[{"publication_identifier":{"eissn":["1742-5662"]},"oa":1,"has_accepted_license":"1","project":[{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"year":"2018","related_material":{"record":[{"relation":"research_data","id":"9814","status":"public"}],"link":[{"relation":"supplementary_material","url":"https://dx.doi.org/10.6084/m9.figshare.c.4028971"}]},"date_updated":"2023-10-18T06:36:00Z","_id":"198","title":"Language acquisition with communication between learners","article_processing_charge":"No","date_published":"2018-03-01T00:00:00Z","day":"01","external_id":{"isi":["000428576200023"],"pmid":["29593089"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:45:09Z","volume":15,"doi":"10.1098/rsif.2018.0073","pmid":1,"status":"public","author":[{"last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Tkadlec, Josef","first_name":"Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec"},{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"oa_version":"Submitted Version","issue":"140","ec_funded":1,"isi":1,"month":"03","intvolume":" 15","article_number":"20180073","ddc":["000"],"type":"journal_article","file":[{"relation":"main_file","file_name":"2018_RS_IbsenJensen.pdf","date_updated":"2020-07-14T12:45:22Z","date_created":"2019-02-12T07:54:37Z","file_size":219837,"creator":"dernst","access_level":"open_access","checksum":"444e1a9d98eb0e780671be82b13025f3","content_type":"application/pdf","file_id":"5955"}],"publication":"Journal of the Royal Society Interface","scopus_import":"1","file_date_updated":"2020-07-14T12:45:22Z","publisher":"The Royal Society","publist_id":"7715","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"abstract":[{"text":"We consider a class of students learning a language from a teacher. The situation can be interpreted as a group of child learners receiving input from the linguistic environment. The teacher provides sample sentences. The students try to learn the grammar from the teacher. In addition to just listening to the teacher, the students can also communicate with each other. The students hold hypotheses about the grammar and change them if they receive counter evidence. The process stops when all students have converged to the correct grammar. We study how the time to convergence depends on the structure of the classroom by introducing and evaluating various complexity measures. We find that structured communication between students, although potentially introducing confusion, can greatly reduce some of the complexity measures. Our theory can also be interpreted as applying to the scientific process, where nature is the teacher and the scientists are the students.","lang":"eng"}],"publication_status":"published","article_type":"original","quality_controlled":"1","citation":{"ama":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Language acquisition with communication between learners. Journal of the Royal Society Interface. 2018;15(140). doi:10.1098/rsif.2018.0073","chicago":"Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Language Acquisition with Communication between Learners.” Journal of the Royal Society Interface. The Royal Society, 2018. https://doi.org/10.1098/rsif.2018.0073.","apa":"Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., & Nowak, M. (2018). Language acquisition with communication between learners. Journal of the Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2018.0073","ieee":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Language acquisition with communication between learners,” Journal of the Royal Society Interface, vol. 15, no. 140. The Royal Society, 2018.","ista":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2018. Language acquisition with communication between learners. Journal of the Royal Society Interface. 15(140), 20180073.","short":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, Journal of the Royal Society Interface 15 (2018).","mla":"Ibsen-Jensen, Rasmus, et al. “Language Acquisition with Communication between Learners.” Journal of the Royal Society Interface, vol. 15, no. 140, 20180073, The Royal Society, 2018, doi:10.1098/rsif.2018.0073."}},{"external_id":{"isi":["000436494200026"]},"day":"12","date_published":"2018-06-12T00:00:00Z","oa_version":"Published Version","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"first_name":"Wen","full_name":"Ma, Wen","last_name":"Ma"},{"last_name":"Veltsos","full_name":"Veltsos, Paris","first_name":"Paris"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","first_name":"Melissa A","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380"},{"full_name":"Rodrigues, Nicolas","first_name":"Nicolas","last_name":"Rodrigues"},{"last_name":"Sermier","first_name":"Roberto","full_name":"Sermier, Roberto"},{"first_name":"Daniel","full_name":"Jeffries, Daniel","last_name":"Jeffries"},{"last_name":"Perrin","first_name":"Nicolas","full_name":"Perrin, Nicolas"}],"doi":"10.3390/genes9060294","volume":9,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:45:09Z","year":"2018","has_accepted_license":"1","oa":1,"article_processing_charge":"No","title":"Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes","_id":"199","date_updated":"2023-09-19T10:15:31Z","abstract":[{"lang":"eng","text":"Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage-or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes."}],"language":[{"iso":"eng"}],"publist_id":"7714","department":[{"_id":"BeVi"}],"publisher":"MDPI AG","publication":"Genes","file":[{"content_type":"application/pdf","checksum":"423069beb1cd3cdd25bf3f464b38f1d7","access_level":"open_access","creator":"dernst","file_id":"5905","relation":"main_file","file_size":3985796,"date_created":"2019-02-01T07:52:28Z","date_updated":"2020-07-14T12:45:22Z","file_name":"2018_Genes_Ma.pdf"}],"file_date_updated":"2020-07-14T12:45:22Z","scopus_import":"1","citation":{"ieee":"W. Ma et al., “Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes,” Genes, vol. 9, no. 6. MDPI AG, 2018.","ista":"Ma W, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries D, Perrin N. 2018. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 9(6), 294.","mla":"Ma, Wen, et al. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes, vol. 9, no. 6, 294, MDPI AG, 2018, doi:10.3390/genes9060294.","short":"W. Ma, P. Veltsos, M.A. Toups, N. Rodrigues, R. Sermier, D. Jeffries, N. Perrin, Genes 9 (2018).","ama":"Ma W, Veltsos P, Toups MA, et al. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 2018;9(6). doi:10.3390/genes9060294","apa":"Ma, W., Veltsos, P., Toups, M. A., Rodrigues, N., Sermier, R., Jeffries, D., & Perrin, N. (2018). Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. MDPI AG. https://doi.org/10.3390/genes9060294","chicago":"Ma, Wen, Paris Veltsos, Melissa A Toups, Nicolas Rodrigues, Roberto Sermier, Daniel Jeffries, and Nicolas Perrin. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes. MDPI AG, 2018. https://doi.org/10.3390/genes9060294."},"quality_controlled":"1","publication_status":"published","article_number":"294","intvolume":" 9","month":"06","isi":1,"issue":"6","type":"journal_article","ddc":["570"]},{"intvolume":" 115","month":"11","isi":1,"ec_funded":1,"page":"12241-12246","issue":"48","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30429320"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Indirect reciprocity explores how humans act when their reputation is at stake, and which social norms they use to assess the actions of others. A crucial question in indirect reciprocity is which social norms can maintain stable cooperation in a society. Past research has highlighted eight such norms, called “leading-eight” strategies. This past research, however, is based on the assumption that all relevant information about other population members is publicly available and that everyone agrees on who is good or bad. Instead, here we explore the reputation dynamics when information is private and noisy. We show that under these conditions, most leading-eight strategies fail to evolve. Those leading-eight strategies that do evolve are unable to sustain full cooperation.Indirect reciprocity is a mechanism for cooperation based on shared moral systems and individual reputations. It assumes that members of a community routinely observe and assess each other and that they use this information to decide who is good or bad, and who deserves cooperation. When information is transmitted publicly, such that all community members agree on each other’s reputation, previous research has highlighted eight crucial moral systems. These “leading-eight” strategies can maintain cooperation and resist invasion by defectors. However, in real populations individuals often hold their own private views of others. Once two individuals disagree about their opinion of some third party, they may also see its subsequent actions in a different light. Their opinions may further diverge over time. Herein, we explore indirect reciprocity when information transmission is private and noisy. We find that in the presence of perception errors, most leading-eight strategies cease to be stable. Even if a leading-eight strategy evolves, cooperation rates may drop considerably when errors are common. Our research highlights the role of reliable information and synchronized reputations to maintain stable moral systems."}],"department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","publication":"PNAS","scopus_import":"1","citation":{"ista":"Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. 2018. Indirect reciprocity with private, noisy, and incomplete information. PNAS. 115(48), 12241–12246.","ieee":"C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, and M. Nowak, “Indirect reciprocity with private, noisy, and incomplete information,” PNAS, vol. 115, no. 48. National Academy of Sciences, pp. 12241–12246, 2018.","mla":"Hilbe, Christian, et al. “Indirect Reciprocity with Private, Noisy, and Incomplete Information.” PNAS, vol. 115, no. 48, National Academy of Sciences, 2018, pp. 12241–46, doi:10.1073/pnas.1810565115.","short":"C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, M. Nowak, PNAS 115 (2018) 12241–12246.","ama":"Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. Indirect reciprocity with private, noisy, and incomplete information. PNAS. 2018;115(48):12241-12246. doi:10.1073/pnas.1810565115","chicago":"Hilbe, Christian, Laura Schmid, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Indirect Reciprocity with Private, Noisy, and Incomplete Information.