[{"title":"Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide","publist_id":"6291","author":[{"full_name":"Di Giglio, Maria","last_name":"Di Giglio","first_name":"Maria"},{"full_name":"Muttenthaler, Markus","last_name":"Muttenthaler","first_name":"Markus"},{"first_name":"Kasper","last_name":"Harpsøe","full_name":"Harpsøe, Kasper"},{"last_name":"Liutkeviciute","full_name":"Liutkeviciute, Zita","first_name":"Zita"},{"last_name":"Keov","full_name":"Keov, Peter","first_name":"Peter"},{"first_name":"Thomas","last_name":"Eder","full_name":"Eder, Thomas"},{"first_name":"Thomas","full_name":"Rattei, Thomas","last_name":"Rattei"},{"full_name":"Arrowsmith, Sarah","last_name":"Arrowsmith","first_name":"Sarah"},{"first_name":"Susan","last_name":"Wray","full_name":"Wray, Susan"},{"first_name":"Ales","last_name":"Marek","full_name":"Marek, Ales"},{"first_name":"Tomas","last_name":"Elbert","full_name":"Elbert, Tomas"},{"full_name":"Alewood, Paul","last_name":"Alewood","first_name":"Paul"},{"first_name":"David","full_name":"Gloriam, David","last_name":"Gloriam"},{"first_name":"Christian","full_name":"Gruber, Christian","last_name":"Gruber"}],"external_id":{"isi":["000393163800001"]},"article_processing_charge":"No","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.","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","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."},"doi":"10.1038/srep41002","date_published":"2017-02-01T00:00:00Z","date_created":"2018-12-11T11:50:04Z","page":"41002","day":"01","publication":"Scientific Reports","has_accepted_license":"1","isi":1,"year":"2017","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"file_date_updated":"2018-12-12T10:14:59Z","ddc":["570","590"],"date_updated":"2023-09-20T11:47:47Z","status":"public","pubrep_id":"790","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":"1086","volume":7,"license":"https://creativecommons.org/licenses/by/4.0/","file":[{"date_created":"2018-12-12T10:14:59Z","file_name":"IST-2017-790-v1+1_srep41002_1_.pdf","creator":"system","date_updated":"2018-12-12T10:14:59Z","file_size":1994139,"file_id":"5115","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"02","intvolume":" 7","scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}]},{"title":"Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis","publist_id":"6294","author":[{"last_name":"Fang","full_name":"Fang, Chong","first_name":"Chong"},{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","first_name":"Anna A","orcid":"0000-0002-1391-8377","full_name":"Nagy-Staron, Anna A","last_name":"Nagy-Staron"},{"first_name":"Martin","last_name":"Grafe","full_name":"Grafe, Martin"},{"full_name":"Heermann, Ralf","last_name":"Heermann","first_name":"Ralf"},{"full_name":"Jung, Kirsten","last_name":"Jung","first_name":"Kirsten"},{"first_name":"Susanne","full_name":"Gebhard, Susanne","last_name":"Gebhard"},{"full_name":"Mascher, Thorsten","last_name":"Mascher","first_name":"Thorsten"}],"external_id":{"isi":["000398059200002"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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","short":"C. Fang, A.A. Nagy-Staron, M. Grafe, R. Heermann, K. Jung, S. Gebhard, T. Mascher, Molecular Microbiology 104 (2017) 16–31.","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."},"publisher":"Wiley-Blackwell","quality_controlled":"1","doi":"10.1111/mmi.13597","date_published":"2017-04-01T00:00:00Z","date_created":"2018-12-11T11:50:03Z","page":"16 - 31","day":"01","publication":"Molecular Microbiology","isi":1,"year":"2017","status":"public","type":"journal_article","_id":"1084","department":[{"_id":"CaGu"}],"date_updated":"2023-09-20T11:48:43Z","month":"04","intvolume":" 104","scopus_import":"1","oa_version":"None","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."}],"volume":104,"issue":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":[" 0950382X"]},"publication_status":"published"},{"intvolume":" 20","month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1603.07368"}],"scopus_import":"1","oa_version":"Submitted Version","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"}],"volume":20,"issue":"2","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["13850172"]},"status":"public","type":"journal_article","_id":"1079","department":[{"_id":"RoSe"}],"date_updated":"2023-09-20T11:53:35Z","oa":1,"quality_controlled":"1","publisher":"Springer","date_created":"2018-12-11T11:50:02Z","doi":"10.1007/s11040-017-9238-0","date_published":"2017-06-01T00:00:00Z","publication":"Mathematical Physics, Analysis and Geometry","day":"01","year":"2017","isi":1,"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"}],"article_number":"6","title":"Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges","external_id":{"isi":["000401270000004"]},"article_processing_charge":"No","publist_id":"6300","author":[{"full_name":"Nam, Phan","last_name":"Nam","first_name":"Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Van Den Bosch","full_name":"Van Den Bosch, Hanne","first_name":"Hanne"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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","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.","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.","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."}},{"scopus_import":"1","month":"01","intvolume":" 14","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","volume":14,"issue":"126","related_material":{"record":[{"id":"9864","status":"public","relation":"research_data"}]},"ec_funded":1,"publication_identifier":{"issn":["17425689"]},"publication_status":"published","file":[{"success":1,"file_id":"5843","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2017_JRSI_Redondo.pdf","date_created":"2019-01-18T09:14:02Z","file_size":1092015,"date_updated":"2019-01-18T09:14:02Z","creator":"dernst"}],"language":[{"iso":"eng"}],"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","file_date_updated":"2019-01-18T09:14:02Z","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"date_updated":"2023-09-20T11:56:34Z","ddc":["570"],"publisher":"Royal Society of London","quality_controlled":"1","oa":1,"date_published":"2017-01-04T00:00:00Z","doi":"10.1098/rsif.2016.0139","date_created":"2018-12-11T11:50:01Z","isi":1,"has_accepted_license":"1","year":"2017","day":"04","publication":"Journal of the Royal Society Interface","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440"}],"article_number":"20160139","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"},{"id":"2A181218-F248-11E8-B48F-1D18A9856A87","first_name":"Harold","full_name":"Vladar, Harold","orcid":"0000-0002-5985-7653","last_name":"Vladar"},{"last_name":"Włodarski","full_name":"Włodarski, Tomasz","first_name":"Tomasz"},{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P"}],"publist_id":"6303","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":{"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.","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.","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.","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"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"oa":1,"publisher":"Cell Press","quality_controlled":"1","year":"2017","isi":1,"has_accepted_license":"1","publication":"Developmental Cell","day":"27","page":"354 - 366","date_created":"2018-12-11T11:49:58Z","doi":"10.1016/j.devcel.2017.01.010","date_published":"2017-02-27T00:00:00Z","project":[{"grant_number":"201439","name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","call_identifier":"FP7","_id":"2524F500-B435-11E9-9278-68D0E5697425"}],"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.","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.","short":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, C.-P.J. Heisenberg, Developmental Cell 40 (2017) 354–366.","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","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","last_name":"Morita","full_name":"Morita, Hitoshi"},{"first_name":"Silvia","last_name":"Grigolon","full_name":"Grigolon, Silvia"},{"first_name":"Martin","full_name":"Bock, Martin","last_name":"Bock"},{"orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel","last_name":"Krens","first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Guillaume","full_name":"Salbreux, Guillaume","last_name":"Salbreux"},{"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","abstract":[{"lang":"eng","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."}],"acknowledged_ssus":[{"_id":"PreCl"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 40","month":"02","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","_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","date_updated":"2023-09-20T12:06:27Z","ddc":["572","597"],"department":[{"_id":"CaHe"}],"file_date_updated":"2018-12-12T10:10:57Z"},{"project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"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"}],"article_processing_charge":"No","external_id":{"isi":["000395807200023"]},"title":"Inferring recent demography from isolation by distance of long shared sequence blocks","citation":{"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.","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.","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.","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","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"Genetics Society of America","oa":1,"page":"1335 - 1351","doi":"10.1534/genetics.116.196220","date_published":"2017-03-01T00:00:00Z","date_created":"2018-12-11T11:50:00Z","isi":1,"year":"2017","day":"01","publication":"Genetics","type":"journal_article","status":"public","_id":"1074","department":[{"_id":"NiBa"}],"date_updated":"2023-09-20T12:00:56Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://www.biorxiv.org/content/early/2016/09/23/076810"}],"month":"03","intvolume":" 205","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."