller, and Bogdan Savchynskyy. “A Study of Lagrangean Decompositions and Dual Ascent Solvers for Graph Matching,” 2017:7062–71. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.747.","ista":"Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. 2017. A study of lagrangean decompositions and dual ascent solvers for graph matching. CVPR: Computer Vision and Pattern Recognition vol. 2017, 7062–7071."},"quality_controlled":"1","publisher":"IEEE","oa":1,"date_published":"2017-01-01T00:00:00Z","doi":"10.1109/CVPR.2017.747","date_created":"2018-12-11T11:49:11Z","page":"7062-7071","day":"01","has_accepted_license":"1","isi":1,"year":"2017"},{"ddc":["000"],"date_updated":"2023-09-26T15:43:27Z","file_date_updated":"2020-07-14T12:48:15Z","department":[{"_id":"VlKo"}],"_id":"915","status":"public","type":"conference","conference":{"name":"CVPR: Computer Vision and Pattern Recognition","end_date":"2017-07-26","location":"Honolulu, HA, United States","start_date":"2017-07-21"},"file":[{"file_size":883264,"date_updated":"2020-07-14T12:48:15Z","creator":"dernst","file_name":"Swoboda_A_Message_Passing_CVPR_2017_paper.pdf","date_created":"2019-01-18T12:52:46Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"7e51dacefa693574581a32da3eff63dc","file_id":"5849"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-153860457-1"]},"publication_status":"published","volume":2017,"ec_funded":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We propose a dual decomposition and linear program relaxation of the NP-hard minimum cost multicut problem. Unlike other polyhedral relaxations of the multicut polytope, it is amenable to efficient optimization by message passing. Like other polyhedral relaxations, it can be tightened efficiently by cutting planes. We define an algorithm that alternates between message passing and efficient separation of cycle- and odd-wheel inequalities. This algorithm is more efficient than state-of-the-art algorithms based on linear programming, including algorithms written in the framework of leading commercial software, as we show in experiments with large instances of the problem from applications in computer vision, biomedical image analysis and data mining."}],"month":"07","intvolume":" 2017","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Swoboda, Paul, and Bjoern Andres. A Message Passing Algorithm for the Minimum Cost Multicut Problem. Vol. 2017, IEEE, 2017, pp. 4990–99, doi:10.1109/CVPR.2017.530.","ieee":"P. Swoboda and B. Andres, “A message passing algorithm for the minimum cost multicut problem,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 4990–4999.","short":"P. Swoboda, B. Andres, in:, IEEE, 2017, pp. 4990–4999.","ama":"Swoboda P, Andres B. A message passing algorithm for the minimum cost multicut problem. In: Vol 2017. IEEE; 2017:4990-4999. doi:10.1109/CVPR.2017.530","apa":"Swoboda, P., & Andres, B. (2017). A message passing algorithm for the minimum cost multicut problem (Vol. 2017, pp. 4990–4999). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.530","chicago":"Swoboda, Paul, and Bjoern Andres. “A Message Passing Algorithm for the Minimum Cost Multicut Problem,” 2017:4990–99. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.530.","ista":"Swoboda P, Andres B. 2017. A message passing algorithm for the minimum cost multicut problem. CVPR: Computer Vision and Pattern Recognition vol. 2017, 4990–4999."},"title":"A message passing algorithm for the minimum cost multicut problem","author":[{"first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","full_name":"Swoboda, Paul"},{"first_name":"Bjoern","last_name":"Andres","full_name":"Andres, Bjoern"}],"publist_id":"6526","article_processing_charge":"No","external_id":{"isi":["000418371405009"]},"project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"day":"01","has_accepted_license":"1","isi":1,"year":"2017","date_published":"2017-07-01T00:00:00Z","doi":"10.1109/CVPR.2017.530","date_created":"2018-12-11T11:49:11Z","page":"4990-4999","publisher":"IEEE","quality_controlled":"1","oa":1},{"author":[{"last_name":"Swoboda","full_name":"Swoboda, Paul","first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","full_name":"Kuske, Jan","last_name":"Kuske"},{"first_name":"Bogdan","full_name":"Savchynskyy, Bogdan","last_name":"Savchynskyy"}],"publist_id":"6524","article_processing_charge":"No","external_id":{"isi":["000418371405005"]},"title":"A dual ascent framework for Lagrangean decomposition of combinatorial problems","citation":{"mla":"Swoboda, Paul, et al. A Dual Ascent Framework for Lagrangean Decomposition of Combinatorial Problems. Vol. 2017, IEEE, 2017, pp. 4950–60, doi:10.1109/CVPR.2017.526.","ama":"Swoboda P, Kuske J, Savchynskyy B. A dual ascent framework for Lagrangean decomposition of combinatorial problems. In: Vol 2017. IEEE; 2017:4950-4960. doi:10.1109/CVPR.2017.526","apa":"Swoboda, P., Kuske, J., & Savchynskyy, B. (2017). A dual ascent framework for Lagrangean decomposition of combinatorial problems (Vol. 2017, pp. 4950–4960). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.526","ieee":"P. Swoboda, J. Kuske, and B. Savchynskyy, “A dual ascent framework for Lagrangean decomposition of combinatorial problems,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 4950–4960.","short":"P. Swoboda, J. Kuske, B. Savchynskyy, in:, IEEE, 2017, pp. 4950–4960.","chicago":"Swoboda, Paul, Jan Kuske, and Bogdan Savchynskyy. “A Dual Ascent Framework for Lagrangean Decomposition of Combinatorial Problems,” 2017:4950–60. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.526.","ista":"Swoboda P, Kuske J, Savchynskyy B. 2017. A dual ascent framework for Lagrangean decomposition of combinatorial problems. CVPR: Computer Vision and Pattern Recognition vol. 2017, 4950–4960."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"}],"page":"4950-4960","doi":"10.1109/CVPR.2017.526","date_published":"2017-07-01T00:00:00Z","date_created":"2018-12-11T11:49:11Z","has_accepted_license":"1","isi":1,"year":"2017","day":"01","publisher":"IEEE","quality_controlled":"1","oa":1,"department":[{"_id":"VlKo"}],"file_date_updated":"2020-07-14T12:48:15Z","date_updated":"2023-09-26T15:41:11Z","ddc":["000"],"type":"conference","conference":{"location":"Honolulu, HA, United States","end_date":"2017-07-26","start_date":"2017-07-21","name":"CVPR: Computer Vision and Pattern Recognition"},"status":"public","_id":"917","volume":2017,"ec_funded":1,"publication_identifier":{"isbn":["978-153860457-1"]},"publication_status":"published","file":[{"file_id":"5847","checksum":"72fd291046bd8e5717961bd68f6b6f03","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-01-18T12:45:55Z","file_name":"2017_CVPR_Swoboda.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:15Z","file_size":898652}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"07","intvolume":" 2017","abstract":[{"text":"We propose a general dual ascent framework for Lagrangean decomposition of combinatorial problems. Although methods of this type have shown their efficiency for a number of problems, so far there was no general algorithm applicable to multiple problem types. In this work, we propose such a general algorithm. It depends on several parameters, which can be used to optimize its performance in each particular setting. We demonstrate efficacy of our method on graph matching and multicut problems, where it outperforms state-of-the-art solvers including those based on subgradient optimization and off-the-shelf linear programming solvers.","lang":"eng"}],"oa_version":"Submitted Version"},{"project":[{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020","grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","grant_number":"201439","_id":"2524F500-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"ama":"Zagórski MP, Tabata Y, Brandenberg N, et al. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 2017;356(6345):1379-1383. doi:10.1126/science.aam5887","apa":"Zagórski, M. P., Tabata, Y., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach, T., … Kicheva, A. (2017). Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aam5887","ieee":"M. P. Zagórski et al., “Decoding of position in the developing neural tube from antiparallel morphogen gradients,” Science, vol. 356, no. 6345. American Association for the Advancement of Science, pp. 1379–1383, 2017.","short":"M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkačik, T. Bollenbach, J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383.","mla":"Zagórski, Marcin P., et al. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science, vol. 356, no. 6345, American Association for the Advancement of Science, 2017, pp. 1379–83, doi:10.1126/science.aam5887.","ista":"Zagórski MP, Tabata Y, Brandenberg N, Lutolf M, Tkačik G, Bollenbach T, Briscoe J, Kicheva A. 2017. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 356(6345), 1379–1383.","chicago":"Zagórski, Marcin P, Yoji Tabata, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik, Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aam5887."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000404351500036"],"pmid":["28663499"]},"article_processing_charge":"No","author":[{"orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P","last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P"},{"full_name":"Tabata, Yoji","last_name":"Tabata","first_name":"Yoji"},{"first_name":"Nathalie","full_name":"Brandenberg, Nathalie","last_name":"Brandenberg"},{"last_name":"Lutolf","full_name":"Lutolf, Matthias","first_name":"Matthias"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"},{"first_name":"Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Tobias"},{"first_name":"James","full_name":"Briscoe, James","last_name":"Briscoe"},{"orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","last_name":"Kicheva","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6474","title":"Decoding of position in the developing neural tube from antiparallel morphogen gradients","oa":1,"publisher":"American Association for the Advancement of Science","quality_controlled":"1","year":"2017","isi":1,"publication":"Science","day":"30","page":"1379 - 1383","date_created":"2018-12-11T11:49:20Z","doi":"10.1126/science.aam5887","date_published":"2017-06-30T00:00:00Z","_id":"943","type":"journal_article","status":"public","date_updated":"2023-09-26T15:38:05Z","department":[{"_id":"AnKi"},{"_id":"GaTk"}],"abstract":[{"lang":"eng","text":"Like many developing tissues, the vertebrate neural tube is patterned by antiparallel morphogen gradients. To understand how these inputs are interpreted, we measured morphogen signaling and target gene expression in mouse embryos and chick ex vivo assays. From these data, we derived and validated a characteristic decoding map that relates morphogen input to the positional identity of neural progenitors. Analysis of the observed responses indicates that the underlying interpretation strategy minimizes patterning errors in response to the joint input of noisy opposing gradients. We reverse-engineered a transcriptional network that provides a mechanistic basis for the observed cell fate decisions and accounts for the precision and dynamics of pattern formation. Together, our data link opposing gradient dynamics in a growing tissue to precise pattern formation."