[{"_id":"8570","conference":{"name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems","location":"Montreal, Canada","end_date":"2019-04-15","start_date":"2019-04-15"},"type":"conference","status":"public","date_updated":"2021-01-12T08:20:05Z","citation":{"ista":"Althoff M, Bak S, Forets M, Frehse G, Kochdumper N, Ray R, Schilling C, Schupp S. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 14–40.","chicago":"Althoff, Matthias, Stanley Bak, Marcelo Forets, Goran Frehse, Niklas Kochdumper, Rajarshi Ray, Christian Schilling, and Stefan Schupp. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Linear Continuous Dynamics.” In EPiC Series in Computing, 61:14–40. EasyChair, 2019. https://doi.org/10.29007/bj1w.","ieee":"M. Althoff et al., “ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics,” in EPiC Series in Computing, Montreal, Canada, 2019, vol. 61, pp. 14–40.","short":"M. Althoff, S. Bak, M. Forets, G. Frehse, N. Kochdumper, R. Ray, C. Schilling, S. Schupp, in:, EPiC Series in Computing, EasyChair, 2019, pp. 14–40.","ama":"Althoff M, Bak S, Forets M, et al. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. In: EPiC Series in Computing. Vol 61. EasyChair; 2019:14-40. doi:10.29007/bj1w","apa":"Althoff, M., Bak, S., Forets, M., Frehse, G., Kochdumper, N., Ray, R., … Schupp, S. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. In EPiC Series in Computing (Vol. 61, pp. 14–40). Montreal, Canada: EasyChair. https://doi.org/10.29007/bj1w","mla":"Althoff, Matthias, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Linear Continuous Dynamics.” EPiC Series in Computing, vol. 61, EasyChair, 2019, pp. 14–40, doi:10.29007/bj1w."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"last_name":"Althoff","full_name":"Althoff, Matthias","first_name":"Matthias"},{"first_name":"Stanley","last_name":"Bak","full_name":"Bak, Stanley"},{"last_name":"Forets","full_name":"Forets, Marcelo","first_name":"Marcelo"},{"first_name":"Goran","full_name":"Frehse, Goran","last_name":"Frehse"},{"last_name":"Kochdumper","full_name":"Kochdumper, Niklas","first_name":"Niklas"},{"first_name":"Rajarshi","full_name":"Ray, Rajarshi","last_name":"Ray"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Schilling","orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian"},{"first_name":"Stefan","full_name":"Schupp, Stefan","last_name":"Schupp"}],"title":"ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics","department":[{"_id":"ToHe"}],"abstract":[{"text":"This report presents the results of a friendly competition for formal verification of continuous and hybrid systems with linear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In its third edition, seven tools have been applied to solve six different benchmark problems in the category for linear continuous dynamics (in alphabetical order): CORA, CORA/SX, HyDRA, Hylaa, JuliaReach, SpaceEx, and XSpeed. This report is a snapshot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results provide one of the most complete assessments of tools for the safety verification of continuous and hybrid systems with linear continuous dynamics up to this date.","lang":"eng"}],"oa_version":"Published Version","oa":1,"main_file_link":[{"url":"https://easychair.org/publications/open/1gbP","open_access":"1"}],"quality_controlled":"1","publisher":"EasyChair","intvolume":" 61","month":"05","year":"2019","publication_status":"published","publication_identifier":{"eissn":["23987340"]},"publication":"EPiC Series in Computing","language":[{"iso":"eng"}],"day":"25","page":"14-40","date_created":"2020-09-26T14:23:54Z","doi":"10.29007/bj1w","date_published":"2019-05-25T00:00:00Z","volume":61},{"citation":{"ista":"Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ. 2019. Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem. 20(7), 891–895.","chicago":"Bakail, May M, Silvia Rodriguez‐Marin, Zsófia Hegedüs, Marie E. Perrin, Françoise Ochsenbein, and Andrew J. Wilson. “Recognition of ASF1 by Using Hydrocarbon‐constrained Peptides.” ChemBioChem. Wiley, 2019. https://doi.org/10.1002/cbic.201800633.","ama":"Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ. Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem. 2019;20(7):891-895. doi:10.1002/cbic.201800633","apa":"Bakail, M. M., Rodriguez‐Marin, S., Hegedüs, Z., Perrin, M. E., Ochsenbein, F., & Wilson, A. J. (2019). Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem. Wiley. https://doi.org/10.1002/cbic.201800633","ieee":"M. M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M. E. Perrin, F. Ochsenbein, and A. J. Wilson, “Recognition of ASF1 by using hydrocarbon‐constrained peptides,” ChemBioChem, vol. 20, no. 7. Wiley, pp. 891–895, 2019.","short":"M.M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M.E. Perrin, F. Ochsenbein, A.J. Wilson, ChemBioChem 20 (2019) 891–895.","mla":"Bakail, May M., et al. “Recognition of ASF1 by Using Hydrocarbon‐constrained Peptides.” ChemBioChem, vol. 20, no. 7, Wiley, 2019, pp. 891–95, doi:10.1002/cbic.201800633."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"last_name":"Bakail","full_name":"Bakail, May M","orcid":"0000-0002-9592-1587","first_name":"May M","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E"},{"first_name":"Silvia","last_name":"Rodriguez‐Marin","full_name":"Rodriguez‐Marin, Silvia"},{"full_name":"Hegedüs, Zsófia","last_name":"Hegedüs","first_name":"Zsófia"},{"last_name":"Perrin","full_name":"Perrin, Marie E.","first_name":"Marie E."},{"full_name":"Ochsenbein, Françoise","last_name":"Ochsenbein","first_name":"Françoise"},{"last_name":"Wilson","full_name":"Wilson, Andrew J.","first_name":"Andrew J."}],"title":"Recognition of ASF1 by using hydrocarbon‐constrained peptides","year":"2019","publication":"ChemBioChem","day":"01","page":"891-895","date_created":"2021-01-19T10:59:14Z","doi":"10.1002/cbic.201800633","date_published":"2019-04-01T00:00:00Z","oa":1,"publisher":"Wiley","quality_controlled":"1","date_updated":"2023-02-23T13:46:48Z","extern":"1","_id":"9016","type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"issn":["1439-4227","1439-7633"]},"language":[{"iso":"eng"}],"issue":"7","volume":20,"abstract":[{"text":"Inhibiting the histone H3–ASF1 (anti‐silencing function 1) protein–protein interaction (PPI) represents a potential approach for treating numerous cancers. As an α‐helix‐mediated PPI, constraining the key histone H3 helix (residues 118–135) is a strategy through which chemical probes might be elaborated to test this hypothesis. In this work, variant H3118–135 peptides bearing pentenylglycine residues at the i and i+4 positions were constrained by olefin metathesis. Biophysical analyses revealed that promotion of a bioactive helical conformation depends on the position at which the constraint is introduced, but that the potency of binding towards ASF1 is unaffected by the constraint and instead that enthalpy–entropy compensation occurs.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"url":" https://doi.org/10.1002/cbic.201800633","open_access":"1"}],"intvolume":" 20","month":"04"},{"publication_identifier":{"issn":["2041-1723"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"70c6e5d6fbea0932b0669505ab6633ec","file_id":"9061","success":1,"date_updated":"2021-02-02T13:47:21Z","file_size":2820337,"creator":"cziletti","date_created":"2021-02-02T13:47:21Z","file_name":"2019_NatureComm_Ramananarivo.pdf"}],"language":[{"iso":"eng"}],"volume":10,"issue":"1","abstract":[{"lang":"eng","text":"Molecular motors are essential to the living, generating fluctuations that boost transport and assist assembly. Active colloids, that consume energy to move, hold similar potential for man-made materials controlled by forces generated from within. Yet, their use as a powerhouse in materials science lacks. Here we show a massive acceleration of the annealing of a monolayer of passive beads by moderate addition of self-propelled microparticles. We rationalize our observations with a model of collisions that drive active fluctuations and activate the annealing. The experiment is quantitatively compared with Brownian dynamic simulations that further unveil a dynamical transition in the mechanism of annealing. Active dopants travel uniformly in the system or co-localize at the grain boundaries as a result of the persistence of their motion. Our findings uncover the potential of internal activity to control materials and lay the groundwork for the rise of materials science beyond equilibrium."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"07","intvolume":" 10","date_updated":"2023-02-23T13:47:59Z","extern":"1","ddc":["530"],"file_date_updated":"2021-02-02T13:47:21Z","_id":"9060","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"has_accepted_license":"1","year":"2019","day":"29","publication":"Nature Communications","doi":"10.1038/s41467-019-11362-y","date_published":"2019-07-29T00:00:00Z","date_created":"2021-02-02T13:43:36Z","quality_controlled":"1","publisher":"Springer Nature","oa":1,"citation":{"mla":"Ramananarivo, Sophie, et al. “Activity-Controlled Annealing of Colloidal Monolayers.” Nature Communications, vol. 10, no. 1, 3380, Springer Nature, 2019, doi:10.1038/s41467-019-11362-y.","ieee":"S. Ramananarivo, E. Ducrot, and J. A. Palacci, “Activity-controlled annealing of colloidal monolayers,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019.","short":"S. Ramananarivo, E. Ducrot, J.A. Palacci, Nature Communications 10 (2019).","ama":"Ramananarivo S, Ducrot E, Palacci JA. Activity-controlled annealing of colloidal monolayers. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-11362-y","apa":"Ramananarivo, S., Ducrot, E., & Palacci, J. A. (2019). Activity-controlled annealing of colloidal monolayers. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-11362-y","chicago":"Ramananarivo, Sophie, Etienne Ducrot, and Jérémie A Palacci. “Activity-Controlled Annealing of Colloidal Monolayers.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-11362-y.","ista":"Ramananarivo S, Ducrot E, Palacci JA. 2019. Activity-controlled annealing of colloidal monolayers. Nature Communications. 10(1), 3380."},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","author":[{"first_name":"Sophie","full_name":"Ramananarivo, Sophie","last_name":"Ramananarivo"},{"full_name":"Ducrot, Etienne","last_name":"Ducrot","first_name":"Etienne"},{"orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","last_name":"Palacci","first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"}],"external_id":{"arxiv":["1909.07382"],"pmid":["31358762"]},"article_processing_charge":"No","title":"Activity-controlled annealing of colloidal monolayers","article_number":"3380"},{"citation":{"ista":"Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL. 2019. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 116(19), 9652–9657.","chicago":"Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman, Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1821435116.","apa":"Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T., & Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1821435116","ama":"Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 2019;116(19):9652-9657. doi:10.1073/pnas.1821435116","ieee":"M. Y. Kim et al., “DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm,” Proceedings of the National Academy of Sciences, vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019.","short":"M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L. Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657.","mla":"Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences, vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:10.1073/pnas.1821435116."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","external_id":{"pmid":["31000601"]},"author":[{"full_name":"Kim, M. Yvonne","last_name":"Kim","first_name":"M. Yvonne"},{"first_name":"Akemi","last_name":"Ono","full_name":"Ono, Akemi"},{"last_name":"Scholten","full_name":"Scholten, Stefan","first_name":"Stefan"},{"full_name":"Kinoshita, Tetsu","last_name":"Kinoshita","first_name":"Tetsu"},{"last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel"},{"first_name":"Takashi","full_name":"Okamoto, Takashi","last_name":"Okamoto"},{"first_name":"Robert L.","last_name":"Fischer","full_name":"Fischer, Robert L."}],"title":"DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm","year":"2019","has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences","day":"07","page":"9652-9657","date_created":"2021-06-04T12:38:20Z","doi":"10.1073/pnas.1821435116","date_published":"2019-05-07T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","date_updated":"2021-12-14T07:52:30Z","ddc":["580"],"extern":"1","file_date_updated":"2021-06-04T12:50:47Z","department":[{"_id":"DaZi"}],"_id":"9460","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","keyword":["Multidisciplinary"],"status":"public","publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2019_PNAS_Kim.pdf","date_created":"2021-06-04T12:50:47Z","creator":"asandaue","file_size":1142540,"date_updated":"2021-06-04T12:50:47Z","success":1,"file_id":"9461","checksum":"5b0ae3779b8b21b5223bd2d3cceede3a","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","issue":"19","volume":116,"abstract":[{"lang":"eng","text":"Epigenetic reprogramming is required for proper regulation of gene expression in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for seed viability, pollen function, and successful reproduction. The DEMETER (DME) DNA glycosylase initiates localized DNA demethylation in vegetative and central cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively. In rice, the central cell genome displays local DNA hypomethylation, suggesting that active DNA demethylation also occurs in rice; however, the enzyme responsible for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING 1a (ROS1a) gene, which is related to DME and is essential for rice seed viability and pollen function. Here, we report genome-wide analyses of DNA methylation in wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative cell genome is locally hypomethylated compared with sperm by a process that requires ROS1a activity. We show that many ROS1a target sequences in the vegetative cell are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation is indirectly promoted by DNA demethylation in the vegetative cell. These results reveal that DNA glycosylase-mediated DNA demethylation processes are conserved in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally, although global non-CG methylation levels of sperm and egg differ, the maternal and paternal embryo genomes show similar non-CG methylation levels, suggesting that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell fusion."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 116","month":"05"},{"citation":{"chicago":"Cheng, Bingqing, Edgar A. Engel, Jörg Behler, Christoph Dellago, and Michele Ceriotti. “Ab Initio Thermodynamics of Liquid and Solid Water.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1815117116.","ista":"Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. 2019. Ab initio thermodynamics of liquid and solid water. Proceedings of the National Academy of Sciences. 116(4), 1110–1115.","mla":"Cheng, Bingqing, et al. “Ab Initio Thermodynamics of Liquid and Solid Water.” Proceedings of the National Academy of Sciences, vol. 116, no. 4, National Academy of Sciences, 2019, pp. 1110–15, doi:10.1073/pnas.1815117116.","ieee":"B. Cheng, E. A. Engel, J. Behler, C. Dellago, and M. Ceriotti, “Ab initio thermodynamics of liquid and solid water,” Proceedings of the National Academy of Sciences, vol. 116, no. 4. National Academy of Sciences, pp. 1110–1115, 2019.","short":"B. Cheng, E.A. Engel, J. Behler, C. Dellago, M. Ceriotti, Proceedings of the National Academy of Sciences 116 (2019) 1110–1115.","apa":"Cheng, B., Engel, E. A., Behler, J., Dellago, C., & Ceriotti, M. (2019). Ab initio thermodynamics of liquid and solid water. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1815117116","ama":"Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. Ab initio thermodynamics of liquid and solid water. Proceedings of the National Academy of Sciences. 2019;116(4):1110-1115. doi:10.1073/pnas.1815117116"},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","external_id":{"pmid":["30610171"],"arxiv":["1811.08630"]},"article_processing_charge":"No","author":[{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"first_name":"Edgar A.","last_name":"Engel","full_name":"Engel, Edgar A."},{"first_name":"Jörg","full_name":"Behler, Jörg","last_name":"Behler"},{"last_name":"Dellago","full_name":"Dellago, Christoph","first_name":"Christoph"},{"full_name":"Ceriotti, Michele","last_name":"Ceriotti","first_name":"Michele"}],"title":"Ab initio thermodynamics of liquid and solid water","year":"2019","publication":"Proceedings of the National Academy of Sciences","day":"22","page":"1110-1115","date_created":"2021-07-19T10:17:09Z","date_published":"2019-01-22T00:00:00Z","doi":"10.1073/pnas.1815117116","oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","date_updated":"2023-02-23T14:05:08Z","extern":"1","_id":"9689","type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"language":[{"iso":"eng"}],"volume":116,"issue":"4","abstract":[{"text":"A central goal of computational physics and chemistry is to predict material properties by using first-principles methods based on the fundamental laws of quantum mechanics. However, the high computational costs of these methods typically prevent rigorous predictions of macroscopic quantities at finite temperatures, such as heat capacity, density, and chemical potential. Here, we enable such predictions by marrying advanced free-energy methods with data-driven machine-learning interatomic potentials. We show that, for the ubiquitous and technologically essential system of water, a first-principles thermodynamic description not only leads to excellent agreement with experiments, but also reveals the crucial role of nuclear quantum fluctuations in modulating the thermodynamic stabilities of different phases of water.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1815117116"}],"scopus_import":"1","intvolume":" 116","month":"01"},{"volume":12,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9784"}]},"publication_status":"published","publication_identifier":{"eissn":["1756-0500"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2019-08-23T11:10:35Z","file_name":"2019_BMC_Antoniou.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:40Z","file_size":1177482,"file_id":"6829","checksum":"4a2bb7994b7f2c432bf44f5127ea3102","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"scopus_import":1,"intvolume":" 12","month":"08","abstract":[{"lang":"eng","text":"Glyphosate (N-phosphonomethyl glycine) and its commercial herbicide formulations have been shown to exert toxicity via various mechanisms. It has been asserted that glyphosate substitutes for glycine in polypeptide chains leading to protein misfolding and toxicity. However, as no direct evidence exists for glycine to glyphosate substitution in proteins, including in mammalian organisms, we tested this claim by conducting a proteomics analysis of MDA-MB-231 human breast cancer cells grown in the presence of 100 mg/L glyphosate for 6 days. Protein extracts from three treated and three untreated cell cultures were analysed as one TMT-6plex labelled sample, to highlight a specific pattern (+/+/+/−/−/−) of reporter intensities for peptides bearing true glyphosate treatment induced-post translational modifications as well as allowing an investigation of the total proteome."}],"oa_version":"Published Version","pmid":1,"department":[{"_id":"LifeSc"}],"file_date_updated":"2020-07-14T12:47:40Z","date_updated":"2023-02-23T14:08:14Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"6819","date_created":"2019-08-18T22:00:39Z","date_published":"2019-08-08T00:00:00Z","doi":"10.1186/s13104-019-4534-3","year":"2019","has_accepted_license":"1","publication":"BMC Research Notes","day":"08","oa":1,"quality_controlled":"1","publisher":"BioMed Central","external_id":{"pmid":["31395095"]},"article_processing_charge":"No","author":[{"first_name":"Michael N.","full_name":"Antoniou, Michael N.","last_name":"Antoniou"},{"full_name":"Nicolas, Armel","last_name":"Nicolas","first_name":"Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mesnage, Robin","last_name":"Mesnage","first_name":"Robin"},{"first_name":"Martina","full_name":"Biserni, Martina","last_name":"Biserni"},{"last_name":"Rao","full_name":"Rao, Francesco V.","first_name":"Francesco V."},{"last_name":"Martin","full_name":"Martin, Cristina Vazquez","first_name":"Cristina Vazquez"}],"title":"Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells","citation":{"ista":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. 12, 494.","chicago":"Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes. BioMed Central, 2019. https://doi.org/10.1186/s13104-019-4534-3.","apa":"Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. BioMed Central. https://doi.org/10.1186/s13104-019-4534-3","ama":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. 2019;12. doi:10.1186/s13104-019-4534-3","ieee":"M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells,” BMC Research Notes, vol. 12. BioMed Central, 2019.","short":"M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, BMC Research Notes 12 (2019).","mla":"Antoniou, Michael N., et al. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes, vol. 12, 494, BioMed Central, 2019, doi:10.1186/s13104-019-4534-3."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"494"},{"status":"public","type":"research_data_reference","_id":"9784","title":"MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells","department":[{"_id":"LifeSc"}],"author":[{"last_name":"Antoniou","full_name":"Antoniou, Michael N.","first_name":"Michael N."},{"full_name":"Nicolas, Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel"},{"first_name":"Robin","last_name":"Mesnage","full_name":"Mesnage, Robin"},{"first_name":"Martina","last_name":"Biserni","full_name":"Biserni, Martina"},{"first_name":"Francesco V.","last_name":"Rao","full_name":"Rao, Francesco V."},{"last_name":"Martin","full_name":"Martin, Cristina Vazquez","first_name":"Cristina Vazquez"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T12:52:29Z","citation":{"ista":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells, Springer Nature, 10.6084/m9.figshare.9411761.v1.","chicago":"Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9411761.v1.","apa":"Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. Springer Nature. https://doi.org/10.6084/m9.figshare.9411761.v1","ama":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. 2019. doi:10.6084/m9.figshare.9411761.v1","short":"M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, (2019).","ieee":"M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells.” Springer Nature, 2019.","mla":"Antoniou, Michael N., et al. MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells. Springer Nature, 2019, doi:10.6084/m9.figshare.9411761.v1."},"month":"08","publisher":"Springer Nature","oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9411761.v1","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1 of seeding flasks and following 6-days of continuous culture. Note: no differences in cell numbers were observed between negative control and glyphosate treated cultures.","lang":"eng"}],"doi":"10.6084/m9.figshare.9411761.v1","related_material":{"record":[{"id":"6819","status":"public","relation":"used_in_publication"}]},"date_published":"2019-08-09T00:00:00Z","date_created":"2021-08-06T08:14:05Z","day":"09","year":"2019"},{"day":"22","year":"2019","doi":"10.5061/dryad.5vv37","date_published":"2019-06-22T00:00:00Z","related_material":{"record":[{"status":"public","id":"315","relation":"used_in_publication"}]},"date_created":"2021-08-09T13:07:28Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range."}],"month":"06","publisher":"Dryad","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.5vv37","open_access":"1"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"chicago":"Polechova, Jitka. “Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” Dryad, 2019. https://doi.org/10.5061/dryad.5vv37.","ista":"Polechova J. 2019. Data from: Is the sky the limit? On the expansion threshold of a species’ range, Dryad, 10.5061/dryad.5vv37.","mla":"Polechova, Jitka. Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range. Dryad, 2019, doi:10.5061/dryad.5vv37.","short":"J. Polechova, (2019).","ieee":"J. Polechova, “Data from: Is the sky the limit? On the expansion threshold of a species’ range.” Dryad, 2019.","ama":"Polechova J. Data from: Is the sky the limit? On the expansion threshold of a species’ range. 2019. doi:10.5061/dryad.5vv37","apa":"Polechova, J. (2019). Data from: Is the sky the limit? On the expansion threshold of a species’ range. Dryad. https://doi.org/10.5061/dryad.5vv37"},"date_updated":"2023-02-23T11:14:30Z","title":"Data from: Is the sky the limit? On the expansion threshold of a species' range","department":[{"_id":"NiBa"}],"author":[{"id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","first_name":"Jitka","orcid":"0000-0003-0951-3112","full_name":"Polechova, Jitka","last_name":"Polechova"}],"article_processing_charge":"No","_id":"9839","status":"public","type":"research_data_reference"},{"publication_status":"published","publication_identifier":{"issn":["0003-9527","1432-0673"]},"language":[{"iso":"eng"}],"volume":233,"issue":"2","abstract":[{"text":"For the Restricted Circular Planar 3 Body Problem, we show that there exists an open set U in phase space of fixed measure, where the set of initial points which lead to collision is O(μ120) dense as μ→0.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1007/s00205-019-01368-7","open_access":"1"}],"intvolume":" 233","month":"03","date_updated":"2021-01-12T08:19:09Z","extern":"1","_id":"8418","article_type":"original","type":"journal_article","keyword":["Mechanical Engineering","Mathematics (miscellaneous)","Analysis"],"status":"public","year":"2019","publication":"Archive for Rational Mechanics and Analysis","day":"12","page":"799-836","date_created":"2020-09-17T10:41:51Z","date_published":"2019-03-12T00:00:00Z","doi":"10.1007/s00205-019-01368-7","oa":1,"quality_controlled":"1","publisher":"Springer Nature","citation":{"apa":"Guardia, M., Kaloshin, V., & Zhang, J. (2019). Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-019-01368-7","ama":"Guardia M, Kaloshin V, Zhang J. Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem. Archive for Rational Mechanics and Analysis. 2019;233(2):799-836. doi:10.1007/s00205-019-01368-7","short":"M. Guardia, V. Kaloshin, J. Zhang, Archive for Rational Mechanics and Analysis 233 (2019) 799–836.","ieee":"M. Guardia, V. Kaloshin, and J. Zhang, “Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem,” Archive for Rational Mechanics and Analysis, vol. 233, no. 2. Springer Nature, pp. 799–836, 2019.","mla":"Guardia, Marcel, et al. “Asymptotic Density of Collision Orbits in the Restricted Circular Planar 3 Body Problem.” Archive for Rational Mechanics and Analysis, vol. 233, no. 2, Springer Nature, 2019, pp. 799–836, doi:10.1007/s00205-019-01368-7.","ista":"Guardia M, Kaloshin V, Zhang J. 2019. Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem. Archive for Rational Mechanics and Analysis. 233(2), 799–836.","chicago":"Guardia, Marcel, Vadim Kaloshin, and Jianlu Zhang. “Asymptotic Density of Collision Orbits in the Restricted Circular Planar 3 Body Problem.” Archive for Rational Mechanics and Analysis. Springer Nature, 2019. https://doi.org/10.1007/s00205-019-01368-7."