}],"oa_version":"Preprint","issue":"3","volume":205,"related_material":{"record":[{"id":"200","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"publication_identifier":{"issn":["00166731"]},"publication_status":"published","language":[{"iso":"eng"}]},{"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"}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1609.07018"}],"month":"02","intvolume":" 95","publication_identifier":{"issn":["24699926"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"2","volume":95,"ec_funded":1,"_id":"1076","type":"journal_article","status":"public","date_updated":"2023-09-20T11:57:23Z","department":[{"_id":"MiLe"}],"quality_controlled":"1","publisher":"American Physical Society","oa":1,"isi":1,"year":"2017","day":"01","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","date_published":"2017-02-01T00:00:00Z","doi":"10.1103/PhysRevA.95.023403","date_created":"2018-12-11T11:50:01Z","article_number":"023403","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"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.","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.","short":"M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, C. Keitel, Physical Review A - Atomic, Molecular, and Optical Physics 95 (2017).","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","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Michael","last_name":"Klaiber","full_name":"Klaiber, Michael"},{"first_name":"Jiří","full_name":"Daněk, Jiří","last_name":"Daněk"},{"first_name":"Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu","orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp"},{"full_name":"Hatsagortsyan, Karen","last_name":"Hatsagortsyan","first_name":"Karen"},{"last_name":"Keitel","full_name":"Keitel, Christoph","first_name":"Christoph"}],"publist_id":"6305","external_id":{"isi":["000400571700011"]},"article_processing_charge":"No","title":"Strong-field ionization via a high-order Coulomb-corrected strong-field approximation"},{"date_updated":"2023-09-20T12:05:56Z","department":[{"_id":"HeEd"}],"_id":"1072","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","volume":369,"issue":"5","ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Given a finite set of points in Rn and a radius parameter, we study the Čech, Delaunay–Čech, Delaunay (or alpha), and Wrap complexes in the light of generalized discrete Morse theory. Establishing the Čech and Delaunay complexes as sublevel sets of generalized discrete Morse functions, we prove that the four complexes are simple-homotopy equivalent by a sequence of simplicial collapses, which are explicitly described by a single discrete gradient field."}],"month":"05","intvolume":" 369","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1312.1231","open_access":"1"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Bauer U, Edelsbrunner H. 2017. The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. 369(5), 3741–3762.","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.","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","ama":"Bauer U, Edelsbrunner H. The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. 2017;369(5):3741-3762. doi:10.1090/tran/6991","short":"U. Bauer, H. Edelsbrunner, Transactions of the American Mathematical Society 369 (2017) 3741–3762.","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.","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."},"title":"The Morse theory of Čech and delaunay complexes","author":[{"full_name":"Bauer, Ulrich","orcid":"0000-0002-9683-0724","last_name":"Bauer","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich"},{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"}],"publist_id":"6311","article_processing_charge":"No","external_id":{"arxiv":["1312.1231"],"isi":["000398030400024"]},"project":[{"grant_number":"318493","name":"Topological Complex Systems","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"day":"01","publication":"Transactions of the American Mathematical Society","isi":1,"year":"2017","doi":"10.1090/tran/6991","date_published":"2017-05-01T00:00:00Z","date_created":"2018-12-11T11:49:59Z","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”.","quality_controlled":"1","publisher":"American Mathematical Society","oa":1},{"quality_controlled":"1","publisher":"Springer","oa":1,"doi":"10.1007/s00454-016-9855-6","date_published":"2017-06-01T00:00:00Z","date_created":"2018-12-11T11:50:00Z","page":"915 - 965","day":"01","publication":"Discrete & Computational Geometry","isi":1,"year":"2017","title":"Algorithmic solvability of the lifting extension problem","author":[{"first_name":"Martin","last_name":"Čadek","full_name":"Čadek, Martin"},{"full_name":"Krcál, Marek","last_name":"Krcál","id":"33E21118-F248-11E8-B48F-1D18A9856A87","first_name":"Marek"},{"first_name":"Lukáš","last_name":"Vokřínek","full_name":"Vokřínek, Lukáš"}],"publist_id":"6309","article_processing_charge":"No","external_id":{"isi":["000400072700008"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","short":"M. Čadek, M. Krcál, L. Vokřínek, Discrete & Computational Geometry 54 (2017) 915–965.","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.","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.","ista":"Čadek M, Krcál M, Vokřínek L. 2017. Algorithmic solvability of the lifting extension problem. Discrete & Computational Geometry. 54(4), 915–965."},"month":"06","intvolume":" 54","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1307.6444","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","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."}],"issue":"4","volume":54,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["01795376"]},"publication_status":"published","status":"public","type":"journal_article","_id":"1073","department":[{"_id":"UlWa"}],"date_updated":"2023-09-20T12:01:28Z"},{"extern":"1","ddc":["579"],"date_updated":"2023-09-20T12:09:21Z","file_date_updated":"2018-12-12T10:16:50Z","_id":"1061","status":"public","pubrep_id":"792","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":[{"date_created":"2018-12-12T10:16:50Z","file_name":"IST-2017-792-v1+1_s12934-017-0645-5.pdf","date_updated":"2018-12-12T10:16:50Z","file_size":1361313,"creator":"system","file_id":"5240","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["14752859"]},"publication_status":"published","volume":16,"issue":"1","oa_version":"Published Version","pmid":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"}],"month":"02","intvolume":" 16","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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).","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","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","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.","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."},"title":"Ethylene production with engineered Synechocystis sp PCC 6803 strains","publist_id":"6325","author":[{"first_name":"Vinod","full_name":"Veetil, Vinod","last_name":"Veetil"},{"id":"4677C796-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Angermayr","orcid":"0000-0001-8619-2223","full_name":"Angermayr, Andreas"},{"first_name":"Klaas","last_name":"Hellingwerf","full_name":"Hellingwerf, Klaas"}],"external_id":{"pmid":["28231787"],"isi":["000397733000001"]},"article_processing_charge":"No","article_number":"34","day":"23","publication":"Microbial Cell Factories","has_accepted_license":"1","isi":1,"year":"2017","date_published":"2017-02-23T00:00:00Z","doi":"10.1186/s12934-017-0645-5","date_created":"2018-12-11T11:49:56Z","publisher":"BioMed Central","quality_controlled":"1","oa":1},{"oa":1,"publisher":"Elsevier","quality_controlled":"1","publication":"Information Processing Letters","day":"01","year":"2017","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:49:57Z","doi":"10.1016/j.ipl.2017.02.003","date_published":"2017-06-01T00:00:00Z","page":"25 - 29","project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Chatterjee K, Osang GF. 2017. Pushdown reachability with constant treewidth. Information Processing Letters. 122, 25–29.","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.","ieee":"K. Chatterjee and G. F. Osang, “Pushdown reachability with constant treewidth,” Information Processing Letters, vol. 122. Elsevier, pp. 25–29, 2017.","short":"K. Chatterjee, G.F. Osang, Information Processing Letters 122 (2017) 25–29.","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","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."},"title":"Pushdown reachability with constant treewidth","article_processing_charge":"No","external_id":{"isi":["000399506600005"]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F","orcid":"0000-0002-8882-5116","full_name":"Osang, Georg F","last_name":"Osang"}],"publist_id":"6323","oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"intvolume":" 122","month":"06","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:13:17Z","file_name":"IST-2018-991-v1+2_2018_Chatterjee_Pushdown_PREPRINT.pdf","creator":"system","date_updated":"2019-10-15T07:44:51Z","file_size":247657,"file_id":"4998","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["00200190"]},"ec_funded":1,"volume":122,"_id":"1065","pubrep_id":"991","status":"public","type":"journal_article","ddc":["000"],"date_updated":"2023-09-20T12:08:18Z","department":[{"_id":"KrCh"},{"_id":"HeEd"}],"file_date_updated":"2019-10-15T07:44:51Z"},{"_id":"1062","status":"public","type":"journal_article","extern":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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","author":[{"first_name":"Laura","full_name":"Guarina, Laura","last_name":"Guarina"},{"full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","last_name":"Vandael","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H"},{"full_name":"Carabelli, Valentina","last_name":"Carabelli","first_name":"Valentina"},{"last_name":"Carbone","full_name":"Carbone, Emilio","first_name":"Emilio"}],"publist_id":"6326","external_id":{"isi":["000399430300022"]},"article_processing_charge":"No","oa_version":"None","abstract":[{"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.","lang":"eng"}],"month":"04","intvolume":" 595","publisher":"Wiley-Blackwell","quality_controlled":"1","day":"15","publication":"Journal of Physiology","language":[{"iso":"eng"}],"isi":1,"year":"2017","publication_status":"published","date_published":"2017-04-15T00:00:00Z","issue":"8","doi":"10.1113/JP273735","volume":595,"date_created":"2018-12-11T11:49:56Z","page":"2587 - 2609 "},{"publisher":"Wiley-Blackwell","quality_controlled":"1","oa":1,"page":"845 - 858","doi":"10.1111/evo.13191","date_published":"2017-04-01T00:00:00Z","date_created":"2018-12-11T11:49:57Z","isi":1,"year":"2017","day":"01","publication":"Evolution","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"author":[{"id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","first_name":"Hildegard","orcid":"0000-0001-9435-2813","full_name":"Uecker, Hildegard","last_name":"Uecker"}],"publist_id":"6327","external_id":{"isi":["000398545200003"]},"article_processing_charge":"No","title":"Evolutionary rescue in randomly mating, selfing, and clonal populations","citation":{"short":"H. Uecker, Evolution 71 (2017) 845–858.","ieee":"H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,” Evolution, vol. 71, no. 4. Wiley-Blackwell, pp. 845–858, 2017.","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","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.","ista":"Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 71(4), 845–858.","chicago":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13191."