}],"oa_version":"Submitted Version","pmid":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568706/","open_access":"1"}],"scopus_import":"1","intvolume":" 356","month":"06","publication_status":"published","publication_identifier":{"issn":["00368075"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"6345","volume":356},{"date_updated":"2023-09-26T15:37:02Z","department":[{"_id":"SiHi"},{"_id":"MaJö"}],"_id":"944","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["08966273"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":94,"issue":"3","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"abstract":[{"lang":"eng","text":"The concerted production of neurons and glia by neural stem cells (NSCs) is essential for neural circuit assembly. In the developing cerebral cortex, radial glia progenitors (RGPs) generate nearly all neocortical neurons and certain glia lineages. RGP proliferation behavior shows a high degree of non-stochasticity, thus a deterministic characteristic of neuron and glia production. However, the cellular and molecular mechanisms controlling RGP behavior and proliferation dynamics in neurogenesis and glia generation remain unknown. By using mosaic analysis with double markers (MADM)-based genetic paradigms enabling the sparse and global knockout with unprecedented single-cell resolution, we identified Lgl1 as a critical regulatory component. We uncover Lgl1-dependent tissue-wide community effects required for embryonic cortical neurogenesis and novel cell-autonomous Lgl1 functions controlling RGP-mediated glia genesis and postnatal NSC behavior. These results suggest that NSC-mediated neuron and glia production is tightly regulated through the concerted interplay of sequential Lgl1-dependent global and cell intrinsic mechanisms."}],"oa_version":"None","scopus_import":"1","intvolume":" 94","month":"05","citation":{"chicago":"Beattie, Robert J, Maria P Postiglione, Laura Burnett, Susanne Laukoter, Carmen Streicher, Florian Pauler, Guanxi Xiao, et al. “Mosaic Analysis with Double Markers Reveals Distinct Sequential Functions of Lgl1 in Neural Stem Cells.” Neuron. Cell Press, 2017. https://doi.org/10.1016/j.neuron.2017.04.012.","ista":"Beattie RJ, Postiglione MP, Burnett L, Laukoter S, Streicher C, Pauler F, Xiao G, Klezovitch O, Vasioukhin V, Ghashghaei T, Hippenmeyer S. 2017. Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. 94(3), 517–533.e3.","mla":"Beattie, Robert J., et al. “Mosaic Analysis with Double Markers Reveals Distinct Sequential Functions of Lgl1 in Neural Stem Cells.” Neuron, vol. 94, no. 3, Cell Press, 2017, p. 517–533.e3, doi:10.1016/j.neuron.2017.04.012.","ieee":"R. J. Beattie et al., “Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells,” Neuron, vol. 94, no. 3. Cell Press, p. 517–533.e3, 2017.","short":"R.J. Beattie, M.P. Postiglione, L. Burnett, S. Laukoter, C. Streicher, F. Pauler, G. Xiao, O. Klezovitch, V. Vasioukhin, T. Ghashghaei, S. Hippenmeyer, Neuron 94 (2017) 517–533.e3.","ama":"Beattie RJ, Postiglione MP, Burnett L, et al. Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. 2017;94(3):517-533.e3. doi:10.1016/j.neuron.2017.04.012","apa":"Beattie, R. J., Postiglione, M. P., Burnett, L., Laukoter, S., Streicher, C., Pauler, F., … Hippenmeyer, S. (2017). Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. Cell Press. https://doi.org/10.1016/j.neuron.2017.04.012"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000400466700011"]},"article_processing_charge":"No","publist_id":"6473","author":[{"orcid":"0000-0002-8483-8753","full_name":"Beattie, Robert J","last_name":"Beattie","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J"},{"id":"2C67902A-F248-11E8-B48F-1D18A9856A87","first_name":"Maria P","last_name":"Postiglione","full_name":"Postiglione, Maria P"},{"last_name":"Burnett","full_name":"Burnett, Laura","orcid":"0000-0002-8937-410X","first_name":"Laura","id":"3B717F68-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Laukoter, Susanne","orcid":"0000-0002-7903-3010","last_name":"Laukoter","first_name":"Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher","full_name":"Streicher, Carmen"},{"last_name":"Pauler","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"full_name":"Xiao, Guanxi","last_name":"Xiao","first_name":"Guanxi"},{"full_name":"Klezovitch, Olga","last_name":"Klezovitch","first_name":"Olga"},{"first_name":"Valeri","last_name":"Vasioukhin","full_name":"Vasioukhin, Valeri"},{"full_name":"Ghashghaei, Troy","last_name":"Ghashghaei","first_name":"Troy"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"title":"Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells","project":[{"grant_number":"618444","name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425"},{"_id":"25D7962E-B435-11E9-9278-68D0E5697425","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","grant_number":"RGP0053/2014"}],"year":"2017","isi":1,"publication":"Neuron","day":"03","page":"517 - 533.e3","date_created":"2018-12-11T11:49:20Z","date_published":"2017-05-03T00:00:00Z","doi":"10.1016/j.neuron.2017.04.012","quality_controlled":"1","publisher":"Cell Press"},{"quality_controlled":"1","publisher":"ACM","date_published":"2017-09-01T00:00:00Z","doi":"10.1145/3106237.3106309","date_created":"2018-12-11T11:49:19Z","page":"593 - 604","day":"01","isi":1,"year":"2017","project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"title":"S3: Syntax- and semantic-guided repair synthesis via programming by examples","publist_id":"6477","author":[{"full_name":"Le, Xuan","last_name":"Le","first_name":"Xuan"},{"id":"3598E630-F248-11E8-B48F-1D18A9856A87","first_name":"Duc Hiep","last_name":"Chu","full_name":"Chu, Duc Hiep"},{"full_name":"Lo, David","last_name":"Lo","first_name":"David"},{"full_name":"Le Goues, Claire","last_name":"Le Goues","first_name":"Claire"},{"first_name":"Willem","last_name":"Visser","full_name":"Visser, Willem"}],"article_processing_charge":"No","external_id":{"isi":["000414279300055"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser. “S3: Syntax- and Semantic-Guided Repair Synthesis via Programming by Examples,” F130154:593–604. ACM, 2017. https://doi.org/10.1145/3106237.3106309.","ista":"Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. S3: Syntax- and semantic-guided repair synthesis via programming by examples. FSE: Foundations of Software Engineering vol. F130154, 593–604.","mla":"Le, Xuan, et al. S3: Syntax- and Semantic-Guided Repair Synthesis via Programming by Examples. Vol. F130154, ACM, 2017, pp. 593–604, doi:10.1145/3106237.3106309.","apa":"Le, X., Chu, D. H., Lo, D., Le Goues, C., & Visser, W. (2017). S3: Syntax- and semantic-guided repair synthesis via programming by examples (Vol. F130154, pp. 593–604). Presented at the FSE: Foundations of Software Engineering, Paderborn, Germany: ACM. https://doi.org/10.1145/3106237.3106309","ama":"Le X, Chu DH, Lo D, Le Goues C, Visser W. S3: Syntax- and semantic-guided repair synthesis via programming by examples. In: Vol F130154. ACM; 2017:593-604. doi:10.1145/3106237.3106309","ieee":"X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “S3: Syntax- and semantic-guided repair synthesis via programming by examples,” presented at the FSE: Foundations of Software Engineering, Paderborn, Germany, 2017, vol. F130154, pp. 593–604.","short":"X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, ACM, 2017, pp. 593–604."},"month":"09","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"A notable class of techniques for automatic program repair is known as semantics-based. Such techniques, e.g., Angelix, infer semantic specifications via symbolic execution, and then use program synthesis to construct new code that satisfies those inferred specifications. However, the obtained specifications are naturally incomplete, leaving the synthesis engine with a difficult task of synthesizing a general solution from a sparse space of many possible solutions that are consistent with the provided specifications but that do not necessarily generalize. We present S3, a new repair synthesis engine that leverages programming-by-examples methodology to synthesize high-quality bug repairs. The novelty in S3 that allows it to tackle the sparse search space to create more general repairs is three-fold: (1) A systematic way to customize and constrain the syntactic search space via a domain-specific language, (2) An efficient enumeration-based search strategy over the constrained search space, and (3) A number of ranking features based on measures of the syntactic and semantic distances between candidate solutions and the original buggy program. We compare S3’s repair effectiveness with state-of-the-art synthesis engines Angelix, Enumerative, and CVC4. S3 can successfully and correctly fix at least three times more bugs than the best baseline on datasets of 52 bugs in small programs, and 100 bugs in real-world large programs. "}],"volume":"F130154","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-145035105-8"]},"publication_status":"published","status":"public","type":"conference","conference":{"name":"FSE: Foundations of Software Engineering","start_date":"2017-09-04","location":"Paderborn, Germany","end_date":"2017-09-08"},"_id":"942","department":[{"_id":"ToHe"}],"date_updated":"2023-09-26T15:38:36Z"},{"article_number":"033905","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Midya B, Konotop V. 2017. Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. 119(3), 033905.","chicago":"Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries: Nonlinearity Controlled by an Exceptional Point and Solitons.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.033905.","apa":"Midya, B., & Konotop, V. (2017). Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.119.033905","ama":"Midya B, Konotop V. Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. 2017;119(3). doi:10.1103/PhysRevLett.119.033905","short":"B. Midya, V. Konotop, Physical Review Letters 119 (2017).","ieee":"B. Midya and V. Konotop, “Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons,” Physical Review Letters, vol. 119, no. 3. American Physical Society, 2017.","mla":"Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries: Nonlinearity Controlled by an Exceptional Point and Solitons.” Physical Review Letters, vol. 119, no. 3, 033905, American Physical Society, 2017, doi:10.1103/PhysRevLett.119.033905."