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Marcel","full_name":"Guardia, Marcel","last_name":"Guardia"},{"full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","last_name":"Kaloshin","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"first_name":"Jianlu","full_name":"Zhang, Jianlu","last_name":"Zhang"}],"title":"Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem"},{"day":"01","publication":"Moscow Mathematical Journal","year":"2019","date_published":"2019-04-01T00:00:00Z","doi":"10.17323/1609-4514-2019-19-2-307-327","date_created":"2020-09-17T10:41:36Z","page":"307-327","quality_controlled":"1","publisher":"American Mathematical Society","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Huang, Guan, and Vadim Kaloshin. “On the Finite Dimensionality of Integrable Deformations of Strictly Convex Integrable Billiard Tables.” Moscow Mathematical Journal. American Mathematical Society, 2019. https://doi.org/10.17323/1609-4514-2019-19-2-307-327.","ista":"Huang G, Kaloshin V. 2019. On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables. Moscow Mathematical Journal. 19(2), 307–327.","mla":"Huang, Guan, and Vadim Kaloshin. “On the Finite Dimensionality of Integrable Deformations of Strictly Convex Integrable Billiard Tables.” Moscow Mathematical Journal, vol. 19, no. 2, American Mathematical Society, 2019, pp. 307–27, doi:10.17323/1609-4514-2019-19-2-307-327.","ama":"Huang G, Kaloshin V. On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables. Moscow Mathematical Journal. 2019;19(2):307-327. doi:10.17323/1609-4514-2019-19-2-307-327","apa":"Huang, G., & Kaloshin, V. (2019). On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables. Moscow Mathematical Journal. American Mathematical Society. https://doi.org/10.17323/1609-4514-2019-19-2-307-327","ieee":"G. Huang and V. Kaloshin, “On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables,” Moscow Mathematical Journal, vol. 19, no. 2. American Mathematical Society, pp. 307–327, 2019.","short":"G. Huang, V. Kaloshin, Moscow Mathematical Journal 19 (2019) 307–327."},"title":"On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables","author":[{"full_name":"Huang, Guan","last_name":"Huang","first_name":"Guan"},{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","last_name":"Kaloshin"}],"external_id":{"arxiv":["1809.09341"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1609-4514"]},"publication_status":"published","volume":19,"issue":"2","oa_version":"Preprint","abstract":[{"text":"In this paper, we show that any smooth one-parameter deformations of a strictly convex integrable billiard table Ω0 preserving the integrability near the boundary have to be tangent to a finite dimensional space passing through Ω0.","lang":"eng"}],"month":"04","intvolume":" 19","main_file_link":[{"url":"https://arxiv.org/abs/1809.09341","open_access":"1"}],"extern":"1","date_updated":"2021-01-12T08:19:08Z","_id":"8416","status":"public","type":"journal_article","article_type":"original"},{"intvolume":" 24","month":"12","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.02523"}],"oa":1,"quality_controlled":"1","publisher":"Springer","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We review V. I. Arnold’s 1963 celebrated paper [1] Proof of A. N. Kolmogorov’s Theorem on the Conservation of Conditionally Periodic Motions with a Small Variation in the Hamiltonian, and prove that, optimising Arnold’s scheme, one can get “sharp” asymptotic quantitative conditions (as ε → 0, ε being the strength of the perturbation). All constants involved are explicitly computed."}],"date_created":"2020-10-21T15:25:45Z","volume":24,"doi":"10.1134/S1560354719060017","date_published":"2019-12-10T00:00:00Z","page":"583–606","language":[{"iso":"eng"}],"publication":"Regular and Chaotic Dynamics","day":"10","year":"2019","publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"8693","title":"V. I. Arnold’s “pointwise” KAM theorem","article_processing_charge":"No","external_id":{"arxiv":["1908.02523"]},"author":[{"first_name":"Luigi","last_name":"Chierchia","full_name":"Chierchia, Luigi"},{"id":"52DF3E68-AEFA-11EA-95A4-124A3DDC885E","first_name":"Edmond","full_name":"Koudjinan, Edmond","orcid":"0000-0003-2640-4049","last_name":"Koudjinan"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2021-01-12T08:20:34Z","citation":{"ista":"Chierchia L, Koudjinan E. 2019. V. I. Arnold’s “pointwise” KAM theorem. Regular and Chaotic Dynamics. 24, 583–606.","chicago":"Chierchia, Luigi, and Edmond Koudjinan. “V. I. Arnold’s ‘Pointwise’ KAM Theorem.” Regular and Chaotic Dynamics. Springer, 2019. https://doi.org/10.1134/S1560354719060017.","short":"L. Chierchia, E. Koudjinan, Regular and Chaotic Dynamics 24 (2019) 583–606.","ieee":"L. Chierchia and E. Koudjinan, “V. I. Arnold’s ‘pointwise’ KAM theorem,” Regular and Chaotic Dynamics, vol. 24. Springer, pp. 583–606, 2019.","apa":"Chierchia, L., & Koudjinan, E. (2019). V. I. Arnold’s “pointwise” KAM theorem. Regular and Chaotic Dynamics. Springer. https://doi.org/10.1134/S1560354719060017","ama":"Chierchia L, Koudjinan E. V. I. Arnold’s “pointwise” KAM theorem. Regular and Chaotic Dynamics. 2019;24:583–606. doi:10.1134/S1560354719060017","mla":"Chierchia, Luigi, and Edmond Koudjinan. “V. I. Arnold’s ‘Pointwise’ KAM Theorem.” Regular and Chaotic Dynamics, vol. 24, Springer, 2019, pp. 583–606, doi:10.1134/S1560354719060017."}},{"publication":"Cell Chemical Biology","day":"21","year":"2019","date_created":"2021-01-19T11:04:50Z","date_published":"2019-11-21T00:00:00Z","doi":"10.1016/j.chembiol.2019.09.002","page":"1573-1585.e10","oa":1,"publisher":"Elsevier","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M.M. Bakail, A. Gaubert, J. Andreani, G. Moal, G. Pinna, E. Boyarchuk, M.-C. Gaillard, R. Courbeyrette, C. Mann, J.-Y. Thuret, B. Guichard, B. Murciano, N. Richet, A. Poitou, C. Frederic, M.-H. Le Du, M. Agez, C. Roelants, Z.A. Gurard-Levin, G. Almouzni, N. Cherradi, R. Guerois, F. Ochsenbein, Cell Chemical Biology 26 (2019) 1573–1585.e10.","ieee":"M. M. Bakail et al., “Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1,” Cell Chemical Biology, vol. 26, no. 11. Elsevier, p. 1573–1585.e10, 2019.","apa":"Bakail, M. M., Gaubert, A., Andreani, J., Moal, G., Pinna, G., Boyarchuk, E., … Ochsenbein, F. (2019). Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. Elsevier. https://doi.org/10.1016/j.chembiol.2019.09.002","ama":"Bakail MM, Gaubert A, Andreani J, et al. Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. 2019;26(11):1573-1585.e10. doi:10.1016/j.chembiol.2019.09.002","mla":"Bakail, May M., et al. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” Cell Chemical Biology, vol. 26, no. 11, Elsevier, 2019, p. 1573–1585.e10, doi:10.1016/j.chembiol.2019.09.002.","ista":"Bakail MM, Gaubert A, Andreani J, Moal G, Pinna G, Boyarchuk E, Gaillard M-C, Courbeyrette R, Mann C, Thuret J-Y, Guichard B, Murciano B, Richet N, Poitou A, Frederic C, Le Du M-H, Agez M, Roelants C, Gurard-Levin ZA, Almouzni G, Cherradi N, Guerois R, Ochsenbein F. 2019. Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. 26(11), 1573–1585.e10.","chicago":"Bakail, May M, Albane Gaubert, Jessica Andreani, Gwenaëlle Moal, Guillaume Pinna, Ekaterina Boyarchuk, Marie-Cécile Gaillard, et al. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” Cell Chemical Biology. Elsevier, 2019. https://doi.org/10.1016/j.chembiol.2019.09.002."},"title":"Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1","external_id":{"pmid":["31543461"]},"article_processing_charge":"No","author":[{"last_name":"Bakail","full_name":"Bakail, May M","orcid":"0000-0002-9592-1587","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","first_name":"May M"},{"first_name":"Albane","last_name":"Gaubert","full_name":"Gaubert, Albane"},{"last_name":"Andreani","full_name":"Andreani, Jessica","first_name":"Jessica"},{"first_name":"Gwenaëlle","full_name":"Moal, Gwenaëlle","last_name":"Moal"},{"last_name":"Pinna","full_name":"Pinna, Guillaume","first_name":"Guillaume"},{"last_name":"Boyarchuk","full_name":"Boyarchuk, Ekaterina","first_name":"Ekaterina"},{"last_name":"Gaillard","full_name":"Gaillard, Marie-Cécile","first_name":"Marie-Cécile"},{"first_name":"Regis","full_name":"Courbeyrette, Regis","last_name":"Courbeyrette"},{"full_name":"Mann, Carl","last_name":"Mann","first_name":"Carl"},{"last_name":"Thuret","full_name":"Thuret, Jean-Yves","first_name":"Jean-Yves"},{"first_name":"Bérengère","last_name":"Guichard","full_name":"Guichard, Bérengère"},{"first_name":"Brice","full_name":"Murciano, Brice","last_name":"Murciano"},{"full_name":"Richet, Nicolas","last_name":"Richet","first_name":"Nicolas"},{"first_name":"Adeline","last_name":"Poitou","full_name":"Poitou, Adeline"},{"first_name":"Claire","last_name":"Frederic","full_name":"Frederic, Claire"},{"last_name":"Le Du","full_name":"Le Du, Marie-Hélène","first_name":"Marie-Hélène"},{"full_name":"Agez, Morgane","last_name":"Agez","first_name":"Morgane"},{"first_name":"Caroline","last_name":"Roelants","full_name":"Roelants, Caroline"},{"last_name":"Gurard-Levin","full_name":"Gurard-Levin, Zachary A.","first_name":"Zachary A."},{"last_name":"Almouzni","full_name":"Almouzni, Geneviève","first_name":"Geneviève"},{"first_name":"Nadia","full_name":"Cherradi, Nadia","last_name":"Cherradi"},{"full_name":"Guerois, Raphael","last_name":"Guerois","first_name":"Raphael"},{"first_name":"Françoise","full_name":"Ochsenbein, Françoise","last_name":"Ochsenbein"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2451-9456"]},"volume":26,"issue":"11","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Anti-silencing function 1 (ASF1) is a conserved H3-H4 histone chaperone involved in histone dynamics during replication, transcription, and DNA repair. Overexpressed in proliferating tissues including many tumors, ASF1 has emerged as a promising therapeutic target. Here, we combine structural, computational, and biochemical approaches to design peptides that inhibit the ASF1-histone interaction. Starting from the structure of the human ASF1-histone complex, we developed a rational design strategy combining epitope tethering and optimization of interface contacts to identify a potent peptide inhibitor with a dissociation constant of 3 nM. When introduced into cultured cells, the inhibitors impair cell proliferation, perturb cell-cycle progression, and reduce cell migration and invasion in a manner commensurate with their affinity for ASF1. Finally, we find that direct injection of the most potent ASF1 peptide inhibitor in mouse allografts reduces tumor growth. Our results open new avenues to use ASF1 inhibitors as promising leads for cancer therapy."}],"intvolume":" 26","month":"11","main_file_link":[{"url":"https://doi.org/10.1016/j.chembiol.2019.09.002","open_access":"1"}],"extern":"1","date_updated":"2023-02-23T13:46:53Z","_id":"9018","keyword":["Clinical Biochemistry","Molecular Medicine","Biochemistry","Molecular Biology","Pharmacology","Drug Discovery"],"status":"public","type":"journal_article","article_type":"original"},{"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Background\r\nDNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional and developmental role of such methylation remains poorly understood. Here, we explore the dynamic range of DNA methylation in honey bee, a model organism for gene body methylation.\r\n\r\nResults\r\nOur data show that CG methylation in gene bodies globally fluctuates during honey bee development. However, these changes cause no gene expression alterations. Intriguingly, despite the global alterations, tissue-specific CG methylation patterns of complete genes or exons are rare, implying robust maintenance of genic methylation during development. Additionally, we show that CG methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Finally, unlike universally present CG methylation, we discovered non-CG methylation specifically in bee heads that resembles such methylation in mammalian brain tissue.\r\n\r\nConclusions\r\nBased on these results, we propose that gene body CG methylation can oscillate during development if it is kept to a level adequate to preserve function. Additionally, our data suggest that heightened non-CG methylation is a conserved regulator of animal nervous systems."}],"intvolume":" 12","month":"10","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"creator":"asandaue","file_size":3221067,"date_updated":"2021-06-08T09:29:19Z","file_name":"2019_EpigeneticsAndChromatin_Harris.pdf","date_created":"2021-06-08T09:29:19Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"9531","checksum":"86ff50a7517891511af2733c76c81b67"}],"publication_status":"published","publication_identifier":{"eissn":["1756-8935"]},"volume":12,"_id":"9530","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["570"],"extern":"1","date_updated":"2021-12-14T07:53:00Z","department":[{"_id":"DaZi"}],"file_date_updated":"2021-06-08T09:29:19Z","oa":1,"publisher":"Springer Nature","quality_controlled":"1","publication":"Epigenetics and Chromatin","day":"10","year":"2019","has_accepted_license":"1","date_created":"2021-06-08T09:21:51Z","doi":"10.1186/s13072-019-0307-4","date_published":"2019-10-10T00:00:00Z","article_number":"62","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Harris, Keith D., James P. B. Lloyd, Katherine Domb, Daniel Zilberman, and Assaf Zemach. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” Epigenetics and Chromatin. Springer Nature, 2019. https://doi.org/10.1186/s13072-019-0307-4.","ista":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. 2019. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 12, 62.","mla":"Harris, Keith D., et al. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” Epigenetics and Chromatin, vol. 12, 62, Springer Nature, 2019, doi:10.1186/s13072-019-0307-4.","ama":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 2019;12. doi:10.1186/s13072-019-0307-4","apa":"Harris, K. D., Lloyd, J. P. B., Domb, K., Zilberman, D., & Zemach, A. (2019). DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. Springer Nature. https://doi.org/10.1186/s13072-019-0307-4","short":"K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics and Chromatin 12 (2019).","ieee":"K. D. Harris, J. P. B. Lloyd, K. Domb, D. Zilberman, and A. Zemach, “DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development,” Epigenetics and Chromatin, vol. 12. Springer Nature, 2019."},"title":"DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development","external_id":{"pmid":["31601251"]},"article_processing_charge":"No","author":[{"first_name":"Keith D.","last_name":"Harris","full_name":"Harris, Keith D."},{"full_name":"Lloyd, James P. B.","last_name":"Lloyd","first_name":"James P. B."},{"full_name":"Domb, Katherine","last_name":"Domb","first_name":"Katherine"},{"last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel"},{"first_name":"Assaf","full_name":"Zemach, Assaf","last_name":"Zemach"}]},{"_id":"9586","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-02-23T14:01:53Z","extern":"1","abstract":[{"lang":"eng","text":"Consider integers 𝑘,ℓ such that 0⩽ℓ⩽(𝑘2) . Given a large graph 𝐺 , what is the fraction of 𝑘 -vertex subsets of 𝐺 which span exactly ℓ edges? When 𝐺 is empty or complete, and ℓ is zero or (𝑘2) , this fraction can be exactly 1. On the other hand, if ℓ is far from these extreme values, one might expect that this fraction is substantially smaller than 1. This was recently proved by Alon, Hefetz, Krivelevich, and Tyomkyn who initiated the systematic study of this question and proposed several natural conjectures.\r\nLet ℓ∗=min{ℓ,(𝑘2)−ℓ} . Our main result is that for any 𝑘 and ℓ , the fraction of 𝑘 -vertex subsets that span ℓ edges is at most log𝑂(1)(ℓ∗/𝑘)√ 𝑘/ℓ∗, which is best-possible up to the logarithmic factor. This improves on multiple results of Alon, Hefetz, Krivelevich, and Tyomkyn, and resolves one of their conjectures. In addition, we also make some first steps towards some analogous questions for hypergraphs.\r\nOur proofs involve some Ramsey-type arguments, and a number of different probabilistic tools, such as polynomial anticoncentration inequalities, hypercontractivity, and a coupling trick for random variables defined on a ‘slice’ of the Boolean hypercube."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1807.05202"}],"month":"05","intvolume":" 99","publication_identifier":{"issn":["0024-6107"],"eissn":["1469-7750"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"3","volume":99,"citation":{"chicago":"Kwan, Matthew Alan, Benny Sudakov, and Tuan Tran. “Anticoncentration for Subgraph Statistics.” Journal of the London Mathematical Society. Wiley, 2019. https://doi.org/10.1112/jlms.12192.","ista":"Kwan MA, Sudakov B, Tran T. 2019. Anticoncentration for subgraph statistics. Journal of the London Mathematical Society. 99(3), 757–777.","mla":"Kwan, Matthew Alan, et al. “Anticoncentration for Subgraph Statistics.” Journal of the London Mathematical Society, vol. 99, no. 3, Wiley, 2019, pp. 757–77, doi:10.1112/jlms.12192.","ama":"Kwan MA, Sudakov B, Tran T. Anticoncentration for subgraph statistics. Journal of the London Mathematical Society. 2019;99(3):757-777. doi:10.1112/jlms.12192","apa":"Kwan, M. A., Sudakov, B., & Tran, T. (2019). Anticoncentration for subgraph statistics. Journal of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.12192","ieee":"M. A. Kwan, B. Sudakov, and T. Tran, “Anticoncentration for subgraph statistics,” Journal of the London Mathematical Society, vol. 99, no. 3. Wiley, pp. 757–777, 2019.","short":"M.A. Kwan, B. Sudakov, T. Tran, Journal of the London Mathematical Society 99 (2019) 757–777."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","first_name":"Matthew Alan","last_name":"Kwan","orcid":"0000-0002-4003-7567","full_name":"Kwan, Matthew Alan"},{"last_name":"Sudakov","full_name":"Sudakov, Benny","first_name":"Benny"},{"last_name":"Tran","full_name":"Tran, Tuan","first_name":"Tuan"}],"article_processing_charge":"No","external_id":{"arxiv":["1807.05202"]},"title":"Anticoncentration for subgraph statistics","quality_controlled":"1","publisher":"Wiley","oa":1,"year":"2019","day":"03","publication":"Journal of the London Mathematical Society","page":"757-777","date_published":"2019-05-03T00:00:00Z","doi":"10.1112/jlms.12192","date_created":"2021-06-22T09:46:03Z"},{"year":"2019","day":"01","publication":"Israel Journal of Mathematics","page":"67-111","doi":"10.1007/s11856-019-1897-z","date_published":"2019-08-01T00:00:00Z","date_created":"2021-06-21T13:36:02Z","quality_controlled":"1","publisher":"Springer","oa":1,"citation":{"mla":"Conlon, David, et al. “Hypergraph Cuts above the Average.” Israel Journal of Mathematics, vol. 233, no. 1, Springer, 2019, pp. 67–111, doi:10.1007/s11856-019-1897-z.","short":"D. Conlon, J. Fox, M.A. Kwan, B. Sudakov, Israel Journal of Mathematics 233 (2019) 67–111.","ieee":"D. Conlon, J. Fox, M. A. Kwan, and B. Sudakov, “Hypergraph cuts above the average,” Israel Journal of Mathematics, vol. 233, no. 1. Springer, pp. 67–111, 2019.","ama":"Conlon D, Fox J, Kwan MA, Sudakov B. Hypergraph cuts above the average. Israel Journal of Mathematics. 2019;233(1):67-111. doi:10.1007/s11856-019-1897-z","apa":"Conlon, D., Fox, J., Kwan, M. A., & Sudakov, B. (2019). Hypergraph cuts above the average. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-019-1897-z","chicago":"Conlon, David, Jacob Fox, Matthew Alan Kwan, and Benny Sudakov. “Hypergraph Cuts above the Average.” Israel Journal of Mathematics. Springer, 2019. https://doi.org/10.1007/s11856-019-1897-z.","ista":"Conlon D, Fox J, Kwan MA, Sudakov B. 2019. Hypergraph cuts above the average. Israel Journal of Mathematics. 233(1), 67–111."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"David","last_name":"Conlon","full_name":"Conlon, David"},{"first_name":"Jacob","last_name":"Fox","full_name":"Fox, Jacob"},{"orcid":"0000-0002-4003-7567","full_name":"Kwan, Matthew Alan","last_name":"Kwan","first_name":"Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3"},{"last_name":"Sudakov","full_name":"Sudakov, Benny","first_name":"Benny"}],"article_processing_charge":"No","external_id":{"arxiv":["1803.08462"]},"title":"Hypergraph cuts above the average","publication_identifier":{"eissn":["1565-8511"],"issn":["0021-2172"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":233,"issue":"1","abstract":[{"text":"An r-cut of a k-uniform hypergraph H is a partition of the vertex set of H into r parts and the size of the cut is the number of edges which have a vertex in each part. A classical result of Edwards says that every m-edge graph has a 2-cut of size m/2+Ω)(m−−√) and this is best possible. That is, there exist cuts which exceed the expected size of a random cut by some multiple of the standard deviation. We study analogues of this and related results in hypergraphs. First, we observe that similarly to graphs, every m-edge k-uniform hypergraph has an r-cut whose size is Ω(m−−√) larger than the expected size of a random r-cut. Moreover, in the case where k = 3 and r = 2 this bound is best possible and is attained by Steiner triple systems. Surprisingly, for all other cases (that is, if k ≥ 4 or r ≥ 3), we show that every m-edge k-uniform hypergraph has an r-cut whose size is Ω(m5/9) larger than the expected size of a random r-cut. This is a significant difference in behaviour, since the amount by which the size of the largest cut exceeds the expected size of a random cut is now considerably larger than the standard deviation.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1803.08462","open_access":"1"}],"month":"08","intvolume":" 233","date_updated":"2023-02-23T14:01:41Z","extern":"1","_id":"9580","article_type":"original","type":"journal_article","status":"public"},{"abstract":[{"text":"An n-vertex graph is called C-Ramsey if it has no clique or independent set of size C log n. All known constructions of Ramsey graphs involve randomness in an essential way, and there is an ongoing line of research towards showing that in fact all Ramsey graphs must obey certain “richness” properties characteristic of random graphs. More than 25 years ago, Erdős, Faudree and Sós conjectured that in any C-Ramsey graph there are Ω(n^5/2) induced subgraphs, no pair of which have the same numbers of vertices and edges. Improving on earlier results of Alon, Balogh, Kostochka and Samotij, in this paper we prove this conjecture.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1090/tran/7729"}],"scopus_import":"1","intvolume":" 372","month":"10","publication_status":"published","publication_identifier":{"issn":["0002-9947"],"eissn":["1088-6850"]},"language":[{"iso":"eng"}],"issue":"8","volume":372,"_id":"9585","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-02-23T14:01:50Z","extern":"1","oa":1,"publisher":"American Mathematical Society","quality_controlled":"1","year":"2019","publication":"Transactions of the American Mathematical Society","day":"15","page":"5571-5594","date_created":"2021-06-22T09:31:45Z","doi":"10.1090/tran/7729","date_published":"2019-10-15T00:00:00Z","citation":{"ista":"Kwan MA, Sudakov B. 2019. Proof of a conjecture on induced subgraphs of Ramsey graphs. Transactions of the American Mathematical Society. 372(8), 5571–5594.","chicago":"Kwan, Matthew Alan, and Benny Sudakov. “Proof of a Conjecture on Induced Subgraphs of Ramsey Graphs.” Transactions of the American Mathematical Society. American Mathematical Society, 2019. https://doi.org/10.1090/tran/7729.","ieee":"M. A. Kwan and B. Sudakov, “Proof of a conjecture on induced subgraphs of Ramsey graphs,” Transactions of the American Mathematical Society, vol. 372, no. 8. American Mathematical Society, pp. 5571–5594, 2019.","short":"M.A. Kwan, B. Sudakov, Transactions of the American Mathematical Society 372 (2019) 5571–5594.","ama":"Kwan MA, Sudakov B. Proof of a conjecture on induced subgraphs of Ramsey graphs. Transactions of the American Mathematical Society. 2019;372(8):5571-5594. doi:10.1090/tran/7729","apa":"Kwan, M. A., & Sudakov, B. (2019). Proof of a conjecture on induced subgraphs of Ramsey graphs. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/7729","mla":"Kwan, Matthew Alan, and Benny Sudakov. “Proof of a Conjecture on Induced Subgraphs of Ramsey Graphs.” Transactions of the American Mathematical Society, vol. 372, no. 8, American Mathematical Society, 2019, pp. 5571–94, doi:10.1090/tran/7729."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","external_id":{"arxiv":["1712.05656"]},"article_processing_charge":"No","author":[{"full_name":"Kwan, Matthew Alan","orcid":"0000-0002-4003-7567","last_name":"Kwan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","first_name":"Matthew Alan"},{"full_name":"Sudakov, Benny","last_name":"Sudakov","first_name":"Benny"}],"title":"Proof of a conjecture on induced subgraphs of Ramsey graphs"},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0010-4655"]},"publication_status":"published","volume":236,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Progress in the atomic-scale modeling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic structure problem explicitly, or by computing accurate approximations of the solution and by the development of techniques that use the Born–Oppenheimer (BO) forces to move the atoms on the BO potential energy surface. As a consequence of these developments it is now possible to identify stable or metastable states, to sample configurations consistent with the appropriate thermodynamic ensemble, and to estimate the kinetics of reactions and phase transitions. All too often, however, progress is slowed down by the bottleneck associated with implementing new optimization algorithms and/or sampling techniques into the many existing electronic-structure and empirical-potential codes. To address this problem, we are thus releasing a new version of the i-PI software. This piece of software is an easily extensible framework for implementing advanced atomistic simulation techniques using interatomic potentials and forces calculated by an external driver code. While the original version of the code (Ceriotti et al., 2014) was developed with a focus on path integral molecular dynamics techniques, this second release of i-PI not only includes several new advanced path integral methods, but also offers other classes of algorithms. In other words, i-PI is moving towards becoming a universal force engine that is both modular and tightly coupled to the driver codes that evaluate the potential energy surface and its derivatives."}],"month":"03","intvolume":" 236","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.03824"}],"extern":"1","date_updated":"2021-08-09T12:37:16Z","_id":"9677","status":"public","type":"journal_article","article_type":"original","day":"01","publication":"Computer Physics Communications","year":"2019","date_published":"2019-03-01T00:00:00Z","doi":"10.1016/j.cpc.2018.09.020","date_created":"2021-07-16T08:53:01Z","page":"214-223","quality_controlled":"1","publisher":"Elsevier","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"chicago":"Kapil, Venkat, Mariana Rossi, Ondrej Marsalek, Riccardo Petraglia, Yair Litman, Thomas Spura, Bingqing Cheng, et al. “I-PI 2.0: A Universal Force Engine for Advanced Molecular Simulations.” Computer Physics Communications. Elsevier, 2019. https://doi.org/10.1016/j.cpc.2018.09.020.","ista":"Kapil V, Rossi M, Marsalek O, Petraglia R, Litman Y, Spura T, Cheng B, Cuzzocrea A, Meißner RH, Wilkins DM, Helfrecht BA, Juda P, Bienvenue SP, Fang W, Kessler J, Poltavsky I, Vandenbrande S, Wieme J, Corminboeuf C, Kühne TD, Manolopoulos DE, Markland TE, Richardson JO, Tkatchenko A, Tribello GA, Van Speybroeck V, Ceriotti M. 2019. i-PI 2.0: A universal force engine for advanced molecular simulations. Computer Physics Communications. 236, 214–223.","mla":"Kapil, Venkat, et al. “I-PI 2.0: A Universal Force Engine for Advanced Molecular Simulations.” Computer Physics Communications, vol. 236, Elsevier, 2019, pp. 214–23, doi:10.1016/j.cpc.2018.09.020.","short":"V. Kapil, M. Rossi, O. Marsalek, R. Petraglia, Y. Litman, T. Spura, B. Cheng, A. Cuzzocrea, R.H. Meißner, D.M. Wilkins, B.A. Helfrecht, P. Juda, S.P. Bienvenue, W. Fang, J. Kessler, I. Poltavsky, S. Vandenbrande, J. Wieme, C. Corminboeuf, T.D. Kühne, D.E. Manolopoulos, T.E. Markland, J.O. Richardson, A. Tkatchenko, G.A. Tribello, V. Van Speybroeck, M. Ceriotti, Computer Physics Communications 236 (2019) 214–223.","ieee":"V. Kapil et al., “i-PI 2.0: A universal force engine for advanced molecular simulations,” Computer Physics Communications, vol. 236. Elsevier, pp. 214–223, 2019.","ama":"Kapil V, Rossi M, Marsalek O, et al. i-PI 2.0: A universal force engine for advanced molecular simulations. Computer Physics Communications. 