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://biorxiv.org/content/early/2016/10/14/081042"}],"month":"04","intvolume":" 71","abstract":[{"lang":"eng","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."}],"oa_version":"Submitted Version","issue":"4","volume":71,"ec_funded":1,"publication_identifier":{"issn":["00143820"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1063","department":[{"_id":"NiBa"}],"date_updated":"2023-09-20T12:10:32Z"},{"author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Otop","full_name":"Otop, Jan"},{"full_name":"Velner, Yaron","last_name":"Velner","first_name":"Yaron"}],"publist_id":"6322","external_id":{"isi":["000402025600002"]},"article_processing_charge":"No","title":"Quantitative fair simulation games","citation":{"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.","ista":"Chatterjee K, Henzinger TA, Otop J, Velner Y. 2017. Quantitative fair simulation games. Information and Computation. 254(2), 143–166.","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.","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","ama":"Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative fair simulation games. Information and Computation. 2017;254(2):143-166. doi:10.1016/j.ic.2016.10.006","short":"K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Information and Computation 254 (2017) 143–166.","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, “Quantitative fair simulation games,” Information and Computation, vol. 254, no. 2. Elsevier, pp. 143–166, 2017."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"page":"143 - 166","doi":"10.1016/j.ic.2016.10.006","date_published":"2017-06-01T00:00:00Z","date_created":"2018-12-11T11:49:58Z","isi":1,"year":"2017","day":"01","publication":"Information and Computation","publisher":"Elsevier","quality_controlled":"1","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2023-09-20T12:07:48Z","type":"journal_article","status":"public","_id":"1066","related_material":{"record":[{"status":"public","id":"5428","relation":"earlier_version"}]},"volume":254,"issue":"2","ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","month":"06","intvolume":" 254","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"}],"oa_version":"None"},{"status":"public","pubrep_id":"802","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":"1023","file_date_updated":"2018-12-12T10:15:29Z","department":[{"_id":"LaEr"}],"ddc":["510"],"date_updated":"2023-09-22T09:27:51Z","month":"02","intvolume":" 22","scopus_import":"1","oa_version":"Published Version","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"}],"volume":22,"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5149","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"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["10836489"]},"publication_status":"published","article_number":"22","title":"Local law for the product of independent non-Hermitian random matrices with independent entries","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"}],"article_processing_charge":"No","external_id":{"isi":["000396611900022"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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","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.","short":"Y. Nemish, Electronic Journal of Probability 22 (2017).","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.","ista":"Nemish Y. 2017. Local law for the product of independent non-Hermitian random matrices with independent entries. Electronic Journal of Probability. 22, 22.","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."},"quality_controlled":"1","publisher":"Institute of Mathematical Statistics","oa":1,"date_published":"2017-02-06T00:00:00Z","doi":"10.1214/17-EJP38","date_created":"2018-12-11T11:49:44Z","day":"06","publication":"Electronic Journal of Probability","isi":1,"has_accepted_license":"1","year":"2017"},{"date_updated":"2023-09-22T09:40:55Z","department":[{"_id":"HeEd"}],"_id":"1022","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["00358711"]},"language":[{"iso":"eng"}],"issue":"4","volume":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","main_file_link":[{"url":"https://arxiv.org/abs/1608.04519","open_access":"1"}],"scopus_import":"1","intvolume":" 465","month":"01","citation":{"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.","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","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000395170200039"]},"article_processing_charge":"No","publist_id":"6373","author":[{"first_name":"Pratyush","full_name":"Pranav, Pratyush","last_name":"Pranav"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"last_name":"Van De Weygaert","full_name":"Van De Weygaert, Rien","first_name":"Rien"},{"full_name":"Vegter, Gert","last_name":"Vegter","first_name":"Gert"},{"first_name":"Michael","full_name":"Kerber, Michael","last_name":"Kerber"},{"last_name":"Jones","full_name":"Jones, Bernard","first_name":"Bernard"},{"id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","first_name":"Mathijs","last_name":"Wintraecken","orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs"}],"title":"The topology of the cosmic web in terms of persistent Betti numbers","year":"2017","isi":1,"publication":"Monthly Notices of the Royal Astronomical Society","day":"01","page":"4281 - 4310","date_created":"2018-12-11T11:49:44Z","date_published":"2017-01-01T00:00:00Z","doi":"10.1093/mnras/stw2862","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.","oa":1,"quality_controlled":"1","publisher":"Oxford University Press"},{"type":"journal_article","article_type":"original","status":"public","_id":"1026","department":[{"_id":"HaJa"}],"date_updated":"2023-09-22T09:26:06Z","scopus_import":"1","month":"12","intvolume":" 48","abstract":[{"lang":"eng","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."}],"oa_version":"None","volume":48,"ec_funded":1,"publication_identifier":{"issn":["09581669"]},"publication_status":"published","language":[{"iso":"eng"}],"project":[{"grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","name":"Microbial Ion Channels for Synthetic Neurobiology","grant_number":"303564"},{"_id":"255A6082-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Drug Targets","grant_number":"W1232-B24"}],"publist_id":"6365","author":[{"last_name":"Agus","full_name":"Agus, Viviana","first_name":"Viviana"},{"orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000418313200003"]},"article_processing_charge":"No","title":"Optogenetic methods in drug screening: Technologies and applications","citation":{"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.","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"Elsevier","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).","page":"8 - 14","doi":"10.1016/j.copbio.2017.02.006","date_published":"2017-12-01T00:00:00Z","date_created":"2018-12-11T11:49:45Z","isi":1,"year":"2017","day":"01","publication":"Current Opinion in Biotechnology"},{"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.","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"day":"08","publication":"ACS Applied Materials and Interfaces","isi":1,"year":"2017","doi":"10.1021/acsami.6b15986","date_published":"2017-03-08T00:00:00Z","date_created":"2018-12-11T11:49:44Z","page":"7885 - 7890","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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.","short":"S. Caixeiro, M. Peruzzo, O. Onelli, S. Vignolini, R. Sapienza, ACS Applied Materials and Interfaces 9 (2017) 7885–7890.","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.","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"},"title":"Disordered cellulose based nanostructures for enhanced light scattering","publist_id":"6372","author":[{"first_name":"Soraya","last_name":"Caixeiro","full_name":"Caixeiro, Soraya"},{"first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","last_name":"Peruzzo","orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda"},{"first_name":"Olimpia","full_name":"Onelli, Olimpia","last_name":"Onelli"},{"full_name":"Vignolini, Silvia","last_name":"Vignolini","first_name":"Silvia"},{"full_name":"Sapienza, Riccardo","last_name":"Sapienza","first_name":"Riccardo"}],"external_id":{"isi":["000396186000002"]},"article_processing_charge":"No","oa_version":"Submitted Version","abstract":[{"lang":"eng","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."}],"month":"03","intvolume":" 9","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1702.01415","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["19448244"]},"publication_status":"published","issue":"9","volume":9,"_id":"1020","status":"public","type":"journal_article","date_updated":"2023-09-22T09:40:14Z","department":[{"_id":"JoFi"}]},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00221120"]},"volume":817,"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"}],"intvolume":" 817","month":"04","main_file_link":[{"url":"https://arxiv.org/abs/1608.05527","open_access":"1"}],"scopus_import":"1","date_updated":"2023-09-22T09:39:46Z","department":[{"_id":"BjHo"}],"_id":"1021","status":"public","type":"journal_article","publication":"Journal of Fluid Mechanics","day":"25","year":"2017","isi":1,"date_created":"2018-12-11T11:49:44Z","date_published":"2017-04-25T00:00:00Z","doi":"10.1017/jfm.2017.109","page":"21 - 34","oa":1,"quality_controlled":"1","publisher":"Cambridge University Press","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","ista":"Lopez Alonso JM, Avila M. 2017. Boundary layer turbulence in experiments on quasi Keplerian flows. Journal of Fluid Mechanics. 