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1810565115.","apa":"Hilbe, C., Schmid, L., Tkadlec, J., Chatterjee, K., & Nowak, M. (2018). Indirect reciprocity with private, noisy, and incomplete information. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1810565115"},"quality_controlled":"1","publication_status":"published","project":[{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23"},{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"year":"2018","oa":1,"title":"Indirect reciprocity with private, noisy, and incomplete information","article_processing_charge":"No","_id":"2","date_updated":"2025-07-14T09:10:09Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/no-cooperation-without-open-communication/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"id":"10293","relation":"dissertation_contains","status":"public"}]},"external_id":{"isi":["000451351000063"],"pmid":["30429320"]},"day":"27","date_published":"2018-11-27T00:00:00Z","oa_version":"Submitted Version","status":"public","author":[{"last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","first_name":"Christian"},{"id":"38B437DE-F248-11E8-B48F-1D18A9856A87","last_name":"Schmid","first_name":"Laura","full_name":"Schmid, Laura","orcid":"0000-0002-6978-7329"},{"last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","first_name":"Josef","full_name":"Tkadlec, Josef"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"pmid":1,"doi":"10.1073/pnas.1810565115","volume":115,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:44:05Z"},{"quality_controlled":"1","citation":{"ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 2018;19(1). doi:10.1186/s12864-018-5173-0","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-018-5173-0","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics. BioMed Central, 2018. https://doi.org/10.1186/s12864-018-5173-0.","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 19(1).","ieee":"J. Higareda Almaraz et al., “Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes,” BMC Genomics, vol. 19, no. 1. BioMed Central, 2018.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, BMC Genomics 19 (2018).","mla":"Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics, vol. 19, no. 1, BioMed Central, 2018, doi:10.1186/s12864-018-5173-0."},"article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"Background: Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level. Results: We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation. In addition, we identified a transcriptional regulatory network with IEGs as master regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover, a functional enrichment analysis and gene clustering into functional modules suggest a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether, our network biology approach explores for the first time the immediate-early systems level response of human adipocytes to acute sympathetic activation, thereby providing a first network basis of early cell fate programs and crosstalks between metabolic and transcriptional networks required for proper WAT function."}],"publist_id":"8035","department":[{"_id":"SiHi"}],"language":[{"iso":"eng"}],"publisher":"BioMed Central","publication":"BMC Genomics","file":[{"creator":"dernst","access_level":"open_access","checksum":"a56516e734dab589dc7f3e1915973b4d","content_type":"application/pdf","file_id":"5712","relation":"main_file","file_name":"2018_BMCGenomics_Higareda.pdf","date_updated":"2020-07-14T12:45:23Z","file_size":4629784,"date_created":"2018-12-17T14:52:57Z"}],"file_date_updated":"2020-07-14T12:45:23Z","scopus_import":"1","ddc":["570"],"type":"journal_article","intvolume":" 19","isi":1,"month":"11","issue":"1","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","author":[{"last_name":"Higareda Almaraz","first_name":"Juan","full_name":"Higareda Almaraz, Juan"},{"last_name":"Karbiener","first_name":"Michael","full_name":"Karbiener, Michael"},{"last_name":"Giroud","full_name":"Giroud, Maude","first_name":"Maude"},{"full_name":"Pauler, Florian","first_name":"Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler"},{"first_name":"Teresa","full_name":"Gerhalter, Teresa","last_name":"Gerhalter"},{"first_name":"Stephan","full_name":"Herzig, Stephan","last_name":"Herzig"},{"full_name":"Scheideler, Marcel","first_name":"Marcel","last_name":"Scheideler"}],"doi":"10.1186/s12864-018-5173-0","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:44:12Z","volume":19,"external_id":{"isi":["000450976700002"]},"day":"03","date_published":"2018-11-03T00:00:00Z","article_processing_charge":"No","title":"Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","date_updated":"2023-09-13T09:10:47Z","_id":"20","related_material":{"record":[{"relation":"research_data","id":"9807","status":"public"},{"id":"9808","status":"public","relation":"research_data"}]},"acknowledgement":"This work was funded by the German Centre for Diabetes Research (DZD) and the Austrian Science Fund (FWF, P25729-B19).","year":"2018","has_accepted_license":"1","oa":1,"publication_identifier":{"issn":["1471-2164"]}},{"date_created":"2018-12-11T11:45:10Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.15479/AT:ISTA:th_963","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"status":"public","author":[{"first_name":"Harald","full_name":"Ringbauer, Harald","orcid":"0000-0002-4884-9682","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","last_name":"Ringbauer"}],"oa_version":"Published Version","date_published":"2018-02-21T00:00:00Z","day":"21","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"563"},{"id":"1074","relation":"part_of_dissertation","status":"public"}]},"_id":"200","date_updated":"2025-05-28T11:57:06Z","title":"Inferring recent demography from spatial genetic structure","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"oa":1,"has_accepted_license":"1","year":"2018","supervisor":[{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","license":"https://creativecommons.org/licenses/by-nc/4.0/","citation":{"chicago":"Ringbauer, Harald. “Inferring Recent Demography from Spatial Genetic Structure.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_963.","apa":"Ringbauer, H. (2018). Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_963","ama":"Ringbauer H. Inferring recent demography from spatial genetic structure. 2018. doi:10.15479/AT:ISTA:th_963","short":"H. Ringbauer, Inferring Recent Demography from Spatial Genetic Structure, Institute of Science and Technology Austria, 2018.","mla":"Ringbauer, Harald. Inferring Recent Demography from Spatial Genetic Structure. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_963.","ista":"Ringbauer H. 2018. Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria.","ieee":"H. Ringbauer, “Inferring recent demography from spatial genetic structure,” Institute of Science and Technology Austria, 2018."},"alternative_title":["ISTA Thesis"],"file":[{"date_created":"2018-12-12T10:14:55Z","file_size":5792935,"file_name":"IST-2018-963-v1+1_thesis.pdf","date_updated":"2020-07-14T12:45:23Z","relation":"main_file","file_id":"5111","checksum":"8cc534d2b528ae017acf80874cce48c9","content_type":"application/pdf","creator":"system","access_level":"open_access"},{"file_id":"6224","access_level":"closed","creator":"dernst","content_type":"application/zip","checksum":"6af18d7e5a7e2728ceda2f41ee24f628","date_updated":"2020-07-14T12:45:23Z","file_name":"2018_thesis_ringbauer_source.zip","file_size":113365,"date_created":"2019-04-05T09:30:12Z","relation":"source_file"}],"file_date_updated":"2020-07-14T12:45:23Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"publist_id":"7713","abstract":[{"lang":"eng","text":"This thesis is concerned with the inference of current population structure based on geo-referenced genetic data. The underlying idea is that population structure affects its spatial genetic structure. Therefore, genotype information can be utilized to estimate important demographic parameters such as migration rates. These indirect estimates of population structure have become very attractive, as genotype data is now widely available. However, there also has been much concern about these approaches. Importantly, genetic structure can be influenced by many complex patterns, which often cannot be disentangled. Moreover, many methods merely fit heuristic patterns of genetic structure, and do not build upon population genetics theory. Here, I describe two novel inference methods that address these shortcomings. In Chapter 2, I introduce an inference scheme based on a new type of signal, identity by descent (IBD) blocks. Recently, it has become feasible to detect such long blocks of genome shared between pairs of samples. These blocks are direct traces of recent coalescence events. As such, they contain ample signal for inferring recent demography. I examine sharing of IBD blocks in two-dimensional populations with local migration. Using a diffusion approximation, I derive formulas for an isolation by distance pattern of long IBD blocks and show that sharing of long IBD blocks approaches rapid exponential decay for growing sample distance. I describe an inference scheme based on these results. It can robustly estimate the dispersal rate and population density, which is demonstrated on simulated data. I also show an application to estimate mean migration and the rate of recent population growth within Eastern Europe. Chapter 3 is about a novel method to estimate barriers to gene flow in a two dimensional population. This inference scheme utilizes geographically localized allele frequency fluctuations - a classical isolation by distance signal. The strength of these local fluctuations increases on average next to a barrier, and there is less correlation across it. I again use a framework of diffusion of ancestral lineages to model this effect, and provide an efficient numerical implementation to fit the results to geo-referenced biallelic SNP data. This inference scheme is able to robustly estimate strong barriers to gene flow, as tests on simulated data confirm."