2019;236:214-223. doi:10.1016/j.cpc.2018.09.020","apa":"Kapil, V., Rossi, M., Marsalek, O., Petraglia, R., Litman, Y., Spura, T., … Ceriotti, M. (2019). i-PI 2.0: A universal force engine for advanced molecular simulations. Computer Physics Communications. Elsevier. https://doi.org/10.1016/j.cpc.2018.09.020"},"title":"i-PI 2.0: A universal force engine for advanced molecular simulations","author":[{"first_name":"Venkat","last_name":"Kapil","full_name":"Kapil, Venkat"},{"first_name":"Mariana","last_name":"Rossi","full_name":"Rossi, Mariana"},{"last_name":"Marsalek","full_name":"Marsalek, Ondrej","first_name":"Ondrej"},{"full_name":"Petraglia, Riccardo","last_name":"Petraglia","first_name":"Riccardo"},{"first_name":"Yair","last_name":"Litman","full_name":"Litman, Yair"},{"full_name":"Spura, Thomas","last_name":"Spura","first_name":"Thomas"},{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing"},{"full_name":"Cuzzocrea, Alice","last_name":"Cuzzocrea","first_name":"Alice"},{"first_name":"Robert H.","last_name":"Meißner","full_name":"Meißner, Robert H."},{"first_name":"David M.","full_name":"Wilkins, David M.","last_name":"Wilkins"},{"last_name":"Helfrecht","full_name":"Helfrecht, Benjamin A.","first_name":"Benjamin A."},{"full_name":"Juda, Przemysław","last_name":"Juda","first_name":"Przemysław"},{"full_name":"Bienvenue, Sébastien P.","last_name":"Bienvenue","first_name":"Sébastien P."},{"first_name":"Wei","full_name":"Fang, Wei","last_name":"Fang"},{"full_name":"Kessler, Jan","last_name":"Kessler","first_name":"Jan"},{"first_name":"Igor","last_name":"Poltavsky","full_name":"Poltavsky, Igor"},{"full_name":"Vandenbrande, Steven","last_name":"Vandenbrande","first_name":"Steven"},{"first_name":"Jelle","full_name":"Wieme, Jelle","last_name":"Wieme"},{"last_name":"Corminboeuf","full_name":"Corminboeuf, Clemence","first_name":"Clemence"},{"first_name":"Thomas D.","full_name":"Kühne, Thomas D.","last_name":"Kühne"},{"first_name":"David E.","full_name":"Manolopoulos, David E.","last_name":"Manolopoulos"},{"full_name":"Markland, Thomas E.","last_name":"Markland","first_name":"Thomas E."},{"last_name":"Richardson","full_name":"Richardson, Jeremy O.","first_name":"Jeremy O."},{"first_name":"Alexandre","last_name":"Tkatchenko","full_name":"Tkatchenko, Alexandre"},{"first_name":"Gareth A.","last_name":"Tribello","full_name":"Tribello, Gareth A."},{"first_name":"Veronique","last_name":"Van Speybroeck","full_name":"Van Speybroeck, Veronique"},{"first_name":"Michele","full_name":"Ceriotti, Michele","last_name":"Ceriotti"}],"external_id":{"arxiv":["1808.03824"]},"article_processing_charge":"No"},{"status":"public","type":"journal_article","article_type":"original","_id":"9680","extern":"1","date_updated":"2021-08-09T12:37:37Z","month":"01","intvolume":" 16","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1911.01140","open_access":"1"}],"oa_version":"Preprint","pmid":1,"abstract":[{"text":"Atomistic modeling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an appropriately chosen set of collective variables can significantly accelerate the exploration of phase space, albeit at the price of distorting the distribution of microstates. Efficient reweighting to recover the unbiased distribution can be nontrivial when employing adaptive sampling techniques such as metadynamics, variationally enhanced sampling, or parallel bias metadynamics, in which the system evolves in a quasi-equilibrium manner under a time-dependent bias. We introduce an iterative unbiasing scheme that makes efficient use of all the trajectory data and that does not require the distribution to be evaluated on a grid. The method can thus be used even when the bias has a high dimensionality. We benchmark this approach against some of the existing schemes on model systems with different complexity and dimensionality.","lang":"eng"}],"volume":16,"issue":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1549-9626"],"issn":["1549-9618"]},"publication_status":"published","title":"Iterative unbiasing of quasi-equilibrium sampling","author":[{"first_name":"F.","last_name":"Giberti","full_name":"Giberti, F."},{"last_name":"Cheng","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing"},{"first_name":"G. A.","full_name":"Tribello, G. A.","last_name":"Tribello"},{"first_name":"M.","full_name":"Ceriotti, M.","last_name":"Ceriotti"}],"external_id":{"arxiv":["1911.01140"],"pmid":["31743021"]},"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"short":"F. Giberti, B. Cheng, G.A. Tribello, M. Ceriotti, Journal of Chemical Theory and Computation 16 (2019) 100–107.","ieee":"F. Giberti, B. Cheng, G. A. Tribello, and M. Ceriotti, “Iterative unbiasing of quasi-equilibrium sampling,” Journal of Chemical Theory and Computation, vol. 16, no. 1. American Chemical Society, pp. 100–107, 2019.","ama":"Giberti F, Cheng B, Tribello GA, Ceriotti M. Iterative unbiasing of quasi-equilibrium sampling. Journal of Chemical Theory and Computation. 2019;16(1):100-107. doi:10.1021/acs.jctc.9b00907","apa":"Giberti, F., Cheng, B., Tribello, G. A., & Ceriotti, M. (2019). Iterative unbiasing of quasi-equilibrium sampling. Journal of Chemical Theory and Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.9b00907","mla":"Giberti, F., et al. “Iterative Unbiasing of Quasi-Equilibrium Sampling.” Journal of Chemical Theory and Computation, vol. 16, no. 1, American Chemical Society, 2019, pp. 100–07, doi:10.1021/acs.jctc.9b00907.","ista":"Giberti F, Cheng B, Tribello GA, Ceriotti M. 2019. Iterative unbiasing of quasi-equilibrium sampling. Journal of Chemical Theory and Computation. 16(1), 100–107.","chicago":"Giberti, F., Bingqing Cheng, G. A. Tribello, and M. Ceriotti. “Iterative Unbiasing of Quasi-Equilibrium Sampling.” Journal of Chemical Theory and Computation. American Chemical Society, 2019. https://doi.org/10.1021/acs.jctc.9b00907."},"quality_controlled":"1","publisher":"American Chemical Society","oa":1,"doi":"10.1021/acs.jctc.9b00907","date_published":"2019-01-14T00:00:00Z","date_created":"2021-07-19T06:56:45Z","page":"100-107","day":"14","publication":"Journal of Chemical Theory and Computation","year":"2019"},{"oa":1,"quality_controlled":"1","publisher":"American Geophysical Union","year":"2019","publication":"Water Resources Research","day":"01","page":"6754-6772","date_created":"2023-02-20T08:12:59Z","date_published":"2019-08-01T00:00:00Z","doi":"10.1029/2019wr024935","citation":{"mla":"Girona‐Mata, Marc, et al. “High‐resolution Snowline Delineation from Landsat Imagery to Infer Snow Cover Controls in a Himalayan Catchment.” Water Resources Research, vol. 55, no. 8, American Geophysical Union, 2019, pp. 6754–72, doi:10.1029/2019wr024935.","short":"M. Girona‐Mata, E.S. Miles, S. Ragettli, F. Pellicciotti, Water Resources Research 55 (2019) 6754–6772.","ieee":"M. Girona‐Mata, E. S. Miles, S. Ragettli, and F. Pellicciotti, “High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment,” Water Resources Research, vol. 55, no. 8. American Geophysical Union, pp. 6754–6772, 2019.","ama":"Girona‐Mata M, Miles ES, Ragettli S, Pellicciotti F. High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment. Water Resources Research. 2019;55(8):6754-6772. doi:10.1029/2019wr024935","apa":"Girona‐Mata, M., Miles, E. S., Ragettli, S., & Pellicciotti, F. (2019). High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment. Water Resources Research. American Geophysical Union. https://doi.org/10.1029/2019wr024935","chicago":"Girona‐Mata, Marc, Evan S. Miles, Silvan Ragettli, and Francesca Pellicciotti. “High‐resolution Snowline Delineation from Landsat Imagery to Infer Snow Cover Controls in a Himalayan Catchment.” Water Resources Research. American Geophysical Union, 2019. https://doi.org/10.1029/2019wr024935.","ista":"Girona‐Mata M, Miles ES, Ragettli S, Pellicciotti F. 2019. High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment. Water Resources Research. 55(8), 6754–6772."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Marc","last_name":"Girona‐Mata","full_name":"Girona‐Mata, Marc"},{"first_name":"Evan S.","last_name":"Miles","full_name":"Miles, Evan S."},{"last_name":"Ragettli","full_name":"Ragettli, Silvan","first_name":"Silvan"},{"full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca"}],"title":"High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment","abstract":[{"lang":"eng","text":"The snow cover dynamics of High Mountain Asia are usually assessed at spatial resolutions of 250 m or greater, but this scale is too coarse to clearly represent the rugged topography common to the region. Higher-resolution measurement of snow-covered area often results in biased sampling due to cloud cover and deep shadows. We therefore develop a Normalized Difference Snow Index-based workflow to delineate snow lines from Landsat Thematic Mapper/Enhanced Thematic Mapper+ imagery and apply it to the upper Langtang Valley in Nepal, processing 194 scenes spanning 1999 to 2013. For each scene, we determine the spatial distribution of snow line altitudes (SLAs) with respect to aspect and across six subcatchments. Our results show that the mean SLA exhibits distinct seasonal behavior based on aspect and subcatchment position. We find that SLA dynamics respond to spatial and seasonal trade-offs in precipitation, temperature, and solar radiation, which act as primary controls. We identify two SLA spatial gradients, which we attribute to the effect of spatially variable precipitation. Our results also reveal that aspect-related SLA differences vary seasonally and are influenced by solar radiation. In terms of seasonal dominant controls, we demonstrate that the snow line is controlled by snow precipitation in winter, melt in premonsoon, a combination of both in postmonsoon, and temperature in monsoon, explaining to a large extent the spatial and seasonal variability of the SLA in the upper Langtang Valley. We conclude that while SLA and snow-covered area are complementary metrics, the SLA has a strong potential for understanding local-scale snow cover dynamics and their controlling mechanisms."}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1029/2019WR024935"}],"scopus_import":"1","intvolume":" 55","month":"08","publication_status":"published","publication_identifier":{"eissn":["1944-7973"],"issn":["0043-1397"]},"language":[{"iso":"eng"}],"volume":55,"issue":"8","_id":"12600","type":"journal_article","article_type":"original","keyword":["Water Science and Technology"],"status":"public","date_updated":"2023-02-28T12:14:18Z","extern":"1"},{"oa_version":"Published Version","abstract":[{"text":"This study aims at developing and applying a spatially-distributed coupled glacier mass balance and ice-flow model to attribute the response of glaciers to natural and anthropogenic climate change. We focus on two glaciers with contrasting surface characteristics: a debris-covered glacier (Langtang Glacier in Nepal) and a clean-ice glacier (Hintereisferner in Austria). The model is applied from the end of the Little Ice Age (1850) to the present-day (2016) and is forced with four bias-corrected General Circulation Models (GCMs) from the historical experiment of the CMIP5 archive. The selected GCMs represent region-specific warm-dry, warm-wet, cold-dry, and cold-wet climate conditions. To isolate the effects of anthropogenic climate change on glacier mass balance and flow runs from these GCMs with and without further anthropogenic forcing after 1970 until 2016 are selected. The outcomes indicate that both glaciers experience the largest reduction in area and volume under warm climate conditions, whereas area and volume reductions are smaller under cold climate conditions. Simultaneously with changes in glacier area and volume, surface velocities generally decrease over time. Without further anthropogenic forcing the results reveal a 3% (9%) smaller decline in glacier area (volume) for the debris-covered glacier and a 18% (39%) smaller decline in glacier area (volume) for the clean-ice glacier. The difference in the magnitude between the two glaciers can mainly be attributed to differences in the response time of the glaciers, where the clean-ice glacier shows a much faster response to climate change. We conclude that the response of the two glaciers can mainly be attributed to anthropogenic climate change and that the impact is larger on the clean-ice glacier. The outcomes show that the model performs well under different climate conditions and that the developed approach can be used for regional-scale glacio-hydrological modeling.","lang":"eng"}],"intvolume":" 7","month":"06","main_file_link":[{"url":"https://doi.org/10.3389/feart.2019.00143","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2296-6463"]},"volume":7,"_id":"12602","status":"public","article_type":"original","type":"journal_article","extern":"1","date_updated":"2023-02-28T12:04:48Z","oa":1,"quality_controlled":"1","publisher":"Frontiers Media","publication":"Frontiers in Earth Science","day":"04","year":"2019","date_created":"2023-02-20T08:13:08Z","date_published":"2019-06-04T00:00:00Z","doi":"10.3389/feart.2019.00143","article_number":"143","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Wijngaard, René R., Jakob F. Steiner, Philip D. A. Kraaijenbrink, Christoph Klug, Surendra Adhikari, Argha Banerjee, Francesca Pellicciotti, et al. “Modeling the Response of the Langtang Glacier and the Hintereisferner to a Changing Climate since the Little Ice Age.” Frontiers in Earth Science. Frontiers Media, 2019. https://doi.org/10.3389/feart.2019.00143.","ista":"Wijngaard RR, Steiner JF, Kraaijenbrink PDA, Klug C, Adhikari S, Banerjee A, Pellicciotti F, van Beek LPH, Bierkens MFP, Lutz AF, Immerzeel WW. 2019. Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age. Frontiers in Earth Science. 7, 143.","mla":"Wijngaard, René R., et al. “Modeling the Response of the Langtang Glacier and the Hintereisferner to a Changing Climate since the Little Ice Age.” Frontiers in Earth Science, vol. 7, 143, Frontiers Media, 2019, doi:10.3389/feart.2019.00143.","ama":"Wijngaard RR, Steiner JF, Kraaijenbrink PDA, et al. Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age. Frontiers in Earth Science. 2019;7. doi:10.3389/feart.2019.00143","apa":"Wijngaard, R. R., Steiner, J. F., Kraaijenbrink, P. D. A., Klug, C., Adhikari, S., Banerjee, A., … Immerzeel, W. W. (2019). Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age. Frontiers in Earth Science. Frontiers Media. https://doi.org/10.3389/feart.2019.00143","short":"R.R. Wijngaard, J.F. Steiner, P.D.A. Kraaijenbrink, C. Klug, S. Adhikari, A. Banerjee, F. Pellicciotti, L.P.H. van Beek, M.F.P. Bierkens, A.F. Lutz, W.W. Immerzeel, Frontiers in Earth Science 7 (2019).","ieee":"R. R. Wijngaard et al., “Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age,” Frontiers in Earth Science, vol. 7. Frontiers Media, 2019."},"title":"Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age","article_processing_charge":"No","author":[{"first_name":"René R.","full_name":"Wijngaard, René R.","last_name":"Wijngaard"},{"full_name":"Steiner, Jakob F.","last_name":"Steiner","first_name":"Jakob F."},{"first_name":"Philip D. A.","last_name":"Kraaijenbrink","full_name":"Kraaijenbrink, Philip D. A."},{"full_name":"Klug, Christoph","last_name":"Klug","first_name":"Christoph"},{"first_name":"Surendra","full_name":"Adhikari, Surendra","last_name":"Adhikari"},{"first_name":"Argha","full_name":"Banerjee, Argha","last_name":"Banerjee"},{"last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"},{"last_name":"van Beek","full_name":"van Beek, Ludovicus P. H.","first_name":"Ludovicus P. H."},{"last_name":"Bierkens","full_name":"Bierkens, Marc F. P.","first_name":"Marc F. P."},{"first_name":"Arthur F.","last_name":"Lutz","full_name":"Lutz, Arthur F."},{"full_name":"Immerzeel, Walter W.","last_name":"Immerzeel","first_name":"Walter W."}]},{"intvolume":" 65","month":"08","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/jog.2019.40"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Ice cliffs and ponds on debris-covered glaciers have received increased attention due to their role in amplifying local melt. However, very few studies have looked at these features on the catchment scale to determine their patterns and changes in space and time. We have compiled a detailed inventory of cliffs and ponds in the Langtang catchment, central Himalaya, from six high-resolution satellite orthoimages and DEMs between 2006 and 2015, and a historic orthophoto from 1974. Cliffs cover between 1.4% (± 0.4%) in the dry and 3.4% (± 0.9%) in the wet seasons and ponds between 0.6% (± 0.1%) and 1.6% (± 0.3%) of the total debris-covered tongues. We find large variations between seasons, as cliffs and ponds tend to grow in the wetter monsoon period, but there is no obvious trend in total area over the study period. The inventory further shows that cliffs are predominately north-facing irrespective of the glacier flow direction. Both cliffs and ponds appear in higher densities several hundred metres from the terminus in areas where tributaries reach the main glacier tongue. On the largest glacier in the catchment ~10% of all cliffs and ponds persisted over nearly a decade.","lang":"eng"}],"volume":65,"issue":"252","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1727-5652"],"issn":["0022-1430"]},"status":"public","type":"journal_article","article_type":"original","_id":"12601","extern":"1","date_updated":"2023-02-28T12:11:07Z","oa":1,"quality_controlled":"1","publisher":"Cambridge University Press","date_created":"2023-02-20T08:13:03Z","doi":"10.1017/jog.2019.40","date_published":"2019-08-01T00:00:00Z","page":"617-632","publication":"Journal of Glaciology","day":"01","year":"2019","title":"Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and characteristics","article_processing_charge":"No","author":[{"first_name":"JAKOB F.","last_name":"STEINER","full_name":"STEINER, JAKOB F."},{"last_name":"BURI","full_name":"BURI, PASCAL","first_name":"PASCAL"},{"first_name":"EVAN S.","full_name":"MILES, EVAN S.","last_name":"MILES"},{"first_name":"SILVAN","last_name":"RAGETTLI","full_name":"RAGETTLI, SILVAN"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"STEINER JF, BURI P, MILES ES, RAGETTLI S, Pellicciotti F. 2019. Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and characteristics. Journal of Glaciology. 65(252), 617–632.","chicago":"STEINER, JAKOB F., PASCAL BURI, EVAN S. MILES, SILVAN RAGETTLI, and Francesca Pellicciotti. “Supraglacial Ice Cliffs and Ponds on Debris-Covered Glaciers: Spatio-Temporal Distribution and Characteristics.” Journal of Glaciology. Cambridge University Press, 2019. https://doi.org/10.1017/jog.2019.40.","ieee":"J. F. STEINER, P. BURI, E. S. MILES, S. RAGETTLI, and F. Pellicciotti, “Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and characteristics,” Journal of Glaciology, vol. 65, no. 252. Cambridge University Press, pp. 617–632, 2019.","short":"J.F. STEINER, P. BURI, E.S. MILES, S. RAGETTLI, F. Pellicciotti, Journal of Glaciology 65 (2019) 617–632.","ama":"STEINER JF, BURI P, MILES ES, RAGETTLI S, Pellicciotti F. Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and characteristics. Journal of Glaciology. 2019;65(252):617-632. doi:10.1017/jog.2019.40","apa":"STEINER, J. F., BURI, P., MILES, E. S., RAGETTLI, S., & Pellicciotti, F. (2019). Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and characteristics. Journal of Glaciology. Cambridge University Press. https://doi.org/10.1017/jog.2019.40","mla":"STEINER, JAKOB F., et al. “Supraglacial Ice Cliffs and Ponds on Debris-Covered Glaciers: Spatio-Temporal Distribution and Characteristics.” Journal of Glaciology, vol. 65, no. 252, Cambridge University Press, 2019, pp. 617–32, doi:10.1017/jog.2019.40."}},{"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6594752/"}],"month":"05","intvolume":" 8","abstract":[{"text":"Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation.","lang":"eng"}],"oa_version":"Published Version","volume":8,"publication_identifier":{"issn":["2050-084X"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"ea6b89c20d59e5eb3646916fe5d568ad","file_id":"12525","success":1,"date_updated":"2023-02-07T09:42:46Z","file_size":2493837,"creator":"alisjak","date_created":"2023-02-07T09:42:46Z","file_name":"2019_elife_He.pdf"}],"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"_id":"12192","department":[{"_id":"XiFe"}],"file_date_updated":"2023-02-07T09:42:46Z","date_updated":"2023-05-08T10:54:12Z","extern":"1","ddc":["580"],"quality_controlled":"1","publisher":"eLife Sciences Publications, Ltd","oa":1,"acknowledgement":"We thank David Twell for the pDONR-P4-P1R-pLAT52 and pDONR-P2R-P3-mRFP vectors, the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy, and the Norwich BioScience Institute Partnership Computing infrastructure for Science Group for High Performance Computing resources. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BB/L025043/1; SH, JZ and XF), a European Research Council Starting Grant ('SexMeth' 804981; XF) and a Grant to Exceptional Researchers by the Gatsby Charitable Foundation (SH and XF).","doi":"10.7554/elife.42530","date_published":"2019-05-28T00:00:00Z","date_created":"2023-01-16T09:17:21Z","has_accepted_license":"1","year":"2019","day":"28","publication":"eLife","article_number":"42530","author":[{"first_name":"Shengbo","last_name":"He","full_name":"He, Shengbo"},{"first_name":"Martin","full_name":"Vickers, Martin","last_name":"Vickers"},{"first_name":"Jingyi","last_name":"Zhang","full_name":"Zhang, Jingyi"},{"last_name":"Feng","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi"}],"external_id":{"unknown":["31135340"]},"article_processing_charge":"No","title":"Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation","citation":{"ista":"He S, Vickers M, Zhang J, Feng X. 2019. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 8, 42530.","chicago":"He, Shengbo, Martin Vickers, Jingyi Zhang, and Xiaoqi Feng. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife. eLife Sciences Publications, Ltd, 2019. https://doi.org/10.7554/elife.42530.","ama":"He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 2019;8. doi:10.7554/elife.42530","apa":"He, S., Vickers, M., Zhang, J., & Feng, X. (2019). Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. ELife. eLife Sciences Publications, Ltd. https://doi.org/10.7554/elife.42530","ieee":"S. He, M. Vickers, J. Zhang, and X. Feng, “Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation,” eLife, vol. 8. eLife Sciences Publications, Ltd, 2019.","short":"S. He, M. Vickers, J. Zhang, X. Feng, ELife 8 (2019).","mla":"He, Shengbo, et al. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife, vol. 8, 42530, eLife Sciences Publications, Ltd, 2019, doi:10.7554/elife.42530."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"author":[{"full_name":"KOKORIS KOGIAS, Eleftherios","last_name":"KOKORIS KOGIAS","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios"},{"last_name":"Spiegelman","full_name":"Spiegelman, Alexander","first_name":"Alexander"},{"full_name":"Malkhi, Dahlia","last_name":"Malkhi","first_name":"Dahlia"},{"first_name":"Ittai","last_name":"Abraham","full_name":"Abraham, Ittai"}],"article_processing_charge":"No","title":"Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation","date_updated":"2023-05-10T09:27:54Z","citation":{"mla":"Kokoris Kogias, Eleftherios, et al. “Bootstrapping Consensus without Trusted Setup: Fully Asynchronous Distributed Key Generation.” Cryptology EPrint Archive, 2019/1015.","ieee":"E. Kokoris Kogias, A. Spiegelman, D. Malkhi, and I. Abraham, “Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation,” Cryptology ePrint Archive. .","short":"E. Kokoris Kogias, A. Spiegelman, D. Malkhi, I. Abraham, Cryptology EPrint Archive (n.d.).","ama":"Kokoris Kogias E, Spiegelman A, Malkhi D, Abraham I. Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation. Cryptology ePrint Archive.","apa":"Kokoris Kogias, E., Spiegelman, A., Malkhi, D., & Abraham, I. (n.d.). Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation. Cryptology ePrint Archive.","chicago":"Kokoris Kogias, Eleftherios, Alexander Spiegelman, Dahlia Malkhi, and Ittai Abraham. “Bootstrapping Consensus without Trusted Setup: Fully Asynchronous Distributed Key Generation.” Cryptology EPrint Archive, n.d.","ista":"Kokoris Kogias E, Spiegelman A, Malkhi D, Abraham I. Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation. Cryptology ePrint Archive, 2019/1015."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"preprint","status":"public","_id":"8305","article_number":"2019/1015","date_published":"2019-09-10T00:00:00Z","date_created":"2020-08-26T12:18:00Z","year":"2019","publication_status":"submitted","day":"10","publication":"Cryptology ePrint Archive","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/1015"}],"oa":1,"month":"09","abstract":[{"text":"In this paper, we present the first fully asynchronous distributed key generation (ADKG) algorithm as well as the first distributed key generation algorithm that can create keys with a dual (f,2f+1)−threshold that are necessary for scalable consensus (which so far needs a trusted dealer assumption). In order to create a DKG with a dual (f,2f+1)− threshold we first answer in the affirmative the open question posed by Cachin et al. how to create an AVSS protocol with recovery thresholds f+1AHPC19 - Austrian HPC Meeting 2019 , 25. Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019.","ista":"Schlögl A, Kiss J, Elefante S. 2019. Is Debian suitable for running an HPC Cluster? AHPC19 - Austrian HPC Meeting 2019 . AHPC: Austrian HPC Meeting, 25.","mla":"Schlögl, Alois, et al. “Is Debian Suitable for Running an HPC Cluster?” AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25.","apa":"Schlögl, A., Kiss, J., & Elefante, S. (2019). Is Debian suitable for running an HPC Cluster? In AHPC19 - Austrian HPC Meeting 2019 (p. 25). Grundlsee, Austria: Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz.","ama":"Schlögl A, Kiss J, Elefante S. Is Debian suitable for running an HPC Cluster? In: AHPC19 - Austrian HPC Meeting 2019 . Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz; 2019:25.","ieee":"A. Schlögl, J. Kiss, and S. Elefante, “Is Debian suitable for running an HPC Cluster?,” in AHPC19 - Austrian HPC Meeting 2019 , Grundlsee, Austria, 2019, p. 25.","short":"A. Schlögl, J. Kiss, S. Elefante, in:, AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25."},"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"last_name":"Schlögl","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kiss, Janos","last_name":"Kiss","first_name":"Janos","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","full_name":"Elefante, Stefano","last_name":"Elefante"}],"title":"Is Debian suitable for running an HPC Cluster?","file_date_updated":"2023-05-16T07:27:09Z","department":[{"_id":"ScienComp"}],"oa_version":"Published Version","oa":1,"main_file_link":[{"url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc19/BOOKLET_AHPC19.pdf","open_access":"1"}],"publisher":"Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz","month":"02","publication_status":"published","year":"2019","has_accepted_license":"1","publication":"AHPC19 - Austrian HPC Meeting 2019 ","language":[{"iso":"eng"}],"day":"27","file":[{"creator":"dernst","file_size":1097603,"date_updated":"2023-05-16T07:27:09Z","file_name":"2019_AHPC_Schloegl.pdf","date_created":"2023-05-16T07:27:09Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"acc8272027faaf30709c51ac5c58ffa4","file_id":"12970"}],"page":"25","date_created":"2023-05-05T12:48:48Z","date_published":"2019-02-27T00:00:00Z"},{"scopus_import":"1","intvolume":" 8","month":"10","abstract":[{"text":"The inner nuclear membrane (INM) is a subdomain of the endoplasmic reticulum (ER) that is gated by the nuclear pore complex. It is unknown whether proteins of the INM and ER are degraded through shared or distinct pathways in mammalian cells. We applied dynamic proteomics to profile protein half-lives and report that INM and ER residents turn over at similar rates, indicating that the INM’s unique topology is not a barrier to turnover. Using a microscopy approach, we observed that the proteasome can degrade INM proteins in situ. However, we also uncovered evidence for selective, vesicular transport-mediated turnover of a single INM protein, emerin, that is potentiated by ER stress. Emerin is rapidly cleared from the INM by a mechanism that requires emerin’s LEM domain to mediate vesicular trafficking to lysosomes. This work demonstrates that the INM can be dynamically remodeled in response to environmental inputs.