817, 21–34.","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.","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.","short":"J.M. Lopez Alonso, M. Avila, Journal of Fluid Mechanics 817 (2017) 21–34.","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","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"},"title":"Boundary layer turbulence in experiments on quasi Keplerian flows","external_id":{"isi":["000398179100006"]},"article_processing_charge":"No","publist_id":"6371","author":[{"orcid":"0000-0002-0384-2022","full_name":"Lopez Alonso, Jose M","last_name":"Lopez Alonso","first_name":"Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Avila, Marc","last_name":"Avila","first_name":"Marc"}],"project":[{"_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012","name":"Information processing and computation in fish groups"}]},{"issue":"7643","volume":543,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00280836"]},"publication_status":"published","month":"03","intvolume":" 543","scopus_import":"1","oa_version":"None","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"}],"department":[{"_id":"CaHe"}],"date_updated":"2023-09-22T09:26:59Z","status":"public","type":"journal_article","_id":"1025","date_published":"2017-03-02T00:00:00Z","doi":"10.1038/nature21502","date_created":"2018-12-11T11:49:45Z","page":"43 - 44","day":"02","publication":"Nature","isi":1,"year":"2017","publisher":"Nature Publishing Group","quality_controlled":"1","title":"Cell biology: Stretched divisions","publist_id":"6367","author":[{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"external_id":{"isi":["000395671500025"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Heisenberg C-PJ. Cell biology: Stretched divisions. Nature. 2017;543(7643):43-44. doi:10.1038/nature21502","apa":"Heisenberg, C.-P. J. (2017). Cell biology: Stretched divisions. Nature. Nature Publishing Group. https://doi.org/10.1038/nature21502","ieee":"C.-P. J. Heisenberg, “Cell biology: Stretched divisions,” Nature, vol. 543, no. 7643. Nature Publishing Group, pp. 43–44, 2017.","short":"C.-P.J. Heisenberg, Nature 543 (2017) 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.","ista":"Heisenberg C-PJ. 2017. Cell biology: Stretched divisions. Nature. 543(7643), 43–44.","chicago":"Heisenberg, Carl-Philipp J. “Cell Biology: Stretched Divisions.” Nature. Nature Publishing Group, 2017. https://doi.org/10.1038/nature21502."}},{"publication_identifier":{"issn":["10447431"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"4742","date_updated":"2018-12-12T10:09:19Z","file_size":1436377,"creator":"system","date_created":"2018-12-12T10:09:19Z","file_name":"IST-2017-806-v1+2_1-s2.0-S1044743116302500-main_1_.pdf"}],"language":[{"iso":"eng"}],"volume":84,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","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","scopus_import":"1","month":"10","intvolume":" 84","date_updated":"2023-09-22T09:42:15Z","ddc":["571"],"file_date_updated":"2018-12-12T10:09:19Z","department":[{"_id":"SiHi"}],"_id":"1017","type":"journal_article","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"},"status":"public","pubrep_id":"806","has_accepted_license":"1","isi":1,"year":"2017","day":"01","publication":"Molecular and Cellular Neuroscience","page":"58 - 67","date_published":"2017-10-01T00:00:00Z","doi":"10.1016/j.mcn.2017.03.002","date_created":"2018-12-11T11:49:42Z","publisher":"Academic Press","quality_controlled":"1","oa":1,"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.","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.","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","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","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","author":[{"first_name":"Martin","full_name":"Breuss, Martin","last_name":"Breuss"},{"first_name":"Ines","last_name":"Leca","full_name":"Leca, Ines"},{"last_name":"Gstrein","full_name":"Gstrein, Thomas","first_name":"Thomas"},{"last_name":"Hansen","full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H"},{"first_name":"David","full_name":"Keays, David","last_name":"Keays"}],"publist_id":"6377","external_id":{"isi":["000415140700007"]},"article_processing_charge":"No","title":"Tubulins and brain development: The origins of functional specification"},{"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","_id":"1015","file_date_updated":"2018-12-12T10:12:32Z","department":[{"_id":"MiLe"}],"date_updated":"2023-09-22T09:43:10Z","ddc":["539"],"scopus_import":"1","intvolume":" 7","month":"04","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","volume":7,"publication_status":"published","publication_identifier":{"issn":["20452322"]},"language":[{"iso":"eng"}],"file":[{"file_id":"4950","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-809-v1+1_srep45702.pdf","date_created":"2018-12-12T10:12:32Z","creator":"system","file_size":478289,"date_updated":"2018-12-12T10:12:32Z"}],"article_number":"45702","article_processing_charge":"No","external_id":{"isi":["000398148100001"]},"publist_id":"6380","author":[{"last_name":"Bighin","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo"},{"first_name":"Luca","full_name":"Salasnich, Luca","last_name":"Salasnich"}],"title":"Vortices and antivortices in two-dimensional ultracold Fermi gases","citation":{"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.","ieee":"G. Bighin and L. Salasnich, “Vortices and antivortices in two-dimensional ultracold Fermi gases,” Scientific Reports, vol. 7. Nature Publishing Group, 2017.","short":"G. Bighin, L. Salasnich, Scientific Reports 7 (2017).","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","date_created":"2018-12-11T11:49:42Z","date_published":"2017-04-04T00:00:00Z","doi":"10.1038/srep45702","year":"2017","has_accepted_license":"1","isi":1,"publication":"Scientific Reports","day":"04"},{"quality_controlled":"1","publisher":"Oxford University Press","page":"258 - 269","date_published":"2017-01-01T00:00:00Z","doi":"10.1093/hmg/ddw383","date_created":"2018-12-11T11:49:42Z","isi":1,"year":"2017","day":"01","publication":"Human Molecular Genetics","author":[{"last_name":"Breuss","full_name":"Breuss, Martin","first_name":"Martin"},{"full_name":"Nguyen, Thai","last_name":"Nguyen","first_name":"Thai"},{"first_name":"Anjana","full_name":"Srivatsan, Anjana","last_name":"Srivatsan"},{"last_name":"Leca","full_name":"Leca, Ines","first_name":"Ines"},{"first_name":"Guoling","last_name":"Tian","full_name":"Tian, Guoling"},{"last_name":"Fritz","full_name":"Fritz, Tanja","first_name":"Tanja"},{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H","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"},{"last_name":"Rosti","full_name":"Rosti, Rasim","first_name":"Rasim"},{"last_name":"Scott","full_name":"Scott, Eric","first_name":"Eric"},{"last_name":"Tan","full_name":"Tan, Uner","first_name":"Uner"},{"full_name":"Kolodner, Richard","last_name":"Kolodner","first_name":"Richard"},{"first_name":"Nicholas","full_name":"Cowan, Nicholas","last_name":"Cowan"},{"last_name":"Keays","full_name":"Keays, David","first_name":"David"},{"last_name":"Gleeson","full_name":"Gleeson, Joseph","first_name":"Joseph"}],"publist_id":"6379","external_id":{"isi":["000397066400002"]},"article_processing_charge":"No","title":"Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability","citation":{"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.","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.","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","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","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","month":"01","intvolume":" 26","abstract":[{"lang":"eng","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."}],"oa_version":"None","volume":26,"issue":"2","publication_identifier":{"issn":["09646906"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1016","department":[{"_id":"SiHi"}],"date_updated":"2023-09-22T09:42:42Z"},{"_id":"1018","type":"journal_article","status":"public","date_updated":"2023-09-22T09:41:48Z","department":[{"_id":"EvBe"}],"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","intvolume":" 174","month":"05","publication_status":"published","language":[{"iso":"eng"}],"volume":174,"issue":"1","citation":{"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","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.","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000402057200028"]},"publist_id":"6375","author":[{"first_name":"Tereza","last_name":"Dobisova","full_name":"Dobisova, Tereza"},{"first_name":"Vendula","full_name":"Hrdinova, Vendula","last_name":"Hrdinova"},{"orcid":"0000-0003-1923-2410","full_name":"Cuesta, Candela","last_name":"Cuesta","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","first_name":"Candela"},{"first_name":"Sarka","last_name":"Michlickova","full_name":"Michlickova, Sarka"},{"full_name":"Urbankova, Ivana","last_name":"Urbankova","first_name":"Ivana"},{"full_name":"Hejatkova, Romana","last_name":"Hejatkova","first_name":"Romana"},{"first_name":"Petra","last_name":"Zadnikova","full_name":"Zadnikova, Petra"},{"first_name":"Markéta","full_name":"Pernisová, Markéta","last_name":"Pernisová"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hejátko","full_name":"Hejátko, Jan","first_name":"Jan"}],"title":"Light regulated expression of sensor histidine kinase CKI1 controls cytokinin related development","publisher":"American Society of Plant Biologists","quality_controlled":"1","year":"2017","isi":1,"publication":"Plant Physiology","day":"17","page":"387 - 404","date_created":"2018-12-11T11:49:43Z","date_published":"2017-05-17T00:00:00Z","doi":"10.1104/pp.16.01964"},{"type":"journal_article","status":"public","_id":"1019","department":[{"_id":"BeVi"}],"date_updated":"2023-09-22T09:41:21Z","scopus_import":"1","intvolume":" 119","month":"07","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":"None","issue":"1","related_material":{"record":[{"id":"9861","status":"public","relation":"research_data"}]},"volume":119,"publication_status":"published","publication_identifier":{"issn":["0018067X"]},"language":[{"iso":"eng"}],"article_processing_charge":"No","external_id":{"isi":["000405397800004"]},"publist_id":"6374","author":[{"full_name":"Argyridou, Eliza","last_name":"Argyridou","first_name":"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","last_name":"Parsch","full_name":"Parsch, John"}],"title":"X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster","citation":{"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.","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.","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.","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.","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"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Nature Publishing Group","quality_controlled":"1","page":"27 - 34","date_created":"2018-12-11T11:49:43Z","date_published":"2017-07-01T00:00:00Z","doi":"10.1038/hdy.2017.12","year":"2017","isi":1,"publication":"Heredity","day":"01"},{"oa_version":"Submitted Version","abstract":[{"lang":"eng","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."