},"title":"Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons","article_processing_charge":"No","external_id":{"isi":["000405718200012"]},"author":[{"last_name":"Midya","full_name":"Midya, Bikashkali","first_name":"Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Vladimir","last_name":"Konotop","full_name":"Konotop, Vladimir"}],"publist_id":"6481","oa":1,"publisher":"American Physical Society","quality_controlled":"1","publication":"Physical Review Letters","day":"18","year":"2017","isi":1,"date_created":"2018-12-11T11:49:18Z","date_published":"2017-07-18T00:00:00Z","doi":"10.1103/PhysRevLett.119.033905","_id":"939","status":"public","type":"journal_article","date_updated":"2023-09-26T15:39:46Z","department":[{"_id":"MiLe"}],"oa_version":"Submitted Version","abstract":[{"text":"We reveal the existence of continuous families of guided single-mode solitons in planar waveguides with weakly nonlinear active core and absorbing boundaries. Stable propagation of TE and TM-polarized solitons is accompanied by attenuation of all other modes, i.e., the waveguide features properties of conservative and dissipative systems. If the linear spectrum of the waveguide possesses exceptional points, which occurs in the case of TM polarization, an originally focusing (defocusing) material nonlinearity may become effectively defocusing (focusing). This occurs due to the geometric phase of the carried eigenmode when the surface impedance encircles the exceptional point. In its turn, the change of the effective nonlinearity ensures the existence of dark (bright) solitons in spite of focusing (defocusing) Kerr nonlinearity of the core. The existence of an exceptional point can also result in anomalous enhancement of the effective nonlinearity. In terms of practical applications, the nonlinearity of the reported waveguide can be manipulated by controlling the properties of the absorbing cladding.","lang":"eng"}],"intvolume":" 119","month":"07","main_file_link":[{"url":"https://arxiv.org/abs/1706.04085 ","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00319007"]},"ec_funded":1,"issue":"3","volume":119},{"date_updated":"2023-09-26T15:45:47Z","citation":{"chicago":"Giehr, Julia, Anna V Grasse, Sylvia Cremer, Jürgen Heinze, and Alexandra Schrempf. “Raw Data from Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” The Royal Society, 2017. https://doi.org/10.6084/m9.figshare.5117788.v1.","ista":"Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. 2017. Raw data from ant queens increase their reproductive efforts after pathogen infection, The Royal Society, 10.6084/m9.figshare.5117788.v1.","mla":"Giehr, Julia, et al. Raw Data from Ant Queens Increase Their Reproductive Efforts after Pathogen Infection. The Royal Society, 2017, doi:10.6084/m9.figshare.5117788.v1.","short":"J. Giehr, A.V. Grasse, S. Cremer, J. Heinze, A. Schrempf, (2017).","ieee":"J. Giehr, A. V. Grasse, S. Cremer, J. Heinze, and A. Schrempf, “Raw data from ant queens increase their reproductive efforts after pathogen infection.” The Royal Society, 2017.","apa":"Giehr, J., Grasse, A. V., Cremer, S., Heinze, J., & Schrempf, A. (2017). Raw data from ant queens increase their reproductive efforts after pathogen infection. The Royal Society. https://doi.org/10.6084/m9.figshare.5117788.v1","ama":"Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. Raw data from ant queens increase their reproductive efforts after pathogen infection. 2017. doi:10.6084/m9.figshare.5117788.v1"},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Giehr","full_name":"Giehr, Julia","first_name":"Julia"},{"full_name":"Grasse, Anna V","last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"},{"first_name":"Jürgen","full_name":"Heinze, Jürgen","last_name":"Heinze"},{"last_name":"Schrempf","full_name":"Schrempf, Alexandra","first_name":"Alexandra"}],"article_processing_charge":"No","title":"Raw data from ant queens increase their reproductive efforts after pathogen infection","department":[{"_id":"SyCr"}],"_id":"9853","type":"research_data_reference","status":"public","year":"2017","day":"19","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"914"}]},"date_published":"2017-06-19T00:00:00Z","doi":"10.6084/m9.figshare.5117788.v1","date_created":"2021-08-10T06:57:57Z","abstract":[{"text":"Egg laying rates and infection loads of C. obscurior queens","lang":"eng"}],"oa_version":"Published Version","publisher":"The Royal Society","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.5117788.v1","open_access":"1"}],"oa":1,"month":"06"},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00278424"]},"ec_funded":1,"volume":114,"issue":"40","pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Polymicrobial infections constitute small ecosystems that accommodate several bacterial species. Commonly, these bacteria are investigated in isolation. However, it is unknown to what extent the isolates interact and whether their interactions alter bacterial growth and ecosystem resilience in the presence and absence of antibiotics. We quantified the complete ecological interaction network for 72 bacterial isolates collected from 23 individuals diagnosed with polymicrobial urinary tract infections and found that most interactions cluster based on evolutionary relatedness. Statistical network analysis revealed that competitive and cooperative reciprocal interactions are enriched in the global network, while cooperative interactions are depleted in the individual host community networks. A population dynamics model parameterized by our measurements suggests that interactions restrict community stability, explaining the observed species diversity of these communities. We further show that the clinical isolates frequently protect each other from clinically relevant antibiotics. Together, these results highlight that ecological interactions are crucial for the growth and survival of bacteria in polymicrobial infection communities and affect their assembly and resilience. "}],"intvolume":" 114","month":"10","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635929/"}],"scopus_import":"1","date_updated":"2023-09-26T16:18:48Z","department":[{"_id":"ToBo"}],"_id":"822","status":"public","type":"journal_article","publication":"PNAS","day":"03","year":"2017","isi":1,"date_created":"2018-12-11T11:48:41Z","date_published":"2017-10-03T00:00:00Z","doi":"10.1073/pnas.1713372114","page":"10666 - 10671","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"de Vos, Marjon, et al. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” PNAS, vol. 114, no. 40, National Academy of Sciences, 2017, pp. 10666–71, doi:10.1073/pnas.1713372114.","ama":"de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. 2017;114(40):10666-10671. doi:10.1073/pnas.1713372114","apa":"de Vos, M., Zagórski, M. P., Mcnally, A., & Bollenbach, M. T. (2017). Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713372114","ieee":"M. de Vos, M. P. Zagórski, A. Mcnally, and M. T. Bollenbach, “Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections,” PNAS, vol. 114, no. 40. National Academy of Sciences, pp. 10666–10671, 2017.","short":"M. de Vos, M.P. Zagórski, A. Mcnally, M.T. Bollenbach, PNAS 114 (2017) 10666–10671.","chicago":"Vos, Marjon de, Marcin P Zagórski, Alan Mcnally, and Mark Tobias Bollenbach. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1713372114.","ista":"de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. 2017. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. 114(40), 10666–10671."},"title":"Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections","external_id":{"isi":["000412130500061"],"pmid":["28923953"]},"article_processing_charge":"No","author":[{"id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","first_name":"Marjon","full_name":"De Vos, Marjon","last_name":"De Vos"},{"orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P","last_name":"Zagórski","first_name":"Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alan","full_name":"Mcnally, Alan","last_name":"Mcnally"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X"}],"publist_id":"6827","project":[{"grant_number":"303507","name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}]},{"quality_controlled":"1","publisher":"Springer","oa":1,"day":"28","isi":1,"year":"2017","doi":"10.1007/978-3-319-64689-3_32","date_published":"2017-07-28T00:00:00Z","date_created":"2018-12-11T11:48:45Z","page":"397 - 409","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Heiss T, Wagner H. Streaming algorithm for Euler characteristic curves of multidimensional images. In: Felsberg M, Heyden A, Krüger N, eds. Vol 10424. Springer; 2017:397-409. doi:10.1007/978-3-319-64689-3_32","apa":"Heiss, T., & Wagner, H. (2017). Streaming algorithm for Euler characteristic curves of multidimensional images. In M. Felsberg, A. Heyden, & N. Krüger (Eds.) (Vol. 10424, pp. 397–409). Presented at the CAIP: Computer Analysis of Images and Patterns, Ystad, Sweden: Springer. https://doi.org/10.1007/978-3-319-64689-3_32","ieee":"T. Heiss and H. Wagner, “Streaming algorithm for Euler characteristic curves of multidimensional images,” presented at the CAIP: Computer Analysis of Images and Patterns, Ystad, Sweden, 2017, vol. 10424, pp. 397–409.","short":"T. Heiss, H. Wagner, in:, M. Felsberg, A. Heyden, N. Krüger (Eds.), Springer, 2017, pp. 397–409.","mla":"Heiss, Teresa, and Hubert Wagner. Streaming Algorithm for Euler Characteristic Curves of Multidimensional Images. Edited by Michael Felsberg et al., vol. 10424, Springer, 2017, pp. 397–409, doi:10.1007/978-3-319-64689-3_32.","ista":"Heiss T, Wagner H. 2017. Streaming algorithm for Euler characteristic curves of multidimensional images. CAIP: Computer Analysis of Images and Patterns, LNCS, vol. 10424, 397–409.","chicago":"Heiss, Teresa, and Hubert Wagner. “Streaming Algorithm for Euler Characteristic Curves of Multidimensional Images.” edited by Michael Felsberg, Anders Heyden, and Norbert Krüger, 10424:397–409. Springer, 2017. https://doi.org/10.1007/978-3-319-64689-3_32."},"title":"Streaming algorithm for Euler characteristic curves of multidimensional images","editor":[{"full_name":"Felsberg, Michael","last_name":"Felsberg","first_name":"Michael"},{"full_name":"Heyden, Anders","last_name":"Heyden","first_name":"Anders"},{"full_name":"Krüger, Norbert","last_name":"Krüger","first_name":"Norbert"}],"publist_id":"6815","author":[{"orcid":"0000-0002-1780-2689","full_name":"Heiss, Teresa","last_name":"Heiss","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","first_name":"Teresa"},{"first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","full_name":"Wagner, Hubert"}],"article_processing_charge":"No","external_id":{"isi":["000432085900032"]},"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We present an efficient algorithm to compute Euler characteristic curves of gray scale images of arbitrary dimension. In various applications the Euler characteristic curve is used as a descriptor of an image. Our algorithm is the first streaming algorithm for Euler characteristic curves. The usage of streaming removes the necessity to store the entire image in RAM. Experiments show that our implementation handles terabyte scale images on commodity hardware. Due to lock-free parallelism, it scales well with the number of processor cores. Additionally, we put the concept of the Euler characteristic curve in the wider context of computational topology. In particular, we explain the connection with persistence diagrams."