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"volume":8,"related_material":{"record":[{"id":"13079","status":"public","relation":"research_data"}]},"publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"1e8672a1e9c3dc0a2d3d0dad89673616","file_id":"11138","success":1,"creator":"dernst","date_updated":"2022-04-08T08:18:01Z","file_size":6984654,"date_created":"2022-04-08T08:18:01Z","file_name":"2019_eLife_Buchwalter.pdf"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"status":"public","_id":"11060","file_date_updated":"2022-04-08T08:18:01Z","date_updated":"2023-05-31T06:36:22Z","ddc":["570"],"extern":"1","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","date_created":"2022-04-07T07:45:02Z","date_published":"2019-10-10T00:00:00Z","doi":"10.7554/elife.49796","year":"2019","has_accepted_license":"1","publication":"eLife","day":"10","article_number":"e49796","external_id":{"pmid":["31599721"]},"article_processing_charge":"No","author":[{"first_name":"Abigail","full_name":"Buchwalter, Abigail","last_name":"Buchwalter"},{"full_name":"Schulte, Roberta","last_name":"Schulte","first_name":"Roberta"},{"first_name":"Hsiao","last_name":"Tsai","full_name":"Tsai, Hsiao"},{"first_name":"Juliana","last_name":"Capitanio","full_name":"Capitanio, Juliana"},{"last_name":"HETZER","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W"}],"title":"Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress","citation":{"mla":"Buchwalter, Abigail, et al. “Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress.” ELife, vol. 8, e49796, eLife Sciences Publications, 2019, doi:10.7554/elife.49796.","short":"A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, M. Hetzer, ELife 8 (2019).","ieee":"A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, and M. Hetzer, “Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress,” eLife, vol. 8. eLife Sciences Publications, 2019.","ama":"Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. eLife. 2019;8. doi:10.7554/elife.49796","apa":"Buchwalter, A., Schulte, R., Tsai, H., Capitanio, J., & Hetzer, M. (2019). Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.49796","chicago":"Buchwalter, Abigail, Roberta Schulte, Hsiao Tsai, Juliana Capitanio, and Martin Hetzer. “Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/elife.49796.","ista":"Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. 2019. Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. eLife. 8, e49796."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd"},{"abstract":[{"text":"The inner nuclear membrane (INM) is a subdomain of the endoplasmic reticulum (ER) that is gated by the nuclear pore complex. It is unknown whether proteins of the INM and ER are degraded through shared or distinct pathways in mammalian cells. We applied dynamic proteomics to profile protein half-lives and report that INM and ER residents turn over at similar rates, indicating that the INM’s unique topology is not a barrier to turnover. Using a microscopy approach, we observed that the proteasome can degrade INM proteins in situ. However, we also uncovered evidence for selective, vesicular transport-mediated turnover of a single INM protein, emerin, that is potentiated by ER stress. Emerin is rapidly cleared from the INM by a mechanism that requires emerin’s LEM domain to mediate vesicular trafficking to lysosomes. This work demonstrates that the INM can be dynamically remodeled in response to environmental inputs.","lang":"eng"}],"oa_version":"Published Version","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.n0r525h","open_access":"1"}],"publisher":"Dryad","month":"10","year":"2019","day":"28","date_created":"2023-05-23T17:09:30Z","doi":"10.5061/DRYAD.N0R525H","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"11060"}]},"date_published":"2019-10-28T00:00:00Z","_id":"13079","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data_reference","status":"public","citation":{"chicago":"Buchwalter, Abigail, Roberta Schulte, Hsiao Tsai, Juliana Capitanio, and Martin Hetzer. “Data from: Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress.” Dryad, 2019. https://doi.org/10.5061/DRYAD.N0R525H.","ista":"Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. 2019. Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress, Dryad, 10.5061/DRYAD.N0R525H.","mla":"Buchwalter, Abigail, et al. Data from: Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress. Dryad, 2019, doi:10.5061/DRYAD.N0R525H.","ieee":"A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, and M. Hetzer, “Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress.” Dryad, 2019.","short":"A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, M. Hetzer, (2019).","apa":"Buchwalter, A., Schulte, R., Tsai, H., Capitanio, J., & Hetzer, M. (2019). Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. Dryad. https://doi.org/10.5061/DRYAD.N0R525H","ama":"Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. 2019. doi:10.5061/DRYAD.N0R525H"},"date_updated":"2023-05-31T06:36:23Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"extern":"1","article_processing_charge":"No","author":[{"first_name":"Abigail","last_name":"Buchwalter","full_name":"Buchwalter, Abigail"},{"first_name":"Roberta","full_name":"Schulte, Roberta","last_name":"Schulte"},{"first_name":"Hsiao","last_name":"Tsai","full_name":"Tsai, Hsiao"},{"last_name":"Capitanio","full_name":"Capitanio, Juliana","first_name":"Juliana"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"HETZER","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X"}],"title":"Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress"},{"publication_status":"published","year":"2019","language":[{"iso":"eng"}],"publication":"Proceedings of the 31st Canadian Conference on Computational Geometry","day":"01","page":"164-170","date_created":"2019-11-04T16:46:11Z","related_material":{"record":[{"relation":"extended_version","status":"public","id":"8317"}]},"date_published":"2019-08-01T00:00:00Z","abstract":[{"lang":"eng","text":"When can a polyomino piece of paper be folded into a unit cube? Prior work studied tree-like polyominoes, but polyominoes with holes remain an intriguing open problem. We present sufficient conditions for a polyomino with hole(s) to fold into a cube, and conditions under which cube folding is impossible. In particular, we show that all but five special simple holes guarantee foldability. "}],"acknowledgement":"This research was performed in part at the 33rd BellairsWinter Workshop on Computational Geometry. Wethank all other participants for a fruitful atmosphere.","oa_version":"Published Version","oa":1,"main_file_link":[{"url":"https://cccg.ca/proceedings/2019/proceedings.pdf","open_access":"1"}],"publisher":"Canadian Conference on Computational Geometry","quality_controlled":"1","scopus_import":"1","month":"08","citation":{"mla":"Aichholzer, Oswin, et al. “Folding Polyominoes with Holes into a Cube.” Proceedings of the 31st Canadian Conference on Computational Geometry, Canadian Conference on Computational Geometry, 2019, pp. 164–70.","ama":"Aichholzer O, Akitaya HA, Cheung KC, et al. Folding polyominoes with holes into a cube. In: Proceedings of the 31st Canadian Conference on Computational Geometry. Canadian Conference on Computational Geometry; 2019:164-170.","apa":"Aichholzer, O., Akitaya, H. A., Cheung, K. C., Demaine, E. D., Demaine, M. L., Fekete, S. P., … Schmidt, C. (2019). Folding polyominoes with holes into a cube. In Proceedings of the 31st Canadian Conference on Computational Geometry (pp. 164–170). Edmonton, Canada: Canadian Conference on Computational Geometry.","short":"O. Aichholzer, H.A. Akitaya, K.C. Cheung, E.D. Demaine, M.L. Demaine, S.P. Fekete, L. Kleist, I. Kostitsyna, M. Löffler, Z. Masárová, K. Mundilova, C. Schmidt, in:, Proceedings of the 31st Canadian Conference on Computational Geometry, Canadian Conference on Computational Geometry, 2019, pp. 164–170.","ieee":"O. Aichholzer et al., “Folding polyominoes with holes into a cube,” in Proceedings of the 31st Canadian Conference on Computational Geometry, Edmonton, Canada, 2019, pp. 164–170.","chicago":"Aichholzer, Oswin, Hugo A Akitaya, Kenneth C Cheung, Erik D Demaine, Martin L Demaine, Sandor P Fekete, Linda Kleist, et al. “Folding Polyominoes with Holes into a Cube.” In Proceedings of the 31st Canadian Conference on Computational Geometry, 164–70. Canadian Conference on Computational Geometry, 2019.","ista":"Aichholzer O, Akitaya HA, Cheung KC, Demaine ED, Demaine ML, Fekete SP, Kleist L, Kostitsyna I, Löffler M, Masárová Z, Mundilova K, Schmidt C. 2019. Folding polyominoes with holes into a cube. Proceedings of the 31st Canadian Conference on Computational Geometry. CCCG: Canadian Conference in Computational Geometry, 164–170."},"date_updated":"2023-08-04T10:57:42Z","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","external_id":{"arxiv":["1910.09917"]},"article_processing_charge":"No","author":[{"full_name":"Aichholzer, Oswin","last_name":"Aichholzer","first_name":"Oswin"},{"full_name":"Akitaya, Hugo A","last_name":"Akitaya","first_name":"Hugo A"},{"first_name":"Kenneth C","full_name":"Cheung, Kenneth C","last_name":"Cheung"},{"full_name":"Demaine, Erik D","last_name":"Demaine","first_name":"Erik D"},{"full_name":"Demaine, Martin L","last_name":"Demaine","first_name":"Martin L"},{"last_name":"Fekete","full_name":"Fekete, Sandor P","first_name":"Sandor P"},{"last_name":"Kleist","full_name":"Kleist, Linda","first_name":"Linda"},{"first_name":"Irina","full_name":"Kostitsyna, Irina","last_name":"Kostitsyna"},{"last_name":"Löffler","full_name":"Löffler, Maarten","first_name":"Maarten"},{"orcid":"0000-0002-6660-1322","full_name":"Masárová, Zuzana","last_name":"Masárová","first_name":"Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mundilova, Klara","last_name":"Mundilova","first_name":"Klara"},{"first_name":"Christiane","full_name":"Schmidt, Christiane","last_name":"Schmidt"}],"title":"Folding polyominoes with holes into a cube","department":[{"_id":"HeEd"}],"_id":"6989","conference":{"name":"CCCG: Canadian Conference in Computational Geometry","end_date":"2019-08-10","location":"Edmonton, Canada","start_date":"2019-08-08"},"type":"conference","status":"public"},{"_id":"13372","article_type":"original","type":"journal_article","status":"public","keyword":["General Chemistry"],"date_updated":"2023-08-07T10:48:31Z","extern":"1","abstract":[{"text":"The capacity to respond or adapt to environmental changes is an intrinsic property of living systems that comprise highly-connected subcomponents communicating through chemical networks. The development of responsive synthetic systems is a relatively new research area that covers different disciplines, among which nanochemistry brings conceptually new demonstrations. Especially attractive are ligand-protected gold nanoparticles, which have been extensively used over the last decade as building blocks in constructing superlattices or dynamic aggregates, under the effect of an applied stimulus. To reflect the importance of surface chemistry and nanoparticle core composition in the dynamic self-assembly of nanoparticles, we provide here an overview of various available stimuli, as tools for synthetic chemists to exploit. Along with this task, the review starts with the use of chemical stimuli such as solvent, pH, gases, metal ions or biomolecules. It then focuses on physical stimuli: temperature, magnetic and electric fields, as well as light. To reflect on the increasing complexity of current architectures, we discuss systems that are responsive to more than one stimulus, to finally encourage further research by proposing future challenges.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1039/C8CS00787J","open_access":"1"}],"month":"01","intvolume":" 48","publication_identifier":{"issn":["0306-0012"],"eissn":["1460-4744"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"5","volume":48,"citation":{"chicago":"Grzelczak, Marek, Luis M. Liz-Marzán, and Rafal Klajn. “Stimuli-Responsive Self-Assembly of Nanoparticles.” Chemical Society Reviews. Royal Society of Chemistry, 2019. https://doi.org/10.1039/c8cs00787j.","ista":"Grzelczak M, Liz-Marzán LM, Klajn R. 2019. Stimuli-responsive self-assembly of nanoparticles. Chemical Society Reviews. 48(5), 1342–1361.","mla":"Grzelczak, Marek, et al. “Stimuli-Responsive Self-Assembly of Nanoparticles.” Chemical Society Reviews, vol. 48, no. 5, Royal Society of Chemistry, 2019, pp. 1342–61, doi:10.1039/c8cs00787j.","short":"M. Grzelczak, L.M. Liz-Marzán, R. Klajn, Chemical Society Reviews 48 (2019) 1342–1361.","ieee":"M. Grzelczak, L. M. Liz-Marzán, and R. Klajn, “Stimuli-responsive self-assembly of nanoparticles,” Chemical Society Reviews, vol. 48, no. 5. Royal Society of Chemistry, pp. 1342–1361, 2019.","apa":"Grzelczak, M., Liz-Marzán, L. M., & Klajn, R. (2019). Stimuli-responsive self-assembly of nanoparticles. Chemical Society Reviews. Royal Society of Chemistry. https://doi.org/10.1039/c8cs00787j","ama":"Grzelczak M, Liz-Marzán LM, Klajn R. Stimuli-responsive self-assembly of nanoparticles. Chemical Society Reviews. 2019;48(5):1342-1361. doi:10.1039/c8cs00787j"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Marek","full_name":"Grzelczak, Marek","last_name":"Grzelczak"},{"full_name":"Liz-Marzán, Luis M.","last_name":"Liz-Marzán","first_name":"Luis M."},{"last_name":"Klajn","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal"}],"article_processing_charge":"No","external_id":{"pmid":["30688963"]},"title":"Stimuli-responsive self-assembly of nanoparticles","publisher":"Royal Society of Chemistry","quality_controlled":"1","oa":1,"year":"2019","day":"28","publication":"Chemical Society Reviews","page":"1342-1361","doi":"10.1039/c8cs00787j","date_published":"2019-01-28T00:00:00Z","date_created":"2023-08-01T09:38:52Z"},{"year":"2019","day":"10","publication":"Beilstein Journal of Organic Chemistry","page":"2398-2407","doi":"10.3762/bjoc.15.232","date_published":"2019-10-10T00:00:00Z","date_created":"2023-08-01T09:38:06Z","publisher":"Beilstein Institut","quality_controlled":"1","oa":1,"citation":{"chicago":"Hanopolskyi, Anton I, Soumen De, Michał J Białek, Yael Diskin-Posner, Liat Avram, Moran Feller, and Rafal Klajn. “Reversible Switching of Arylazopyrazole within a Metal–Organic Cage.” Beilstein Journal of Organic Chemistry. Beilstein Institut, 2019. https://doi.org/10.3762/bjoc.15.232.","ista":"Hanopolskyi AI, De S, Białek MJ, Diskin-Posner Y, Avram L, Feller M, Klajn R. 2019. Reversible switching of arylazopyrazole within a metal–organic cage. Beilstein Journal of Organic Chemistry. 15, 2398–2407.","mla":"Hanopolskyi, Anton I., et al. “Reversible Switching of Arylazopyrazole within a Metal–Organic Cage.” Beilstein Journal of Organic Chemistry, vol. 15, Beilstein Institut, 2019, pp. 2398–407, doi:10.3762/bjoc.15.232.","ama":"Hanopolskyi AI, De S, Białek MJ, et al. Reversible switching of arylazopyrazole within a metal–organic cage. Beilstein Journal of Organic Chemistry. 2019;15:2398-2407. doi:10.3762/bjoc.15.232","apa":"Hanopolskyi, A. I., De, S., Białek, M. J., Diskin-Posner, Y., Avram, L., Feller, M., & Klajn, R. (2019). Reversible switching of arylazopyrazole within a metal–organic cage. Beilstein Journal of Organic Chemistry. Beilstein Institut. https://doi.org/10.3762/bjoc.15.232","short":"A.I. Hanopolskyi, S. De, M.J. Białek, Y. Diskin-Posner, L. Avram, M. Feller, R. Klajn, Beilstein Journal of Organic Chemistry 15 (2019) 2398–2407.","ieee":"A. I. Hanopolskyi et al., “Reversible switching of arylazopyrazole within a metal–organic cage,” Beilstein Journal of Organic Chemistry, vol. 15. Beilstein Institut, pp. 2398–2407, 2019."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Anton I","full_name":"Hanopolskyi, Anton I","last_name":"Hanopolskyi"},{"first_name":"Soumen","full_name":"De, Soumen","last_name":"De"},{"full_name":"Białek, Michał J","last_name":"Białek","first_name":"Michał J"},{"first_name":"Yael","last_name":"Diskin-Posner","full_name":"Diskin-Posner, Yael"},{"full_name":"Avram, Liat","last_name":"Avram","first_name":"Liat"},{"first_name":"Moran","full_name":"Feller, Moran","last_name":"Feller"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn","full_name":"Klajn, Rafal"}],"article_processing_charge":"No","external_id":{"pmid":["31666874"]},"title":"Reversible switching of arylazopyrazole within a metal–organic cage","publication_identifier":{"eissn":["1860-5397"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":15,"abstract":[{"text":"Arylazopyrazoles represent a new family of molecular photoswitches characterized by a near-quantitative conversion between two states and long thermal half-lives of the metastable state. Here, we investigated the behavior of a model arylazopyrazole in the presence of a self-assembled cage based on Pd–imidazole coordination. Owing to its high water solubility, the cage can solubilize the E isomer of arylazopyrazole, which, by itself, is not soluble in water. NMR spectroscopy and X-ray crystallography have independently demonstrated that each cage can encapsulate two molecules of E-arylazopyrazole. UV-induced switching to the Z isomer was accompanied by the release of one of the two guests from the cage and the formation of a 1:1 cage/Z-arylazopyrazole inclusion complex. DFT calculations suggest that this process involves a dramatic change in the conformation of the cage. Back-isomerization was induced with green light and resulted in the initial 1:2 cage/E-arylazopyrazole complex. This back-isomerization reaction also proceeded in the dark, with a rate significantly higher than in the absence of the cage.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3762/bjoc.15.232"}],"month":"10","intvolume":" 15","date_updated":"2023-08-07T10:34:56Z","extern":"1","_id":"13369","type":"journal_article","article_type":"original","status":"public","keyword":["Organic Chemistry"]},{"citation":{"mla":"Białek, Michał J., and Rafal Klajn. “Diamond Grows Up.” Chem, vol. 5, no. 9, Elsevier, 2019, pp. 2283–85, doi:10.1016/j.chempr.2019.08.012.","apa":"Białek, M. J., & Klajn, R. (2019). Diamond grows up. Chem. Elsevier. https://doi.org/10.1016/j.chempr.2019.08.012","ama":"Białek MJ, Klajn R. Diamond grows up. Chem. 2019;5(9):2283-2285. doi:10.1016/j.chempr.2019.08.012","short":"M.J. Białek, R. Klajn, Chem 5 (2019) 2283–2285.","ieee":"M. J. Białek and R. Klajn, “Diamond grows up,” Chem, vol. 5, no. 9. Elsevier, pp. 2283–2285, 2019.","chicago":"Białek, Michał J., and Rafal Klajn. “Diamond Grows Up.” Chem. Elsevier, 2019. https://doi.org/10.1016/j.chempr.2019.08.012.","ista":"Białek MJ, Klajn R. 2019. Diamond grows up. Chem. 5(9), 2283–2285."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Michał J.","last_name":"Białek","full_name":"Białek, Michał J."},{"last_name":"Klajn","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal"}],"article_processing_charge":"No","title":"Diamond grows up","year":"2019","day":"12","publication":"Chem","page":"2283-2285","doi":"10.1016/j.chempr.2019.08.012","date_published":"2019-09-12T00:00:00Z","date_created":"2023-08-01T09:38:38Z","publisher":"Elsevier","quality_controlled":"1","oa":1,"date_updated":"2023-08-07T10:46:50Z","extern":"1","_id":"13371","type":"journal_article","article_type":"original","status":"public","keyword":["Materials Chemistry","Biochemistry (medical)","General Chemical Engineering","Environmental Chemistry","Biochemistry","General Chemistry"],"publication_identifier":{"eissn":["2451-9294"],"issn":["2451-9308"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":5,"issue":"9","abstract":[{"lang":"eng","text":"Diamondoid nanoporous crystals represent a synthetically challenging class of materials that typically have been obtained from tetrahedral building blocks. In this issue of Chem, Stoddart and coworkers demonstrate that it is possible to generate diamondoid frameworks from a hexacationic building block lacking a tetrahedral symmetry. These results highlight the great potential of self-assembly for rapidly transforming small molecules into structurally complex functional materials."}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.chempr.2019.08.012","open_access":"1"}],"month":"09","intvolume":" 5"},{"volume":138,"related_material":{"record":[{"relation":"later_version","status":"public","id":"9239"}]},"ec_funded":1,"file":[{"file_id":"6913","checksum":"6346e116a4f4ed1414174d96d2c4fbd7","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2019_LIPIcs_Avni.pdf","date_created":"2019-09-27T11:45:15Z","creator":"kschuh","file_size":554457,"date_updated":"2020-07-14T12:47:42Z"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"08","intvolume":" 138","scopus_import":1,"alternative_title":["LIPIcs"],"oa_version":"Published Version","abstract":[{"text":"In two-player games on graphs, the players move a token through a graph to produce a finite or infinite path, which determines the qualitative winner or quantitative payoff of the game. We study bidding games in which the players bid for the right to move the token. Several bidding rules were studied previously. In Richman bidding, in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Poorman bidding is similar except that the winner of the bidding pays the \"bank\" rather than the other player. Taxman bidding spans the spectrum between Richman and poorman bidding. They are parameterized by a constant tau in [0,1]: portion tau of the winning bid is paid to the other player, and portion 1-tau to the bank. While finite-duration (reachability) taxman games have been studied before, we present, for the first time, results on infinite-duration taxman games. It was previously shown that both Richman and poorman infinite-duration games with qualitative objectives reduce to reachability games, and we show a similar result here. Our most interesting results concern quantitative taxman games, namely mean-payoff games, where poorman and Richman bidding differ significantly. A central quantity in these games is the ratio between the two players' initial budgets. While in poorman mean-payoff games, the optimal payoff of a player depends on the initial ratio, in Richman bidding, the payoff depends only on the structure of the game. In both games the optimal payoffs can be found using (different) probabilistic connections with random-turn games in which in each turn, instead of bidding, a coin is tossed to determine which player moves. While the value with Richman bidding equals the value of a random-turn game with an un-biased coin, with poorman bidding, the bias in the coin is the initial ratio of the budgets. We give a complete classification of mean-payoff taxman games that is based on a probabilistic connection: the value of a taxman bidding game with parameter tau and initial ratio r, equals the value of a random-turn game that uses a coin with bias F(tau, r) = (r+tau * (1-r))/(1+tau). Thus, we show that Richman bidding is the exception; namely, for every tau <1, the value of the game depends on the initial ratio. Our proof technique simplifies and unifies the previous proof techniques for both Richman and poorman bidding. ","lang":"eng"}],"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:47:42Z","ddc":["004"],"date_updated":"2023-08-07T14:08:34Z","status":"public","type":"conference","conference":{"name":"MFCS: nternational Symposium on Mathematical Foundations of Computer Science","start_date":"2019-08-26","location":"Aachen, Germany","end_date":"2019-08-30"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"6884","doi":"10.4230/LIPICS.MFCS.2019.11","date_published":"2019-08-01T00:00:00Z","date_created":"2019-09-18T08:04:26Z","day":"01","has_accepted_license":"1","year":"2019","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"title":"Bidding mechanisms in graph games","author":[{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy","last_name":"Avni","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"last_name":"Zikelic","full_name":"Zikelic, Dorde","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["1905.03835"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Avni, Guy, et al. Bidding Mechanisms in Graph Games. Vol. 138, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.MFCS.2019.11.","apa":"Avni, G., Henzinger, T. A., & Zikelic, D. (2019). Bidding mechanisms in graph games (Vol. 138). Presented at the MFCS: nternational Symposium on Mathematical Foundations of Computer Science, Aachen, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2019.11","ama":"Avni G, Henzinger TA, Zikelic D. Bidding mechanisms in graph games. In: Vol 138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.MFCS.2019.11","ieee":"G. Avni, T. A. Henzinger, and D. Zikelic, “Bidding mechanisms in graph games,” presented at the MFCS: nternational Symposium on Mathematical Foundations of Computer Science, Aachen, Germany, 2019, vol. 138.","short":"G. Avni, T.A. Henzinger, D. Zikelic, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","chicago":"Avni, Guy, Thomas A Henzinger, and Dorde Zikelic. “Bidding Mechanisms in Graph Games,” Vol. 138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.MFCS.2019.11.","ista":"Avni G, Henzinger TA, Zikelic D. 2019. Bidding mechanisms in graph games. MFCS: nternational Symposium on Mathematical Foundations of Computer Science, LIPIcs, vol. 138, 11."},"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"grant_number":"M02369","name":"Formal Methods meets Algorithmic Game Theory","_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"},{"_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S11402-N23"}],"article_number":"11"},{"_id":"13471","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"status":"public","article_type":"original","type":"journal_article","extern":"1","date_updated":"2023-08-09T12:26:08Z","oa_version":"Published Version","abstract":[{"text":"We perform an extensive numerical study of the evolution of massive binary systems to predict the peculiar velocities that stars obtain when their companion collapses and disrupts the system. Our aim is to (i) identify which predictions are robust against model uncertainties and assess their implications, (ii) investigate which physical processes leave a clear imprint and may therefore be constrained observationally, and (iii) provide a suite of publicly available model predictions to allow for the use of kinematic constraints from the Gaia mission. We find that 22+26−8% of all massive binary systems merge prior to the first core-collapse in the system. Of the remainder, 86+11−9% become unbound because of the core-collapse. Remarkably, this rarely produces runaway stars (observationally defined as stars with velocities above 30 km s−1). These are outnumbered by more than an order of magnitude by slower unbound companions, or “walkaway stars”. This is a robust outcome of our simulations and is due to the reversal of the mass ratio prior to the explosion and widening of the orbit, as we show analytically and numerically. For stars more massive than 15 M⊙, we estimate that 10+5−8% are walkaways and only 0.5+1.0−0.4% are runaways, nearly all of which have accreted mass from their companion. Our findings are consistent with earlier studies; however, the low runaway fraction we find is in tension with observed fractions of about 10%. Thus, astrometric data on presently single massive stars can potentially constrain the physics of massive binary evolution. Finally, we show that the high end of the mass distributions of runaway stars is very sensitive to the assumed black hole natal kicks, and we propose this as a potentially stringent test for the explosion mechanism. We also discuss companions remaining bound that can evolve into X-ray and gravitational wave sources.","lang":"eng"}],"intvolume":" 624","month":"04","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1051/0004-6361/201833297"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"volume":624,"article_number":"A66","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Renzo, M., E. Zapartas, S. E. de Mink, Ylva Louise Linsdotter Götberg, S. Justham, R. J. Farmer, R. G. Izzard, S. Toonen, and H. Sana. “Massive Runaway and Walkaway Stars.