}],"month":"01","intvolume":" 49","main_file_link":[{"url":"https://arxiv.org/abs/1703.04328","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00361410"]},"publication_status":"published","issue":"1","volume":49,"_id":"1014","status":"public","type":"journal_article","extern":"1","date_updated":"2023-09-22T09:43:36Z","publisher":"Society for Industrial and Applied Mathematics ","quality_controlled":"1","oa":1,"day":"12","publication":"SIAM Journal on Mathematical Analysis","isi":1,"year":"2017","doi":"10.1137/16M1070384","date_published":"2017-01-12T00:00:00Z","date_created":"2018-12-11T11:49:41Z","page":"82 - 114","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","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","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.","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.","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."},"title":"Liouville principles and a large-scale regularity theory for random elliptic operators on the half-space","publist_id":"6381","author":[{"full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L"},{"first_name":"Claudia","last_name":"Raithel","full_name":"Raithel, Claudia"}],"article_processing_charge":"No","external_id":{"isi":["000396681800004"]}},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-22T09:41:20Z","citation":{"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.","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.","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.","short":"E. Argyridou, A.K. Huylmans, A. Königer, J. Parsch, (2017).","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","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"},"title":"Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster","department":[{"_id":"BeVi"}],"article_processing_charge":"No","author":[{"first_name":"Eliza","last_name":"Argyridou","full_name":"Argyridou, Eliza"},{"first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","last_name":"Huylmans"},{"first_name":"Annabella","last_name":"Königer","full_name":"Königer, Annabella"},{"first_name":"John","last_name":"Parsch","full_name":"Parsch, John"}],"_id":"9861","status":"public","type":"research_data_reference","day":"14","year":"2017","date_created":"2021-08-10T08:12:52Z","doi":"10.5061/dryad.02f6r","related_material":{"record":[{"id":"1019","status":"public","relation":"used_in_publication"}]},"date_published":"2017-02-14T00:00:00Z","oa_version":"Published Version","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."}],"month":"02","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.02f6r","open_access":"1"}],"publisher":"Dryad"},{"publication_status":"published","publication_identifier":{"issn":["14712164"]},"language":[{"iso":"eng"}],"file":[{"file_id":"5236","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:16:46Z","file_name":"IST-2017-814-v1+1_s12864-017-3705-7.pdf","date_updated":"2018-12-12T10:16:46Z","file_size":2379672,"creator":"system"}],"related_material":{"record":[{"id":"9859","status":"public","relation":"research_data"},{"id":"9860","status":"public","relation":"research_data"}]},"volume":18,"issue":"1","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 18","month":"04","date_updated":"2023-09-22T09:47:44Z","ddc":["570"],"department":[{"_id":"SyCr"}],"file_date_updated":"2018-12-12T10:16:46Z","_id":"1006","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":"814","status":"public","year":"2017","has_accepted_license":"1","isi":1,"publication":"BMC Genomics","day":"26","page":"329","date_created":"2018-12-11T11:49:39Z","date_published":"2017-04-26T00:00:00Z","doi":"10.1186/s12864-017-3705-7","oa":1,"quality_controlled":"1","publisher":"BioMed Central","citation":{"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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000400625200004"]},"article_processing_charge":"No","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","last_name":"Essar","full_name":"Essar, Daniela"},{"first_name":"Philip","full_name":"Rosenstiel, Philip","last_name":"Rosenstiel"},{"last_name":"Schulenburg","full_name":"Schulenburg, Hinrich","first_name":"Hinrich"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"}],"title":"Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae"},{"oa":1,"publisher":"Springer","quality_controlled":"1","page":"287 - 313","date_created":"2018-12-11T11:49:41Z","date_published":"2017-03-19T00:00:00Z","doi":"10.1007/978-3-662-54434-1_11","year":"2017","isi":1,"day":"19","project":[{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_processing_charge":"No","external_id":{"isi":["000681702400011"]},"author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard","full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","last_name":"Kragl"},{"full_name":"Mishra, Samarth","last_name":"Mishra","first_name":"Samarth"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"}],"publist_id":"6384","editor":[{"first_name":"Hongseok","full_name":"Yang, Hongseok","last_name":"Yang"}],"title":"Faster algorithms for weighted recursive state machines","citation":{"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.","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.","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.","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","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1701.04914"}],"scopus_import":"1","alternative_title":["LNCS"],"intvolume":" 10201","month":"03","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","ec_funded":1,"volume":10201,"publication_status":"published","publication_identifier":{"issn":["03029743"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2017-04-29","location":"Uppsala, Sweden","start_date":"2017-04-22","name":"ESOP: European Symposium on Programming"},"type":"conference","status":"public","_id":"1011","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2023-09-22T09:44:50Z"},{"project":[{"name":"Hormone cross-talk drives nutrient dependent plant development","grant_number":"I 1774-B16","call_identifier":"FWF","_id":"2542D156-B435-11E9-9278-68D0E5697425"}],"author":[{"id":"29B901B0-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztina","full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983","last_name":"Ötvös"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6394","external_id":{"isi":["000404880400013"],"pmid":["28391060"]},"article_processing_charge":"No","title":"Spatiotemporal mechanisms of root branching","citation":{"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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Elsevier","quality_controlled":"1","oa":1,"page":"82 - 89","doi":"10.1016/j.gde.2017.03.010","date_published":"2017-08-01T00:00:00Z","date_created":"2018-12-11T11:49:38Z","isi":1,"has_accepted_license":"1","year":"2017","day":"01","publication":"Current Opinion in Genetics & Development","type":"journal_article","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"},"status":"public","pubrep_id":"1017","_id":"1004","file_date_updated":"2019-04-17T08:00:36Z","department":[{"_id":"EvBe"}],"date_updated":"2023-09-22T09:48:15Z","ddc":["575"],"scopus_import":"1","month":"08","intvolume":" 45","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","volume":45,"publication_identifier":{"issn":["0959437X"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"6336","file_size":364133,"date_updated":"2019-04-17T08:00:36Z","creator":"dernst","file_name":"Otvos_Benkova_CurOpDevBiol_2017.pdf","date_created":"2019-04-17T08:00:36Z"}],"language":[{"iso":"eng"}]},{"publication_status":"published","publication_identifier":{"issn":["10836489"]},"language":[{"iso":"eng"}],"file":[{"file_id":"5024","relation":"main_file","access_level":"open_access","content_type":"application/pdf","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"}],"ec_funded":1,"volume":22,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"149"}]},"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","date_updated":"2023-09-22T09:45:23Z","ddc":["510","539"],"file_date_updated":"2018-12-12T10:13:39Z","department":[{"_id":"LaEr"}],"_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","year":"2017","isi":1,"has_accepted_license":"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","oa":1,"publisher":"Institute of Mathematical Statistics","quality_controlled":"1","citation":{"ista":"Alt J, Erdös L, Krüger TH. 2017. Local law for random Gram matrices. Electronic Journal of Probability. 22, 25.","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.","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.","short":"J. Alt, L. Erdös, T.H. Krüger, Electronic Journal of Probability 22 (2017).","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","ama":"Alt J, Erdös L, Krüger TH. Local law for random Gram matrices. Electronic Journal of Probability. 2017;22. doi:10.1214/17-EJP42","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"arxiv":["1606.07353"],"isi":["000396611900025"]},"author":[{"last_name":"Alt","full_name":"Alt, Johannes","first_name":"Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H","last_name":"Krüger","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H"}],"publist_id":"6386","title":"Local law for random Gram matrices","article_number":"25","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}]},{"quality_controlled":"1","publisher":"AAAI Press","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].","date_published":"2017-01-01T00:00:00Z","date_created":"2018-12-11T11:49:40Z","page":"3725 - 3732","day":"01","publication":"Proceedings of the 31st AAAI Conference on Artificial Intelligence","isi":1,"year":"2017","project":[{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"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","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"}],"title":"Optimizing expectation with guarantees in POMDPs","publist_id":"6387","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotny","full_name":"Novotny, Petr"},{"first_name":"Guillermo","full_name":"Pérez, Guillermo","last_name":"Pérez"},{"last_name":"Raskin","full_name":"Raskin, Jean","first_name":"Jean"},{"first_name":"Djordje","last_name":"Zikelic","full_name":"Zikelic, Djordje"}],"external_id":{"isi":["000485630703107"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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.","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.","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.","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.","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."