}],"type":"dissertation","ddc":["576"],"degree_awarded":"PhD","page":"146","month":"02","pubrep_id":"963"},{"type":"dissertation","ddc":["514","516"],"page":"171","degree_awarded":"PhD","pubrep_id":"1026","month":"06","supervisor":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"}],"publication_status":"published","citation":{"ama":"Iglesias Ham M. Multiple covers with balls. 2018. doi:10.15479/AT:ISTA:th_1026","apa":"Iglesias Ham, M. (2018). Multiple covers with balls. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1026","chicago":"Iglesias Ham, Mabel. “Multiple Covers with Balls.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1026.","ieee":"M. Iglesias Ham, “Multiple covers with balls,” Institute of Science and Technology Austria, 2018.","ista":"Iglesias Ham M. 2018. Multiple covers with balls. Institute of Science and Technology Austria.","short":"M. Iglesias Ham, Multiple Covers with Balls, Institute of Science and Technology Austria, 2018.","mla":"Iglesias Ham, Mabel. Multiple Covers with Balls. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1026."},"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","file":[{"relation":"source_file","file_size":11827713,"date_created":"2019-02-05T07:43:31Z","date_updated":"2020-07-14T12:45:24Z","file_name":"IST-2018-1025-v2+5_ist-thesis-iglesias-11June2018(1).zip","content_type":"application/zip","checksum":"dd699303623e96d1478a6ae07210dd05","access_level":"closed","creator":"kschuh","file_id":"5918"},{"file_size":4783846,"date_created":"2019-02-05T07:43:45Z","file_name":"IST-2018-1025-v2+4_ThesisIglesiasFinal11June2018.pdf","date_updated":"2020-07-14T12:45:24Z","relation":"main_file","file_id":"5919","checksum":"ba163849a190d2b41d66fef0e4983294","content_type":"application/pdf","creator":"kschuh","access_level":"open_access"}],"file_date_updated":"2020-07-14T12:45:24Z","abstract":[{"lang":"eng","text":"We describe arrangements of three-dimensional spheres from a geometrical and topological point of view. Real data (fitting this setup) often consist of soft spheres which show certain degree of deformation while strongly packing against each other. In this context, we answer the following questions: If we model a soft packing of spheres by hard spheres that are allowed to overlap, can we measure the volume in the overlapped areas? Can we be more specific about the overlap volume, i.e. quantify how much volume is there covered exactly twice, three times, or k times? What would be a good optimization criteria that rule the arrangement of soft spheres while making a good use of the available space? Fixing a particular criterion, what would be the optimal sphere configuration? The first result of this thesis are short formulas for the computation of volumes covered by at least k of the balls. The formulas exploit information contained in the order-k Voronoi diagrams and its closely related Level-k complex. The used complexes lead to a natural generalization into poset diagrams, a theoretical formalism that contains the order-k and degree-k diagrams as special cases. In parallel, we define different criteria to determine what could be considered an optimal arrangement from a geometrical point of view. Fixing a criterion, we find optimal soft packing configurations in 2D and 3D where the ball centers lie on a lattice. As a last step, we use tools from computational topology on real physical data, to show the potentials of higher-order diagrams in the description of melting crystals. The results of the experiments leaves us with an open window to apply the theories developed in this thesis in real applications."}],"language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"publist_id":"7712","_id":"201","date_updated":"2023-09-07T12:25:32Z","title":"Multiple covers with balls","article_processing_charge":"No","oa":1,"publication_identifier":{"issn":["2663-337X"]},"year":"2018","has_accepted_license":"1","doi":"10.15479/AT:ISTA:th_1026","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:45:10Z","oa_version":"Published Version","author":[{"id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","last_name":"Iglesias Ham","full_name":"Iglesias Ham, Mabel","first_name":"Mabel"}],"status":"public","day":"11","date_published":"2018-06-11T00:00:00Z"},{"year":"2018","oa":1,"title":"Learning directed acyclic graphs based on sparsest permutations","article_processing_charge":"No","_id":"2015","date_updated":"2021-01-12T06:54:44Z","external_id":{"arxiv":["1307.0366"]},"date_published":"2018-04-17T00:00:00Z","day":"17","extern":"1","status":"public","author":[{"first_name":"Garvesh","full_name":"Raskutti, Garvesh","last_name":"Raskutti"},{"last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","first_name":"Caroline","full_name":"Uhler, Caroline"}],"oa_version":"Preprint","volume":7,"date_created":"2018-12-11T11:55:13Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1002/sta4.183","month":"04","article_number":"e183","intvolume":" 7","issue":"1","arxiv":1,"main_file_link":[{"url":"http://arxiv.org/abs/1307.0366","open_access":"1"}],"type":"journal_article","language":[{"iso":"eng"}],"publist_id":"5061","abstract":[{"lang":"eng","text":"We consider the problem of learning a Bayesian network or directed acyclic graph model from observational data. A number of constraint‐based, score‐based and hybrid algorithms have been developed for this purpose. Statistical consistency guarantees of these algorithms rely on the faithfulness assumption, which has been shown to be restrictive especially for graphs with cycles in the skeleton. We here propose the sparsest permutation (SP) algorithm, showing that learning Bayesian networks is possible under strictly weaker assumptions than faithfulness. This comes at a computational price, thereby indicating a statistical‐computational trade‐off for causal inference algorithms. In the Gaussian noiseless setting, we prove that the SP algorithm boils down to finding the permutation of the variables with the sparsest Cholesky decomposition of the inverse covariance matrix, which is equivalent to ℓ0‐penalized maximum likelihood estimation. We end with a simulation study showing that in line with the proven stronger consistency guarantees, and the SP algorithm compares favourably to standard causal inference algorithms in terms of accuracy for a given sample size."}],"publication":"STAT","publisher":"Wiley","citation":{"ama":"Raskutti G, Uhler C. Learning directed acyclic graphs based on sparsest permutations. STAT. 2018;7(1). doi:10.1002/sta4.183","chicago":"Raskutti, Garvesh, and Caroline Uhler. “Learning Directed Acyclic Graphs Based on Sparsest Permutations.” STAT. Wiley, 2018. https://doi.org/10.1002/sta4.183.","apa":"Raskutti, G., & Uhler, C. (2018). Learning directed acyclic graphs based on sparsest permutations. STAT. Wiley. https://doi.org/10.1002/sta4.183","ieee":"G. Raskutti and C. Uhler, “Learning directed acyclic graphs based on sparsest permutations,” STAT, vol. 7, no. 1. Wiley, 2018.","ista":"Raskutti G, Uhler C. 2018. Learning directed acyclic graphs based on sparsest permutations. STAT. 7(1), e183.","mla":"Raskutti, Garvesh, and Caroline Uhler. “Learning Directed Acyclic Graphs Based on Sparsest Permutations.” STAT, vol. 7, no. 1, e183, Wiley, 2018, doi:10.1002/sta4.183.","short":"G. Raskutti, C. Uhler, STAT 7 (2018)."},"quality_controlled":"1","publication_status":"published","article_type":"original"},{"main_file_link":[{"url":"http://eprints.nottingham.ac.uk/52388/","open_access":"1"}],"type":"journal_article","month":"06","isi":1,"intvolume":" 115","issue":"26","ec_funded":1,"page":"6864-6869","citation":{"short":"M. Abbas, G.J. Hernández, S. Pollmann, S.L. Samodelov, M. Kolb, J. Friml, U.Z. Hammes, M.D. Zurbriggen, M. Blázquez, D. Alabadí, PNAS 115 (2018) 6864–6869.","mla":"Abbas, Mohamad, et al. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS, vol. 115, no. 26, National Academy of Sciences, 2018, pp. 6864–69, doi:10.1073/pnas.1806565115.","ista":"Abbas M, Hernández GJ, Pollmann S, Samodelov SL, Kolb M, Friml J, Hammes UZ, Zurbriggen MD, Blázquez M, Alabadí D. 2018. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 115(26), 6864–6869.","ieee":"M. Abbas et al., “Auxin methylation is required for differential growth in Arabidopsis,” PNAS, vol. 115, no. 26. National Academy of Sciences, pp. 6864–6869, 2018.","chicago":"Abbas, Mohamad, García J Hernández, Stephan Pollmann, Sophia L Samodelov, Martina Kolb, Jiří Friml, Ulrich Z Hammes, Matias D Zurbriggen, Miguel Blázquez, and David Alabadí. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1806565115.","apa":"Abbas, M., Hernández, G. J., Pollmann, S., Samodelov, S. L., Kolb, M., Friml, J., … Alabadí, D. (2018). Auxin methylation is required for differential growth in Arabidopsis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1806565115","ama":"Abbas M, Hernández GJ, Pollmann S, et al. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 2018;115(26):6864-6869. doi:10.1073/pnas.1806565115"},"quality_controlled":"1","publication_status":"published","publist_id":"7710","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"abstract":[{"text":"Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase in PIN gene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation in the iamt1 mutant could be restored with either endodermis-specific expression of IAMT1 or partial inhibition of polar auxin transport, which also results in normal PIN gene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses.","lang":"eng"}],"scopus_import":"1","publication":"PNAS","publisher":"National Academy of Sciences","title":"Auxin methylation is required for differential growth in Arabidopsis","article_processing_charge":"No","_id":"203","date_updated":"2025-05-07T11:12:32Z","year":"2018","project":[{"call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants"}],"oa":1,"author":[{"full_name":"Abbas, Mohamad","first_name":"Mohamad","last_name":"Abbas","id":"47E8FC1C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hernández","first_name":"García J","full_name":"Hernández, García J"},{"first_name":"Stephan","full_name":"Pollmann, Stephan","last_name":"Pollmann"},{"first_name":"Sophia L","full_name":"Samodelov, Sophia L","last_name":"Samodelov"},{"first_name":"Martina","full_name":"Kolb, Martina","last_name":"Kolb"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí"},{"last_name":"Hammes","first_name":"Ulrich Z","full_name":"Hammes, Ulrich Z"},{"last_name":"Zurbriggen","first_name":"Matias D","full_name":"Zurbriggen, Matias D"},{"full_name":"Blázquez, Miguel","first_name":"Miguel","last_name":"Blázquez"},{"first_name":"David","full_name":"Alabadí, David","last_name":"Alabadí"}],"status":"public","oa_version":"None","volume":115,"date_created":"2018-12-11T11:45:11Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1073/pnas.1806565115","external_id":{"isi":["000436245000096"]},"date_published":"2018-06-26T00:00:00Z","day":"26"},{"intvolume":" 9","article_number":"641","month":"02","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-017-02715-6"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Confining molecules to volumes only slightly larger than the molecules themselves can profoundly alter their properties. Molecular switches—entities that can be toggled between two or more forms upon exposure to an external stimulus—often require conformational freedom to isomerize. Therefore, placing these switches in confined spaces can render them non-operational. To preserve the switchability of these species under confinement, we work with a water-soluble coordination cage that is flexible enough to adapt its shape to the conformation of the encapsulated guest. We show that owing to its flexibility, the cage is not only capable of accommodating—and solubilizing in water—several light-responsive spiropyran-based molecular switches, but, more importantly, it also provides an environment suitable for the efficient, reversible photoisomerization of the bound guests. Our findings pave the way towards studying various molecular switching processes in confined environments."}],"language":[{"iso":"eng"}],"publisher":"Springer Nature","publication":"Nature Communications","scopus_import":"1","quality_controlled":"1","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"citation":{"mla":"Samanta, Dipak, et al. “Reversible Chromism of Spiropyran in the Cavity of a Flexible Coordination Cage.” Nature Communications, vol. 9, 641, Springer Nature, 2018, doi:10.1038/s41467-017-02715-6.","short":"D. Samanta, D. Galaktionova, J. Gemen, L.J.W. Shimon, Y. Diskin-Posner, L. Avram, P. Král, R. Klajn, Nature Communications 9 (2018).","ista":"Samanta D, Galaktionova D, Gemen J, Shimon LJW, Diskin-Posner Y, Avram L, Král P, Klajn R. 2018. Reversible chromism of spiropyran in the cavity of a flexible coordination cage. Nature Communications. 9, 641.","ieee":"D. Samanta et al., “Reversible chromism of spiropyran in the cavity of a flexible coordination cage,” Nature Communications, vol. 9. Springer Nature, 2018.","chicago":"Samanta, Dipak, Daria Galaktionova, Julius Gemen, Linda J. W. Shimon, Yael Diskin-Posner, Liat Avram, Petr Král, and Rafal Klajn. “Reversible Chromism of Spiropyran in the Cavity of a Flexible Coordination Cage.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-017-02715-6.","apa":"Samanta, D., Galaktionova, D., Gemen, J., Shimon, L. J. W., Diskin-Posner, Y., Avram, L., … Klajn, R. (2018). Reversible chromism of spiropyran in the cavity of a flexible coordination cage. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-017-02715-6","ama":"Samanta D, Galaktionova D, Gemen J, et al. Reversible chromism of spiropyran in the cavity of a flexible coordination cage. Nature Communications. 2018;9. doi:10.1038/s41467-017-02715-6"},"article_type":"original","publication_status":"published","year":"2018","oa":1,"publication_identifier":{"eissn":["2041-1723"]},"title":"Reversible chromism of spiropyran in the cavity of a flexible coordination cage","article_processing_charge":"No","date_updated":"2023-08-07T10:54:05Z","_id":"13374","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-018-03701-2","relation":"erratum"}]},"external_id":{"pmid":["29440687"]},"day":"13","date_published":"2018-02-13T00:00:00Z","oa_version":"Published Version","status":"public","author":[{"last_name":"Samanta","full_name":"Samanta, Dipak","first_name":"Dipak"},{"full_name":"Galaktionova, Daria","first_name":"Daria","last_name":"Galaktionova"},{"first_name":"Julius","full_name":"Gemen, Julius","last_name":"Gemen"},{"last_name":"Shimon","full_name":"Shimon, Linda J. W.","first_name":"Linda J. W."},{"full_name":"Diskin-Posner, Yael","first_name":"Yael","last_name":"Diskin-Posner"},{"first_name":"Liat","full_name":"Avram, Liat","last_name":"Avram"},{"first_name":"Petr","full_name":"Král, Petr","last_name":"Král"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","first_name":"Rafal","full_name":"Klajn, Rafal"}],"extern":"1","doi":"10.1038/s41467-017-02715-6","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-01T09:39:32Z","volume":9},{"type":"journal_article","issue":"41","month":"10","intvolume":" 30","article_number":"1706750","publication_status":"published","article_type":"original","quality_controlled":"1","citation":{"mla":"De, Soumen, and Rafal Klajn. “Dissipative Self-Assembly Driven by the Consumption of Chemical Fuels.” Advanced Materials, vol. 30, no. 41, 1706750, Wiley, 2018, doi:10.1002/adma.201706750.","short":"S. De, R. Klajn, Advanced Materials 30 (2018).","ista":"De S, Klajn R. 2018. Dissipative self-assembly driven by the consumption of chemical fuels. Advanced Materials. 30(41), 1706750.","ieee":"S. De and R. Klajn, “Dissipative self-assembly driven by the consumption of chemical fuels,” Advanced Materials, vol. 30, no. 41. Wiley, 2018.","apa":"De, S., & Klajn, R. (2018). Dissipative self-assembly driven by the consumption of chemical fuels. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201706750","chicago":"De, Soumen, and Rafal Klajn. “Dissipative Self-Assembly Driven by the Consumption of Chemical Fuels.” Advanced Materials. Wiley, 2018. https://doi.org/10.1002/adma.201706750.","ama":"De S, Klajn R. Dissipative self-assembly driven by the consumption of chemical fuels. Advanced Materials. 2018;30(41). doi:10.1002/adma.201706750"},"keyword":["Mechanical Engineering","Mechanics of Materials","General Materials Science"],"scopus_import":"1","publication":"Advanced Materials","publisher":"Wiley","language":[{"iso":"eng"}],"abstract":[{"text":"Dissipative self-assembly leads to structures and materials that exist away from equilibrium by continuously exchanging energy and materials with the external environment. Although this mode of self-assembly is ubiquitous in nature, where it gives rise to functions such as signal processing, motility, self-healing, self-replication, and ultimately life, examples of dissipative self-assembly processes in man-made systems are few and far between. Herein, recent progress in developing diverse synthetic dissipative self-assembly systems is discussed. The systems reported thus far can be categorized into three classes, in which: i) the fuel chemically modifies the building blocks, thus triggering their self-assembly, ii) the fuel acts as a template interacting with the building blocks noncovalently, and iii) transient states are induced by the addition of two mutually exclusive stimuli. These early studies give rise to materials that would be difficult to obtain otherwise, including hydrogels with programmable lifetimes, vesicular nanoreactors, and membranes exhibiting transient conductivity.","lang":"eng"}],"date_updated":"2023-08-07T10:56:26Z","_id":"13375","title":"Dissipative self-assembly driven by the consumption of chemical fuels","article_processing_charge":"No","publication_identifier":{"issn":["0935-9648"],"eissn":["1521-4095"]},"year":"2018","date_created":"2023-08-01T09:39:46Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":30,"doi":"10.1002/adma.201706750","pmid":1,"author":[{"full_name":"De, Soumen","first_name":"Soumen","last_name":"De"},{"full_name":"Klajn, Rafal","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn"}],"status":"public","extern":"1","oa_version":"None","date_published":"2018-10-11T00:00:00Z","day":"11","external_id":{"pmid":["29520846"]}},{"article_processing_charge":"No","title":"Reversible photoswitching of encapsulated azobenzenes in water","_id":"13376","date_updated":"2023-08-07T10:58:11Z","year":"2018","oa":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"oa_version":"Published Version","extern":"1","status":"public","author":[{"full_name":"Samanta, Dipak","first_name":"Dipak","last_name":"Samanta"},{"last_name":"Gemen","full_name":"Gemen, Julius","first_name":"Julius"},{"first_name":"Zonglin","full_name":"Chu, Zonglin","last_name":"Chu"},{"full_name":"Diskin-Posner, Yael","first_name":"Yael","last_name":"Diskin-Posner"},{"first_name":"Linda J. W.","full_name":"Shimon, Linda J. W.","last_name":"Shimon"},{"first_name":"Rafal","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn"}],"doi":"10.1073/pnas.1712787115","pmid":1,"volume":115,"date_created":"2023-08-01T09:40:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["29717041"]},"day":"01","date_published":"2018-05-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1712787115"}],"type":"journal_article","intvolume":" 115","month":"05","page":"9379-9384","issue":"38","keyword":["Multidisciplinary"],"citation":{"chicago":"Samanta, Dipak, Julius Gemen, Zonglin Chu, Yael Diskin-Posner, Linda J. W. Shimon, and Rafal Klajn. “Reversible Photoswitching of Encapsulated Azobenzenes in Water.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1712787115.","apa":"Samanta, D., Gemen, J., Chu, Z., Diskin-Posner, Y., Shimon, L. J. W., & Klajn, R. (2018). Reversible photoswitching of encapsulated azobenzenes in water. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1712787115","ama":"Samanta D, Gemen J, Chu Z, Diskin-Posner Y, Shimon LJW, Klajn R. Reversible photoswitching of encapsulated azobenzenes in water. Proceedings of the National Academy of Sciences. 