}],"month":"07","intvolume":" 10424","scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"url":"https://arxiv.org/abs/1705.02045","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["03029743"]},"publication_status":"published","volume":10424,"_id":"833","status":"public","type":"conference","conference":{"start_date":"2017-08-22","end_date":"2017-08-24","location":"Ystad, Sweden","name":"CAIP: Computer Analysis of Images and Patterns"},"date_updated":"2023-09-26T16:10:03Z","department":[{"_id":"HeEd"}]},{"publication":"Development","language":[{"iso":"eng"}],"day":"31","year":"2017","publication_status":"published","isi":1,"date_created":"2018-12-11T11:48:36Z","date_published":"2017-10-31T00:00:00Z","doi":"10.1242/dev.145698","volume":144,"page":"3917 - 3931","oa_version":"None","abstract":[{"text":"During corticogenesis, distinct classes of neurons are born from progenitor cells located in the ventricular and subventricular zones, from where they migrate towards the pial surface to assemble into highly organized layer-specific circuits. However, the precise and coordinated transcriptional network activity defining neuronal identity is still not understood. Here, we show that genetic depletion of the basic helix-loop-helix (bHLH) transcription factor E2A splice variant E47 increased the number of Tbr1-positive deep layer and Satb2-positive upper layer neurons at E14.5, while depletion of the alternatively spliced E12 variant did not affect layer-specific neurogenesis. While ChIP-Seq identified a big overlap for E12- and E47-specific binding sites in embryonic NSCs, including sites at the cyclin-dependent kinase inhibitor (CDKI) Cdkn1c gene locus, RNA-Seq revealed a unique transcriptional regulation by each splice variant. E47 activated the expression of the CDKI Cdkn1c through binding to a distal enhancer. Finally, overexpression of E47 in embryonic NSCs in vitro impaired neurite outgrowth and E47 overexpression in vivo by in utero electroporation disturbed proper layer-specific neurogenesis and upregulated p57(KIP2) expression. Overall, this study identified E2A target genes in embryonic NSCs and demonstrates that E47 regulates neuronal differentiation via p57(KIP2).","lang":"eng"}],"intvolume":" 144","month":"10","publisher":"Company of Biologists","quality_controlled":"1","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Pfurr, Sabrina, Yu Chu, Christian Bohrer, Franziska Greulich, Robert J Beattie, Könül Mammadzada, Miriam Hils, et al. “The E2A Splice Variant E47 Regulates the Differentiation of Projection Neurons via P57(KIP2) during Cortical Development.” Development. Company of Biologists, 2017. https://doi.org/10.1242/dev.145698.","ista":"Pfurr S, Chu Y, Bohrer C, Greulich F, Beattie RJ, Mammadzada K, Hils M, Arnold S, Taylor V, Schachtrup K, Uhlenhaut NH, Schachtrup C. 2017. The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development. Development. 144, 3917–3931.","mla":"Pfurr, Sabrina, et al. “The E2A Splice Variant E47 Regulates the Differentiation of Projection Neurons via P57(KIP2) during Cortical Development.” Development, vol. 144, Company of Biologists, 2017, pp. 3917–31, doi:10.1242/dev.145698.","ama":"Pfurr S, Chu Y, Bohrer C, et al. The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development. Development. 2017;144:3917-3931. doi:10.1242/dev.145698","apa":"Pfurr, S., Chu, Y., Bohrer, C., Greulich, F., Beattie, R. J., Mammadzada, K., … Schachtrup, C. (2017). The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development. Development. Company of Biologists. https://doi.org/10.1242/dev.145698","short":"S. Pfurr, Y. Chu, C. Bohrer, F. Greulich, R.J. Beattie, K. Mammadzada, M. Hils, S. Arnold, V. Taylor, K. Schachtrup, N.H. Uhlenhaut, C. Schachtrup, Development 144 (2017) 3917–3931.","ieee":"S. Pfurr et al., “The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development,” Development, vol. 144. Company of Biologists, pp. 3917–3931, 2017."},"date_updated":"2023-09-26T16:20:09Z","department":[{"_id":"SiHi"}],"title":"The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development","external_id":{"isi":["000414025600007"]},"article_processing_charge":"No","author":[{"last_name":"Pfurr","full_name":"Pfurr, Sabrina","first_name":"Sabrina"},{"full_name":"Chu, Yu","last_name":"Chu","first_name":"Yu"},{"full_name":"Bohrer, Christian","last_name":"Bohrer","first_name":"Christian"},{"first_name":"Franziska","last_name":"Greulich","full_name":"Greulich, Franziska"},{"full_name":"Beattie, Robert J","orcid":"0000-0002-8483-8753","last_name":"Beattie","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J"},{"first_name":"Könül","last_name":"Mammadzada","full_name":"Mammadzada, Könül"},{"first_name":"Miriam","last_name":"Hils","full_name":"Hils, Miriam"},{"first_name":"Sebastian","full_name":"Arnold, Sebastian","last_name":"Arnold"},{"first_name":"Verdon","last_name":"Taylor","full_name":"Taylor, Verdon"},{"first_name":"Kristina","full_name":"Schachtrup, Kristina","last_name":"Schachtrup"},{"first_name":"N Henriette","full_name":"Uhlenhaut, N Henriette","last_name":"Uhlenhaut"},{"last_name":"Schachtrup","full_name":"Schachtrup, Christian","first_name":"Christian"}],"publist_id":"6846","_id":"805","status":"public","type":"journal_article"},{"article_number":"104201","citation":{"chicago":"Serbyn, Maksym, Papic Zlatko, and Dmitry Abanin. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.104201.","ista":"Serbyn M, Zlatko P, Abanin D. 2017. Thouless energy and multifractality across the many-body localization transition. Physical Review B - Condensed Matter and Materials Physics. 96(10), 104201.","mla":"Serbyn, Maksym, et al. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 10, 104201, American Physical Society, 2017, doi:10.1103/PhysRevB.96.104201.","apa":"Serbyn, M., Zlatko, P., & Abanin, D. (2017). Thouless energy and multifractality across the many-body localization transition. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.96.104201","ama":"Serbyn M, Zlatko P, Abanin D. Thouless energy and multifractality across the many-body localization transition. Physical Review B - Condensed Matter and Materials Physics. 2017;96(10). doi:10.1103/PhysRevB.96.104201","ieee":"M. Serbyn, P. Zlatko, and D. Abanin, “Thouless energy and multifractality across the many-body localization transition,” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 10. American Physical Society, 2017.","short":"M. Serbyn, P. Zlatko, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 96 (2017)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000409429300004"]},"publist_id":"6814","author":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"},{"full_name":"Zlatko, Papic","last_name":"Zlatko","first_name":"Papic"},{"full_name":"Abanin, Dmitry","last_name":"Abanin","first_name":"Dmitry"}],"title":"Thouless energy and multifractality across the many-body localization transition","acknowledgement":"We acknowledge useful discussions with V. Kravtsov, T. Grover, and R. Vasseur. M.S. was supported by Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant GBMF4307. M.S. and D.A. acknowledge hospitality of KITP, where parts of this work were completed (supported in part by the National Science Foundation under Grant No. NSF PHY11-25915)","oa":1,"publisher":"American Physical Society","quality_controlled":"1","year":"2017","isi":1,"publication":"Physical Review B - Condensed Matter and Materials Physics","day":"06","date_created":"2018-12-11T11:48:45Z","doi":"10.1103/PhysRevB.96.104201","date_published":"2017-09-06T00:00:00Z","_id":"834","type":"journal_article","status":"public","date_updated":"2023-09-26T15:51:54Z","department":[{"_id":"MaSe"}],"abstract":[{"lang":"eng","text":"Thermal and many-body localized phases are separated by a dynamical phase transition of a new kind. We analyze the distribution of off-diagonal matrix elements of local operators across this transition in two different models of disordered spin chains. We show that the behavior of matrix elements can be used to characterize the breakdown of thermalization and to extract the many-body Thouless energy. We find that upon increasing the disorder strength the system enters a critical region around the many-body localization transition. The properties of the system in this region are: (i) the Thouless energy becomes smaller than the level spacing, (ii) the matrix elements show critical dependence on the energy difference, and (iii) the matrix elements, viewed as amplitudes of a fictitious wave function, exhibit strong multifractality. This critical region decreases with the system size, which we interpret as evidence for a diverging correlation length at the many-body localization transition. Our findings show that the correlation length becomes larger than the accessible system sizes in a broad range of disorder strength values and shed light on the critical behavior near the many-body localization transition."}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1610.02389"}],"scopus_import":"1","intvolume":" 96","month":"09","publication_status":"published","publication_identifier":{"issn":["24699950"]},"language":[{"iso":"eng"}],"volume":96,"issue":"10"},{"oa":1,"quality_controlled":"1","publisher":"IOPscience","year":"2017","isi":1,"publication":" Journal of Statistical Mechanics: Theory and Experiment","day":"26","date_created":"2018-12-11T11:48:41Z","doi":"10.1088/1742-5468/aa85c3","date_published":"2017-09-26T00:00:00Z","article_number":"093404","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Colabrese, Simona, et al. “Phase Transitions in Integer Linear Problems.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2017, no. 9, 093404, IOPscience, 2017, doi:10.1088/1742-5468/aa85c3.","short":"S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari, Journal of Statistical Mechanics: Theory and Experiment 2017 (2017).","ieee":"S. Colabrese, D. De Martino, L. Leuzzi, and E. Marinari, “Phase transitions in integer linear problems,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2017, no. 9. IOPscience, 2017.","ama":"Colabrese S, De Martino D, Leuzzi L, Marinari E. Phase transitions in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment. 2017;2017(9). doi:10.1088/1742-5468/aa85c3","apa":"Colabrese, S., De Martino, D., Leuzzi, L., & Marinari, E. (2017). Phase transitions in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa85c3","chicago":"Colabrese, Simona, Daniele De Martino, Luca Leuzzi, and Enzo Marinari. “Phase Transitions in Integer Linear Problems.” Journal of Statistical Mechanics: Theory and Experiment. IOPscience, 2017. https://doi.org/10.1088/1742-5468/aa85c3.","ista":"Colabrese S, De Martino D, Leuzzi L, Marinari E. 2017. Phase transitions in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment. 2017(9), 093404."