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201833297.","ista":"Renzo M, Zapartas E, de Mink SE, Götberg YLL, Justham S, Farmer RJ, Izzard RG, Toonen S, Sana H. 2019. Massive runaway and walkaway stars. Astronomy & Astrophysics. 624, A66.","mla":"Renzo, M., et al. “Massive Runaway and Walkaway Stars.” Astronomy & Astrophysics, vol. 624, A66, EDP Sciences, 2019, doi:10.1051/0004-6361/201833297.","ieee":"M. Renzo et al., “Massive runaway and walkaway stars,” Astronomy & Astrophysics, vol. 624. EDP Sciences, 2019.","short":"M. Renzo, E. Zapartas, S.E. de Mink, Y.L.L. Götberg, S. Justham, R.J. Farmer, R.G. Izzard, S. Toonen, H. Sana, Astronomy & Astrophysics 624 (2019).","apa":"Renzo, M., Zapartas, E., de Mink, S. E., Götberg, Y. L. L., Justham, S., Farmer, R. J., … Sana, H. (2019). Massive runaway and walkaway stars. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201833297","ama":"Renzo M, Zapartas E, de Mink SE, et al. Massive runaway and walkaway stars. Astronomy & Astrophysics. 2019;624. doi:10.1051/0004-6361/201833297"},"title":"Massive runaway and walkaway stars","external_id":{"arxiv":["1804.09164"]},"article_processing_charge":"No","author":[{"last_name":"Renzo","full_name":"Renzo, M.","first_name":"M."},{"first_name":"E.","last_name":"Zapartas","full_name":"Zapartas, E."},{"first_name":"S. E.","last_name":"de Mink","full_name":"de Mink, S. E."},{"full_name":"Götberg, Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","last_name":"Götberg","first_name":"Ylva Louise Linsdotter","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d"},{"full_name":"Justham, S.","last_name":"Justham","first_name":"S."},{"first_name":"R. J.","full_name":"Farmer, R. J.","last_name":"Farmer"},{"last_name":"Izzard","full_name":"Izzard, R. G.","first_name":"R. G."},{"first_name":"S.","full_name":"Toonen, S.","last_name":"Toonen"},{"full_name":"Sana, H.","last_name":"Sana","first_name":"H."}],"oa":1,"publisher":"EDP Sciences","quality_controlled":"1","publication":"Astronomy & Astrophysics","day":"11","year":"2019","date_created":"2023-08-03T10:14:18Z","date_published":"2019-04-11T00:00:00Z","doi":"10.1051/0004-6361/201833297"},{"_id":"13470","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"status":"public","type":"journal_article","article_type":"original","extern":"1","date_updated":"2023-08-09T12:29:58Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Context. Massive Wolf–Rayet (WR) stars dominate the radiative and mechanical energy budget of galaxies and probe a critical phase in the evolution of massive stars prior to core collapse. It is not known whether core He-burning WR stars (classical WR; cWR) form predominantly through wind stripping (w-WR) or binary stripping (b-WR). Whereas spectroscopy of WR binaries has so-far largely been avoided because of its complexity, our study focuses on the 44 WR binaries and binary candidates of the Large Magellanic Cloud (LMC; metallicity Z ≈ 0.5 Z⊙), which were identified on the basis of radial velocity variations, composite spectra, or high X-ray luminosities.\r\n\r\nAims. Relying on a diverse spectroscopic database, we aim to derive the physical and orbital parameters of our targets, confronting evolution models of evolved massive stars at subsolar metallicity and constraining the impact of binary interaction in forming these stars.\r\n\r\nMethods. Spectroscopy was performed using the Potsdam Wolf–Rayet (PoWR) code and cross-correlation techniques. Disentanglement was performed using the code Spectangular or the shift-and-add algorithm. Evolutionary status was interpreted using the Binary Population and Spectral Synthesis (BPASS) code, exploring binary interaction and chemically homogeneous evolution.\r\n\r\nResults. Among our sample, 28/44 objects show composite spectra and are analyzed as such. An additional five targets show periodically moving WR primaries but no detected companions (SB1); two (BAT99 99 and 112) are potential WR + compact-object candidates owing to their high X-ray luminosities. We cannot confirm the binary nature of the remaining 11 candidates. About two-thirds of the WN components in binaries are identified as cWR, and one-third as hydrogen-burning WR stars. We establish metallicity-dependent mass-loss recipes, which broadly agree with those recently derived for single WN stars, and in which so-called WN3/O3 stars are clear outliers. We estimate that 45 ± 30% of the cWR stars in our sample have interacted with a companion via mass transfer. However, only ≈12 ± 7% of the cWR stars in our sample naively appear to have formed purely owing to stripping via a companion (12% b-WR). Assuming that apparently single WR stars truly formed as single stars, this comprises ≈4% of the whole LMC WN population, which is about ten times less than expected. No obvious differences in the properties of single and binary WN stars, whose luminosities extend down to log L ≈ 5.2 [L⊙], are apparent. With the exception of a few systems (BAT99 19, 49, and 103), the equatorial rotational velocities of the OB-type companions are moderate (veq ≲ 250 km s−1) and challenge standard formalisms of angular-momentum accretion. For most objects, chemically homogeneous evolution can be rejected for the secondary, but not for the WR progenitor.\r\n\r\nConclusions. No obvious dichotomy in the locations of apparently single and binary WN stars on the Hertzsprung-Russell diagram is apparent. According to commonly used stellar evolution models (BPASS, Geneva), most apparently single WN stars could not have formed as single stars, implying that they were stripped by an undetected companion. Otherwise, it must follow that pre-WR mass-loss/mixing (e.g., during the red supergiant phase) are strongly underestimated in standard stellar evolution models."}],"intvolume":" 627","month":"07","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1051/0004-6361/201935684"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"volume":627,"related_material":{"link":[{"url":"https://doi.org/10.1051/0004-6361/201935684e","relation":"erratum"}]},"article_number":"A151","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Shenar, T., et al. “The Wolf–Rayet Binaries of the Nitrogen Sequence in the Large Magellanic Cloud.” Astronomy & Astrophysics, vol. 627, A151, EDP Sciences, 2019, doi:10.1051/0004-6361/201935684.","apa":"Shenar, T., Sablowski, D. P., Hainich, R., Todt, H., Moffat, A. F. J., Oskinova, L. M., … Hamann, W.-R. (2019). The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic Cloud. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201935684","ama":"Shenar T, Sablowski DP, Hainich R, et al. The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic Cloud. Astronomy & Astrophysics. 2019;627. doi:10.1051/0004-6361/201935684","ieee":"T. Shenar et al., “The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic Cloud,” Astronomy & Astrophysics, vol. 627. EDP Sciences, 2019.","short":"T. Shenar, D.P. Sablowski, R. Hainich, H. Todt, A.F.J. Moffat, L.M. Oskinova, V. Ramachandran, H. Sana, A.A.C. Sander, O. Schnurr, N. St-Louis, D. Vanbeveren, Y.L.L. Götberg, W.-R. Hamann, Astronomy & Astrophysics 627 (2019).","chicago":"Shenar, T., D. P. Sablowski, R. Hainich, H. Todt, A. F. J. Moffat, L. M. Oskinova, V. Ramachandran, et al. “The Wolf–Rayet Binaries of the Nitrogen Sequence in the Large Magellanic Cloud.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201935684.","ista":"Shenar T, Sablowski DP, Hainich R, Todt H, Moffat AFJ, Oskinova LM, Ramachandran V, Sana H, Sander AAC, Schnurr O, St-Louis N, Vanbeveren D, Götberg YLL, Hamann W-R. 2019. The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic Cloud. Astronomy & Astrophysics. 627, A151."},"title":"The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic Cloud","article_processing_charge":"No","author":[{"first_name":"T.","last_name":"Shenar","full_name":"Shenar, T."},{"last_name":"Sablowski","full_name":"Sablowski, D. P.","first_name":"D. P."},{"full_name":"Hainich, R.","last_name":"Hainich","first_name":"R."},{"full_name":"Todt, H.","last_name":"Todt","first_name":"H."},{"first_name":"A. F. J.","last_name":"Moffat","full_name":"Moffat, A. F. J."},{"last_name":"Oskinova","full_name":"Oskinova, L. M.","first_name":"L. M."},{"last_name":"Ramachandran","full_name":"Ramachandran, V.","first_name":"V."},{"first_name":"H.","full_name":"Sana, H.","last_name":"Sana"},{"last_name":"Sander","full_name":"Sander, A. A. C.","first_name":"A. A. C."},{"full_name":"Schnurr, O.","last_name":"Schnurr","first_name":"O."},{"first_name":"N.","full_name":"St-Louis, N.","last_name":"St-Louis"},{"last_name":"Vanbeveren","full_name":"Vanbeveren, D.","first_name":"D."},{"id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","first_name":"Ylva Louise Linsdotter","last_name":"Götberg","full_name":"Götberg, Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911"},{"first_name":"W.-R.","full_name":"Hamann, W.-R.","last_name":"Hamann"}],"oa":1,"quality_controlled":"1","publisher":"EDP Sciences","publication":"Astronomy & Astrophysics","day":"16","year":"2019","date_created":"2023-08-03T10:14:09Z","doi":"10.1051/0004-6361/201935684","date_published":"2019-07-16T00:00:00Z"},{"oa":1,"quality_controlled":"1","publisher":"EDP Sciences","date_created":"2023-08-03T10:14:27Z","date_published":"2019-03-27T00:00:00Z","doi":"10.1051/0004-6361/201732206","publication":"Astronomy & Astrophysics","day":"27","year":"2019","article_number":"A34","title":"No surviving non-compact stellar companion to Cassiopeia A","article_processing_charge":"No","external_id":{"arxiv":["1711.00055"]},"author":[{"full_name":"Kerzendorf, Wolfgang E.","last_name":"Kerzendorf","first_name":"Wolfgang E."},{"full_name":"Do, Tuan","last_name":"Do","first_name":"Tuan"},{"full_name":"de Mink, Selma E.","last_name":"de Mink","first_name":"Selma E."},{"full_name":"Götberg, Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","last_name":"Götberg","first_name":"Ylva Louise Linsdotter","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d"},{"full_name":"Milisavljevic, Dan","last_name":"Milisavljevic","first_name":"Dan"},{"first_name":"Emmanouil","full_name":"Zapartas, Emmanouil","last_name":"Zapartas"},{"first_name":"Mathieu","last_name":"Renzo","full_name":"Renzo, Mathieu"},{"full_name":"Justham, Stephen","last_name":"Justham","first_name":"Stephen"},{"last_name":"Podsiadlowski","full_name":"Podsiadlowski, Philipp","first_name":"Philipp"},{"full_name":"Fesen, Robert A.","last_name":"Fesen","first_name":"Robert A."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kerzendorf, Wolfgang E., Tuan Do, Selma E. de Mink, Ylva Louise Linsdotter Götberg, Dan Milisavljevic, Emmanouil Zapartas, Mathieu Renzo, Stephen Justham, Philipp Podsiadlowski, and Robert A. Fesen. “No Surviving Non-Compact Stellar Companion to Cassiopeia A.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201732206.","ista":"Kerzendorf WE, Do T, de Mink SE, Götberg YLL, Milisavljevic D, Zapartas E, Renzo M, Justham S, Podsiadlowski P, Fesen RA. 2019. No surviving non-compact stellar companion to Cassiopeia A. Astronomy & Astrophysics. 623, A34.","mla":"Kerzendorf, Wolfgang E., et al. “No Surviving Non-Compact Stellar Companion to Cassiopeia A.” Astronomy & Astrophysics, vol. 623, A34, EDP Sciences, 2019, doi:10.1051/0004-6361/201732206.","apa":"Kerzendorf, W. E., Do, T., de Mink, S. E., Götberg, Y. L. L., Milisavljevic, D., Zapartas, E., … Fesen, R. A. (2019). No surviving non-compact stellar companion to Cassiopeia A. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201732206","ama":"Kerzendorf WE, Do T, de Mink SE, et al. No surviving non-compact stellar companion to Cassiopeia A. Astronomy & Astrophysics. 2019;623. doi:10.1051/0004-6361/201732206","short":"W.E. Kerzendorf, T. Do, S.E. de Mink, Y.L.L. Götberg, D. Milisavljevic, E. Zapartas, M. Renzo, S. Justham, P. Podsiadlowski, R.A. Fesen, Astronomy & Astrophysics 623 (2019).","ieee":"W. E. Kerzendorf et al., “No surviving non-compact stellar companion to Cassiopeia A,” Astronomy & Astrophysics, vol. 623. EDP Sciences, 2019."},"intvolume":" 623","month":"03","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1051/0004-6361/201732206"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Massive stars in binaries can give rise to extreme phenomena such as X-ray binaries and gravitational wave sources after one or both stars end their lives as core-collapse supernovae. Stars in close orbit around a stellar or compact companion are expected to explode as “stripped-envelope supernovae”, showing no (Type Ib/c) or little (Type IIb) signs of hydrogen in the spectra, because hydrogen-rich progenitors are too large to fit. The physical processes responsible for the stripping process and the fate of the companion are still very poorly understood. Aiming to find new clues, we investigate Cas A, which is a very young (∼340 yr) and near (∼3.4 kpc) remnant of a core-collapse supernova. Cas A has been subject to several searches for possible companions, all unsuccessfully. We present new measurements of the proper motions and photometry of stars in the vicinity based on deep HST ACS/WFC and WFC3-IR data. We identify stellar sources that are close enough in projection but using their proper motions we show that none are compatible with being at the location of center at the time of explosion, in agreement with earlier findings. Our photometric measurements allow us to place much deeper (order-of-magnitude) upper limits on the brightness of possible undetected companions. We systematically compare them with model predictions for a wide variety of scenarios. We can confidently rule out the presence of any stellar companion of any reasonable mass and age (main sequence, pre main sequence or stripped) ruling out what many considered to be likely evolutionary scenarios for Type IIb supernova (SN IIb). More exotic scenarios that predict the presence of a compact companion (white dwarf, neutron star or black hole) are still possible as well as scenarios where the progenitor of Cas A was single at the moment of explosion (either because it was truly single, or resulted from a binary that was disrupted, or from a binary merger). The presence of a compact companion would imply that Cas A is of interest to study exotic outcomes of binary evolution. The single-at-death solution would still require fine-tuning of the process that removed most of the envelope through a mass-loss mechanism yet to be identified. We discuss how future constraints from Gaia and even deeper photometric studies may help to place further constraints.","lang":"eng"}],"volume":623,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"status":"public","type":"journal_article","article_type":"original","_id":"13472","extern":"1","date_updated":"2023-08-09T12:28:17Z"},{"article_processing_charge":"No","external_id":{"arxiv":["1907.06687"]},"author":[{"full_name":"Zapartas, Emmanouil","last_name":"Zapartas","first_name":"Emmanouil"},{"last_name":"de Mink","full_name":"de Mink, Selma E.","first_name":"Selma E."},{"full_name":"Justham, Stephen","last_name":"Justham","first_name":"Stephen"},{"last_name":"Smith","full_name":"Smith, Nathan","first_name":"Nathan"},{"last_name":"de Koter","full_name":"de Koter, Alex","first_name":"Alex"},{"last_name":"Renzo","full_name":"Renzo, Mathieu","first_name":"Mathieu"},{"first_name":"Iair","full_name":"Arcavi, Iair","last_name":"Arcavi"},{"last_name":"Farmer","full_name":"Farmer, Rob","first_name":"Rob"},{"id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","first_name":"Ylva Louise Linsdotter","last_name":"Götberg","orcid":"0000-0002-6960-6911","full_name":"Götberg, Ylva Louise Linsdotter"},{"first_name":"Silvia","full_name":"Toonen, Silvia","last_name":"Toonen"}],"title":"The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction","citation":{"mla":"Zapartas, Emmanouil, et al. “The Diverse Lives of Progenitors of Hydrogen-Rich Core-Collapse Supernovae: The Role of Binary Interaction.” Astronomy & Astrophysics, vol. 631, A5, EDP Sciences, 2019, doi:10.1051/0004-6361/201935854.","short":"E. Zapartas, S.E. de Mink, S. Justham, N. Smith, A. de Koter, M. Renzo, I. Arcavi, R. Farmer, Y.L.L. Götberg, S. Toonen, Astronomy & Astrophysics 631 (2019).","ieee":"E. Zapartas et al., “The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction,” Astronomy & Astrophysics, vol. 631. EDP Sciences, 2019.","ama":"Zapartas E, de Mink SE, Justham S, et al. The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction. Astronomy & Astrophysics. 2019;631. doi:10.1051/0004-6361/201935854","apa":"Zapartas, E., de Mink, S. E., Justham, S., Smith, N., de Koter, A., Renzo, M., … Toonen, S. (2019). The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201935854","chicago":"Zapartas, Emmanouil, Selma E. de Mink, Stephen Justham, Nathan Smith, Alex de Koter, Mathieu Renzo, Iair Arcavi, Rob Farmer, Ylva Louise Linsdotter Götberg, and Silvia Toonen. “The Diverse Lives of Progenitors of Hydrogen-Rich Core-Collapse Supernovae: The Role of Binary Interaction.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201935854.","ista":"Zapartas E, de Mink SE, Justham S, Smith N, de Koter A, Renzo M, Arcavi I, Farmer R, Götberg YLL, Toonen S. 2019. The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction. Astronomy & Astrophysics. 631, A5."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"A5","date_created":"2023-08-03T10:13:52Z","doi":"10.1051/0004-6361/201935854","date_published":"2019-11-20T00:00:00Z","year":"2019","publication":"Astronomy & Astrophysics","day":"20","oa":1,"quality_controlled":"1","publisher":"EDP Sciences","date_updated":"2023-08-09T12:36:09Z","extern":"1","type":"journal_article","article_type":"original","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"status":"public","_id":"13468","volume":631,"publication_status":"published","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1051/0004-6361/201935854","open_access":"1"}],"scopus_import":"1","intvolume":" 631","month":"11","abstract":[{"text":"Hydrogen-rich supernovae, known as Type II (SNe II), are the most common class of explosions observed following the collapse of the core of massive stars. We used analytical estimates and population synthesis simulations to assess the fraction of SNe II progenitors that are expected to have exchanged mass with a companion prior to explosion. We estimate that 1/3 to 1/2 of SN II progenitors have a history of mass exchange with a binary companion before exploding. The dominant binary channels leading to SN II progenitors involve the merger of binary stars. Mergers are expected to produce a diversity of SN II progenitor characteristics, depending on the evolutionary timing and properties of the merger. Alternatively, SN II progenitors from interacting binaries may have accreted mass from their companion, and subsequently been ejected from the binary system after their companion exploded. We show that the overall fraction of SN II progenitors that are predicted to have experienced binary interaction is robust against the main physical uncertainties in our models. However, the relative importance of different binary evolutionary channels is affected by changing physical assumptions. We further discuss ways in which binarity might contribute to the observed diversity of SNe II by considering potential observational signatures arising from each binary channel. For supernovae which have a substantial H-rich envelope at explosion (i.e., excluding Type IIb SNe), a surviving non-compact companion would typically indicate that the supernova progenitor star was in a wide, non-interacting binary. We argue that a significant fraction of even Type II-P SNe are expected to have gained mass from a companion prior to explosion.","lang":"eng"}],"oa_version":"Published Version"},{"extern":"1","date_updated":"2023-08-09T12:34:11Z","_id":"13469","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"volume":629,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Stars stripped of their envelopes from interaction with a binary companion emit a significant fraction of their radiation as ionizing photons. They are potentially important stellar sources of ionizing radiation, however, they are still often neglected in spectral synthesis simulations or simulations of stellar feedback. In anticipating the large datasets of galaxy spectra from the upcoming James Webb Space Telescope, we modeled the radiative contribution from stripped stars by using detailed evolutionary and spectral models. We estimated their impact on the integrated spectra and specifically on the emission rates of H I-, He I-, and He II-ionizing photons from stellar populations. We find that stripped stars have the largest impact on the ionizing spectrum of a population in which star formation halted several Myr ago. In such stellar populations, stripped stars dominate the emission of ionizing photons, mimicking a younger stellar population in which massive stars are still present. Our models also suggest that stripped stars have harder ionizing spectra than massive stars. The additional ionizing radiation, with which stripped stars contribute affects observable properties that are related to the emission of ionizing photons from stellar populations. In co-eval stellar populations, the ionizing radiation from stripped stars increases the ionization parameter and the production efficiency of hydrogen ionizing photons. They also cause high values for these parameters for about ten times longer than what is predicted for massive stars. The effect on properties related to non-ionizing wavelengths is less pronounced, such as on the ultraviolet continuum slope or stellar contribution to emission lines. However, the hard ionizing radiation from stripped stars likely introduces a characteristic ionization structure of the nebula, which leads to the emission of highly ionized elements such as O2+ and C3+. We, therefore, expect that the presence of stripped stars affects the location in the BPT diagram and the diagnostic ratio of O III to O II nebular emission lines. Our models are publicly available through CDS database and on the STARBURST99 website."}],"intvolume":" 629","month":"09","main_file_link":[{"url":"https://doi.org/10.1051/0004-6361/201834525","open_access":"1"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Götberg, Y. L. L., de Mink, S. E., Groh, J. H., Leitherer, C., & Norman, C. (2019). The impact of stars stripped in binaries on the integrated spectra of stellar populations. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201834525","ama":"Götberg YLL, de Mink SE, Groh JH, Leitherer C, Norman C. The impact of stars stripped in binaries on the integrated spectra of stellar populations. Astronomy & Astrophysics. 2019;629. doi:10.1051/0004-6361/201834525","short":"Y.L.L. Götberg, S.E. de Mink, J.H. Groh, C. Leitherer, C. Norman, Astronomy & Astrophysics 629 (2019).","ieee":"Y. L. L. Götberg, S. E. de Mink, J. H. Groh, C. Leitherer, and C. Norman, “The impact of stars stripped in binaries on the integrated spectra of stellar populations,” Astronomy & Astrophysics, vol. 629. EDP Sciences, 2019.","mla":"Götberg, Ylva Louise Linsdotter, et al. “The Impact of Stars Stripped in Binaries on the Integrated Spectra of Stellar Populations.” Astronomy & Astrophysics, vol. 629, A134, EDP Sciences, 2019, doi:10.1051/0004-6361/201834525.","ista":"Götberg YLL, de Mink SE, Groh JH, Leitherer C, Norman C. 2019. The impact of stars stripped in binaries on the integrated spectra of stellar populations. Astronomy & Astrophysics. 629, A134.","chicago":"Götberg, Ylva Louise Linsdotter, S. E. de Mink, J. H. Groh, C. Leitherer, and C. Norman. “The Impact of Stars Stripped in Binaries on the Integrated Spectra of Stellar Populations.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201834525."},"title":"The impact of stars stripped in binaries on the integrated spectra of stellar populations","article_processing_charge":"No","external_id":{"arxiv":["1908.06102"]},"author":[{"last_name":"Götberg","orcid":"0000-0002-6960-6911","full_name":"Götberg, Ylva Louise Linsdotter","first_name":"Ylva Louise Linsdotter","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d"},{"first_name":"S. E.","full_name":"de Mink, S. E.","last_name":"de Mink"},{"last_name":"Groh","full_name":"Groh, J. H.","first_name":"J. H."},{"first_name":"C.","last_name":"Leitherer","full_name":"Leitherer, C."},{"last_name":"Norman","full_name":"Norman, C.","first_name":"C."}],"article_number":"A134","publication":"Astronomy & Astrophysics","day":"17","year":"2019","date_created":"2023-08-03T10:14:00Z","date_published":"2019-09-17T00:00:00Z","doi":"10.1051/0004-6361/201834525","oa":1,"publisher":"EDP Sciences","quality_controlled":"1"},{"day":"13","publication":"Proceedings of the National Academy of Sciences","year":"2019","date_published":"2019-11-13T00:00:00Z","doi":"10.1073/pnas.1907189116","date_created":"2023-08-09T13:10:36Z","page":"23923-23929","quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Baykusheva DR, Zindel D, Svoboda V, Bommeli E, Ochsner M, Tehlar A, Wörner HJ. 2019. Real-time probing of chirality during a chemical reaction. Proceedings of the National Academy of Sciences. 116(48), 23923–23929.","chicago":"Baykusheva, Denitsa Rangelova, Daniel Zindel, Vít Svoboda, Elias Bommeli, Manuel Ochsner, Andres Tehlar, and Hans Jakob Wörner. “Real-Time Probing of Chirality during a Chemical Reaction.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1907189116.","ieee":"D. R. Baykusheva et al., “Real-time probing of chirality during a chemical reaction,” Proceedings of the National Academy of Sciences, vol. 116, no. 48. Proceedings of the National Academy of Sciences, pp. 23923–23929, 2019.","short":"D.R. Baykusheva, D. Zindel, V. Svoboda, E. Bommeli, M. Ochsner, A. Tehlar, H.J. Wörner, Proceedings of the National Academy of Sciences 116 (2019) 23923–23929.","ama":"Baykusheva DR, Zindel D, Svoboda V, et al. Real-time probing of chirality during a chemical reaction. Proceedings of the National Academy of Sciences. 2019;116(48):23923-23929. doi:10.1073/pnas.1907189116","apa":"Baykusheva, D. R., Zindel, D., Svoboda, V., Bommeli, E., Ochsner, M., Tehlar, A., & Wörner, H. J. (2019). Real-time probing of chirality during a chemical reaction. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1907189116","mla":"Baykusheva, Denitsa Rangelova, et al. “Real-Time Probing of Chirality during a Chemical Reaction.” Proceedings of the National Academy of Sciences, vol. 116, no. 48, Proceedings of the National Academy of Sciences, 2019, pp. 23923–29, doi:10.1073/pnas.1907189116."