},"month":"01","intvolume":" 5","scopus_import":"1","main_file_link":[{"url":"http://www.aaai.org/ocs/index.php/AAAI/AAAI17/paper/download/14354/14092","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","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."}],"volume":5,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"conference","conference":{"start_date":"2017-02-04","location":"San Francisco, CA, United States","end_date":"2017-02-10","name":"AAAI: Conference on Artificial Intelligence"},"_id":"1009","department":[{"_id":"KrCh"}],"date_updated":"2023-09-22T09:46:41Z"},{"year":"2017","day":"26","date_published":"2017-04-26T00:00:00Z","doi":"10.6084/m9.figshare.c.3756974_d1.v1","related_material":{"record":[{"relation":"used_in_publication","id":"1006","status":"public"}]},"date_created":"2021-08-10T07:59:02Z","abstract":[{"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)","lang":"eng"}],"oa_version":"Published Version","publisher":"Springer Nature","oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.c.3756974_d1.v1","open_access":"1"}],"month":"04","date_updated":"2023-09-22T09:47:44Z","citation":{"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.","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.","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.","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 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","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","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."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Greenwood","full_name":"Greenwood, Jenny","first_name":"Jenny"},{"last_name":"Milutinovic","full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara"},{"last_name":"Peuß","full_name":"Peuß, Robert","first_name":"Robert"},{"first_name":"Sarah","last_name":"Behrens","full_name":"Behrens, Sarah"},{"first_name":"Daniela","full_name":"Essar, Daniela","last_name":"Essar"},{"full_name":"Rosenstiel, Philip","last_name":"Rosenstiel","first_name":"Philip"},{"first_name":"Hinrich","last_name":"Schulenburg","full_name":"Schulenburg, Hinrich"},{"first_name":"Joachim","last_name":"Kurtz","full_name":"Kurtz, Joachim"}],"article_processing_charge":"No","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"}],"_id":"9859","type":"research_data_reference","status":"public"},{"publisher":"Springer Nature","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.c.3756974_d5.v1"}],"month":"04","oa_version":"Published Version","doi":"10.6084/m9.figshare.c.3756974_d5.v1","date_published":"2017-04-26T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1006"}]},"date_created":"2021-08-10T08:07:12Z","year":"2017","day":"26","type":"research_data_reference","status":"public","_id":"9860","author":[{"first_name":"Jenny","full_name":"Greenwood, Jenny","last_name":"Greenwood"},{"first_name":"Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758","last_name":"Milutinovic"},{"last_name":"Peuß","full_name":"Peuß, Robert","first_name":"Robert"},{"full_name":"Behrens, Sarah","last_name":"Behrens","first_name":"Sarah"},{"full_name":"Essar, Daniela","last_name":"Essar","first_name":"Daniela"},{"first_name":"Philip","last_name":"Rosenstiel","full_name":"Rosenstiel, Philip"},{"first_name":"Hinrich","last_name":"Schulenburg","full_name":"Schulenburg, Hinrich"},{"first_name":"Joachim","last_name":"Kurtz","full_name":"Kurtz, Joachim"}],"article_processing_charge":"No","title":"Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae","department":[{"_id":"SyCr"}],"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.","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 5: Table S3. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae.” Springer Nature, 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"},{"status":"public","pubrep_id":"1050","type":"conference","conference":{"name":"SIGGRAPH: Computer Graphics and Interactive Techniques","start_date":"2017-07-30","location":"Los Angeles, CA, United States ","end_date":"2017-08-03"},"_id":"1002","file_date_updated":"2018-12-12T10:09:05Z","department":[{"_id":"BeBi"}],"ddc":["003","004"],"date_updated":"2023-09-22T09:49:31Z","month":"06","intvolume":" 36","alternative_title":["ACM Transactions on Graphics"],"scopus_import":"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"}],"volume":36,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8386"}]},"issue":"4","ec_funded":1,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4728","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"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["07300301"]},"publication_status":"published","project":[{"name":"Distributed 3D Object Design","grant_number":"642841","_id":"2508E324-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"81","title":"Functionality-aware retargeting of mechanisms to 3D shapes","publist_id":"6396","author":[{"last_name":"Zhang","full_name":"Zhang, Ran","orcid":"0000-0002-3808-281X","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","first_name":"Ran"},{"id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Auzinger","full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265"},{"first_name":"Duygu","last_name":"Ceylan","full_name":"Ceylan, Duygu"},{"full_name":"Li, Wilmot","last_name":"Li","first_name":"Wilmot"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385"}],"article_processing_charge":"No","external_id":{"isi":["000406432100049"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"R. Zhang, T. Auzinger, D. Ceylan, W. Li, B. Bickel, in:, ACM, 2017.","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.","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","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.","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.","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."},"quality_controlled":"1","publisher":"ACM","oa":1,"date_published":"2017-06-01T00:00:00Z","doi":"10.1145/3072959.3073710","date_created":"2018-12-11T11:49:38Z","day":"01","isi":1,"has_accepted_license":"1","year":"2017"},{"external_id":{"isi":["000406432100032"]},"article_processing_charge":"No","publist_id":"6397","author":[{"id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ruslan","orcid":"0000-0001-9819-5077","full_name":"Guseinov, Ruslan","last_name":"Guseinov"},{"first_name":"Eder","full_name":"Miguel, Eder","last_name":"Miguel"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"title":"CurveUps: Shaping objects from flat plates with tension-actuated curvature","citation":{"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.","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.","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","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","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.","short":"R. Guseinov, E. Miguel, B. Bickel, in:, ACM, 2017."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"H2020","_id":"25082902-B435-11E9-9278-68D0E5697425","name":"Soft-bodied intelligence for Manipulation","grant_number":"645599"},{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"article_number":"64","date_created":"2018-12-11T11:49:38Z","date_published":"2017-01-01T00:00:00Z","doi":"10.1145/3072959.3073709","year":"2017","has_accepted_license":"1","isi":1,"day":"01","oa":1,"publisher":"ACM","quality_controlled":"1","department":[{"_id":"BeBi"}],"file_date_updated":"2018-12-12T10:10:24Z","date_updated":"2023-09-22T09:49:58Z","ddc":["003","004"],"conference":{"name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","end_date":"2017-08-25","location":"Los Angeles, CA, United States","start_date":"2017-08-19"},"type":"conference","pubrep_id":"1053","status":"public","_id":"1001","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"8366","status":"public"}]},"issue":"4","volume":36,"publication_status":"published","language":[{"iso":"eng"}],"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"}],"alternative_title":["ACM Transactions on Graphics"],"intvolume":" 36","month":"01","abstract":[{"lang":"eng","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."}],"oa_version":"Submitted Version"},{"publication_status":"published","publication_identifier":{"issn":["10450823"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:16:58Z","file_name":"IST-2017-818-v1+1_allIJCAI_CR.pdf","creator":"system","date_updated":"2018-12-12T10:16:58Z","file_size":365172,"file_id":"5249","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"related_material":{"record":[{"relation":"later_version","id":"6006","status":"public"}]},"abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","month":"05","date_updated":"2023-09-22T09:49:00Z","ddc":["004"],"file_date_updated":"2018-12-12T10:16:58Z","department":[{"_id":"ToHe"}],"_id":"1003","conference":{"end_date":"2017-08-25","location":"Melbourne, Australia","start_date":"2017-08-19","name":"IJCAI: International Joint Conference on Artificial Intelligence "},"type":"conference","pubrep_id":"818","status":"public","year":"2017","isi":1,"has_accepted_license":"1","day":"30","page":"70 - 76","date_created":"2018-12-11T11:49:38Z","doi":"10.24963/ijcai.2017/11","date_published":"2017-05-30T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"AAAI Press","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.","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","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","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.","short":"G. Avni, S. Guha, O. Kupferman, in:, AAAI Press, 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","external_id":{"isi":["000764137500011"]},"article_processing_charge":"No","publist_id":"6395","author":[{"last_name":"Avni","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy"},{"full_name":"Guha, Shibashis","last_name":"Guha","first_name":"Shibashis"},{"last_name":"Kupferman","full_name":"Kupferman, Orna","first_name":"Orna"}],"title":"An abstraction-refinement methodology for reasoning about network games","project":[{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"}]},{"_id":"1000","status":"public","conference":{"location":"Sydney, Australia","end_date":"2017-08-11","start_date":"2017-08-06","name":"ICML: International Conference on Machine Learning"},"type":"conference","date_updated":"2023-09-22T09:50:41Z","department":[{"_id":"ChLa"}],"oa_version":"Submitted Version","abstract":[{"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. ","lang":"eng"}],"intvolume":" 70","month":"08","main_file_link":[{"url":"https://arxiv.org/abs/1612.08185","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-151085514-4"]},"ec_funded":1,"volume":70,"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","short":"A. Kolesnikov, C. Lampert, in:, 34th International Conference on Machine Learning, JMLR, 2017, pp. 