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000411842900001"]},"publist_id":"6826","author":[{"full_name":"Colabrese, Simona","last_name":"Colabrese","first_name":"Simona"},{"full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino","first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Luca","full_name":"Leuzzi, Luca","last_name":"Leuzzi"},{"first_name":"Enzo","full_name":"Marinari, Enzo","last_name":"Marinari"}],"title":"Phase transitions in integer linear problems","abstract":[{"text":"The resolution of a linear system with positive integer variables is a basic yet difficult computational problem with many applications. We consider sparse uncorrelated random systems parametrised by the density c and the ratio α=N/M between number of variables N and number of constraints M. By means of ensemble calculations we show that the space of feasible solutions endows a Van-Der-Waals phase diagram in the plane (c, α). We give numerical evidence that the associated computational problems become more difficult across the critical point and in particular in the coexistence region.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.06303"}],"scopus_import":"1","intvolume":" 2017","month":"09","publication_status":"published","publication_identifier":{"issn":["17425468"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":2017,"issue":"9","_id":"823","type":"journal_article","status":"public","date_updated":"2023-09-26T16:18:12Z","department":[{"_id":"GaTk"}]},{"publication_identifier":{"issn":["00221120"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":827,"abstract":[{"lang":"eng","text":"In shear flows at transitional Reynolds numbers, localized patches of turbulence, known as puffs, coexist with the laminar flow. Recently, Avila et al. (Phys. Rev. Lett., vol. 110, 2013, 224502) discovered two spatially localized relative periodic solutions for pipe flow, which appeared in a saddle-node bifurcation at low Reynolds number. Combining slicing methods for continuous symmetry reduction with Poincaré sections for the first time in a shear flow setting, we compute and visualize the unstable manifold of the lower-branch solution and show that it extends towards the neighbourhood of the upper-branch solution. Surprisingly, this connection even persists far above the bifurcation point and appears to mediate the first stage of the puff generation: amplification of streamwise localized fluctuations. When the state-space trajectories on the unstable manifold reach the vicinity of the upper branch, corresponding fluctuations expand in space and eventually take the usual shape of a puff."}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1703.10484","open_access":"1"}],"month":"08","intvolume":" 827","date_updated":"2023-09-26T16:17:43Z","department":[{"_id":"BjHo"}],"_id":"824","type":"journal_article","status":"public","isi":1,"year":"2017","day":"18","publication":"Journal of Fluid Mechanics","date_published":"2017-08-18T00:00:00Z","doi":"10.1017/jfm.2017.516","date_created":"2018-12-11T11:48:42Z","quality_controlled":"1","publisher":"Cambridge University Press","oa":1,"citation":{"chicago":"Budanur, Nazmi B, and Björn Hof. “Heteroclinic Path to Spatially Localized Chaos in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2017. https://doi.org/10.1017/jfm.2017.516.","ista":"Budanur NB, Hof B. 2017. Heteroclinic path to spatially localized chaos in pipe flow. Journal of Fluid Mechanics. 827, R1.","mla":"Budanur, Nazmi B., and Björn Hof. “Heteroclinic Path to Spatially Localized Chaos in Pipe Flow.” Journal of Fluid Mechanics, vol. 827, R1, Cambridge University Press, 2017, doi:10.1017/jfm.2017.516.","ama":"Budanur NB, Hof B. Heteroclinic path to spatially localized chaos in pipe flow. Journal of Fluid Mechanics. 2017;827. doi:10.1017/jfm.2017.516","apa":"Budanur, N. B., & Hof, B. (2017). Heteroclinic path to spatially localized chaos in pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.516","short":"N.B. Budanur, B. Hof, Journal of Fluid Mechanics 827 (2017).","ieee":"N. B. Budanur and B. Hof, “Heteroclinic path to spatially localized chaos in pipe flow,” Journal of Fluid Mechanics, vol. 827. Cambridge University Press, 2017."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","last_name":"Budanur","orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"}],"publist_id":"6824","article_processing_charge":"No","external_id":{"isi":["000408326300001"]},"title":"Heteroclinic path to spatially localized chaos in pipe flow","article_number":"R1"},{"oa":1,"publisher":"Oxford University Press","quality_controlled":"1","date_created":"2018-12-11T11:48:34Z","doi":"10.1093/pcp/pcx118","date_published":"2017-08-21T00:00:00Z","publication":"Plant and Cell Physiology","day":"21","year":"2017","isi":1,"has_accepted_license":"1","article_number":"1801-1811","title":"BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana","article_processing_charge":"No","external_id":{"isi":["000413220400019"],"pmid":["29016942"]},"author":[{"first_name":"Saeko","full_name":"Kitakura, Saeko","last_name":"Kitakura"},{"last_name":"Adamowski","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Matsuura, Yuki","last_name":"Matsuura","first_name":"Yuki"},{"last_name":"Santuari","full_name":"Santuari, Luca","first_name":"Luca"},{"first_name":"Hirotaka","full_name":"Kouno, Hirotaka","last_name":"Kouno"},{"first_name":"Kohei","full_name":"Arima, Kohei","last_name":"Arima"},{"full_name":"Hardtke, Christian","last_name":"Hardtke","first_name":"Christian"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tatsuo","last_name":"Kakimoto","full_name":"Kakimoto, Tatsuo"},{"first_name":"Hirokazu","last_name":"Tanaka","full_name":"Tanaka, Hirokazu"}],"publist_id":"6854","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Kitakura, Saeko, et al. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” Plant and Cell Physiology, vol. 58, no. 10, 1801–1811, Oxford University Press, 2017, doi:10.1093/pcp/pcx118.","ieee":"S. Kitakura et al., “BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana,” Plant and Cell Physiology, vol. 58, no. 10. Oxford University Press, 2017.","short":"S. Kitakura, M. Adamowski, Y. Matsuura, L. Santuari, H. Kouno, K. Arima, C. Hardtke, J. Friml, T. Kakimoto, H. Tanaka, Plant and Cell Physiology 58 (2017).","apa":"Kitakura, S., Adamowski, M., Matsuura, Y., Santuari, L., Kouno, H., Arima, K., … Tanaka, H. (2017). BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcx118","ama":"Kitakura S, Adamowski M, Matsuura Y, et al. BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. 2017;58(10). doi:10.1093/pcp/pcx118","chicago":"Kitakura, Saeko, Maciek Adamowski, Yuki Matsuura, Luca Santuari, Hirotaka Kouno, Kohei Arima, Christian Hardtke, Jiří Friml, Tatsuo Kakimoto, and Hirokazu Tanaka. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” Plant and Cell Physiology. Oxford University Press, 2017. https://doi.org/10.1093/pcp/pcx118.","ista":"Kitakura S, Adamowski M, Matsuura Y, Santuari L, Kouno H, Arima K, Hardtke C, Friml J, Kakimoto T, Tanaka H. 2017. BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. 58(10), 1801–1811."},"intvolume":" 58","month":"08","scopus_import":"1","oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"Membrane traffic at the trans-Golgi network (TGN) is crucial for correctly distributing various membrane proteins to their destination. Polarly localized auxin efflux proteins, including PIN-FORMED1 (PIN1), are dynamically transported between the endosomes and the plasma membrane (PM) in the plant cells. The intracellular trafficking of PIN1 protein is sensitive to a fungal toxin brefeldin A (BFA), which is known to inhibit guanine-nucleotide exchange factors for ADP ribosylation factors (ARF GEFs) such as GNOM. However, the molecular details of the BFA-sensitive trafficking pathway have not been revealed fully. In a previous study, we have identified an Arabidopsis mutant BFA-visualized endocytic trafficking defective 3 (ben3) which exhibited reduced sensitivity to BFA in terms of BFA-induced intracellular PIN1 agglomeration. Here, we show that BEN3 encodes a member of BIG family ARF GEFs, BIG2. Fluorescent proteins tagged BEN3/BIG2 co-localized with markers for TGN / early endosome (EE). Inspection of conditionally induced de novo synthesized PIN1 confirmed that its secretion to the PM is BFA-sensitive and established BEN3/BIG2 as a crucial component of this BFA action at the level of TGN/EE. Furthermore, ben3 mutation alleviated BFA-induced agglomeration of another TGN-localized ARF GEF BEN1/MIN7. Taken together our results suggest that BEN3/BIG2 is an ARF GEF component, which confers BFA sensitivity to the TGN/EE in Arabidopsis.","lang":"eng"}],"volume":58,"issue":"10","language":[{"iso":"eng"}],"file":[{"checksum":"bd3e3a94d55416739cbb19624bb977f8","file_id":"6333","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2017_PlantCellPhysio_Kitakura.pdf","date_created":"2019-04-17T07:52:34Z","creator":"dernst","file_size":1352913,"date_updated":"2020-07-14T12:48:06Z"}],"publication_status":"published","publication_identifier":{"issn":["00320781"]},"pubrep_id":"1009","status":"public","type":"journal_article","_id":"799","file_date_updated":"2020-07-14T12:48:06Z","department":[{"_id":"JiFr"}],"ddc":["581"],"date_updated":"2023-09-27T11:00:19Z"},{"file_date_updated":"2020-07-14T12:48:07Z","department":[{"_id":"PeJo"}],"date_updated":"2023-09-27T10:59:41Z","ddc":["571"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"914","_id":"800","volume":8,"issue":"1","ec_funded":1,"publication_identifier":{"issn":["20411723"]},"publication_status":"published","file":[{"checksum":"7e2c7621afd5f802338e92e8619f024d","file_id":"5135","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-914-v1+1_s41467-017-00936-3.pdf","date_created":"2018-12-12T10:15:17Z","creator":"system","file_size":4261832,"date_updated":"2020-07-14T12:48:07Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"10","intvolume":" 8","abstract":[{"lang":"eng","text":"Gamma oscillations (30–150 Hz) in neuronal networks are associated with the processing and recall of information. We measured local field potentials in the dentate gyrus of freely moving mice and found that gamma activity occurs in bursts, which are highly heterogeneous in their spatial extensions, ranging from focal to global coherent events. Synaptic communication among perisomatic-inhibitory interneurons (PIIs) is thought to play an important role in the generation of hippocampal gamma patterns. However, how neuronal circuits can generate synchronous oscillations at different spatial scales is unknown. We analyzed paired recordings in dentate gyrus slices and show that synaptic signaling at interneuron-interneuron synapses is distance dependent. Synaptic strength declines whereas the duration of inhibitory signals increases with axonal distance among interconnected PIIs. Using neuronal network modeling, we show that distance-dependent inhibition generates multiple highly synchronous focal gamma bursts allowing the network to process complex inputs in parallel in flexibly organized neuronal centers."