2018;115(38):9379-9384. doi:10.1073/pnas.1712787115","short":"D. Samanta, J. Gemen, Z. Chu, Y. Diskin-Posner, L.J.W. Shimon, R. Klajn, Proceedings of the National Academy of Sciences 115 (2018) 9379–9384.","mla":"Samanta, Dipak, et al. “Reversible Photoswitching of Encapsulated Azobenzenes in Water.” Proceedings of the National Academy of Sciences, vol. 115, no. 38, Proceedings of the National Academy of Sciences, 2018, pp. 9379–84, doi:10.1073/pnas.1712787115.","ista":"Samanta D, Gemen J, Chu Z, Diskin-Posner Y, Shimon LJW, Klajn R. 2018. Reversible photoswitching of encapsulated azobenzenes in water. Proceedings of the National Academy of Sciences. 115(38), 9379–9384.","ieee":"D. Samanta, J. Gemen, Z. Chu, Y. Diskin-Posner, L. J. W. Shimon, and R. Klajn, “Reversible photoswitching of encapsulated azobenzenes in water,” Proceedings of the National Academy of Sciences, vol. 115, no. 38. Proceedings of the National Academy of Sciences, pp. 9379–9384, 2018."},"quality_controlled":"1","article_type":"original","publication_status":"published","abstract":[{"text":"Efficient molecular switching in confined spaces is critical for the successful development of artificial molecular machines. However, molecular switching events often entail large structural changes and therefore require conformational freedom, which is typically limited under confinement conditions. Here, we investigated the behavior of azobenzene—the key building block of light-controlled molecular machines—in a confined environment that is flexible and can adapt its shape to that of the bound guest. To this end, we encapsulated several structurally diverse azobenzenes within the cavity of a flexible, water-soluble coordination cage, and investigated their light-responsive behavior. Using UV/Vis absorption spectroscopy and a combination of NMR methods, we showed that each of the encapsulated azobenzenes exhibited distinct switching properties. An azobenzene forming a 1:1 host–guest inclusion complex could be efficiently photoisomerized in a reversible fashion. In contrast, successful switching in inclusion complexes incorporating two azobenzene guests was dependent on the availability of free cages in the system, and it involved reversible trafficking of azobenzene between the cages. In the absence of extra cages, photoswitching was either suppressed or it involved expulsion of azobenzene from the cage and consequently its precipitation from the solution. This finding was utilized to develop an information storage medium in which messages could be written and erased in a reversible fashion using light.","lang":"eng"}],"language":[{"iso":"eng"}],"publisher":"Proceedings of the National Academy of Sciences","scopus_import":"1","publication":"Proceedings of the National Academy of Sciences"},{"oa":1,"publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"year":"2018","_id":"13377","date_updated":"2023-08-07T11:14:28Z","title":"“Precipitation on nanoparticles”: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles","article_processing_charge":"No","day":"11","date_published":"2018-06-11T00:00:00Z","external_id":{"pmid":["29673022"]},"doi":"10.1002/anie.201800673","pmid":1,"volume":57,"date_created":"2023-08-01T09:40:16Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","extern":"1","status":"public","author":[{"first_name":"Zonglin","full_name":"Chu, Zonglin","last_name":"Chu"},{"full_name":"Han, Yanxiao","first_name":"Yanxiao","last_name":"Han"},{"last_name":"Král","full_name":"Král, Petr","first_name":"Petr"},{"full_name":"Klajn, Rafal","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn"}],"page":"7023-7027","issue":"24","intvolume":" 57","month":"06","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1002/anie.201800673","open_access":"1"}],"publisher":"Wiley","scopus_import":"1","publication":"Angewandte Chemie International Edition","abstract":[{"lang":"eng","text":"Confining organic molecules to the surfaces of inorganic nanoparticles can induce intermolecular interactions between them, which can affect the composition of the mixed self-assembled monolayers obtained by co-adsorption from solution of two different molecules. Two thiolated ligands (a dialkylviologen and a zwitterionic sulfobetaine) that can interact with each other electrostatically were coadsorbed onto gold nanoparticles. The nanoparticles favor a narrow range of ratios of these two molecules that is largely independent of the molar ratio in solution. Changing the solution molar ratio of the two ligands by a factor of 5 000 affects the on-nanoparticle ratio of these ligands by only threefold. This behavior is reminiscent of the formation of insoluble inorganic salts (such as AgCl), which similarly compensate positive and negative charges upon crystallizing. Our results pave the way towards developing well-defined hybrid organic–inorganic nanostructures."}],"language":[{"iso":"eng"}],"article_type":"original","publication_status":"published","keyword":["General Chemistry","Catalysis"],"citation":{"short":"Z. Chu, Y. Han, P. Král, R. Klajn, Angewandte Chemie International Edition 57 (2018) 7023–7027.","mla":"Chu, Zonglin, et al. “‘Precipitation on Nanoparticles’: Attractive Intermolecular Interactions Stabilize Specific Ligand Ratios on the Surfaces of Nanoparticles.” Angewandte Chemie International Edition, vol. 57, no. 24, Wiley, 2018, pp. 7023–27, doi:10.1002/anie.201800673.","ieee":"Z. Chu, Y. Han, P. Král, and R. Klajn, “‘Precipitation on nanoparticles’: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles,” Angewandte Chemie International Edition, vol. 57, no. 24. Wiley, pp. 7023–7027, 2018.","ista":"Chu Z, Han Y, Král P, Klajn R. 2018. “Precipitation on nanoparticles”: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles. Angewandte Chemie International Edition. 57(24), 7023–7027.","chicago":"Chu, Zonglin, Yanxiao Han, Petr Král, and Rafal Klajn. “‘Precipitation on Nanoparticles’: Attractive Intermolecular Interactions Stabilize Specific Ligand Ratios on the Surfaces of Nanoparticles.” Angewandte Chemie International Edition. Wiley, 2018. https://doi.org/10.1002/anie.201800673.","apa":"Chu, Z., Han, Y., Král, P., & Klajn, R. (2018). “Precipitation on nanoparticles”: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201800673","ama":"Chu Z, Han Y, Král P, Klajn R. “Precipitation on nanoparticles”: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles. Angewandte Chemie International Edition. 2018;57(24):7023-7027. doi:10.1002/anie.201800673"},"quality_controlled":"1"},{"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/marc.201700827"}],"issue":"1","month":"01","intvolume":" 39","article_number":"1700827","publication_status":"published","article_type":"letter_note","quality_controlled":"1","keyword":["Materials Chemistry","Polymers and Plastics","Organic Chemistry"],"citation":{"short":"D. Bléger, R. Klajn, Macromolecular Rapid Communications 39 (2018).","mla":"Bléger, David, and Rafal Klajn. “Integrating Macromolecules with Molecular Switches.” Macromolecular Rapid Communications, vol. 39, no. 1, 1700827, Wiley, 2018, doi:10.1002/marc.201700827.","ista":"Bléger D, Klajn R. 2018. Integrating macromolecules with molecular switches. Macromolecular Rapid Communications. 39(1), 1700827.","ieee":"D. Bléger and R. Klajn, “Integrating macromolecules with molecular switches,” Macromolecular Rapid Communications, vol. 39, no. 1. Wiley, 2018.","chicago":"Bléger, David, and Rafal Klajn. “Integrating Macromolecules with Molecular Switches.” Macromolecular Rapid Communications. Wiley, 2018. https://doi.org/10.1002/marc.201700827.","apa":"Bléger, D., & Klajn, R. (2018). Integrating macromolecules with molecular switches. Macromolecular Rapid Communications. Wiley. https://doi.org/10.1002/marc.201700827","ama":"Bléger D, Klajn R. Integrating macromolecules with molecular switches. Macromolecular Rapid Communications. 2018;39(1). doi:10.1002/marc.201700827"},"scopus_import":"1","publication":"Macromolecular Rapid Communications","publisher":"Wiley","language":[{"iso":"eng"}],"date_updated":"2023-08-07T11:16:49Z","_id":"13379","title":"Integrating macromolecules with molecular switches","article_processing_charge":"No","publication_identifier":{"eissn":["1521-3927"],"issn":["1022-1336"]},"oa":1,"year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-01T09:40:48Z","volume":39,"doi":"10.1002/marc.201700827","pmid":1,"status":"public","author":[{"last_name":"Bléger","full_name":"Bléger, David","first_name":"David"},{"first_name":"Rafal","full_name":"Klajn, Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"extern":"1","oa_version":"Published Version","date_published":"2018-01-08T00:00:00Z","day":"08","external_id":{"pmid":["29314396"]}},{"ddc":["000"],"type":"journal_article","intvolume":" 37","article_number":"94","month":"07","isi":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"ec_funded":1,"issue":"4","alternative_title":["SIGGRAPH"],"quality_controlled":"1","citation":{"apa":"Jeschke, S., Skrivan, T., Mueller Fischer, M., Chentanez, N., Macklin, M., & Wojtan, C. (2018). Water surface wavelets. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3197517.3201336","chicago":"Jeschke, Stefan, Tomas Skrivan, Matthias Mueller Fischer, Nuttapong Chentanez, Miles Macklin, and Chris Wojtan. “Water Surface Wavelets.” ACM Transactions on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201336.","ama":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. Water surface wavelets. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201336","short":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, C. Wojtan, ACM Transactions on Graphics 37 (2018).","mla":"Jeschke, Stefan, et al. “Water Surface Wavelets.” ACM Transactions on Graphics, vol. 37, no. 4, 94, ACM, 2018, doi:10.1145/3197517.3201336.","ieee":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, and C. Wojtan, “Water surface wavelets,” ACM Transactions on Graphics, vol. 37, no. 4. ACM, 2018.","ista":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. 2018. Water surface wavelets. ACM Transactions on Graphics. 37(4), 94."