},"title":"Real-time probing of chirality during a chemical reaction","author":[{"first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova"},{"last_name":"Zindel","full_name":"Zindel, Daniel","first_name":"Daniel"},{"first_name":"Vít","last_name":"Svoboda","full_name":"Svoboda, Vít"},{"first_name":"Elias","full_name":"Bommeli, Elias","last_name":"Bommeli"},{"last_name":"Ochsner","full_name":"Ochsner, Manuel","first_name":"Manuel"},{"full_name":"Tehlar, Andres","last_name":"Tehlar","first_name":"Andres"},{"first_name":"Hans Jakob","full_name":"Wörner, Hans Jakob","last_name":"Wörner"}],"article_processing_charge":"No","external_id":{"pmid":["31723044"],"arxiv":["1906.10818"]},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","issue":"48","volume":116,"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Chiral molecules interact and react differently with other chiral objects, depending on their handedness. Therefore, it is essential to understand and ultimately control the evolution of molecular chirality during chemical reactions. Although highly sophisticated techniques for the controlled synthesis of chiral molecules have been developed, the observation of chirality on the natural femtosecond time scale of a chemical reaction has so far remained out of reach in the gas phase. Here, we demonstrate a general experimental technique, based on high-harmonic generation in tailored laser fields, and apply it to probe the time evolution of molecular chirality during the photodissociation of 2-iodobutane. These measurements show a change in sign and a pronounced increase in the magnitude of the chiral response over the first 100 fs, followed by its decay within less than 500 fs, revealing the photodissociation to achiral products. The observed time evolution is explained in terms of the variation of the electric and magnetic transition-dipole moments between the lowest electronic states of the cation as a function of the reaction coordinate. These results open the path to investigations of the chirality of molecular-reaction pathways, light-induced chirality in chemical processes, and the control of molecular chirality through tailored laser pulses."}],"month":"11","intvolume":" 116","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1907189116","open_access":"1"}],"extern":"1","date_updated":"2023-08-22T07:40:05Z","_id":"14001","status":"public","keyword":["Multidisciplinary"],"type":"journal_article","article_type":"original"},{"file_date_updated":"2020-07-14T12:47:36Z","department":[{"_id":"HeEd"}],"date_updated":"2023-08-22T12:37:47Z","ddc":["000"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"6671","ec_funded":1,"volume":3,"issue":"1-2","publication_status":"published","publication_identifier":{"eissn":["2367-1734"],"issn":["2367-1726"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2019-07-31T08:09:56Z","file_name":"2019_JournAppliedComputTopol_Boissonnat.pdf","date_updated":"2020-07-14T12:47:36Z","file_size":2215157,"creator":"dernst","file_id":"6741","checksum":"a5b244db9f751221409cf09c97ee0935","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"intvolume":" 3","month":"06","abstract":[{"text":"In this paper we discuss three results. The first two concern general sets of positive reach: we first characterize the reach of a closed set by means of a bound on the metric distortion between the distance measured in the ambient Euclidean space and the shortest path distance measured in the set. Secondly, we prove that the intersection of a ball with radius less than the reach with the set is geodesically convex, meaning that the shortest path between any two points in the intersection lies itself in the intersection. For our third result we focus on manifolds with positive reach and give a bound on the angle between tangent spaces at two different points in terms of the reach and the distance between the two points.","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Jean-Daniel","last_name":"Boissonnat","full_name":"Boissonnat, Jean-Daniel"},{"last_name":"Lieutier","full_name":"Lieutier, André","first_name":"André"},{"last_name":"Wintraecken","full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","first_name":"Mathijs"}],"title":"The reach, metric distortion, geodesic convexity and the variation of tangent spaces","citation":{"mla":"Boissonnat, Jean-Daniel, et al. “The Reach, Metric Distortion, Geodesic Convexity and the Variation of Tangent Spaces.” Journal of Applied and Computational Topology, vol. 3, no. 1–2, Springer Nature, 2019, pp. 29–58, doi:10.1007/s41468-019-00029-8.","short":"J.-D. Boissonnat, A. Lieutier, M. Wintraecken, Journal of Applied and Computational Topology 3 (2019) 29–58.","ieee":"J.-D. Boissonnat, A. Lieutier, and M. Wintraecken, “The reach, metric distortion, geodesic convexity and the variation of tangent spaces,” Journal of Applied and Computational Topology, vol. 3, no. 1–2. Springer Nature, pp. 29–58, 2019.","apa":"Boissonnat, J.-D., Lieutier, A., & Wintraecken, M. (2019). The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-019-00029-8","ama":"Boissonnat J-D, Lieutier A, Wintraecken M. The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. 2019;3(1-2):29–58. doi:10.1007/s41468-019-00029-8","chicago":"Boissonnat, Jean-Daniel, André Lieutier, and Mathijs Wintraecken. “The Reach, Metric Distortion, Geodesic Convexity and the Variation of Tangent Spaces.” Journal of Applied and Computational Topology. Springer Nature, 2019. https://doi.org/10.1007/s41468-019-00029-8.","ista":"Boissonnat J-D, Lieutier A, Wintraecken M. 2019. The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. 3(1–2), 29–58."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"page":"29–58","date_created":"2019-07-24T08:37:29Z","doi":"10.1007/s41468-019-00029-8","date_published":"2019-06-01T00:00:00Z","year":"2019","has_accepted_license":"1","publication":"Journal of Applied and Computational Topology","day":"01","oa":1,"publisher":"Springer Nature","quality_controlled":"1"},{"oa":1,"quality_controlled":"1","publisher":"Elsevier","publication":"Stochastic Processes and their Applications","day":"01","year":"2019","isi":1,"date_created":"2018-12-11T11:45:42Z","doi":"10.1016/j.spa.2018.04.003","date_published":"2019-03-01T00:00:00Z","page":"995-1012","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"M. Gerencser, I. Gyöngy, Stochastic Processes and Their Applications 129 (2019) 995–1012.","ieee":"M. Gerencser and I. Gyöngy, “A Feynman–Kac formula for stochastic Dirichlet problems,” Stochastic Processes and their Applications, vol. 129, no. 3. Elsevier, pp. 995–1012, 2019.","apa":"Gerencser, M., & Gyöngy, I. (2019). A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and Their Applications. Elsevier. https://doi.org/10.1016/j.spa.2018.04.003","ama":"Gerencser M, Gyöngy I. A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and their Applications. 2019;129(3):995-1012. doi:10.1016/j.spa.2018.04.003","mla":"Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet Problems.” Stochastic Processes and Their Applications, vol. 129, no. 3, Elsevier, 2019, pp. 995–1012, doi:10.1016/j.spa.2018.04.003.","ista":"Gerencser M, Gyöngy I. 2019. A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and their Applications. 129(3), 995–1012.","chicago":"Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet Problems.” Stochastic Processes and Their Applications. Elsevier, 2019. https://doi.org/10.1016/j.spa.2018.04.003."},"title":"A Feynman–Kac formula for stochastic Dirichlet problems","external_id":{"isi":["000458945300012"],"arxiv":["1611.04177"]},"article_processing_charge":"No","author":[{"id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate","full_name":"Gerencser, Mate","last_name":"Gerencser"},{"full_name":"Gyöngy, István","last_name":"Gyöngy","first_name":"István"}],"oa_version":"Preprint","abstract":[{"text":"A representation formula for solutions of stochastic partial differential equations with Dirichlet boundary conditions is proved. The scope of our setting is wide enough to cover the general situation when the backward characteristics that appear in the usual formulation are not even defined in the Itô sense.","lang":"eng"}],"intvolume":" 129","month":"03","main_file_link":[{"url":"https://arxiv.org/abs/1611.04177","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","issue":"3","volume":129,"_id":"301","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-24T14:20:49Z","department":[{"_id":"JaMa"}]},{"ddc":["530"],"date_updated":"2023-08-24T14:27:51Z","file_date_updated":"2020-07-14T12:48:07Z","department":[{"_id":"RoSe"}],"_id":"80","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"creator":"dernst","date_updated":"2020-07-14T12:48:07Z","file_size":893902,"date_created":"2018-12-17T10:34:06Z","file_name":"2018_CommunMathPhys_Deuchert.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5688","checksum":"c7e9880b43ac726712c1365e9f2f73a6"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":368,"issue":"2","ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We consider an interacting, dilute Bose gas trapped in a harmonic potential at a positive temperature. The system is analyzed in a combination of a thermodynamic and a Gross–Pitaevskii (GP) limit where the trap frequency ω, the temperature T, and the particle number N are related by N∼ (T/ ω) 3→ ∞ while the scattering length is so small that the interaction energy per particle around the center of the trap is of the same order of magnitude as the spectral gap in the trap. We prove that the difference between the canonical free energy of the interacting gas and the one of the noninteracting system can be obtained by minimizing the GP energy functional. We also prove Bose–Einstein condensation in the following sense: The one-particle density matrix of any approximate minimizer of the canonical free energy functional is to leading order given by that of the noninteracting gas but with the free condensate wavefunction replaced by the GP minimizer."}],"month":"06","intvolume":" 368","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Deuchert, Andreas, et al. “Bose–Einstein Condensation in a Dilute, Trapped Gas at Positive Temperature.” Communications in Mathematical Physics, vol. 368, no. 2, Springer, 2019, pp. 723–76, doi:10.1007/s00220-018-3239-0.","apa":"Deuchert, A., Seiringer, R., & Yngvason, J. (2019). Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-018-3239-0","ama":"Deuchert A, Seiringer R, Yngvason J. Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. 2019;368(2):723-776. doi:10.1007/s00220-018-3239-0","ieee":"A. Deuchert, R. Seiringer, and J. Yngvason, “Bose–Einstein condensation in a dilute, trapped gas at positive temperature,” Communications in Mathematical Physics, vol. 368, no. 2. Springer, pp. 723–776, 2019.","short":"A. Deuchert, R. Seiringer, J. Yngvason, Communications in Mathematical Physics 368 (2019) 723–776.","chicago":"Deuchert, Andreas, Robert Seiringer, and Jakob Yngvason. “Bose–Einstein Condensation in a Dilute, Trapped Gas at Positive Temperature.” Communications in Mathematical Physics. Springer, 2019. https://doi.org/10.1007/s00220-018-3239-0.","ista":"Deuchert A, Seiringer R, Yngvason J. 2019. Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. 368(2), 723–776."},"title":"Bose–Einstein condensation in a dilute, trapped gas at positive temperature","publist_id":"7974","author":[{"orcid":"0000-0003-3146-6746","full_name":"Deuchert, Andreas","last_name":"Deuchert","first_name":"Andreas","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"first_name":"Jakob","last_name":"Yngvason","full_name":"Yngvason, Jakob"}],"external_id":{"isi":["000467796800007"]},"article_processing_charge":"Yes (via OA deal)","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"},{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"day":"01","publication":"Communications in Mathematical Physics","isi":1,"has_accepted_license":"1","year":"2019","doi":"10.1007/s00220-018-3239-0","date_published":"2019-06-01T00:00:00Z","date_created":"2018-12-11T11:44:31Z","page":"723-776","quality_controlled":"1","publisher":"Springer","oa":1},{"date_updated":"2023-08-24T14:29:48Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"NiBa"}],"_id":"5911","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"issn":["01695347"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"7245","checksum":"ef24572d6ebcc1452c067e05410cc4a2","date_updated":"2020-07-14T12:47:13Z","file_size":1946795,"creator":"cziletti","date_created":"2020-01-09T10:55:58Z","file_name":"2019_Trends_Evolution_Faria.pdf"}],"ec_funded":1,"issue":"3","volume":34,"abstract":[{"text":"Empirical data suggest that inversions in many species contain genes important for intraspecific divergence and speciation, yet mechanisms of evolution remain unclear. While genes inside an inversion are tightly linked, inversions are not static but evolve separately from the rest of the genome by new mutations, recombination within arrangements, and gene flux between arrangements. Inversion polymorphisms are maintained by different processes, for example, divergent or balancing selection, or a mix of multiple processes. Moreover, the relative roles of selection, drift, mutation, and recombination will change over the lifetime of an inversion and within its area of distribution. We believe inversions are central to the evolution of many species, but we need many more data and new models to understand the complex mechanisms involved.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 34","month":"03","citation":{"ieee":"R. Faria, K. Johannesson, R. K. Butlin, and A. M. Westram, “Evolving inversions,” Trends in Ecology and Evolution, vol. 34, no. 3. Elsevier, pp. 239–248, 2019.","short":"R. Faria, K. Johannesson, R.K. Butlin, A.M. Westram, Trends in Ecology and Evolution 34 (2019) 239–248.","ama":"Faria R, Johannesson K, Butlin RK, Westram AM. Evolving inversions. Trends in Ecology and Evolution. 2019;34(3):239-248. doi:10.1016/j.tree.2018.12.005","apa":"Faria, R., Johannesson, K., Butlin, R. K., & Westram, A. M. (2019). Evolving inversions. Trends in Ecology and Evolution. Elsevier. https://doi.org/10.1016/j.tree.2018.12.005","mla":"Faria, Rui, et al. “Evolving Inversions.” Trends in Ecology and Evolution, vol. 34, no. 3, Elsevier, 2019, pp. 239–48, doi:10.1016/j.tree.2018.12.005.","ista":"Faria R, Johannesson K, Butlin RK, Westram AM. 2019. Evolving inversions. Trends in Ecology and Evolution. 34(3), 239–248.","chicago":"Faria, Rui, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram. “Evolving Inversions.” Trends in Ecology and Evolution. Elsevier, 2019. https://doi.org/10.1016/j.tree.2018.12.005."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000459899000013"]},"article_processing_charge":"No","author":[{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"},{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"}],"title":"Evolving inversions","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"year":"2019","has_accepted_license":"1","isi":1,"publication":"Trends in Ecology and Evolution","day":"01","page":"239-248","date_created":"2019-02-03T22:59:15Z","doi":"10.1016/j.tree.2018.12.005","date_published":"2019-03-01T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Elsevier"},{"project":[{"_id":"25E549F4-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"320593","name":"Arithmetic and physics of Higgs moduli spaces"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Hausel T, Mereb M, Wong M. 2019. Arithmetic and representation theory of wild character varieties. Journal of the European Mathematical Society. 21(10), 2995–3052.","chicago":"Hausel, Tamás, Martin Mereb, and Michael Wong. “Arithmetic and Representation Theory of Wild Character Varieties.” Journal of the European Mathematical Society. European Mathematical Society, 2019. https://doi.org/10.4171/JEMS/896.","ieee":"T. Hausel, M. Mereb, and M. Wong, “Arithmetic and representation theory of wild character varieties,” Journal of the European Mathematical Society, vol. 21, no. 10. European Mathematical Society, pp. 2995–3052, 2019.","short":"T. Hausel, M. Mereb, M. Wong, Journal of the European Mathematical Society 21 (2019) 2995–3052.","apa":"Hausel, T., Mereb, M., & Wong, M. (2019). Arithmetic and representation theory of wild character varieties. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/896","ama":"Hausel T, Mereb M, Wong M. Arithmetic and representation theory of wild character varieties. Journal of the European Mathematical Society. 2019;21(10):2995-3052. doi:10.4171/JEMS/896","mla":"Hausel, Tamás, et al. “Arithmetic and Representation Theory of Wild Character Varieties.” Journal of the European Mathematical Society, vol. 21, no. 10, European Mathematical Society, 2019, pp. 2995–3052, doi:10.4171/JEMS/896."},"title":"Arithmetic and representation theory of wild character varieties","external_id":{"isi":["000480413600002"],"arxiv":["1604.03382"]},"article_processing_charge":"No","publist_id":"7384","author":[{"last_name":"Hausel","full_name":"Hausel, Tamas","first_name":"Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87"},{"id":"43D735EE-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Mereb","full_name":"Mereb, Martin"},{"full_name":"Wong, Michael","last_name":"Wong","first_name":"Michael"}],"oa":1,"quality_controlled":"1","publisher":"European Mathematical Society","publication":"Journal of the European Mathematical Society","day":"01","year":"2019","isi":1,"date_created":"2018-12-11T11:46:29Z","date_published":"2019-10-01T00:00:00Z","doi":"10.4171/JEMS/896","page":"2995-3052","_id":"439","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-08-24T14:24:49Z","department":[{"_id":"TaHa"}],"oa_version":"Preprint","abstract":[{"text":"We count points over a finite field on wild character varieties,of Riemann surfaces for singularities with regular semisimple leading term. The new feature in our counting formulas is the appearance of characters of Yokonuma–Hecke algebras. Our result leads to the conjecture that the mixed Hodge polynomials of these character varieties agree with previously conjectured perverse Hodge polynomials of certain twisted parabolic Higgs moduli spaces, indicating the\r\npossibility of a P = W conjecture for a suitable wild Hitchin system.","lang":"eng"}],"intvolume":" 21","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/1604.03382","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1435-9855"]},"ec_funded":1,"volume":21,"issue":"10"},{"publication_status":"published","language":[{"iso":"eng"}],"volume":27,"abstract":[{"lang":"eng","text":"Clinical Utility Gene Card. 1. Name of Disease (Synonyms): Pontocerebellar hypoplasia type 9 (PCH9) and spastic paraplegia-63 (SPG63). 2. OMIM# of the Disease: 615809 and 615686. 3. Name of the Analysed Genes or DNA/Chromosome Segments: AMPD2 at 1p13.3. 4. OMIM# of the Gene(s): 102771."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41431-018-0231-2"}],"month":"01","intvolume":" 27","date_updated":"2023-08-24T14:28:24Z","department":[{"_id":"GaNo"}],"_id":"105","type":"journal_article","article_type":"original","status":"public","isi":1,"year":"2019","day":"01","publication":"European Journal of Human Genetics","page":"161-166","date_published":"2019-01-01T00:00:00Z","doi":"10.1038/s41431-018-0231-2","date_created":"2018-12-11T11:44:39Z","acknowledgement":"This work was supported by EuroGentest2 (Unit 2: “Genetic testing as part of health care”), a Coordination Action under FP7 (Grant Agreement Number 261469) and the European Society of Human Genetics. We acknowledge the participation of the patients and their families in these studies, as well as the generous financial support of the Lefroy and Handbury families. APLM was supported by an Australian Postgraduate Award. PJL is supported by an NHMRC Career Development Fellowship (GNT1032364). RJL is supported by a Melbourne Children’s Clinician Scientist Fellowship.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"citation":{"chicago":"Marsh, Ashley, Gaia Novarino, Paul Lockhart, and Richard Leventer. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” European Journal of Human Genetics. Springer Nature, 2019. https://doi.org/10.1038/s41431-018-0231-2.","ista":"Marsh A, Novarino G, Lockhart P, Leventer R. 2019. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 27, 161–166.","mla":"Marsh, Ashley, et al. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” European Journal of Human Genetics, vol. 27, Springer Nature, 2019, pp. 161–66, doi:10.1038/s41431-018-0231-2.","short":"A. Marsh, G. Novarino, P. Lockhart, R. Leventer, European Journal of Human Genetics 27 (2019) 161–166.","ieee":"A. Marsh, G. Novarino, P. Lockhart, and R. Leventer, “CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63,” European Journal of Human Genetics, vol. 27. Springer Nature, pp. 161–166, 2019.","ama":"Marsh A, Novarino G, Lockhart P, Leventer R. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 2019;27:161-166. doi:10.1038/s41431-018-0231-2","apa":"Marsh, A., Novarino, G., Lockhart, P., & Leventer, R. (2019). CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. Springer Nature. https://doi.org/10.1038/s41431-018-0231-2"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Marsh, Ashley","last_name":"Marsh","first_name":"Ashley"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino"},{"full_name":"Lockhart, Paul","last_name":"Lockhart","first_name":"Paul"},{"first_name":"Richard","last_name":"Leventer","full_name":"Leventer, Richard"}],"publist_id":"7949","article_processing_charge":"No","external_id":{"isi":["000454111500019"],"pmid":["30089829"]},"title":"CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Dareiotis, Konstantinos, Mate Gerencser, and Benjamin Gess. “Entropy Solutions for Stochastic Porous Media Equations.” Journal of Differential Equations. Elsevier, 2019. https://doi.org/10.1016/j.jde.2018.09.012.","ista":"Dareiotis K, Gerencser M, Gess B. 2019. Entropy solutions for stochastic porous media equations. Journal of Differential Equations. 266(6), 3732–3763.","mla":"Dareiotis, Konstantinos, et al. “Entropy Solutions for Stochastic Porous Media Equations.” Journal of Differential Equations, vol. 266, no. 6, Elsevier, 2019, pp. 3732–63, doi:10.1016/j.jde.2018.09.012.","ieee":"K. Dareiotis, M. Gerencser, and B. Gess, “Entropy solutions for stochastic porous media equations,” Journal of Differential Equations, vol. 266, no. 6. Elsevier, pp. 3732–3763, 2019.","short":"K. Dareiotis, M. Gerencser, B. Gess, Journal of Differential Equations 266 (2019) 3732–3763.","apa":"Dareiotis, K., Gerencser, M., & Gess, B. (2019). Entropy solutions for stochastic porous media equations. Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2018.09.012","ama":"Dareiotis K, Gerencser M, Gess B. Entropy solutions for stochastic porous media equations. Journal of Differential Equations. 2019;266(6):3732-3763. doi:10.1016/j.jde.2018.09.012"},"title":"Entropy solutions for stochastic porous media equations","article_processing_charge":"No","external_id":{"arxiv":["1803.06953"],"isi":["000456332500026"]},"author":[{"last_name":"Dareiotis","full_name":"Dareiotis, Konstantinos","first_name":"Konstantinos"},{"last_name":"Gerencser","full_name":"Gerencser, Mate","first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gess, Benjamin","last_name":"Gess","first_name":"Benjamin"}],"publist_id":"7989","oa":1,"quality_controlled":"1","publisher":"Elsevier","publication":"Journal of Differential Equations","day":"5","year":"2019","isi":1,"date_created":"2018-12-11T11:44:26Z","date_published":"2019-03-05T00:00:00Z","doi":"10.1016/j.jde.2018.09.012","page":"3732-3763","_id":"65","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-08-24T14:30:16Z","department":[{"_id":"JaMa"}],"oa_version":"Preprint","abstract":[{"text":"We provide an entropy formulation for porous medium-type equations with a stochastic, non-linear, spatially inhomogeneous forcing. Well-posedness and L1-contraction is obtained in the class of entropy solutions. Our scope allows for porous medium operators Δ(|u|m−1u) for all m∈(1,∞), and Hölder continuous diffusion nonlinearity with exponent 1/2.","lang":"eng"}],"intvolume":" 266","month":"03","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1803.06953"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","issue":"6","volume":266},{"_id":"5907","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","date_updated":"2023-08-24T14:33:16Z","ddc":["580"],"file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"FlSc"}],"abstract":[{"text":"Microalgae of the genus Chlorella vulgaris are candidates for the production of lipids for biofuel production. Besides that, Chlorella vulgaris is marketed as protein and vitamin rich food additive. Its potential as a novel expression system for recombinant proteins inspired us to study its asparagine-linked oligosaccharides (N-glycans) by mass spectrometry, chromatography and gas chromatography. Oligomannosidic N-glycans with up to nine mannoses were the structures found in culture collection strains as well as several commercial products. These glycans co-eluted with plant N-glycans in the highly shape selective porous graphitic carbon chromatography. Thus, Chlorella vulgaris generates oligomannosidic N-glycans of the structural type known from land plants and animals. In fact, Man5 (Man5GlcNAc2) served as substrate for GlcNAc-transferase I and a trace of an endogenous structure with terminal GlcNAc was seen. The unusual more linear Man5 structure recently found on glycoproteins of Chlamydomonas reinhardtii occurred - if at all - in traces only. Notably, a majority of the oligomannosidic glycans was multiply O-methylated with 3-O-methyl and 3,6-di-O-methyl mannoses at the non-reducing termini. This modification has so far been neither found on plant nor vertebrate N-glycans. It’s possible immunogenicity raises concerns as to the use of C. vulgaris for production of pharmaceutical glycoproteins.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 9","month":"01","publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"4129c7d7663d1f8a1edf8c4232372f66","file_id":"5923","file_size":2124292,"date_updated":"2020-07-14T12:47:13Z","creator":"dernst","file_name":"2019_ScientificReports_Mocsai.pdf","date_created":"2019-02-05T13:10:02Z"}],"issue":"1","volume":9,"article_number":"331","citation":{"short":"R. Mócsai, R. Figl, C. Troschl, R. Strasser, E. Svehla, M. Windwarder, A. Thader, F. Altmann, Scientific Reports 9 (2019).","ieee":"R. Mócsai et al., “N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated,” Scientific Reports, vol. 9, no. 1. Nature Publishing Group, 2019.","ama":"Mócsai R, Figl R, Troschl C, et al. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. 2019;9(1). doi:10.1038/s41598-018-36884-1","apa":"Mócsai, R., Figl, R., Troschl, C., Strasser, R., Svehla, E., Windwarder, M., … Altmann, F. (2019). N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-36884-1","mla":"Mócsai, Réka, et al. “N-Glycans of the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.” Scientific Reports, vol. 9, no. 1, 331, Nature Publishing Group, 2019, doi:10.1038/s41598-018-36884-1.","ista":"Mócsai R, Figl R, Troschl C, Strasser R, Svehla E, Windwarder M, Thader A, Altmann F. 2019. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. 9(1), 331.","chicago":"Mócsai, Réka, Rudolf Figl, Clemens Troschl, Richard Strasser, Elisabeth Svehla, Markus Windwarder, Andreas Thader, and Friedrich Altmann. “N-Glycans of the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.” Scientific Reports. Nature Publishing Group, 2019. https://doi.org/10.1038/s41598-018-36884-1."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000456392400012"]},"author":[{"first_name":"Réka","full_name":"Mócsai, Réka","last_name":"Mócsai"},{"first_name":"Rudolf","last_name":"Figl","full_name":"Figl, Rudolf"},{"last_name":"Troschl","full_name":"Troschl, Clemens","first_name":"Clemens"},{"first_name":"Richard","last_name":"Strasser","full_name":"Strasser, Richard"},{"first_name":"Elisabeth","last_name":"Svehla","full_name":"Svehla, Elisabeth"},{"last_name":"Windwarder","full_name":"Windwarder, Markus","first_name":"Markus"},{"last_name":"Thader","full_name":"Thader, Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"first_name":"Friedrich","last_name":"Altmann","full_name":"Altmann, Friedrich"}],"title":"N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","year":"2019","has_accepted_license":"1","isi":1,"publication":"Scientific Reports","day":"23","date_created":"2019-02-03T22:59:13Z","date_published":"2019-01-23T00:00:00Z","doi":"10.1038/s41598-018-36884-1"},{"author":[{"last_name":"Lee","full_name":"Lee, Eunkyoung","first_name":"Eunkyoung"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"first_name":"Jessica","full_name":"Pérez-Sancho, Jessica","last_name":"Pérez-Sancho"},{"last_name":"Benitez-Fuente","full_name":"Benitez-Fuente, Francisco","first_name":"Francisco"},{"first_name":"Matthew","full_name":"Strelau, Matthew","last_name":"Strelau"},{"full_name":"Macho, Alberto P.","last_name":"Macho","first_name":"Alberto P."