}],"oa_version":"Published Version","publist_id":"6853","author":[{"full_name":"Strüber, Michael","last_name":"Strüber","first_name":"Michael"},{"last_name":"Sauer","full_name":"Sauer, Jonas","first_name":"Jonas"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"},{"last_name":"Bartos","full_name":"Bartos, Marlene","first_name":"Marlene"}],"article_processing_charge":"No","external_id":{"isi":["000412053100004"]},"title":"Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus","citation":{"mla":"Strüber, Michael, et al. “Distance-Dependent Inhibition Facilitates Focality of Gamma Oscillations in the Dentate Gyrus.” Nature Communications, vol. 8, no. 1, 758, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00936-3.","ieee":"M. Strüber, J. Sauer, P. M. Jonas, and M. Bartos, “Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","short":"M. Strüber, J. Sauer, P.M. Jonas, M. Bartos, Nature Communications 8 (2017).","ama":"Strüber M, Sauer J, Jonas PM, Bartos M. Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-00936-3","apa":"Strüber, M., Sauer, J., Jonas, P. M., & Bartos, M. (2017). Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00936-3","chicago":"Strüber, Michael, Jonas Sauer, Peter M Jonas, and Marlene Bartos. “Distance-Dependent Inhibition Facilitates Focality of Gamma Oscillations in the Dentate Gyrus.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00936-3.","ista":"Strüber M, Sauer J, Jonas PM, Bartos M. 2017. Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications. 8(1), 758."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FP7","_id":"25C0F108-B435-11E9-9278-68D0E5697425","grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons"}],"article_number":"758","date_published":"2017-10-02T00:00:00Z","doi":"10.1038/s41467-017-00936-3","date_created":"2018-12-11T11:48:34Z","has_accepted_license":"1","isi":1,"year":"2017","day":"02","publication":"Nature Communications","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1},{"issue":"5","volume":170,"publication_status":"published","publication_identifier":{"issn":["00928674"]},"language":[{"iso":"eng"}],"file":[{"checksum":"64897b0c5373f22273f598e4672c60ff","file_id":"5852","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-01-18T13:45:40Z","file_name":"2017_Cell_Samwer.pdf","date_updated":"2020-07-14T12:48:08Z","file_size":17666637,"creator":"dernst"}],"scopus_import":"1","intvolume":" 170","month":"08","acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Eukaryotic cells store their chromosomes in a single nucleus. This is important to maintain genomic integrity, as chromosomes packaged into separate nuclei (micronuclei) are prone to massive DNA damage. During mitosis, higher eukaryotes disassemble their nucleus and release individualized chromosomes for segregation. How numerous chromosomes subsequently reform a single nucleus has remained unclear. Using image-based screening of human cells, we identified barrier-to-autointegration factor (BAF) as a key factor guiding membranes to form a single nucleus. Unexpectedly, nuclear assembly does not require BAF?s association with inner nuclear membrane proteins but instead relies on BAF?s ability to bridge distant DNA sites. Live-cell imaging and in vitro reconstitution showed that BAF enriches around the mitotic chromosome ensemble to induce a densely cross-bridged chromatin layer that is mechanically stiff and limits membranes to the surface. Our study reveals that BAF-mediated changes in chromosome mechanics underlie nuclear assembly with broad implications for proper genome function."}],"oa_version":"Published Version","department":[{"_id":"CaHe"}],"file_date_updated":"2020-07-14T12:48:08Z","date_updated":"2023-09-27T10:59:14Z","ddc":["570"],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","status":"public","_id":"803","page":"956 - 972","date_created":"2018-12-11T11:48:35Z","doi":"10.1016/j.cell.2017.07.038","date_published":"2017-08-24T00:00:00Z","year":"2017","isi":1,"has_accepted_license":"1","publication":"Cell","day":"24","oa":1,"publisher":"Cell Press","quality_controlled":"1","external_id":{"isi":["000408372400014"]},"article_processing_charge":"No","publist_id":"6848","author":[{"first_name":"Matthias","full_name":"Samwer, Matthias","last_name":"Samwer"},{"last_name":"Schneider","full_name":"Schneider, Maximilian","first_name":"Maximilian"},{"full_name":"Hoefler, Rudolf","last_name":"Hoefler","first_name":"Rudolf"},{"id":"309D50DA-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp S","last_name":"Schmalhorst","full_name":"Schmalhorst, Philipp S","orcid":"0000-0002-5795-0133"},{"last_name":"Jude","full_name":"Jude, Julian","first_name":"Julian"},{"first_name":"Johannes","last_name":"Zuber","full_name":"Zuber, Johannes"},{"full_name":"Gerlic, Daniel","last_name":"Gerlic","first_name":"Daniel"}],"title":"DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes","citation":{"mla":"Samwer, Matthias, et al. “DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes.” Cell, vol. 170, no. 5, Cell Press, 2017, pp. 956–72, doi:10.1016/j.cell.2017.07.038.","ama":"Samwer M, Schneider M, Hoefler R, et al. DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. Cell. 2017;170(5):956-972. doi:10.1016/j.cell.2017.07.038","apa":"Samwer, M., Schneider, M., Hoefler, R., Schmalhorst, P. S., Jude, J., Zuber, J., & Gerlic, D. (2017). DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. Cell. Cell Press. https://doi.org/10.1016/j.cell.2017.07.038","ieee":"M. Samwer et al., “DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes,” Cell, vol. 170, no. 5. Cell Press, pp. 956–972, 2017.","short":"M. Samwer, M. Schneider, R. Hoefler, P.S. Schmalhorst, J. Jude, J. Zuber, D. Gerlic, Cell 170 (2017) 956–972.","chicago":"Samwer, Matthias, Maximilian Schneider, Rudolf Hoefler, Philipp S Schmalhorst, Julian Jude, Johannes Zuber, and Daniel Gerlic. “DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes.” Cell. Cell Press, 2017. https://doi.org/10.1016/j.cell.2017.07.038.","ista":"Samwer M, Schneider M, Hoefler R, Schmalhorst PS, Jude J, Zuber J, Gerlic D. 2017. DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. Cell. 170(5), 956–972."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["15499618"]},"volume":13,"issue":"10","oa_version":"Submitted Version","abstract":[{"text":"Polysaccharides (carbohydrates) are key regulators of a large number of cell biological processes. However, precise biochemical or genetic manipulation of these often complex structures is laborious and hampers experimental structure–function studies. Molecular Dynamics (MD) simulations provide a valuable alternative tool to generate and test hypotheses on saccharide function. Yet, currently used MD force fields often overestimate the aggregation propensity of polysaccharides, affecting the usability of those simulations. Here we tested MARTINI, a popular coarse-grained (CG) force field for biological macromolecules, for its ability to accurately represent molecular forces between saccharides. To this end, we calculated a thermodynamic solution property, the second virial coefficient of the osmotic pressure (B22). Comparison with light scattering experiments revealed a nonphysical aggregation of a prototypical polysaccharide in MARTINI, pointing at an imbalance of the nonbonded solute–solute, solute–water, and water–water interactions. This finding also applies to smaller oligosaccharides which were all found to aggregate in simulations even at moderate concentrations, well below their solubility limit. Finally, we explored the influence of the Lennard-Jones (LJ) interaction between saccharide molecules and propose a simple scaling of the LJ interaction strength that makes MARTINI more reliable for the simulation of saccharides.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"intvolume":" 13","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/1704.03773","open_access":"1"}],"scopus_import":"1","date_updated":"2023-09-27T10:58:45Z","department":[{"_id":"CaHe"}],"_id":"804","status":"public","type":"journal_article","publication":"Journal of Chemical Theory and Computation","day":"10","year":"2017","isi":1,"date_created":"2018-12-11T11:48:35Z","doi":"10.1021/acs.jctc.7b00374","date_published":"2017-10-10T00:00:00Z","page":"5039 - 5053","acknowledgement":"P.S.S. was supported by research fellowship 2811/1-1 from the German Research Foundation (DFG), and M.S. was supported by EMBO Long Term Fellowship ALTF 187-2013 and Grant GC65-32 from the Interdisciplinary Centre for Mathematical and Computational Modelling (ICM), University of Warsaw, Poland. The authors thank Antje Potthast, Marek Cieplak, Tomasz Włodarski, and Damien Thompson for fruitful discussions and the IST Austria Scientific Computing Facility for support.","oa":1,"quality_controlled":"1","publisher":"American Chemical Society","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. 2017. Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. Journal of Chemical Theory and Computation. 13(10), 5039–5053.","chicago":"Schmalhorst, Philipp S, Felix Deluweit, Roger Scherrers, Carl-Philipp J Heisenberg, and Mateusz K Sikora. “Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides.” Journal of Chemical Theory and Computation. American Chemical Society, 2017. https://doi.org/10.1021/acs.jctc.7b00374.","ama":"Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. Journal of Chemical Theory and Computation. 2017;13(10):5039-5053. doi:10.1021/acs.jctc.7b00374","apa":"Schmalhorst, P. S., Deluweit, F., Scherrers, R., Heisenberg, C.-P. J., & Sikora, M. K. (2017). Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. Journal of Chemical Theory and Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.7b00374","short":"P.S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P.J. Heisenberg, M.K. Sikora, Journal of Chemical Theory and Computation 13 (2017) 5039–5053.","ieee":"P. S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P. J. Heisenberg, and M. K. Sikora, “Overcoming the limitations of the MARTINI force field in simulations of polysaccharides,” Journal of Chemical Theory and Computation, vol. 13, no. 10. American Chemical Society, pp. 5039–5053, 2017.","mla":"Schmalhorst, Philipp S., et al. “Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides.” Journal of Chemical Theory and Computation, vol. 13, no. 10, American Chemical Society, 2017, pp. 5039–53, doi:10.1021/acs.jctc.7b00374."