},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","publication_status":"published","abstract":[{"lang":"eng","text":"The current state of the art in real-time two-dimensional water wave simulation requires developers to choose between efficient Fourier-based methods, which lack interactions with moving obstacles, and finite-difference or finite element methods, which handle environmental interactions but are significantly more expensive. This paper attempts to bridge this long-standing gap between complexity and performance, by proposing a new wave simulation method that can faithfully simulate wave interactions with moving obstacles in real time while simultaneously preserving minute details and accommodating very large simulation domains.\r\n\r\nPrevious methods for simulating 2D water waves directly compute the change in height of the water surface, a strategy which imposes limitations based on the CFL condition (fast moving waves require small time steps) and Nyquist's limit (small wave details require closely-spaced simulation variables). This paper proposes a novel wavelet transformation that discretizes the liquid motion in terms of amplitude-like functions that vary over space, frequency, and direction, effectively generalizing Fourier-based methods to handle local interactions. Because these new variables change much more slowly over space than the original water height function, our change of variables drastically reduces the limitations of the CFL condition and Nyquist limit, allowing us to simulate highly detailed water waves at very large visual resolutions. Our discretization is amenable to fast summation and easy to parallelize. We also present basic extensions like pre-computed wave paths and two-way solid fluid coupling. Finally, we argue that our discretization provides a convenient set of variables for artistic manipulation, which we illustrate with a novel wave-painting interface."}],"publist_id":"7789","language":[{"iso":"eng"}],"department":[{"_id":"ChWo"}],"publisher":"ACM","scopus_import":"1","publication":"ACM Transactions on Graphics","file_date_updated":"2020-07-14T12:44:45Z","file":[{"file_id":"5744","checksum":"db75ebabe2ec432bf41389e614d6ef62","content_type":"application/pdf","creator":"dernst","access_level":"open_access","date_created":"2018-12-18T09:59:23Z","file_size":22185016,"file_name":"2018_ACM_Jeschke.pdf","date_updated":"2020-07-14T12:44:45Z","relation":"main_file"}],"article_processing_charge":"No","title":"Water surface wavelets","date_updated":"2024-02-28T13:58:51Z","_id":"134","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-water-simulation-captures-small-details-even-in-large-scenes/"}]},"project":[{"grant_number":"638176","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425"},{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"year":"2018","has_accepted_license":"1","oa":1,"oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"author":[{"id":"44D6411A-F248-11E8-B48F-1D18A9856A87","last_name":"Jeschke","first_name":"Stefan","full_name":"Jeschke, Stefan"},{"full_name":"Skrivan, Tomas","first_name":"Tomas","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","last_name":"Skrivan"},{"last_name":"Mueller Fischer","full_name":"Mueller Fischer, Matthias","first_name":"Matthias"},{"first_name":"Nuttapong","full_name":"Chentanez, Nuttapong","last_name":"Chentanez"},{"last_name":"Macklin","first_name":"Miles","full_name":"Macklin, Miles"},{"last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","first_name":"Christopher J"}],"status":"public","doi":"10.1145/3197517.3201336","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:44:48Z","volume":37,"external_id":{"isi":["000448185000055"]},"day":"30","date_published":"2018-07-30T00:00:00Z"},{"intvolume":" 615","article_number":"A30","month":"07","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1051/0004-6361/201731194"}],"arxiv":1,"publisher":"EDP Sciences","scopus_import":"1","publication":"Astronomy & Astrophysics","abstract":[{"lang":"eng","text":"Stripped-envelope stars form in binary systems after losing mass through Roche-lobe overflow. They bear astrophysical significance as sources of UV and ionizing radiation in older stellar populations and, if sufficiently massive, as stripped supernova progenitors. Binary evolutionary models predict that they are common, but only a handful of subdwarfs with B-type companions are known. The question is whether a large population of such systems has evaded detection as a result of biases, or whether the model predictions are wrong. We reanalyze the well-studied post-interaction binary φ Persei. Recently, new data have improved the orbital solution of the system, which contains an ~1.2M⊙ stripped-envelope star and a rapidly rotating ~9.6M⊙ Be star. We compare with an extensive grid of evolutionary models using a Bayesian approach and constrain the initial masses of the progenitor to 7.2 ± 0.4M⊙ for the stripped star and 3.8 ± 0.4M⊙ for the Be star. The system must have evolved through near-conservative mass transfer. These findings are consistent with earlier studies. The age we obtain, 57 ± 9 Myr, is in excellent agreement with the age of the α Persei cluster. We note that neither star was initially massive enough to produce a core-collapse supernova, but mass exchange pushed the Be star above the mass threshold. We find that the subdwarf is overluminous for its mass by almost an order of magnitude, compared to the expectations for a helium core burning star. We can only reconcile this if the subdwarf resides in a late phase of helium shell burning, which lasts only 2–3% of the total lifetime as a subdwarf. Assuming continuous star formation implies that up to ~50 less evolved, dimmer subdwarfs exist for each system similar to φ Persei, but have evaded detection so far. Our findings can be interpreted as a strong indication that a substantial population of stripped-envelope stars indeed exists, but has so far evaded detection because of observational biases and lack of large-scale systematic searches."}],"language":[{"iso":"eng"}],"article_type":"original","publication_status":"published","quality_controlled":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"citation":{"ama":"Schootemeijer A, Götberg YLL, de Mink SE, Gies D, Zapartas E. Clues about the scarcity of stripped-envelope stars from the evolutionary state of the sdO+Be binary system φ Persei. Astronomy & Astrophysics. 2018;615. doi:10.1051/0004-6361/201731194","chicago":"Schootemeijer, A., Ylva Louise Linsdotter Götberg, S. E. de Mink, D. Gies, and E. Zapartas. “Clues about the Scarcity of Stripped-Envelope Stars from the Evolutionary State of the SdO+Be Binary System φ Persei.” Astronomy & Astrophysics. EDP Sciences, 2018. https://doi.org/10.1051/0004-6361/201731194.","apa":"Schootemeijer, A., Götberg, Y. L. L., de Mink, S. E., Gies, D., & Zapartas, E. (2018). Clues about the scarcity of stripped-envelope stars from the evolutionary state of the sdO+Be binary system φ Persei. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201731194","ista":"Schootemeijer A, Götberg YLL, de Mink SE, Gies D, Zapartas E. 2018. Clues about the scarcity of stripped-envelope stars from the evolutionary state of the sdO+Be binary system φ Persei. Astronomy & Astrophysics. 615, A30.","ieee":"A. Schootemeijer, Y. L. L. Götberg, S. E. de Mink, D. Gies, and E. Zapartas, “Clues about the scarcity of stripped-envelope stars from the evolutionary state of the sdO+Be binary system φ Persei,” Astronomy & Astrophysics, vol. 615. EDP Sciences, 2018.","mla":"Schootemeijer, A., et al. “Clues about the Scarcity of Stripped-Envelope Stars from the Evolutionary State of the SdO+Be Binary System φ Persei.” Astronomy & Astrophysics, vol. 615, A30, EDP Sciences, 2018, doi:10.1051/0004-6361/201731194.","short":"A. Schootemeijer, Y.L.L. Götberg, S.E. de Mink, D. Gies, E. Zapartas, Astronomy & Astrophysics 615 (2018)."},"oa":1,"publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"year":"2018","date_updated":"2023-08-09T12:22:52Z","_id":"13473","article_processing_charge":"No","title":"Clues about the scarcity of stripped-envelope stars from the evolutionary state of the sdO+Be binary system φ Persei","day":"06","date_published":"2018-07-06T00:00:00Z","external_id":{"arxiv":["1803.02379"]},"doi":"10.1051/0004-6361/201731194","date_created":"2023-08-03T10:14:37Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":615,"oa_version":"Published Version","author":[{"full_name":"Schootemeijer, A.","first_name":"A.","last_name":"Schootemeijer"},{"orcid":"0000-0002-6960-6911","first_name":"Ylva Louise Linsdotter","full_name":"Götberg, Ylva Louise Linsdotter","last_name":"Götberg","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d"},{"first_name":"S. E.","full_name":"de Mink, S. E.","last_name":"de Mink"},{"last_name":"Gies","first_name":"D.","full_name":"Gies, D."},{"last_name":"Zapartas","full_name":"Zapartas, E.","first_name":"E."}],"status":"public","extern":"1"},{"publisher":"Oxford University Press","scopus_import":"1","publication":"Monthly Notices of the Royal Astronomical Society","abstract":[{"lang":"eng","text":"Recent surveys of the Magellanic Clouds have revealed a subtype of Wolf–Rayet (WR) star with peculiar properties. WN3/O3 spectra exhibit both WR-like emission and O3 V-like absorption – but at lower luminosity than O3 V or WN stars. We examine the projected spatial distribution of WN3/O3 stars in the Large Magellanic Cloud as compared to O-type stars. Surprisingly, WN3/O3 stars are among the most isolated of all classes of massive stars; they have a distribution similar to red supergiants dominated by initial masses of 10–15 M⊙, and are far more dispersed than classical WR stars or luminous blue variables. Their lack of association with clusters of O-type stars suggests strongly that WN3/O3 stars are not the descendants of single massive stars (30 M⊙ or above). Instead, they are likely products of interacting binaries at lower initial mass (10–18 M⊙). Comparison with binary models suggests a probable origin with primaries in this mass range that were stripped of their H envelopes through non-conservative mass transfer by a low-mass secondary. We show that model spectra and positions on the Hertzsprung–Russell diagram for binary-stripped stars are consistent with WN3/O3 stars. Monitoring radial velocities with high-resolution spectra can test for low-mass companions or runaway velocities. With lower initial mass and environments that avoid very massive stars, the WN3/O3 stars fit expectations for progenitors of Type Ib and possibly Type Ibn supernovae."