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.","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.","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.","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."},"title":"PixelCNN models with auxiliary variables for natural image modeling","external_id":{"arxiv":["1612.08185"],"isi":["000683309501102"]},"article_processing_charge":"No","author":[{"last_name":"Kolesnikov","full_name":"Kolesnikov, Alexander","first_name":"Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6398","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","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:49:37Z","date_published":"2017-08-01T00:00:00Z","page":"1905 - 1914"},{"publication_identifier":{"isbn":["978-153860457-1"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":2017,"ec_funded":1,"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. "}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1611.07725"}],"month":"04","intvolume":" 2017","date_updated":"2023-09-22T09:51:58Z","department":[{"_id":"ChLa"},{"_id":"ChWo"}],"_id":"998","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"},"status":"public","isi":1,"year":"2017","day":"14","page":"5533 - 5542","date_published":"2017-04-14T00:00:00Z","doi":"10.1109/CVPR.2017.587","date_created":"2018-12-11T11:49:37Z","quality_controlled":"1","publisher":"IEEE","oa":1,"citation":{"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.","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.","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","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","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.","mla":"Rebuffi, Sylvestre Alvise, et al. ICaRL: Incremental Classifier and Representation Learning. 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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"}],"intvolume":" 71","month":"06","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_name":"2017_Evolution_Sachdeva_supplement.pdf","date_created":"2019-04-17T07:37:04Z","creator":"dernst","file_size":625260,"date_updated":"2020-07-14T12:48:18Z","file_id":"6329","checksum":"6d4c38cb1347fd43620d1736c6df5c79","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"file_size":520110,"date_updated":"2020-07-14T12:48:18Z","creator":"dernst","file_name":"2017_Evolution_Sachdeva_article.pdf","date_created":"2019-04-17T07:37:04Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"f1d90dd8831b44baf49b4dd176f263af","file_id":"6330"}],"publication_status":"published","publication_identifier":{"issn":["00143820"]},"ec_funded":1,"volume":71,"issue":"6","_id":"990","pubrep_id":"977","status":"public","type":"journal_article","ddc":["576"],"date_updated":"2023-09-22T09:55:13Z","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:48:18Z","oa":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","publication":"Evolution; International Journal of Organic Evolution","day":"01","year":"2017","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:49:34Z","date_published":"2017-06-01T00:00:00Z","doi":"10.1111/evo.13252","page":"1478 - 1493 ","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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.","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","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.","short":"H. Sachdeva, N.H. Barton, Evolution; International Journal of Organic Evolution 71 (2017) 1478–1493.","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."},"title":"Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow","article_processing_charge":"No","external_id":{"pmid":["28419447"],"isi":["000403014800005"]},"author":[{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6409"},{"pubrep_id":"826","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":"988","department":[{"_id":"NanoFab"}],"file_date_updated":"2020-07-14T12:48:18Z","ddc":["621"],"date_updated":"2023-09-22T09:56:21Z","intvolume":" 17","month":"05","scopus_import":"1","oa_version":"Published Version","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."}],"issue":"6","volume":17,"language":[{"iso":"eng"}],"file":[{"file_id":"5037","checksum":"22021daa90cf13b01becd776838acb7b","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-826-v1+1_2017_Aguilera-Servin_Current.pdf","date_created":"2018-12-12T10:13:50Z","creator":"system","file_size":508638,"date_updated":"2020-07-14T12:48:18Z"}],"publication_status":"published","publication_identifier":{"issn":["15306984"]},"title":"Current-phase relation of ballistic graphene Josephson junctions","article_processing_charge":"No","external_id":{"isi":["000403631600011"]},"author":[{"first_name":"Gaurav","last_name":"Nanda","full_name":"Nanda, Gaurav"},{"full_name":"Aguilera Servin, Juan L","orcid":"0000-0002-2862-8372","last_name":"Aguilera Servin","first_name":"Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Péter","full_name":"Rakyta, Péter","last_name":"Rakyta"},{"first_name":"Andor","last_name":"Kormányos","full_name":"Kormányos, Andor"},{"full_name":"Kleiner, Reinhold","last_name":"Kleiner","first_name":"Reinhold"},{"full_name":"Koelle, Dieter","last_name":"Koelle","first_name":"Dieter"},{"last_name":"Watanabe","full_name":"Watanabe, Kazuo","first_name":"Kazuo"},{"first_name":"Takashi","last_name":"Taniguchi","full_name":"Taniguchi, Takashi"},{"full_name":"Vandersypen, Lieven","last_name":"Vandersypen","first_name":"Lieven"},{"first_name":"Srijit","last_name":"Goswami","full_name":"Goswami, Srijit"}],"publist_id":"6412","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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","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","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.","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.","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.","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.","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."},"oa":1,"publisher":"American Chemical Society","quality_controlled":"1","date_created":"2018-12-11T11:49:33Z","doi":"10.1021/acs.nanolett.7b00097","date_published":"2017-05-05T00:00:00Z","page":"3396 - 3401","publication":"Nano Letters","day":"05","year":"2017","has_accepted_license":"1","isi":1},{"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","scopus_import":"1","intvolume":" 8","month":"05","publication_status":"published","publication_identifier":{"issn":["20411723"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:15:05Z","file_name":"IST-2017-819-v1+1_2017_Levina_SubsamplingScaling.pdf","creator":"system","date_updated":"2020-07-14T12:48:19Z","file_size":746224,"checksum":"9880212f8c4c53404c7c6fbf9023c53a","file_id":"5122","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"ec_funded":1,"volume":8,"_id":"993","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","date_updated":"2023-09-22T09:54:07Z","ddc":["005","571"],"file_date_updated":"2020-07-14T12:48:19Z","department":[{"_id":"GaTk"},{"_id":"JoCs"}],"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","year":"2017","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"04","date_created":"2018-12-11T11:49:35Z","doi":"10.1038/ncomms15140","date_published":"2017-05-04T00:00:00Z","article_number":"15140","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” Nature Communications, vol. 8, 15140, Nature Publishing Group, 2017, doi: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.","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","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","external_id":{"isi":["000400560700001"]},"article_processing_charge":"Yes (in subscription journal)","publist_id":"6406","author":[{"id":"35AF8020-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","full_name":"Levina (Martius), Anna","last_name":"Levina (Martius)"},{"full_name":"Priesemann, Viola","last_name":"Priesemann","first_name":"Viola"}],"title":"Subsampling scaling"},{"external_id":{"isi":["000407017100009"]},"article_processing_charge":"No","author":[{"id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo","last_name":"Bighin","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777"},{"last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}],"publist_id":"6404","title":"Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment","citation":{"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.","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.","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.","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","short":"G. Bighin, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 96 (2017).","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment"}],"article_number":"085410","date_created":"2018-12-11T11:49:36Z","date_published":"2017-08-07T00:00:00Z","doi":"10.1103/PhysRevB.96.085410","year":"2017","isi":1,"publication":"Physical Review B - Condensed Matter and Materials Physics","day":"07","oa":1,"publisher":"American Physical Society","quality_controlled":"1","department":[{"_id":"MiLe"}],"date_updated":"2023-09-22T09:53:17Z","type":"journal_article","status":"public","_id":"995","issue":"8","volume":96,"publication_status":"published","publication_identifier":{"issn":["24699950"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1704.02616","open_access":"1"}],"scopus_import":"1","intvolume":" 96","month":"08","abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version"},{"title":"Transport based image morphing with intensity modulation","editor":[{"first_name":"François","last_name":"Lauze","full_name":"Lauze, François"},{"last_name":"Dong","full_name":"Dong, Yiqiu","first_name":"Yiqiu"},{"full_name":"Bjorholm Dahl, Anders","last_name":"Bjorholm Dahl","first_name":"Anders"}],"article_processing_charge":"No","external_id":{"isi":["000432210900045"]},"publist_id":"6410","author":[{"last_name":"Maas","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"first_name":"Martin","full_name":"Rumpf, Martin","last_name":"Rumpf"},{"first_name":"Stefan","last_name":"Simon","full_name":"Simon, Stefan"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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.","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","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","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."