},"title":"Overcoming the limitations of the MARTINI force field in simulations of polysaccharides","external_id":{"isi":["000412965700036"]},"article_processing_charge":"No","author":[{"id":"309D50DA-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp S","last_name":"Schmalhorst","orcid":"0000-0002-5795-0133","full_name":"Schmalhorst, Philipp S"},{"first_name":"Felix","full_name":"Deluweit, Felix","last_name":"Deluweit"},{"first_name":"Roger","full_name":"Scherrers, Roger","last_name":"Scherrers"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"last_name":"Sikora","full_name":"Sikora, Mateusz K","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6847"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"915","status":"public","_id":"746","department":[{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:47:58Z","date_updated":"2023-09-27T12:27:30Z","ddc":["571"],"scopus_import":"1","intvolume":" 8","month":"12","abstract":[{"lang":"eng","text":"Metabotropic glutamate receptor subtype 5 (mGluR5) is crucially implicated in the pathophysiology of Fragile X Syndrome (FXS); however, its dysfunction at the sub-cellular level, and related synaptic and cognitive phenotypes are unexplored. Here, we probed the consequences of mGluR5/Homer scaffold disruption for mGluR5 cell-surface mobility, synaptic N-methyl-D-Aspartate receptor (NMDAR) function, and behavioral phenotypes in the second-generation Fmr1 knockout (KO) mouse. Using single-molecule tracking, we found that mGluR5 was significantly more mobile at synapses in hippocampal Fmr1 KO neurons, causing an increased synaptic surface co-clustering of mGluR5 and NMDAR. This correlated with a reduced amplitude of synaptic NMDAR currents, a lack of their mGluR5-Activated long-Term depression, and NMDAR/hippocampus dependent cognitive deficits. These synaptic and behavioral phenomena were reversed by knocking down Homer1a in Fmr1 KO mice. Our study provides a mechanistic link between changes of mGluR5 dynamics and pathological phenotypes of FXS, unveiling novel targets for mGluR5-based therapeutics."}],"oa_version":"Published Version","issue":"1","volume":8,"publication_status":"published","publication_identifier":{"issn":["20411723"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"99ceee57549dc0461e3adfc037ec70a9","file_id":"5287","creator":"system","date_updated":"2020-07-14T12:47:58Z","file_size":1841650,"date_created":"2018-12-12T10:17:32Z","file_name":"IST-2017-915-v1+1_s41467-017-01191-2.pdf"}],"article_number":"1103","article_processing_charge":"No","external_id":{"isi":["000413571300004"]},"publist_id":"6921","author":[{"first_name":"Elisabetta","last_name":"Aloisi","full_name":"Aloisi, Elisabetta"},{"first_name":"Katy","last_name":"Le Corf","full_name":"Le Corf, Katy"},{"first_name":"Julien","full_name":"Dupuis, Julien","last_name":"Dupuis"},{"first_name":"Pei","last_name":"Zhang","full_name":"Zhang, Pei"},{"first_name":"Melanie","last_name":"Ginger","full_name":"Ginger, Melanie"},{"first_name":"Virginie","full_name":"Labrousse, Virginie","last_name":"Labrousse"},{"first_name":"Michela","last_name":"Spatuzza","full_name":"Spatuzza, Michela"},{"full_name":"Georg Haberl, Matthias","last_name":"Georg Haberl","first_name":"Matthias"},{"full_name":"Costa, Lara","last_name":"Costa","first_name":"Lara"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"},{"first_name":"Anke","last_name":"Tappe Theodor","full_name":"Tappe Theodor, Anke"},{"full_name":"Drago, Fillippo","last_name":"Drago","first_name":"Fillippo"},{"last_name":"Vincenzo Piazza","full_name":"Vincenzo Piazza, Pier","first_name":"Pier"},{"full_name":"Mulle, Christophe","last_name":"Mulle","first_name":"Christophe"},{"full_name":"Groc, Laurent","last_name":"Groc","first_name":"Laurent"},{"full_name":"Ciranna, Lucia","last_name":"Ciranna","first_name":"Lucia"},{"full_name":"Catania, Maria","last_name":"Catania","first_name":"Maria"},{"first_name":"Andreas","last_name":"Frick","full_name":"Frick, Andreas"}],"title":"Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice","citation":{"chicago":"Aloisi, Elisabetta, Katy Le Corf, Julien Dupuis, Pei Zhang, Melanie Ginger, Virginie Labrousse, Michela Spatuzza, et al. “Altered Surface MGluR5 Dynamics Provoke Synaptic NMDAR Dysfunction and Cognitive Defects in Fmr1 Knockout Mice.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01191-2.","ista":"Aloisi E, Le Corf K, Dupuis J, Zhang P, Ginger M, Labrousse V, Spatuzza M, Georg Haberl M, Costa L, Shigemoto R, Tappe Theodor A, Drago F, Vincenzo Piazza P, Mulle C, Groc L, Ciranna L, Catania M, Frick A. 2017. Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice. Nature Communications. 8(1), 1103.","mla":"Aloisi, Elisabetta, et al. “Altered Surface MGluR5 Dynamics Provoke Synaptic NMDAR Dysfunction and Cognitive Defects in Fmr1 Knockout Mice.” Nature Communications, vol. 8, no. 1, 1103, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01191-2.","ama":"Aloisi E, Le Corf K, Dupuis J, et al. Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01191-2","apa":"Aloisi, E., Le Corf, K., Dupuis, J., Zhang, P., Ginger, M., Labrousse, V., … Frick, A. (2017). Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01191-2","short":"E. Aloisi, K. Le Corf, J. Dupuis, P. Zhang, M. Ginger, V. Labrousse, M. Spatuzza, M. Georg Haberl, L. Costa, R. Shigemoto, A. Tappe Theodor, F. Drago, P. Vincenzo Piazza, C. Mulle, L. Groc, L. Ciranna, M. Catania, A. Frick, Nature Communications 8 (2017).","ieee":"E. Aloisi et al., “Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","date_created":"2018-12-11T11:48:17Z","date_published":"2017-12-01T00:00:00Z","doi":"10.1038/s41467-017-01191-2","year":"2017","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"01"},{"volume":21,"issue":"8","related_material":{"record":[{"id":"324","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"publication_identifier":{"issn":["22111247"]},"publication_status":"published","file":[{"creator":"system","date_updated":"2020-07-14T12:47:59Z","file_size":2759195,"date_created":"2018-12-12T10:09:14Z","file_name":"IST-2017-874-v1+1_PIIS2211124717316029.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"a6afa3764909bf6edafa07982d8e1cee","file_id":"4737"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"11","intvolume":" 21","abstract":[{"text":"Synaptotagmin 7 (Syt7) is thought to be a Ca2+ sensor that mediates asynchronous transmitter release and facilitation at synapses. However, Syt7 is strongly expressed in fast-spiking, parvalbumin-expressing GABAergic interneurons, and the output synapses of these neurons produce only minimal asynchronous release and show depression rather than facilitation. To resolve this apparent contradiction, we examined the effects of genetic elimination of Syt7 on synaptic transmission at the GABAergic basket cell (BC)-Purkinje cell (PC) synapse in cerebellum. Our results indicate that at the BC-PC synapse, Syt7 contributes to asynchronous release, pool replenishment, and facilitation. In combination, these three effects ensure efficient transmitter release during high-frequency activity and guarantee frequency independence of inhibition. Our results identify a distinct function of Syt7: ensuring the efficiency of high-frequency inhibitory synaptic transmission","lang":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"}],"oa_version":"Published Version","department":[{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:47:59Z","date_updated":"2023-09-27T12:26:04Z","ddc":["570","571"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"874","_id":"749","page":"2082 - 2089","date_published":"2017-11-21T00:00:00Z","doi":"10.1016/j.celrep.2017.10.122","date_created":"2018-12-11T11:48:18Z","has_accepted_license":"1","isi":1,"year":"2017","day":"21","publication":"Cell Reports","quality_controlled":"1","publisher":"Cell Press","oa":1,"author":[{"first_name":"Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chong","last_name":"Chen"},{"full_name":"Satterfield, Rachel","last_name":"Satterfield","first_name":"Rachel"},{"last_name":"Young","full_name":"Young, Samuel","first_name":"Samuel"},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6907","external_id":{"isi":["000416216700007"]},"article_processing_charge":"No","title":"Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses","citation":{"mla":"Chen, Chong, et al. “Triple Function of Synaptotagmin 7 Ensures Efficiency of High-Frequency Transmission at Central GABAergic Synapses.” Cell Reports, vol. 21, no. 8, Cell Press, 2017, pp. 2082–89, doi:10.1016/j.celrep.2017.10.122.","ama":"Chen C, Satterfield R, Young S, Jonas PM. Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses. Cell Reports. 2017;21(8):2082-2089. doi:10.1016/j.celrep.2017.10.122","apa":"Chen, C., Satterfield, R., Young, S., & Jonas, P. M. (2017). Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2017.10.122","short":"C. Chen, R. Satterfield, S. Young, P.M. Jonas, Cell Reports 21 (2017) 2082–2089.","ieee":"C. Chen, R. Satterfield, S. Young, and P. M. Jonas, “Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses,” Cell Reports, vol. 21, no. 8. Cell Press, pp. 2082–2089, 2017.","chicago":"Chen, Chong, Rachel Satterfield, Samuel Young, and Peter M Jonas. “Triple Function of Synaptotagmin 7 Ensures Efficiency of High-Frequency Transmission at Central GABAergic Synapses.” Cell Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2017.10.122.","ista":"Chen C, Satterfield R, Young S, Jonas PM. 2017. Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses. Cell Reports. 21(8), 2082–2089."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"P24909-B24","name":"Mechanisms of transmitter release at GABAergic synapses","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692"}]},{"day":"21","publication":" Journal of Theoretical Biology","has_accepted_license":"1","isi":1,"year":"2017","doi":"10.1016/j.jtbi.2017.08.025","date_published":"2017-11-21T00:00:00Z","date_created":"2018-12-11T11:48:16Z","page":"64 - 72","quality_controlled":"1","publisher":"Elsevier","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Priklopil T, Chatterjee K, Nowak M. 2017. Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma. Journal of Theoretical Biology. 433, 64–72.","chicago":"Priklopil, Tadeas, Krishnendu Chatterjee, and Martin Nowak. “Optional Interactions and Suspicious Behaviour Facilitates Trustful Cooperation in Prisoners Dilemma.” Journal of Theoretical Biology. Elsevier, 2017. https://doi.org/10.1016/j.jtbi.2017.08.025.","ieee":"T. Priklopil, K. Chatterjee, and M. Nowak, “Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma,” Journal of Theoretical Biology, vol. 433. Elsevier, pp. 64–72, 2017.","short":"T. Priklopil, K. Chatterjee, M. Nowak, Journal of Theoretical Biology 433 (2017) 64–72.","ama":"Priklopil T, Chatterjee K, Nowak M. Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma. Journal of Theoretical Biology. 2017;433:64-72. doi:10.1016/j.jtbi.2017.08.025","apa":"Priklopil, T., Chatterjee, K., & Nowak, M. (2017). Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2017.08.025","mla":"Priklopil, Tadeas, et al. “Optional Interactions and Suspicious Behaviour Facilitates Trustful Cooperation in Prisoners Dilemma.” Journal of Theoretical Biology, vol. 433, Elsevier, 2017, pp. 64–72, doi:10.1016/j.jtbi.2017.08.025."