}],"language":[{"iso":"eng"}],"article_type":"original","publication_status":"published","quality_controlled":"1","citation":{"chicago":"Smith, Nathan, Ylva Louise Linsdotter Götberg, and Selma E de Mink. “Extreme Isolation of WN3/O3 Stars and Implications for Their Evolutionary Origin as the Elusive Stripped Binaries.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/stx3181.","apa":"Smith, N., Götberg, Y. L. L., & de Mink, S. E. (2018). Extreme isolation of WN3/O3 stars and implications for their evolutionary origin as the elusive stripped binaries. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stx3181","ama":"Smith N, Götberg YLL, de Mink SE. Extreme isolation of WN3/O3 stars and implications for their evolutionary origin as the elusive stripped binaries. Monthly Notices of the Royal Astronomical Society. 2018;475(1):772-782. doi:10.1093/mnras/stx3181","short":"N. Smith, Y.L.L. Götberg, S.E. de Mink, Monthly Notices of the Royal Astronomical Society 475 (2018) 772–782.","mla":"Smith, Nathan, et al. “Extreme Isolation of WN3/O3 Stars and Implications for Their Evolutionary Origin as the Elusive Stripped Binaries.” Monthly Notices of the Royal Astronomical Society, vol. 475, no. 1, Oxford University Press, 2018, pp. 772–82, doi:10.1093/mnras/stx3181.","ista":"Smith N, Götberg YLL, de Mink SE. 2018. Extreme isolation of WN3/O3 stars and implications for their evolutionary origin as the elusive stripped binaries. Monthly Notices of the Royal Astronomical Society. 475(1), 772–782.","ieee":"N. Smith, Y. L. L. Götberg, and S. E. de Mink, “Extreme isolation of WN3/O3 stars and implications for their evolutionary origin as the elusive stripped binaries,” Monthly Notices of the Royal Astronomical Society, vol. 475, no. 1. Oxford University Press, pp. 772–782, 2018."},"keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"page":"772-782","issue":"1","intvolume":" 475","month":"03","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1093/mnras/stx3181","open_access":"1"}],"arxiv":1,"day":"01","date_published":"2018-03-01T00:00:00Z","external_id":{"arxiv":["1704.03516"]},"doi":"10.1093/mnras/stx3181","date_created":"2023-08-03T10:14:47Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":475,"oa_version":"Published Version","status":"public","author":[{"last_name":"Smith","first_name":"Nathan","full_name":"Smith, Nathan"},{"last_name":"Götberg","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","orcid":"0000-0002-6960-6911","full_name":"Götberg, Ylva Louise Linsdotter","first_name":"Ylva Louise Linsdotter"},{"last_name":"de Mink","first_name":"Selma E","full_name":"de Mink, Selma E"}],"extern":"1","oa":1,"publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"year":"2018","date_updated":"2023-08-09T12:17:34Z","_id":"13474","title":"Extreme isolation of WN3/O3 stars and implications for their evolutionary origin as the elusive stripped binaries","article_processing_charge":"No"},{"external_id":{"arxiv":["1802.03018"]},"day":"17","date_published":"2018-07-17T00:00:00Z","oa_version":"Published Version","extern":"1","status":"public","author":[{"id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","last_name":"Götberg","full_name":"Götberg, Ylva Louise Linsdotter","first_name":"Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911"},{"last_name":"de Mink","first_name":"S. E.","full_name":"de Mink, S. E."},{"full_name":"Groh, J. H.","first_name":"J. H.","last_name":"Groh"},{"first_name":"T.","full_name":"Kupfer, T.","last_name":"Kupfer"},{"first_name":"P. A.","full_name":"Crowther, P. A.","last_name":"Crowther"},{"last_name":"Zapartas","full_name":"Zapartas, E.","first_name":"E."},{"full_name":"Renzo, M.","first_name":"M.","last_name":"Renzo"}],"doi":"10.1051/0004-6361/201732274","volume":615,"date_created":"2023-08-03T10:15:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","oa":1,"publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"title":"Spectral models for binary products: Unifying subdwarfs and Wolf-Rayet stars as a sequence of stripped-envelope stars","article_processing_charge":"No","_id":"13475","date_updated":"2023-08-09T11:22:17Z","abstract":[{"text":"Stars stripped of their hydrogen-rich envelope through interaction with a binary companion are generally not considered when accounting for ionizing radiation from stellar populations, despite the expectation that stripped stars emit hard ionizing radiation, form frequently, and live 10–100 times longer than single massive stars. We compute the first grid of evolutionary and spectral models specially made for stars stripped in binaries for a range of progenitor masses (2–20 M⊙) and metallicities ranging from solar to values representative for pop II stars. For stripped stars with masses in the range 0.3–7 M⊙, we find consistently high effective temperatures (20 000–100 000 K, increasing with mass), small radii (0.2–1 R⊙), and high bolometric luminosities, comparable to that of their progenitor before stripping. The spectra show a continuous sequence that naturally bridges subdwarf-type stars at the low-mass end and Wolf-Rayet-like spectra at the high-mass end. For intermediate masses we find hybrid spectral classes showing a mixture of absorption and emission lines. These appear for stars with mass-loss rates of 10−8−10−6 M⊙ yr−1, which have semi-transparent atmospheres. At low metallicity, substantial hydrogen-rich layers are left at the surface and we predict spectra that resemble O-type stars instead. We obtain spectra undistinguishable from subdwarfs for stripped stars with masses up to 1.7 M⊙, which questions whether the widely adopted canonical value of 0.47 M⊙ is uniformly valid. Only a handful of stripped stars of intermediate mass have currently been identified observationally. Increasing this sample will provide necessary tests for the physics of interaction, internal mixing, and stellar winds. We use our model spectra to investigate the feasibility to detect stripped stars next to an optically bright companion and recommend systematic searches for their UV excess and possible emission lines, most notably HeII λ4686 in the optical and HeII λ1640 in the UV. Our models are publicly available for further investigations or inclusion in spectral synthesis simulations.","lang":"eng"}],"language":[{"iso":"eng"}],"publisher":"EDP Sciences","publication":"Astronomy & Astrophysics","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"citation":{"chicago":"Götberg, Ylva Louise Linsdotter, S. E. de Mink, J. H. Groh, T. Kupfer, P. A. Crowther, E. Zapartas, and M. Renzo. “Spectral Models for Binary Products: Unifying Subdwarfs and Wolf-Rayet Stars as a Sequence of Stripped-Envelope Stars.” Astronomy & Astrophysics. EDP Sciences, 2018. https://doi.org/10.1051/0004-6361/201732274.","apa":"Götberg, Y. L. L., de Mink, S. E., Groh, J. H., Kupfer, T., Crowther, P. A., Zapartas, E., & Renzo, M. (2018). Spectral models for binary products: Unifying subdwarfs and Wolf-Rayet stars as a sequence of stripped-envelope stars. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201732274","ama":"Götberg YLL, de Mink SE, Groh JH, et al. Spectral models for binary products: Unifying subdwarfs and Wolf-Rayet stars as a sequence of stripped-envelope stars. Astronomy & Astrophysics. 2018;615. doi:10.1051/0004-6361/201732274","mla":"Götberg, Ylva Louise Linsdotter, et al. “Spectral Models for Binary Products: Unifying Subdwarfs and Wolf-Rayet Stars as a Sequence of Stripped-Envelope Stars.” Astronomy & Astrophysics, vol. 615, A78, EDP Sciences, 2018, doi:10.1051/0004-6361/201732274.","short":"Y.L.L. Götberg, S.E. de Mink, J.H. Groh, T. Kupfer, P.A. Crowther, E. Zapartas, M. Renzo, Astronomy & Astrophysics 615 (2018).","ieee":"Y. L. L. Götberg et al., “Spectral models for binary products: Unifying subdwarfs and Wolf-Rayet stars as a sequence of stripped-envelope stars,” Astronomy & Astrophysics, vol. 615. EDP Sciences, 2018.","ista":"Götberg YLL, de Mink SE, Groh JH, Kupfer T, Crowther PA, Zapartas E, Renzo M. 2018. Spectral models for binary products: Unifying subdwarfs and Wolf-Rayet stars as a sequence of stripped-envelope stars. Astronomy & Astrophysics. 615, A78."},"quality_controlled":"1","article_type":"original","publication_status":"published","article_number":"A78","intvolume":" 615","month":"07","arxiv":1,"main_file_link":[{"url":"https://doi.org/10.1051/0004-6361/201732274","open_access":"1"}],"type":"journal_article"},{"citation":{"apa":"Sato, T., Wojtan, C., Thuerey, N., Igarashi, T., & Ando, R. (2018). Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13351","chicago":"Sato, Takahiro, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi Ando. “Extended Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum. Wiley, 2018. https://doi.org/10.1111/cgf.13351.","ama":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. 2018;37(2):169-177. doi:10.1111/cgf.13351","mla":"Sato, Takahiro, et al. “Extended Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum, vol. 37, no. 2, Wiley, 2018, pp. 169–77, doi:10.1111/cgf.13351.","short":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, Computer Graphics Forum 37 (2018) 169–177.","ista":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. 2018. Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. 37(2), 169–177.","ieee":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Extended narrow band FLIP for liquid simulations,” Computer Graphics Forum, vol. 37, no. 2. Wiley, pp. 169–177, 2018."