},{"last_name":"Botella","full_name":"Botella, Miguel A.","first_name":"Miguel A."},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"full_name":"Rosado, Abel","last_name":"Rosado","first_name":"Abel"}],"article_processing_charge":"No","external_id":{"pmid":["30610176"],"isi":["000456336100050"]},"title":"Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis","citation":{"ista":"Lee E, Vanneste S, Pérez-Sancho J, Benitez-Fuente F, Strelau M, Macho AP, Botella MA, Friml J, Rosado A. 2019. Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 116(4), 1420–1429.","chicago":"Lee, Eunkyoung, Steffen Vanneste, Jessica Pérez-Sancho, Francisco Benitez-Fuente, Matthew Strelau, Alberto P. Macho, Miguel A. Botella, Jiří Friml, and Abel Rosado. “Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated SYT1 Contact Site Expansion in Arabidopsis.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1818099116.","apa":"Lee, E., Vanneste, S., Pérez-Sancho, J., Benitez-Fuente, F., Strelau, M., Macho, A. P., … Rosado, A. (2019). Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1818099116","ama":"Lee E, Vanneste S, Pérez-Sancho J, et al. Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(4):1420-1429. doi:10.1073/pnas.1818099116","short":"E. Lee, S. Vanneste, J. Pérez-Sancho, F. Benitez-Fuente, M. Strelau, A.P. Macho, M.A. Botella, J. Friml, A. Rosado, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 1420–1429.","ieee":"E. Lee et al., “Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 4. National Academy of Sciences, pp. 1420–1429, 2019.","mla":"Lee, Eunkyoung, et al. “Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated SYT1 Contact Site Expansion in Arabidopsis.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 4, National Academy of Sciences, 2019, pp. 1420–29, doi:10.1073/pnas.1818099116."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"1420-1429","doi":"10.1073/pnas.1818099116","date_published":"2019-01-22T00:00:00Z","date_created":"2019-02-03T22:59:14Z","isi":1,"year":"2019","day":"22","publication":"Proceedings of the National Academy of Sciences of the United States of America","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"department":[{"_id":"JiFr"}],"date_updated":"2023-08-24T14:31:09Z","type":"journal_article","article_type":"original","status":"public","_id":"5908","volume":116,"issue":"4","publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1818099116"}],"month":"01","intvolume":" 116","abstract":[{"lang":"eng","text":"The interorganelle communication mediated by membrane contact sites (MCSs) is an evolutionary hallmark of eukaryotic cells. MCS connections enable the nonvesicular exchange of information between organelles and allow them to coordinate responses to changing cellular environments. In plants, the importance of MCS components in the responses to environmental stress has been widely established, but the molecular mechanisms regulating interorganelle connectivity during stress still remain opaque. In this report, we use the model plant Arabidopsis thaliana to show that ionic stress increases endoplasmic reticulum (ER)–plasma membrane (PM) connectivity by promoting the cortical expansion of synaptotagmin 1 (SYT1)-enriched ER–PM contact sites (S-EPCSs). We define differential roles for the cortical cytoskeleton in the regulation of S-EPCS dynamics and ER–PM connectivity, and we identify the accumulation of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] at the PM as a molecular signal associated with the ER–PM connectivity changes. Our study highlights the functional conservation of EPCS components and PM phosphoinositides as modulators of ER–PM connectivity in eukaryotes, and uncovers unique aspects of the spatiotemporal regulation of ER–PM connectivity in plants."}],"pmid":1,"oa_version":"Published Version"},{"department":[{"_id":"UlWa"}],"date_updated":"2023-08-24T14:30:43Z","type":"journal_article","article_type":"original","status":"public","_id":"5790","ec_funded":1,"issue":"4","volume":91,"publication_status":"published","publication_identifier":{"issn":["03649024"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1309.2399"}],"scopus_import":"1","intvolume":" 91","month":"08","abstract":[{"lang":"eng","text":"The partial representation extension problem is a recently introduced generalization of the recognition problem. A circle graph is an intersection graph of chords of a circle. We study the partial representation extension problem for circle graphs, where the input consists of a graph G and a partial representation R′ giving some predrawn chords that represent an induced subgraph of G. The question is whether one can extend R′ to a representation R of the entire graph G, that is, whether one can draw the remaining chords into a partially predrawn representation to obtain a representation of G. Our main result is an O(n3) time algorithm for partial representation extension of circle graphs, where n is the number of vertices. To show this, we describe the structure of all representations of a circle graph using split decomposition. This can be of independent interest."}],"oa_version":"Preprint","external_id":{"arxiv":["1309.2399"],"isi":["000485392800004"]},"article_processing_charge":"No","author":[{"last_name":"Chaplick","full_name":"Chaplick, Steven","first_name":"Steven"},{"first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek"},{"first_name":"Pavel","last_name":"Klavík","full_name":"Klavík, Pavel"}],"title":"Extending partial representations of circle graphs","citation":{"mla":"Chaplick, Steven, et al. “Extending Partial Representations of Circle Graphs.” Journal of Graph Theory, vol. 91, no. 4, Wiley, 2019, pp. 365–94, doi:10.1002/jgt.22436.","short":"S. Chaplick, R. Fulek, P. Klavík, Journal of Graph Theory 91 (2019) 365–394.","ieee":"S. Chaplick, R. Fulek, and P. Klavík, “Extending partial representations of circle graphs,” Journal of Graph Theory, vol. 91, no. 4. Wiley, pp. 365–394, 2019.","apa":"Chaplick, S., Fulek, R., & Klavík, P. (2019). Extending partial representations of circle graphs. Journal of Graph Theory. Wiley. https://doi.org/10.1002/jgt.22436","ama":"Chaplick S, Fulek R, Klavík P. Extending partial representations of circle graphs. Journal of Graph Theory. 2019;91(4):365-394. doi:10.1002/jgt.22436","chicago":"Chaplick, Steven, Radoslav Fulek, and Pavel Klavík. “Extending Partial Representations of Circle Graphs.” Journal of Graph Theory. Wiley, 2019. https://doi.org/10.1002/jgt.22436.","ista":"Chaplick S, Fulek R, Klavík P. 2019. Extending partial representations of circle graphs. Journal of Graph Theory. 91(4), 365–394."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"page":"365-394","date_created":"2018-12-30T22:59:15Z","date_published":"2019-08-01T00:00:00Z","doi":"10.1002/jgt.22436","year":"2019","isi":1,"publication":"Journal of Graph Theory","day":"01","oa":1,"quality_controlled":"1","publisher":"Wiley"},{"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"D. Virosztek, Linear Algebra and Its Applications 576 (2019) 67–78.","ieee":"D. Virosztek, “Jointly convex quantum Jensen divergences,” Linear Algebra and Its Applications, vol. 576. Elsevier, pp. 67–78, 2019.","apa":"Virosztek, D. (2019). Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. Elsevier. https://doi.org/10.1016/j.laa.2018.03.002","ama":"Virosztek D. Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. 2019;576:67-78. doi:10.1016/j.laa.2018.03.002","mla":"Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” Linear Algebra and Its Applications, vol. 576, Elsevier, 2019, pp. 67–78, doi:10.1016/j.laa.2018.03.002.","ista":"Virosztek D. 2019. Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. 576, 67–78.","chicago":"Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” Linear Algebra and Its Applications. Elsevier, 2019. https://doi.org/10.1016/j.laa.2018.03.002."},"title":"Jointly convex quantum Jensen divergences","article_processing_charge":"No","external_id":{"arxiv":["1712.05324"],"isi":["000470955300005"]},"author":[{"first_name":"Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","last_name":"Virosztek","orcid":"0000-0003-1109-5511","full_name":"Virosztek, Daniel"}],"publist_id":"7424","acknowledgement":"The author was supported by the ISTFELLOW program of the Institute of Science and Technology Austria (project code IC1027FELL01) and partially supported by the Hungarian National Research, Development and Innovation Office – NKFIH (grant no. K124152)","oa":1,"publisher":"Elsevier","quality_controlled":"1","publication":"Linear Algebra and Its Applications","day":"01","year":"2019","isi":1,"date_created":"2018-12-11T11:46:17Z","doi":"10.1016/j.laa.2018.03.002","date_published":"2019-09-01T00:00:00Z","page":"67-78","_id":"405","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-08-24T14:31:47Z","department":[{"_id":"LaEr"}],"oa_version":"Preprint","abstract":[{"text":"We investigate the quantum Jensen divergences from the viewpoint of joint convexity. It turns out that the set of the functions which generate jointly convex quantum Jensen divergences on positive matrices coincides with the Matrix Entropy Class which has been introduced by Chen and Tropp quite recently.","lang":"eng"}],"intvolume":" 576","month":"09","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.05324"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":576},{"oa_version":"Preprint","abstract":[{"text":"An upper bound sieve for rational points on suitable varieties isdeveloped, together with applications tocounting rational points in thin sets,to local solubility in families, and to the notion of “friable” rational pointswith respect to divisors. In the special case of quadrics, sharper estimates areobtained by developing a version of the Selberg sieve for rational points.","lang":"eng"}],"month":"04","intvolume":" 371","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.01999"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["10886850"],"issn":["00029947"]},"publication_status":"published","volume":371,"issue":"8","_id":"175","status":"public","type":"journal_article","date_updated":"2023-08-24T14:34:56Z","department":[{"_id":"TiBr"}],"quality_controlled":"1","publisher":"American Mathematical Society","oa":1,"day":"15","publication":"Transactions of the American Mathematical Society","isi":1,"year":"2019","doi":"10.1090/tran/7514","date_published":"2019-04-15T00:00:00Z","date_created":"2018-12-11T11:45:01Z","page":"5757-5785","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"T.D. Browning, D. Loughran, Transactions of the American Mathematical Society 371 (2019) 5757–5785.","ieee":"T. D. Browning and D. Loughran, “Sieving rational points on varieties,” Transactions of the American Mathematical Society, vol. 371, no. 8. American Mathematical Society, pp. 5757–5785, 2019.","ama":"Browning TD, Loughran D. Sieving rational points on varieties. Transactions of the American Mathematical Society. 2019;371(8):5757-5785. doi:10.1090/tran/7514","apa":"Browning, T. D., & Loughran, D. (2019). Sieving rational points on varieties. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/7514","mla":"Browning, Timothy D., and Daniel Loughran. “Sieving Rational Points on Varieties.” Transactions of the American Mathematical Society, vol. 371, no. 8, American Mathematical Society, 2019, pp. 5757–85, doi:10.1090/tran/7514.","ista":"Browning TD, Loughran D. 2019. Sieving rational points on varieties. Transactions of the American Mathematical Society. 371(8), 5757–5785.","chicago":"Browning, Timothy D, and Daniel Loughran. “Sieving Rational Points on Varieties.” Transactions of the American Mathematical Society. American Mathematical Society, 2019. https://doi.org/10.1090/tran/7514."},"title":"Sieving rational points on varieties","author":[{"last_name":"Browning","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Daniel","last_name":"Loughran","full_name":"Loughran, Daniel"}],"publist_id":"7746","article_processing_charge":"No","external_id":{"arxiv":["1705.01999"],"isi":["000464034200019"]}},{"page":"697–758","doi":"10.1007/s00440-018-0841-1","date_published":"2019-04-01T00:00:00Z","date_created":"2018-12-11T11:45:48Z","has_accepted_license":"1","isi":1,"year":"2019","day":"01","publication":"Probability Theory and Related Fields","quality_controlled":"1","publisher":"Springer","oa":1,"acknowledgement":"MG thanks the support of the LMS Postdoctoral Mobility Grant.\r\n\r\n","author":[{"id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate","full_name":"Gerencser, Mate","last_name":"Gerencser"},{"full_name":"Hairer, Martin","last_name":"Hairer","first_name":"Martin"}],"publist_id":"7546","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000463613800001"]},"title":"Singular SPDEs in domains with boundaries","citation":{"ista":"Gerencser M, Hairer M. 2019. Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. 173(3–4), 697–758.","chicago":"Gerencser, Mate, and Martin Hairer. “Singular SPDEs in Domains with Boundaries.” Probability Theory and Related Fields. Springer, 2019. https://doi.org/10.1007/s00440-018-0841-1.","apa":"Gerencser, M., & Hairer, M. (2019). Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-018-0841-1","ama":"Gerencser M, Hairer M. Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. 2019;173(3-4):697–758. doi:10.1007/s00440-018-0841-1","ieee":"M. Gerencser and M. Hairer, “Singular SPDEs in domains with boundaries,” Probability Theory and Related Fields, vol. 173, no. 3–4. Springer, pp. 697–758, 2019.","short":"M. Gerencser, M. Hairer, Probability Theory and Related Fields 173 (2019) 697–758.","mla":"Gerencser, Mate, and Martin Hairer. “Singular SPDEs in Domains with Boundaries.” Probability Theory and Related Fields, vol. 173, no. 3–4, Springer, 2019, pp. 697–758, doi:10.1007/s00440-018-0841-1."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"issue":"3-4","volume":173,"publication_identifier":{"eissn":["14322064"],"issn":["01788051"]},"publication_status":"published","file":[{"file_id":"5722","checksum":"288d16ef7291242f485a9660979486e3","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-17T16:25:24Z","file_name":"2018_ProbTheory_Gerencser.pdf","creator":"dernst","date_updated":"2020-07-14T12:46:03Z","file_size":893182}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"04","intvolume":" 173","abstract":[{"text":"We study spaces of modelled distributions with singular behaviour near the boundary of a domain that, in the context of the theory of regularity structures, allow one to give robust solution theories for singular stochastic PDEs with boundary conditions. The calculus of modelled distributions established in Hairer (Invent Math 198(2):269–504, 2014. https://doi.org/10.1007/s00222-014-0505-4) is extended to this setting. We formulate and solve fixed point problems in these spaces with a class of kernels that is sufficiently large to cover in particular the Dirichlet and Neumann heat kernels. These results are then used to provide solution theories for the KPZ equation with Dirichlet and Neumann boundary conditions and for the 2D generalised parabolic Anderson model with Dirichlet boundary conditions. In the case of the KPZ equation with Neumann boundary conditions, we show that, depending on the class of mollifiers one considers, a “boundary renormalisation” takes place. In other words, there are situations in which a certain boundary condition is applied to an approximation to the KPZ equation, but the limiting process is the Hopf–Cole solution to the KPZ equation with a different boundary condition.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:46:03Z","date_updated":"2023-08-24T14:38:32Z","ddc":["510"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"319"},{"ec_funded":1,"volume":173,"issue":"1-2","language":[{"iso":"eng"}],"file":[{"file_size":1201840,"date_updated":"2020-07-14T12:46:26Z","creator":"dernst","file_name":"2018_ProbTheory_Ajanki.pdf","date_created":"2018-12-17T16:12:08Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"f9354fa5c71f9edd17132588f0dc7d01","file_id":"5720"}],"publication_status":"published","publication_identifier":{"eissn":["14322064"],"issn":["01788051"]},"intvolume":" 173","month":"02","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We consider real symmetric or complex hermitian random matrices with correlated entries. We prove local laws for the resolvent and universality of the local eigenvalue statistics in the bulk of the spectrum. The correlations have fast decay but are otherwise of general form. The key novelty is the detailed stability analysis of the corresponding matrix valued Dyson equation whose solution is the deterministic limit of the resolvent.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:26Z","department":[{"_id":"LaEr"}],"ddc":["510"],"date_updated":"2023-08-24T14:39:00Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"429","date_created":"2018-12-11T11:46:25Z","doi":"10.1007/s00440-018-0835-z","date_published":"2019-02-01T00:00:00Z","page":"293–373","publication":"Probability Theory and Related Fields","day":"01","year":"2019","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).\r\n","title":"Stability of the matrix Dyson equation and random matrices with correlations","external_id":{"isi":["000459396500007"]},"article_processing_charge":"Yes (via OA deal)","publist_id":"7394","author":[{"first_name":"Oskari H","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","last_name":"Ajanki","full_name":"Ajanki, Oskari H"},{"last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Ajanki, Oskari H., et al. “Stability of the Matrix Dyson Equation and Random Matrices with Correlations.” Probability Theory and Related Fields, vol. 173, no. 1–2, Springer, 2019, pp. 293–373, doi:10.1007/s00440-018-0835-z.","short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields 173 (2019) 293–373.","ieee":"O. H. Ajanki, L. Erdös, and T. H. Krüger, “Stability of the matrix Dyson equation and random matrices with correlations,” Probability Theory and Related Fields, vol. 173, no. 1–2. Springer, pp. 293–373, 2019.","ama":"Ajanki OH, Erdös L, Krüger TH. Stability of the matrix Dyson equation and random matrices with correlations. Probability Theory and Related Fields. 2019;173(1-2):293–373. doi:10.1007/s00440-018-0835-z","apa":"Ajanki, O. H., Erdös, L., & Krüger, T. H. (2019). Stability of the matrix Dyson equation and random matrices with correlations. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-018-0835-z","chicago":"Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Stability of the Matrix Dyson Equation and Random Matrices with Correlations.” Probability Theory and Related Fields. Springer, 2019. https://doi.org/10.1007/s00440-018-0835-z.","ista":"Ajanki OH, Erdös L, Krüger TH. 2019. Stability of the matrix Dyson equation and random matrices with correlations. Probability Theory and Related Fields. 173(1–2), 293–373."},"project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}]},{"title":"A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries","author":[{"first_name":"Bapi","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Bapi","orcid":"0000-0002-2742-4028"},{"first_name":"Sathya","full_name":"Peri, Sathya","last_name":"Peri"},{"first_name":"Muktikanta","last_name":"Sa","full_name":"Sa, Muktikanta"},{"full_name":"Singhal, Nandini","last_name":"Singhal","first_name":"Nandini"}],"article_processing_charge":"No","external_id":{"isi":["000484491600019"],"arxiv":["1809.00896"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Chatterjee, Bapi, et al. “A Simple and Practical Concurrent Non-Blocking Unbounded Graph with Linearizable Reachability Queries.” ACM International Conference Proceeding Series, ACM, 2019, pp. 168–77, doi:10.1145/3288599.3288617.","ieee":"B. Chatterjee, S. Peri, M. Sa, and N. Singhal, “A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries,” in ACM International Conference Proceeding Series, Bangalore, India, 2019, pp. 168–177.","short":"B. Chatterjee, S. Peri, M. Sa, N. Singhal, in:, ACM International Conference Proceeding Series, ACM, 2019, pp. 168–177.","ama":"Chatterjee B, Peri S, Sa M, Singhal N. A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. In: ACM International Conference Proceeding Series. ACM; 2019:168-177. doi:10.1145/3288599.3288617","apa":"Chatterjee, B., Peri, S., Sa, M., & Singhal, N. (2019). A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. In ACM International Conference Proceeding Series (pp. 168–177). Bangalore, India: ACM. https://doi.org/10.1145/3288599.3288617","chicago":"Chatterjee, Bapi, Sathya Peri, Muktikanta Sa, and Nandini Singhal. “A Simple and Practical Concurrent Non-Blocking Unbounded Graph with Linearizable Reachability Queries.” In ACM International Conference Proceeding Series, 168–77. ACM, 2019. https://doi.org/10.1145/3288599.3288617.","ista":"Chatterjee B, Peri S, Sa M, Singhal N. 2019. A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. ACM International Conference Proceeding Series. ICDCN: Conference on Distributed Computing and Networking, 168–177."},"publisher":"ACM","quality_controlled":"1","oa":1,"doi":"10.1145/3288599.3288617","date_published":"2019-01-04T00:00:00Z","date_created":"2019-02-10T22:59:17Z","page":"168-177","day":"04","publication":"ACM International Conference Proceeding Series","isi":1,"year":"2019","status":"public","type":"conference","conference":{"location":"Bangalore, India","end_date":"2019-01-07","start_date":"2019-01-04","name":"ICDCN: Conference on Distributed Computing and Networking"},"_id":"5947","department":[{"_id":"DaAl"}],"date_updated":"2023-08-24T14:41:53Z","month":"01","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1809.00896","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"Graph algorithms applied in many applications, including social networks, communication networks, VLSI design, graphics, and several others, require dynamic modifications - addition and removal of vertices and/or edges - in the graph. This paper presents a novel concurrent non-blocking algorithm to implement a dynamic unbounded directed graph in a shared-memory machine. The addition and removal operations of vertices and edges are lock-free. For a finite sized graph, the lookup operations are wait-free. Most significant component of the presented algorithm is the reachability query in a concurrent graph. The reachability queries in our algorithm are obstruction-free and thus impose minimal additional synchronization cost over other operations. We prove that each of the data structure operations are linearizable. We extensively evaluate a sample C/C++ implementation of the algorithm through a number of micro-benchmarks. The experimental results show that the proposed algorithm scales well with the number of threads and on an average provides 5 to 7x performance improvement over a concurrent graph implementation using coarse-grained locking.","lang":"eng"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-1-4503-6094-4 "]},"publication_status":"published"},{"oa_version":"Preprint","abstract":[{"text":"A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is [Formula presented](n−1), and that this bound is best possible for infinitely many values of n.","lang":"eng"}],"month":"04","intvolume":" 259","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1708.08037","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0166218X"]},"publication_status":"published","related_material":{"record":[{"id":"433","status":"public","relation":"earlier_version"}]},"issue":"4","volume":259,"_id":"5857","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-08-24T14:39:33Z","department":[{"_id":"UlWa"}],"quality_controlled":"1","publisher":"Elsevier","oa":1,"day":"30","publication":"Discrete Applied Mathematics","isi":1,"year":"2019","doi":"10.1016/j.dam.2018.12.025","date_published":"2019-04-30T00:00:00Z","date_created":"2019-01-20T22:59:17Z","page":"266-231","project":[{"grant_number":"M02281","name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.” Discrete Applied Mathematics, vol. 259, no. 4, Elsevier, 2019, pp. 266–231, doi:10.1016/j.dam.2018.12.025.","ama":"Fulek R, Pach J. Thrackles: An improved upper bound. Discrete Applied Mathematics. 2019;259(4):266-231. doi:10.1016/j.dam.2018.12.025","apa":"Fulek, R., & Pach, J. (2019). Thrackles: An improved upper bound. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2018.12.025","ieee":"R. Fulek and J. Pach, “Thrackles: An improved upper bound,” Discrete Applied Mathematics, vol. 259, no. 4. Elsevier, pp. 266–231, 2019.","short":"R. Fulek, J. Pach, Discrete Applied Mathematics 259 (2019) 266–231.","chicago":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.” Discrete Applied Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.dam.2018.12.025.","ista":"Fulek R, Pach J. 2019. Thrackles: An improved upper bound. Discrete Applied Mathematics. 259(4), 266–231."},"title":"Thrackles: An improved upper bound","author":[{"last_name":"Fulek","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pach","full_name":"Pach, János","first_name":"János"}],"article_processing_charge":"No","external_id":{"arxiv":["1708.08037"],"isi":["000466061100020"]}},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” Life, vol. 9, no. 1, 9, MDPI, 2019, doi:10.3390/life9010009.","ama":"Corominas-Murtra B. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 2019;9(1). doi:10.3390/life9010009","apa":"Corominas-Murtra, B. (2019). Thermodynamics of duplication thresholds in synthetic protocell systems. Life. MDPI. https://doi.org/10.3390/life9010009","short":"B. Corominas-Murtra, Life 9 (2019).","ieee":"B. Corominas-Murtra, “Thermodynamics of duplication thresholds in synthetic protocell systems,” Life, vol. 9, no. 1. MDPI, 2019.","chicago":"Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” Life. MDPI, 2019. https://doi.org/10.3390/life9010009.","ista":"Corominas-Murtra B. 2019. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 9(1), 9."},"title":"Thermodynamics of duplication thresholds in synthetic protocell systems","author":[{"first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra","orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat"}],"external_id":{"isi":["000464125500001"]},"article_processing_charge":"No","article_number":"9","day":"15","publication":"Life","isi":1,"has_accepted_license":"1","year":"2019","date_published":"2019-01-15T00:00:00Z","doi":"10.3390/life9010009","date_created":"2019-02-10T22:59:15Z","quality_controlled":"1","publisher":"MDPI","oa":1,"ddc":["570"],"date_updated":"2023-08-24T14:43:41Z","file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"EdHa"}],"_id":"5944","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_size":963454,"date_updated":"2020-07-14T12:47:13Z","creator":"dernst","file_name":"2019_Life_Corominas.pdf","date_created":"2019-02-11T10:45:27Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"7d2322cd96ace41959909b66702d5cf4","file_id":"5951"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20751729"]},"publication_status":"published","issue":"1","volume":9,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy gradients and entropic contributions that underlie duplication. The study of synthetic, feasible systems reproducing part of the key ingredients of living entities but overcoming major sources of biological complexity is of great relevance to deepen the comprehension of the fundamental thermodynamic processes underlying life and its prevalence. In this paper an abstract—yet realistic—synthetic system made of small synthetic protocell aggregates is studied in detail. A fundamental relation between free energy and entropic gradients is derived for a general, non-equilibrium scenario, setting the thermodynamic conditions for the occurrence and prevalence of duplication phenomena. This relation sets explicitly how the energy gradients invested in creating and maintaining structural—and eventually, functional—elements of the system must always compensate the entropic gradients, whose contributions come from changes in the translational, configurational, and macrostate entropies, as well as from dissipation due to irreversible transitions. Work/energy relations are also derived, defining lower bounds on the energy required for the duplication event to take place. A specific example including real ternary emulsions is provided in order to grasp the orders of magnitude involved in the problem. It is found that the minimal work invested over the system to trigger a duplication event is around ~ 10−13J , which results, in the case of duplication of all the vesicles contained in a liter of emulsion, in an amount of energy around ~ 1kJ . Without aiming to describe a truly biological process of duplication, this theoretical contribution seeks to explicitly define and identify the key actors that participate in it."