},"title":"Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma","publist_id":"6923","author":[{"last_name":"Priklopil","full_name":"Priklopil, Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","first_name":"Tadeas"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"article_processing_charge":"No","external_id":{"pmid":["28867224"],"isi":["000412039800007"]},"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"file":[{"file_id":"7047","checksum":"4b43af1615ebf1a861840cb03d8a320c","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-11-19T07:57:39Z","file_name":"2017_JournTheoretBio_Priklopil.pdf","date_updated":"2020-07-14T12:47:58Z","file_size":537323,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00225193"]},"publication_status":"published","volume":433,"ec_funded":1,"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"In evolutionary game theory interactions between individuals are often assumed obligatory. However, in many real-life situations, individuals can decide to opt out of an interaction depending on the information they have about the opponent. We consider a simple evolutionary game theoretic model to study such a scenario, where at each encounter between two individuals the type of the opponent (cooperator/defector) is known with some probability, and where each individual either accepts or opts out of the interaction. If the type of the opponent is unknown, a trustful individual accepts the interaction, whereas a suspicious individual opts out of the interaction. If either of the two individuals opt out both individuals remain without an interaction. We show that in the prisoners dilemma optional interactions along with suspicious behaviour facilitates the emergence of trustful cooperation."}],"month":"11","intvolume":" 433","scopus_import":"1","ddc":["000","570"],"date_updated":"2023-09-27T12:29:02Z","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:47:58Z","_id":"744","status":"public","type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"}},{"project":[{"call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425","name":"Decoding the complexity of turbulence at its origin","grant_number":"306589"}],"citation":{"mla":"Xu, Duo, et al. “Transition to Turbulence in Pulsating Pipe Flow.” Journal of Fluid Mechanics, vol. 831, Cambridge University Press, 2017, pp. 418–32, doi:10.1017/jfm.2017.620.","ama":"Xu D, Warnecke S, Song B, Ma X, Hof B. Transition to turbulence in pulsating pipe flow. Journal of Fluid Mechanics. 2017;831:418-432. doi:10.1017/jfm.2017.620","apa":"Xu, D., Warnecke, S., Song, B., Ma, X., & Hof, B. (2017). Transition to turbulence in pulsating pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.620","ieee":"D. Xu, S. Warnecke, B. Song, X. Ma, and B. Hof, “Transition to turbulence in pulsating pipe flow,” Journal of Fluid Mechanics, vol. 831. Cambridge University Press, pp. 418–432, 2017.","short":"D. Xu, S. Warnecke, B. Song, X. Ma, B. Hof, Journal of Fluid Mechanics 831 (2017) 418–432.","chicago":"Xu, Duo, Sascha Warnecke, Baofang Song, Xingyu Ma, and Björn Hof. “Transition to Turbulence in Pulsating Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2017. https://doi.org/10.1017/jfm.2017.620.","ista":"Xu D, Warnecke S, Song B, Ma X, Hof B. 2017. Transition to turbulence in pulsating pipe flow. Journal of Fluid Mechanics. 831, 418–432."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000412934800005"]},"author":[{"full_name":"Xu, Duo","last_name":"Xu","id":"3454D55E-F248-11E8-B48F-1D18A9856A87","first_name":"Duo"},{"first_name":"Sascha","last_name":"Warnecke","full_name":"Warnecke, Sascha"},{"first_name":"Baofang","last_name":"Song","full_name":"Song, Baofang"},{"first_name":"Xingyu","id":"34BADBA6-F248-11E8-B48F-1D18A9856A87","full_name":"Ma, Xingyu","orcid":"0000-0002-0179-9737","last_name":"Ma"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"publist_id":"6922","title":"Transition to turbulence in pulsating pipe flow","oa":1,"quality_controlled":"1","publisher":"Cambridge University Press","year":"2017","isi":1,"publication":"Journal of Fluid Mechanics","day":"25","page":"418 - 432","date_created":"2018-12-11T11:48:17Z","date_published":"2017-11-25T00:00:00Z","doi":"10.1017/jfm.2017.620","_id":"745","type":"journal_article","status":"public","date_updated":"2023-09-27T12:28:12Z","department":[{"_id":"BjHo"}],"abstract":[{"lang":"eng","text":"Fluid flows in nature and applications are frequently subject to periodic velocity modulations. Surprisingly, even for the generic case of flow through a straight pipe, there is little consensus regarding the influence of pulsation on the transition threshold to turbulence: while most studies predict a monotonically increasing threshold with pulsation frequency (i.e. Womersley number, ), others observe a decreasing threshold for identical parameters and only observe an increasing threshold at low . In the present study we apply recent advances in the understanding of transition in steady shear flows to pulsating pipe flow. For moderate pulsation amplitudes we find that the first instability encountered is subcritical (i.e. requiring finite amplitude disturbances) and gives rise to localized patches of turbulence ('puffs') analogous to steady pipe flow. By monitoring the impact of pulsation on the lifetime of turbulence we map the onset of turbulence in parameter space. Transition in pulsatile flow can be separated into three regimes. At small Womersley numbers the dynamics is dominated by the decay turbulence suffers during the slower part of the cycle and hence transition is delayed significantly. As shown in this regime thresholds closely agree with estimates based on a quasi-steady flow assumption only taking puff decay rates into account. The transition point predicted in the zero limit equals to the critical point for steady pipe flow offset by the oscillation Reynolds number (i.e. the dimensionless oscillation amplitude). In the high frequency limit on the other hand, puff lifetimes are identical to those in steady pipe flow and hence the transition threshold appears to be unaffected by flow pulsation. In the intermediate frequency regime the transition threshold sharply drops (with increasing ) from the decay dominated (quasi-steady) threshold to the steady pipe flow level."}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://arxiv.org/abs/1709.03738","open_access":"1"}],"scopus_import":"1","intvolume":" 831","month":"11","publication_status":"published","publication_identifier":{"issn":["00221120"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":831},{"department":[{"_id":"GaNo"}],"date_updated":"2023-09-27T12:26:59Z","type":"journal_article","article_type":"original","status":"public","_id":"747","volume":365,"publication_status":"published","publication_identifier":{"issn":["03064522"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798458"}],"scopus_import":"1","intvolume":" 365","month":"12","abstract":[{"lang":"eng","text":"Bradykinin (BK), a component of the kallikrein-kininogen-kinin system exerts multiple effects via B1 and B2 receptor activation. In the cardiovascular system, bradykinin has cardioprotective and vasodilator properties. We investigated the effect of BK on cardiac-projecting neurons of nucleus ambiguus, a key site for the parasympathetic cardiac regulation. BK produced a dose-dependent increase in cytosolic Ca2+ concentration. Pretreatment with HOE140, a B2 receptor antagonist, but not with R715, a B1 receptor antagonist, abolished the response to BK. A selective B2 receptor agonist, but not a B1 receptor agonist, elicited an increase in cytosolic Ca2+ similarly to BK. Inhibition of N-type voltage-gated Ca2+ channels with ω-conotoxin GVIA had no effect on the Ca2+ signal produced by BK, while pretreatment with ω-conotoxin MVIIC, a blocker of P/Q-type of Ca2+ channels, significantly diminished the effect of BK. Pretreatment with xestospongin C and 2-aminoethoxydiphenyl borate, antagonists of inositol 1,4,5-trisphosphate receptors, abolished the response to BK. Inhibition of ryanodine receptors reduced the BK-induced Ca2+ increase, while disruption of lysosomal Ca2+ stores with bafilomycin A1 did not affect the response. BK produced a dose-dependent depolarization of nucleus ambiguus neurons, which was prevented by the B2 receptor antagonist. In vivo studies indicate that microinjection of BK into nucleus ambiguus elicited bradycardia in conscious rats via B2 receptors. In summary, in cardiac vagal neurons of nucleus ambiguus, BK activates B2 receptors promoting Ca2+ influx and Ca2+ release from endoplasmic reticulum, and membrane depolarization; these effects are translated in vivo by bradycardia."}],"pmid":1,"oa_version":"Submitted Version","article_processing_charge":"No","external_id":{"pmid":["28951324"],"isi":["000415966200003"]},"publist_id":"6911","author":[{"first_name":"Eugen","last_name":"Brǎiloiu","full_name":"Brǎiloiu, Eugen"},{"first_name":"Matthew","last_name":"Mcguire","full_name":"Mcguire, Matthew"},{"full_name":"Shuler, Shadaria","last_name":"Shuler","first_name":"Shadaria"},{"full_name":"Deliu, Elena","orcid":"0000-0002-7370-5293","last_name":"Deliu","first_name":"Elena","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barr, Jeffrey","last_name":"Barr","first_name":"Jeffrey"},{"full_name":"Abood, Mary","last_name":"Abood","first_name":"Mary"},{"last_name":"Brailoiu","full_name":"Brailoiu, Gabriela","first_name":"Gabriela"}],"title":"Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus","citation":{"short":"E. Brǎiloiu, M. Mcguire, S. Shuler, E. Deliu, J. Barr, M. Abood, G. Brailoiu, Neuroscience 365 (2017) 23–32.","ieee":"E. Brǎiloiu et al., “Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus,” Neuroscience, vol. 365. Elsevier, pp. 23–32, 2017.","ama":"Brǎiloiu E, Mcguire M, Shuler S, et al. Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus. Neuroscience. 2017;365:23-32. doi:10.1016/j.neuroscience.2017.09.034","apa":"Brǎiloiu, E., Mcguire, M., Shuler, S., Deliu, E., Barr, J., Abood, M., & Brailoiu, G. (2017). Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus. Neuroscience. Elsevier. https://doi.org/10.1016/j.neuroscience.2017.09.034","mla":"Brǎiloiu, Eugen, et al. “Modulation of Cardiac Vagal Tone by Bradykinin Acting on Nucleus Ambiguus.” Neuroscience, vol. 365, Elsevier, 2017, pp. 23–32, doi:10.1016/j.neuroscience.2017.09.034.","ista":"Brǎiloiu E, Mcguire M, Shuler S, Deliu E, Barr J, Abood M, Brailoiu G. 2017. Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus. Neuroscience. 365, 23–32.","chicago":"Brǎiloiu, Eugen, Matthew Mcguire, Shadaria Shuler, Elena Deliu, Jeffrey Barr, Mary Abood, and Gabriela Brailoiu. “Modulation of Cardiac Vagal Tone by Bradykinin Acting on Nucleus Ambiguus.” Neuroscience. Elsevier, 2017. https://doi.org/10.1016/j.neuroscience.2017.09.034."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"23 - 32","date_created":"2018-12-11T11:48:17Z","date_published":"2017-12-04T00:00:00Z","doi":"10.1016/j.neuroscience.2017.09.034","year":"2017","isi":1,"publication":"Neuroscience","day":"04","oa":1,"publisher":"Elsevier","quality_controlled":"1"}]