},"alternative_title":["Eurographics"],"quality_controlled":"1","publication_status":"published","article_type":"original","department":[{"_id":"ChWo"}],"language":[{"iso":"eng"}],"abstract":[{"text":"The Fluid Implicit Particle method (FLIP) reduces numerical dissipation by combining particles with grids. To improve performance, the subsequent narrow band FLIP method (NB‐FLIP) uses a FLIP‐based fluid simulation only near the liquid surface and a traditional grid‐based fluid simulation away from the surface. This spatially‐limited FLIP simulation significantly reduces the number of particles and alleviates a computational bottleneck. In this paper, we extend the NB‐FLIP idea even further, by allowing a simulation to transition between a FLIP‐like fluid simulation and a grid‐based simulation in arbitrary locations, not just near the surface. This approach leads to even more savings in memory and computation, because we can concentrate the particles only in areas where they are needed. More importantly, this new method allows us to seamlessly transition to smooth implicit surface geometry wherever the particle‐based simulation is unnecessary. Consequently, our method leads to a practical algorithm for avoiding the noisy surface artifacts associated with particle‐based liquid simulations, while simultaneously maintaining the benefits of a FLIP simulation in regions of dynamic motion.","lang":"eng"}],"publication":"Computer Graphics Forum","file_date_updated":"2020-10-08T08:38:23Z","file":[{"file_id":"8627","checksum":"8edb90da8a72395eb5d970580e0925b6","content_type":"application/pdf","access_level":"open_access","creator":"wojtan","date_created":"2020-10-08T08:38:23Z","success":1,"file_size":54309947,"date_updated":"2020-10-08T08:38:23Z","file_name":"exnbflip.pdf","relation":"main_file"}],"scopus_import":"1","publisher":"Wiley","type":"journal_article","ddc":["006"],"month":"05","isi":1,"intvolume":" 37","issue":"2","ec_funded":1,"page":"169 - 177","status":"public","author":[{"first_name":"Takahiro","full_name":"Sato, Takahiro","last_name":"Sato"},{"first_name":"Christopher J","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan"},{"full_name":"Thuerey, Nils","first_name":"Nils","last_name":"Thuerey"},{"full_name":"Igarashi, Takeo","first_name":"Takeo","last_name":"Igarashi"},{"last_name":"Ando","first_name":"Ryoichi","full_name":"Ando, Ryoichi"}],"oa_version":"Submitted Version","volume":37,"date_created":"2018-12-11T11:44:49Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1111/cgf.13351","external_id":{"isi":["000434085600016"]},"date_published":"2018-05-22T00:00:00Z","day":"22","article_processing_charge":"No","title":"Extended narrow band FLIP for liquid simulations","_id":"135","date_updated":"2023-09-11T14:00:26Z","has_accepted_license":"1","year":"2018","project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","call_identifier":"H2020"}],"publication_identifier":{"issn":["0167-7055"]},"oa":1},{"year":"2018","oa":1,"article_processing_charge":"No","title":"Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow","date_updated":"2023-10-10T13:29:10Z","_id":"136","external_id":{"isi":["000441466800010"],"arxiv":["1808.02088"]},"date_published":"2018-08-13T00:00:00Z","day":"13","author":[{"full_name":"Suri, Balachandra","first_name":"Balachandra","last_name":"Suri","id":"47A5E706-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jeffrey","full_name":"Tithof, Jeffrey","last_name":"Tithof"},{"last_name":"Grigoriev","full_name":"Grigoriev, Roman","first_name":"Roman"},{"last_name":"Schatz","first_name":"Michael","full_name":"Schatz, Michael"}],"status":"public","oa_version":"Submitted Version","date_created":"2018-12-11T11:44:49Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":98,"doi":"10.1103/PhysRevE.98.023105","month":"08","isi":1,"intvolume":" 98","issue":"2","main_file_link":[{"url":"https://arxiv.org/abs/1808.02088","open_access":"1"}],"arxiv":1,"type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"BjHo"}],"abstract":[{"lang":"eng","text":"Recent studies suggest that unstable, nonchaotic solutions of the Navier-Stokes equation may provide deep insights into fluid turbulence. In this article, we present a combined experimental and numerical study exploring the dynamical role of unstable equilibrium solutions and their invariant manifolds in a weakly turbulent, electromagnetically driven, shallow fluid layer. Identifying instants when turbulent evolution slows down, we compute 31 unstable equilibria of a realistic two-dimensional model of the flow. We establish the dynamical relevance of these unstable equilibria by showing that they are closely visited by the turbulent flow. We also establish the dynamical relevance of unstable manifolds by verifying that they are shadowed by turbulent trajectories departing from the neighborhoods of unstable equilibria over large distances in state space."}],"publication":"Physical Review E","scopus_import":"1","publisher":"American Physical Society","quality_controlled":"1","citation":{"ieee":"B. Suri, J. Tithof, R. Grigoriev, and M. Schatz, “Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow,” Physical Review E, vol. 98, no. 2. American Physical Society, 2018.","ista":"Suri B, Tithof J, Grigoriev R, Schatz M. 2018. Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. 98(2).","mla":"Suri, Balachandra, et al. “Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like Flow.” Physical Review E, vol. 98, no. 2, American Physical Society, 2018, doi:10.1103/PhysRevE.98.023105.","short":"B. Suri, J. Tithof, R. Grigoriev, M. Schatz, Physical Review E 98 (2018).","ama":"Suri B, Tithof J, Grigoriev R, Schatz M. Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. 2018;98(2). doi:10.1103/PhysRevE.98.023105","chicago":"Suri, Balachandra, Jeffrey Tithof, Roman Grigoriev, and Michael Schatz. “Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like Flow.” Physical Review E. American Physical Society, 2018. https://doi.org/10.1103/PhysRevE.98.023105.","apa":"Suri, B., Tithof, J., Grigoriev, R., & Schatz, M. (2018). Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.98.023105"},"publication_status":"published"},{"date_updated":"2023-09-13T08:58:05Z","_id":"137","article_processing_charge":"No","title":"Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS","oa":1,"project":[{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","grant_number":"RGY0084/2012"}],"year":"2018","pmid":1,"doi":"10.1038/s41589-018-0108-2","date_created":"2018-12-11T11:44:49Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":14,"oa_version":"Submitted Version","author":[{"last_name":"Zhang","full_name":"Zhang, William","first_name":"William"},{"first_name":"Michel","full_name":"Herde, Michel","last_name":"Herde"},{"first_name":"Joshua","full_name":"Mitchell, Joshua","last_name":"Mitchell"},{"first_name":"Jason","full_name":"Whitfield, Jason","last_name":"Whitfield"},{"last_name":"Wulff","full_name":"Wulff, Andreas","first_name":"Andreas"},{"last_name":"Vongsouthi","first_name":"Vanessa","full_name":"Vongsouthi, Vanessa"},{"first_name":"Inmaculada","full_name":"Sanchez Romero, Inmaculada","last_name":"Sanchez Romero","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Polina","full_name":"Gulakova, Polina","last_name":"Gulakova"},{"full_name":"Minge, Daniel","first_name":"Daniel","last_name":"Minge"},{"last_name":"Breithausen","first_name":"Björn","full_name":"Breithausen, Björn"},{"last_name":"Schoch","full_name":"Schoch, Susanne","first_name":"Susanne"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315"},{"first_name":"Colin","full_name":"Jackson, Colin","last_name":"Jackson"},{"last_name":"Henneberger","first_name":"Christian","full_name":"Henneberger, Christian"}],"status":"public","day":"30","date_published":"2018-07-30T00:00:00Z","external_id":{"pmid":["30061718 "],"isi":["000442174500013"]},"type":"journal_article","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30061718","open_access":"1"}],"page":"861 - 869","issue":"9","intvolume":" 14","month":"07","isi":1,"article_type":"original","publication_status":"published","quality_controlled":"1","citation":{"short":"W. Zhang, M. Herde, J. Mitchell, J. Whitfield, A. Wulff, V. Vongsouthi, I. Sanchez-Romero, P. Gulakova, D. Minge, B. Breithausen, S. Schoch, H.L. Janovjak, C. Jackson, C. Henneberger, Nature Chemical Biology 14 (2018) 861–869.","mla":"Zhang, William, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical Biology, vol. 14, no. 9, Nature Publishing Group, 2018, pp. 861–69, doi:10.1038/s41589-018-0108-2.","ista":"Zhang W, Herde M, Mitchell J, Whitfield J, Wulff A, Vongsouthi V, Sanchez-Romero I, Gulakova P, Minge D, Breithausen B, Schoch S, Janovjak HL, Jackson C, Henneberger C. 2018. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. 14(9), 861–869.","ieee":"W. Zhang et al., “Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS,” Nature Chemical Biology, vol. 14, no. 9. Nature Publishing Group, pp. 861–869, 2018.","apa":"Zhang, W., Herde, M., Mitchell, J., Whitfield, J., Wulff, A., Vongsouthi, V., … Henneberger, C. (2018). Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0108-2","chicago":"Zhang, William, Michel Herde, Joshua Mitchell, Jason Whitfield, Andreas Wulff, Vanessa Vongsouthi, Inmaculada Sanchez-Romero, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0108-2.","ama":"Zhang W, Herde M, Mitchell J, et al. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. 2018;14(9):861-869. doi:10.1038/s41589-018-0108-2"},"publisher":"Nature Publishing Group","scopus_import":"1","publication":"Nature Chemical Biology","abstract":[{"lang":"eng","text":"Fluorescent sensors are an essential part of the experimental toolbox of the life sciences, where they are used ubiquitously to visualize intra- and extracellular signaling. In the brain, optical neurotransmitter sensors can shed light on temporal and spatial aspects of signal transmission by directly observing, for instance, neurotransmitter release and spread. Here we report the development and application of the first optical sensor for the amino acid glycine, which is both an inhibitory neurotransmitter and a co-agonist of the N-methyl-d-aspartate receptors (NMDARs) involved in synaptic plasticity. Computational design of a glycine-specific binding protein allowed us to produce the optical glycine FRET sensor (GlyFS), which can be used with single and two-photon excitation fluorescence microscopy. We took advantage of this newly developed sensor to test predictions about the uneven spatial distribution of glycine in extracellular space and to demonstrate that extracellular glycine levels are controlled by plasticity-inducing stimuli."}],"language":[{"iso":"eng"}],"department":[{"_id":"HaJa"}],"publist_id":"7786"}]