},"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,"quality_controlled":"1","publisher":"Springer","department":[{"_id":"JaMa"}],"date_updated":"2023-09-22T09:55:50Z","status":"public","conference":{"name":"SSVM: Scale Space and Variational Methods in Computer Vision","start_date":"2017-06-04","location":"Kolding, Denmark","end_date":"2017-06-08"},"type":"conference","_id":"989","volume":10302,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["03029743"]},"intvolume":" 10302","month":"05","scopus_import":"1","alternative_title":["LNCS"],"oa_version":"None","abstract":[{"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.","lang":"eng"}]},{"date_updated":"2023-09-22T09:53:42Z","department":[{"_id":"MiLe"}],"_id":"994","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":1,"issue":"3","oa_version":"Submitted Version","abstract":[{"lang":"eng","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."}],"intvolume":" 1","month":"08","main_file_link":[{"url":"https://arxiv.org/abs/1705.09220","open_access":"1"}],"scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","ista":"Cherepanov I, Lemeshko M. 2017. Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules. Physical Review Materials. 1(3).","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.","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","short":"I. Cherepanov, M. Lemeshko, Physical Review Materials 1 (2017).","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."},"title":"Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules","article_processing_charge":"No","external_id":{"isi":["000416564000004"]},"publist_id":"6405","author":[{"last_name":"Cherepanov","full_name":"Cherepanov, Igor","first_name":"Igor","id":"339C7E5A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"}],"project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment"},{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"publication":"Physical Review Materials","day":"08","year":"2017","isi":1,"date_created":"2018-12-11T11:49:35Z","date_published":"2017-08-08T00:00:00Z","doi":"10.1103/PhysRevMaterials.1.035602","oa":1,"quality_controlled":"1","publisher":"American Physical Society"},{"publication_identifier":{"issn":["08966273"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"4","volume":94,"abstract":[{"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.","lang":"eng"}],"oa_version":"None","scopus_import":"1","month":"05","intvolume":" 94","date_updated":"2023-09-22T09:54:37Z","department":[{"_id":"PeJo"}],"_id":"991","type":"journal_article","status":"public","isi":1,"year":"2017","day":"17","publication":"Neuron","page":"694 - 696","doi":"10.1016/j.neuron.2017.05.011","date_published":"2017-05-17T00:00:00Z","date_created":"2018-12-11T11:49:34Z","publisher":"Elsevier","quality_controlled":"1","citation":{"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.","short":"C. Chen, P.M. Jonas, Neuron 94 (2017) 694–696.","ieee":"C. Chen and P. M. Jonas, “Synaptotagmins: That’s why so many,” Neuron, vol. 94, no. 4. Elsevier, pp. 694–696, 2017.","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","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.","ista":"Chen C, Jonas PM. 2017. Synaptotagmins: That’s why so many. Neuron. 94(4), 694–696."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Chen, Chong","last_name":"Chen","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","first_name":"Chong"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"publist_id":"6408","article_processing_charge":"No","external_id":{"isi":["000401415100002"]},"title":"Synaptotagmins: That’s why so many"},{"oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","year":"2017","isi":1,"has_accepted_license":"1","publication":"eLife","day":"18","date_created":"2018-12-11T11:49:23Z","doi":"10.7554/eLife.25192","date_published":"2017-05-18T00:00:00Z","article_number":"e25192","project":[{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"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.","short":"M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017).","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.","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","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"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000404024800001"]},"article_processing_charge":"Yes","author":[{"last_name":"Lagator","full_name":"Lagator, Mato","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","last_name":"Paixao","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"}],"publist_id":"6460","title":"On the mechanistic nature of epistasis in a canonical cis-regulatory element","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","scopus_import":"1","intvolume":" 6","month":"05","publication_status":"published","publication_identifier":{"issn":["2050084X"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:48:16Z","file_size":2441529,"creator":"system","date_created":"2018-12-12T10:17:49Z","file_name":"IST-2017-841-v1+1_elife-25192-v2.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"59cdd4400fb41280122d414fea971546","file_id":"5306"},{"file_name":"IST-2017-841-v1+2_elife-25192-figures-v2.pdf","date_created":"2018-12-12T10:17:50Z","file_size":3752660,"date_updated":"2020-07-14T12:48:16Z","creator":"system","checksum":"b69024880558b858eb8c5d47a92b6377","file_id":"5307","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"ec_funded":1,"volume":6,"_id":"954","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":"841","status":"public","date_updated":"2023-09-22T10:01:17Z","ddc":["576"],"department":[{"_id":"CaGu"},{"_id":"NiBa"},{"_id":"JoBo"}],"file_date_updated":"2020-07-14T12:48:16Z"},{"title":"Evolution of new regulatory functions on biophysically realistic fitness landscapes","external_id":{"isi":["000407198800005"]},"article_processing_charge":"Yes (in subscription journal)","publist_id":"6459","author":[{"first_name":"Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","full_name":"Friedlander, Tamar","last_name":"Friedlander"},{"full_name":"Prizak, Roshan","last_name":"Prizak","id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"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","short":"T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017).","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.","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."},"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"}],"article_number":"216","date_created":"2018-12-11T11:49:23Z","date_published":"2017-08-09T00:00:00Z","doi":"10.1038/s41467-017-00238-8","publication":"Nature Communications","day":"09","year":"2017","isi":1,"has_accepted_license":"1","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:48:16Z","ddc":["539","576"],"date_updated":"2023-09-22T10:00:49Z","pubrep_id":"864","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":"955","ec_funded":1,"volume":8,"related_material":{"record":[{"id":"6071","status":"public","relation":"dissertation_contains"}]},"issue":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"29a1b5db458048d3bd5c67e0e2a56818","file_id":"5064","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"},{"file_id":"5065","checksum":"7b78401e52a576cf3e6bbf8d0abadc17","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:14:15Z","file_name":"IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf","date_updated":"2020-07-14T12:48:16Z","file_size":9715993,"creator":"system"}],"publication_status":"published","publication_identifier":{"issn":["20411723"]},"intvolume":" 8","month":"08","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","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."}]},{"department":[{"_id":"ToHe"}],"date_updated":"2023-09-22T09:58:02Z","status":"public","conference":{"name":"CAV: Computer Aided Verification","location":"Heidelberg, Germany","end_date":"2017-07-28","start_date":"2017-07-24"},"type":"conference","_id":"962","volume":10427,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["03029743"]},"intvolume":" 10427","month":"01","scopus_import":"1","alternative_title":["LNCS"],"oa_version":"None","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."}],"title":"Model counting for recursively-defined strings","editor":[{"first_name":"Rupak","full_name":"Majumdar, Rupak","last_name":"Majumdar"},{"first_name":"Viktor","last_name":"Kunčak","full_name":"Kunčak, Viktor"}],"article_processing_charge":"No","external_id":{"isi":["000431900900021"]},"publist_id":"6443","author":[{"first_name":"Minh","full_name":"Trinh, Minh","last_name":"Trinh"},{"first_name":"Duc Hiep","id":"3598E630-F248-11E8-B48F-1D18A9856A87","last_name":"Chu","full_name":"Chu, Duc Hiep"},{"full_name":"Jaffar, Joxan","last_name":"Jaffar","first_name":"Joxan"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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."},"project":[{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"date_created":"2018-12-11T11:49:26Z","date_published":"2017-01-01T00:00:00Z","doi":"10.1007/978-3-319-63390-9_21","page":"399 - 418","day":"01","year":"2017","isi":1,"publisher":"Springer","quality_controlled":"1"},{"date_created":"2018-12-11T11:49:23Z","date_published":"2017-05-31T00:00:00Z","doi":"10.1098/rspb.2016.2864","year":"2017","isi":1,"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","day":"31","oa":1,"quality_controlled":"1","publisher":"Royal Society, The","article_processing_charge":"No","external_id":{"pmid":["28566483"],"isi":["000405148800021"]},"author":[{"full_name":"Charlesworth, Deborah","last_name":"Charlesworth","first_name":"Deborah"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Brian","full_name":"Charlesworth, Brian","last_name":"Charlesworth"}],"publist_id":"6462","title":"The sources of adaptive evolution","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"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"20162864","volume":284,"issue":"1855","publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454256/"}],"scopus_import":"1","intvolume":" 284","month":"05","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"}],"oa_version":"Submitted Version","pmid":1,"department":[{"_id":"NiBa"}],"date_updated":"2023-09-22T10:01:48Z","type":"journal_article","status":"public","_id":"953"}]