}],"month":"01","intvolume":" 9","scopus_import":"1"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Lindner, Marco, et al. “A Fast and Simple Contact Printing Approach to Generate 2D Protein Nanopatterns.” Frontiers in Chemistry, vol. 6, 655, Frontiers Media S.A., 2019, doi:10.3389/fchem.2018.00655.","short":"M. Lindner, A. Tresztenyak, G. Fülöp, W. Jahr, A. Prinz, I. Prinz, J.G. Danzl, G.J. Schütz, E. Sevcsik, Frontiers in Chemistry 6 (2019).","ieee":"M. Lindner et al., “A fast and simple contact printing approach to generate 2D protein nanopatterns,” Frontiers in Chemistry, vol. 6. Frontiers Media S.A., 2019.","ama":"Lindner M, Tresztenyak A, Fülöp G, et al. A fast and simple contact printing approach to generate 2D protein nanopatterns. Frontiers in Chemistry. 2019;6. doi:10.3389/fchem.2018.00655","apa":"Lindner, M., Tresztenyak, A., Fülöp, G., Jahr, W., Prinz, A., Prinz, I., … Sevcsik, E. (2019). A fast and simple contact printing approach to generate 2D protein nanopatterns. Frontiers in Chemistry. Frontiers Media S.A. https://doi.org/10.3389/fchem.2018.00655","chicago":"Lindner, Marco, Aliz Tresztenyak, Gergö Fülöp, Wiebke Jahr, Adrian Prinz, Iris Prinz, Johann G Danzl, Gerhard J. Schütz, and Eva Sevcsik. “A Fast and Simple Contact Printing Approach to Generate 2D Protein Nanopatterns.” Frontiers in Chemistry. Frontiers Media S.A., 2019. https://doi.org/10.3389/fchem.2018.00655.","ista":"Lindner M, Tresztenyak A, Fülöp G, Jahr W, Prinz A, Prinz I, Danzl JG, Schütz GJ, Sevcsik E. 2019. A fast and simple contact printing approach to generate 2D protein nanopatterns. Frontiers in Chemistry. 6, 655."},"title":"A fast and simple contact printing approach to generate 2D protein nanopatterns","author":[{"first_name":"Marco","last_name":"Lindner","full_name":"Lindner, Marco"},{"full_name":"Tresztenyak, Aliz","last_name":"Tresztenyak","first_name":"Aliz"},{"full_name":"Fülöp, Gergö","last_name":"Fülöp","first_name":"Gergö"},{"last_name":"Jahr","full_name":"Jahr, Wiebke","first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Prinz, Adrian","last_name":"Prinz","first_name":"Adrian"},{"last_name":"Prinz","full_name":"Prinz, Iris","first_name":"Iris"},{"orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schütz","full_name":"Schütz, Gerhard J.","first_name":"Gerhard J."},{"first_name":"Eva","last_name":"Sevcsik","full_name":"Sevcsik, Eva"}],"article_processing_charge":"No","external_id":{"isi":["000456718000001"]},"article_number":"655","day":"24","publication":"Frontiers in Chemistry","has_accepted_license":"1","isi":1,"year":"2019","date_published":"2019-01-24T00:00:00Z","doi":"10.3389/fchem.2018.00655","date_created":"2019-02-17T22:59:24Z","publisher":"Frontiers Media S.A.","quality_controlled":"1","oa":1,"ddc":["540"],"date_updated":"2023-08-24T14:45:38Z","file_date_updated":"2020-07-14T12:47:17Z","department":[{"_id":"JoDa"}],"_id":"6029","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"date_created":"2019-02-18T15:10:34Z","file_name":"2019_frontiers_Lindner.pdf","date_updated":"2020-07-14T12:47:17Z","file_size":1766820,"creator":"dernst","file_id":"6039","checksum":"7841301d7c53b56ef873791b4b6f7b24","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["22962646"]},"publication_status":"published","volume":6,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Protein micropatterning has become an important tool for many biomedical applications as well as in academic research. Current techniques that allow to reduce the feature size of patterns below 1 μm are, however, often costly and require sophisticated equipment. We present here a straightforward and convenient method to generate highly condensed nanopatterns of proteins without the need for clean room facilities or expensive equipment. Our approach is based on nanocontact printing and allows for the fabrication of protein patterns with feature sizes of 80 nm and periodicities down to 140 nm. This was made possible by the use of the material X-poly(dimethylsiloxane) (X-PDMS) in a two-layer stamp layout for protein printing. In a proof of principle, different proteins at various scales were printed and the pattern quality was evaluated by atomic force microscopy (AFM) and super-resolution fluorescence microscopy."}],"month":"01","intvolume":" 6","scopus_import":"1"},{"scopus_import":"1","month":"02","intvolume":" 72","abstract":[{"text":"We give a construction allowing us to build local renormalized solutions to general quasilinear stochastic PDEs within the theory of regularity structures, thus greatly generalizing the recent results of [1, 5, 11]. Loosely speaking, our construction covers quasilinear variants of all classes of equations for which the general construction of [3, 4, 7] applies, including in particular one‐dimensional systems with KPZ‐type nonlinearities driven by space‐time white noise. In a less singular and more specific case, we furthermore show that the counterterms introduced by the renormalization procedure are given by local functionals of the solution. The main feature of our construction is that it allows exploitation of a number of existing results developed for the semilinear case, so that the number of additional arguments it requires is relatively small.","lang":"eng"}],"oa_version":"Published Version","issue":"9","volume":72,"publication_status":"published","file":[{"checksum":"09aec427eb48c0f96a1cce9ff53f013b","file_id":"7237","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-01-07T13:25:55Z","file_name":"2019_Wiley_Gerencser.pdf","date_updated":"2020-07-14T12:47:17Z","file_size":381350,"creator":"kschuh"}],"language":[{"iso":"eng"}],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"6028","file_date_updated":"2020-07-14T12:47:17Z","department":[{"_id":"JaMa"}],"date_updated":"2023-08-24T14:44:31Z","ddc":["500"],"publisher":"Wiley","quality_controlled":"1","oa":1,"page":"1983-2005","doi":"10.1002/cpa.21816","date_published":"2019-02-08T00:00:00Z","date_created":"2019-02-17T22:59:24Z","has_accepted_license":"1","isi":1,"year":"2019","day":"08","publication":"Communications on Pure and Applied Mathematics","author":[{"full_name":"Gerencser, Mate","last_name":"Gerencser","first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hairer, Martin","last_name":"Hairer","first_name":"Martin"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000475465000003"]},"title":"A solution theory for quasilinear singular SPDEs","citation":{"short":"M. Gerencser, M. Hairer, Communications on Pure and Applied Mathematics 72 (2019) 1983–2005.","ieee":"M. Gerencser and M. Hairer, “A solution theory for quasilinear singular SPDEs,” Communications on Pure and Applied Mathematics, vol. 72, no. 9. Wiley, pp. 1983–2005, 2019.","apa":"Gerencser, M., & Hairer, M. (2019). A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21816","ama":"Gerencser M, Hairer M. A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. 2019;72(9):1983-2005. doi:10.1002/cpa.21816","mla":"Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” Communications on Pure and Applied Mathematics, vol. 72, no. 9, Wiley, 2019, pp. 1983–2005, doi:10.1002/cpa.21816.","ista":"Gerencser M, Hairer M. 2019. A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. 72(9), 1983–2005.","chicago":"Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” Communications on Pure and Applied Mathematics. Wiley, 2019. https://doi.org/10.1002/cpa.21816."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"day":"07","publication":"Cell","isi":1,"year":"2019","date_published":"2019-02-07T00:00:00Z","doi":"10.1016/j.cell.2019.01.007","date_created":"2019-02-10T22:59:16Z","page":"844-855.e15","publisher":"Cell Press","quality_controlled":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Petkova, Mariela D., et al. “Optimal Decoding of Cellular Identities in a Genetic Network.” Cell, vol. 176, no. 4, Cell Press, 2019, p. 844–855.e15, doi:10.1016/j.cell.2019.01.007.","ieee":"M. D. Petkova, G. Tkačik, W. Bialek, E. F. Wieschaus, and T. Gregor, “Optimal decoding of cellular identities in a genetic network,” Cell, vol. 176, no. 4. Cell Press, p. 844–855.e15, 2019.","short":"M.D. Petkova, G. Tkačik, W. Bialek, E.F. Wieschaus, T. Gregor, Cell 176 (2019) 844–855.e15.","ama":"Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. Optimal decoding of cellular identities in a genetic network. Cell. 2019;176(4):844-855.e15. doi:10.1016/j.cell.2019.01.007","apa":"Petkova, M. D., Tkačik, G., Bialek, W., Wieschaus, E. F., & Gregor, T. (2019). Optimal decoding of cellular identities in a genetic network. Cell. Cell Press. https://doi.org/10.1016/j.cell.2019.01.007","chicago":"Petkova, Mariela D., Gašper Tkačik, William Bialek, Eric F. Wieschaus, and Thomas Gregor. “Optimal Decoding of Cellular Identities in a Genetic Network.” Cell. Cell Press, 2019. https://doi.org/10.1016/j.cell.2019.01.007.","ista":"Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. 2019. Optimal decoding of cellular identities in a genetic network. Cell. 176(4), 844–855.e15."},"title":"Optimal decoding of cellular identities in a genetic network","author":[{"first_name":"Mariela D.","last_name":"Petkova","full_name":"Petkova, Mariela D."},{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"full_name":"Bialek, William","last_name":"Bialek","first_name":"William"},{"last_name":"Wieschaus","full_name":"Wieschaus, Eric F.","first_name":"Eric F."},{"full_name":"Gregor, Thomas","last_name":"Gregor","first_name":"Thomas"}],"external_id":{"isi":["000457969200015"],"pmid":["30712870"]},"article_processing_charge":"No","project":[{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"4","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/cells-find-their-identity-using-a-mathematically-optimal-strategy/"}]},"volume":176,"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In developing organisms, spatially prescribed cell identities are thought to be determined by the expression levels of multiple genes. Quantitative tests of this idea, however, require a theoretical framework capable of exposing the rules and precision of cell specification over developmental time. We use the gap gene network in the early fly embryo as an example to show how expression levels of the four gap genes can be jointly decoded into an optimal specification of position with 1% accuracy. The decoder correctly predicts, with no free parameters, the dynamics of pair-rule expression patterns at different developmental time points and in various mutant backgrounds. Precise cellular identities are thus available at the earliest stages of development, contrasting the prevailing view of positional information being slowly refined across successive layers of the patterning network. Our results suggest that developmental enhancers closely approximate a mathematically optimal decoding strategy."}],"month":"02","intvolume":" 176","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2019.01.007","open_access":"1"}],"date_updated":"2023-08-24T14:42:47Z","department":[{"_id":"GaTk"}],"_id":"5945","status":"public","article_type":"original","type":"journal_article"},{"publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"day":"25","publication":"Journal of Fluid Mechanics","isi":1,"year":"2019","date_published":"2019-03-25T00:00:00Z","doi":"10.1017/jfm.2018.974","date_created":"2019-02-10T22:59:15Z","page":"386-406","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Klotz L, Gumowski K, Wesfreid JE. 2019. Experiments on a jet in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics. 863, 386–406.","chicago":"Klotz, Lukasz, Konrad Gumowski, and José Eduardo Wesfreid. “Experiments on a Jet in a Crossflow in the Low-Velocity-Ratio Regime.” Journal of Fluid Mechanics. Cambridge University Press, 2019. https://doi.org/10.1017/jfm.2018.974.","apa":"Klotz, L., Gumowski, K., & Wesfreid, J. E. (2019). Experiments on a jet in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2018.974","ama":"Klotz L, Gumowski K, Wesfreid JE. Experiments on a jet in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics. 2019;863:386-406. doi:10.1017/jfm.2018.974","short":"L. Klotz, K. Gumowski, J.E. Wesfreid, Journal of Fluid Mechanics 863 (2019) 386–406.","ieee":"L. Klotz, K. Gumowski, and J. E. Wesfreid, “Experiments on a jet in a crossflow in the low-velocity-ratio regime,” Journal of Fluid Mechanics, vol. 863. Cambridge University Press, pp. 386–406, 2019.","mla":"Klotz, Lukasz, et al. “Experiments on a Jet in a Crossflow in the Low-Velocity-Ratio Regime.” Journal of Fluid Mechanics, vol. 863, Cambridge University Press, 2019, pp. 386–406, doi:10.1017/jfm.2018.974."},"title":"Experiments on a jet in a crossflow in the low-velocity-ratio regime","author":[{"id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87","first_name":"Lukasz","last_name":"Klotz","full_name":"Klotz, Lukasz","orcid":"0000-0003-1740-7635"},{"last_name":"Gumowski","full_name":"Gumowski, Konrad","first_name":"Konrad"},{"last_name":"Wesfreid","full_name":"Wesfreid, José Eduardo","first_name":"José Eduardo"}],"external_id":{"arxiv":["1902.07931"],"isi":["000526029100016"]},"article_processing_charge":"No","oa_version":"Preprint","abstract":[{"text":"The hairpin instability of a jet in a crossflow (JICF) for a low jet-to-crossflow velocity ratio is investigated experimentally for a velocity ratio range of R ∈ (0.14, 0.75) and crossflow Reynolds numbers ReD ∈ (260, 640). From spectral analysis we characterize the Strouhal number and amplitude of the hairpin instability as a function of R and ReD. We demonstrate that the dynamics of the hairpins is well described by the Landau model, and, hence, that the instability occurs through Hopf bifurcation, similarly to other hydrodynamical oscillators such as wake behind different bluff bodies. Using the Landau model, we determine the precise threshold values of hairpin shedding. We also study the spatial dependence of this hydrodynamical instability, which shows a global behaviour.","lang":"eng"}],"month":"03","intvolume":" 863","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1902.07931","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":863,"ec_funded":1,"_id":"5943","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-08-24T14:43:13Z","department":[{"_id":"BjHo"}]},{"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"citation":{"chicago":"Christakis, Maria, Matthias Heizmann, Muhammad Numair Mansur, Christian Schilling, and Valentin Wüstholz. “Semantic Fault Localization and Suspiciousness Ranking.” In 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , 11427:226–43. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-17462-0_13.","ista":"Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. 2019. Semantic fault localization and suspiciousness ranking. 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 11427, 226–243.","mla":"Christakis, Maria, et al. “Semantic Fault Localization and Suspiciousness Ranking.” 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , vol. 11427, Springer Nature, 2019, pp. 226–43, doi:10.1007/978-3-030-17462-0_13.","short":"M. Christakis, M. Heizmann, M.N. Mansur, C. Schilling, V. Wüstholz, in:, 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , Springer Nature, 2019, pp. 226–243.","ieee":"M. Christakis, M. Heizmann, M. N. Mansur, C. Schilling, and V. Wüstholz, “Semantic fault localization and suspiciousness ranking,” in 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , Prague, Czech Republic, 2019, vol. 11427, pp. 226–243.","ama":"Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. Semantic fault localization and suspiciousness ranking. In: 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems . Vol 11427. Springer Nature; 2019:226-243. doi:10.1007/978-3-030-17462-0_13","apa":"Christakis, M., Heizmann, M., Mansur, M. N., Schilling, C., & Wüstholz, V. (2019). Semantic fault localization and suspiciousness ranking. In 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems (Vol. 11427, pp. 226–243). Prague, Czech Republic: Springer Nature. https://doi.org/10.1007/978-3-030-17462-0_13"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000681166500013"]},"author":[{"last_name":"Christakis","full_name":"Christakis, Maria","first_name":"Maria"},{"first_name":"Matthias","full_name":"Heizmann, Matthias","last_name":"Heizmann"},{"first_name":"Muhammad Numair","last_name":"Mansur","full_name":"Mansur, Muhammad Numair"},{"first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065","last_name":"Schilling"},{"last_name":"Wüstholz","full_name":"Wüstholz, Valentin","first_name":"Valentin"}],"title":"Semantic fault localization and suspiciousness ranking","oa":1,"quality_controlled":"1","publisher":"Springer Nature","year":"2019","has_accepted_license":"1","isi":1,"publication":"25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems ","day":"04","page":"226-243","date_created":"2019-02-18T16:44:06Z","doi":"10.1007/978-3-030-17462-0_13","date_published":"2019-04-04T00:00:00Z","_id":"6042","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2019-04-06","end_date":"2019-04-11","location":"Prague, Czech Republic"},"type":"conference","status":"public","date_updated":"2023-08-24T14:47:45Z","ddc":["000"],"file_date_updated":"2020-07-14T12:47:17Z","department":[{"_id":"ToHe"}],"abstract":[{"text":"Static program analyzers are increasingly effective in checking correctness properties of programs and reporting any errors found, often in the form of error traces. However, developers still spend a significant amount of time on debugging. This involves processing long error traces in an effort to localize a bug to a relatively small part of the program and to identify its cause. In this paper, we present a technique for automated fault localization that, given a program and an error trace, efficiently narrows down the cause of the error to a few statements. These statements are then ranked in terms of their suspiciousness. Our technique relies only on the semantics of the given program and does not require any test cases or user guidance. In experiments on a set of C benchmarks, we show that our technique is effective in quickly isolating the cause of error while out-performing other state-of-the-art fault-localization techniques.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","alternative_title":["LNCS"],"intvolume":" 11427","month":"04","publication_status":"published","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"9998496f6fe202c0a19124b4209154c6","file_id":"6408","creator":"dernst","file_size":773083,"date_updated":"2020-07-14T12:47:17Z","file_name":"2019_LNCS_Christakis.pdf","date_created":"2019-05-10T14:16:05Z"}],"ec_funded":1,"volume":11427},{"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We present JuliaReach, a toolbox for set-based reachability analysis of dynamical systems. JuliaReach consists of two main packages: Reachability, containing implementations of reachability algorithms for continuous and hybrid systems, and LazySets, a standalone library that implements state-of-the-art algorithms for calculus with convex sets. The library offers both concrete and lazy set representations, where the latter stands for the ability to delay set computations until they are needed. The choice of the programming language Julia and the accompanying documentation of our toolbox allow researchers to easily translate set-based algorithms from mathematics to software in a platform-independent way, while achieving runtime performance that is comparable to statically compiled languages. Combining lazy operations in high dimensions and explicit computations in low dimensions, JuliaReach can be applied to solve complex, large-scale problems."}],"month":"04","intvolume":" 22","scopus_import":"1","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"28ed56439aea5991c3122d4730fd828f","file_id":"6067","date_updated":"2020-07-14T12:47:17Z","file_size":3784414,"creator":"cschilli","date_created":"2019-03-05T09:27:18Z","file_name":"hscc19.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450362825"]},"publication_status":"published","volume":22,"ec_funded":1,"_id":"6035","status":"public","keyword":["reachability analysis","hybrid systems","lazy computation"],"type":"conference","conference":{"end_date":"2019-04-18","location":"Montreal, QC, Canada","start_date":"2019-04-16","name":"HSCC: Hybrid Systems Computation and Control"},"ddc":["000"],"date_updated":"2023-08-24T14:47:21Z","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:17Z","quality_controlled":"1","publisher":"ACM","oa":1,"day":"16","publication":"Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control","isi":1,"has_accepted_license":"1","year":"2019","doi":"10.1145/3302504.3311804","date_published":"2019-04-16T00:00:00Z","date_created":"2019-02-18T14:43:28Z","page":"39-44","project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “JuliaReach: A Toolbox for Set-Based Reachability.” In Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, 22:39–44. ACM, 2019. https://doi.org/10.1145/3302504.3311804.","ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2019. JuliaReach: A toolbox for set-based reachability. Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems Computation and Control vol. 22, 39–44.","mla":"Bogomolov, Sergiy, et al. “JuliaReach: A Toolbox for Set-Based Reachability.” Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, vol. 22, ACM, 2019, pp. 39–44, doi:10.1145/3302504.3311804.","ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. JuliaReach: A toolbox for set-based reachability. In: Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control. Vol 22. ACM; 2019:39-44. doi:10.1145/3302504.3311804","apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2019). JuliaReach: A toolbox for set-based reachability. In Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control (Vol. 22, pp. 39–44). Montreal, QC, Canada: ACM. https://doi.org/10.1145/3302504.3311804","ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “JuliaReach: A toolbox for set-based reachability,” in Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, Montreal, QC, Canada, 2019, vol. 22, pp. 39–44.","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 39–44."},"title":"JuliaReach: A toolbox for set-based reachability","author":[{"id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy","last_name":"Bogomolov","full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365"},{"first_name":"Marcelo","full_name":"Forets, Marcelo","last_name":"Forets"},{"first_name":"Goran","last_name":"Frehse","full_name":"Frehse, Goran"},{"first_name":"Kostiantyn","last_name":"Potomkin","full_name":"Potomkin, Kostiantyn"},{"orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"}],"article_processing_charge":"No","external_id":{"arxiv":["1901.10736"],"isi":["000516713900005"]}},{"oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","page":"832–863","date_created":"2019-02-24T22:59:20Z","date_published":"2019-03-01T00:00:00Z","doi":"10.1038/s41596-018-0117-3","year":"2019","has_accepted_license":"1","isi":1,"publication":"Nature Protocols","day":"01","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules"}],"article_processing_charge":"No","external_id":{"isi":["000459890700008"],"pmid":["30778205"]},"author":[{"last_name":"Truckenbrodt","full_name":"Truckenbrodt, Sven M","first_name":"Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","last_name":"Sommer","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Silvio O","full_name":"Rizzoli, Silvio O","last_name":"Rizzoli"},{"orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"title":"A practical guide to optimization in X10 expansion microscopy","citation":{"chicago":"Truckenbrodt, Sven M, Christoph M Sommer, Silvio O Rizzoli, and Johann G Danzl. “A Practical Guide to Optimization in X10 Expansion Microscopy.” Nature Protocols. Nature Publishing Group, 2019. https://doi.org/10.1038/s41596-018-0117-3.","ista":"Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. 2019. A practical guide to optimization in X10 expansion microscopy. Nature Protocols. 14(3), 832–863.","mla":"Truckenbrodt, Sven M., et al. “A Practical Guide to Optimization in X10 Expansion Microscopy.” Nature Protocols, vol. 14, no. 3, Nature Publishing Group, 2019, pp. 832–863, doi:10.1038/s41596-018-0117-3.","ieee":"S. M. Truckenbrodt, C. M. Sommer, S. O. Rizzoli, and J. G. Danzl, “A practical guide to optimization in X10 expansion microscopy,” Nature Protocols, vol. 14, no. 3. Nature Publishing Group, pp. 832–863, 2019.","short":"S.M. Truckenbrodt, C.M. Sommer, S.O. Rizzoli, J.G. Danzl, Nature Protocols 14 (2019) 832–863.","ama":"Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. A practical guide to optimization in X10 expansion microscopy. Nature Protocols. 2019;14(3):832–863. doi:10.1038/s41596-018-0117-3","apa":"Truckenbrodt, S. M., Sommer, C. M., Rizzoli, S. O., & Danzl, J. G. (2019). A practical guide to optimization in X10 expansion microscopy. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/s41596-018-0117-3"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","intvolume":" 14","month":"03","abstract":[{"lang":"eng","text":"Expansion microscopy is a relatively new approach to super-resolution imaging that uses expandable hydrogels to isotropically increase the physical distance between fluorophores in biological samples such as cell cultures or tissue slices. The classic gel recipe results in an expansion factor of ~4×, with a resolution of 60–80 nm. We have recently developed X10 microscopy, which uses a gel that achieves an expansion factor of ~10×, with a resolution of ~25 nm. Here, we provide a step-by-step protocol for X10 expansion microscopy. A typical experiment consists of seven sequential stages: (i) immunostaining, (ii) anchoring, (iii) polymerization, (iv) homogenization, (v) expansion, (vi) imaging, and (vii) validation. The protocol presented here includes recommendations for optimization, pitfalls and their solutions, and detailed guidelines that should increase reproducibility. Although our protocol focuses on X10 expansion microscopy, we detail which of these suggestions are also applicable to classic fourfold expansion microscopy. We exemplify our protocol using primary hippocampal neurons from rats, but our approach can be used with other primary cells or cultured cell lines of interest. This protocol will enable any researcher with basic experience in immunostainings and access to an epifluorescence microscope to perform super-resolution microscopy with X10. The procedure takes 3 d and requires ~5 h of actively handling the sample for labeling and expansion, and another ~3 h for imaging and analysis."}],"pmid":1,"oa_version":"Submitted Version","ec_funded":1,"volume":14,"issue":"3","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"181031_Truckenbrodt_ExM_NatProtoc.docx","date_created":"2021-06-29T14:41:46Z","file_size":84478958,"date_updated":"2021-06-29T14:41:46Z","creator":"kschuh","success":1,"file_id":"9619","checksum":"7efb9951e7ddf3e3dcc2fb92b859c623","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"main_file","access_level":"open_access"}],"type":"journal_article","article_type":"original","status":"public","_id":"6052","department":[{"_id":"JoDa"},{"_id":"Bio"}],"file_date_updated":"2021-06-29T14:41:46Z","date_updated":"2023-08-24T14:48:33Z","ddc":["570"]},{"abstract":[{"lang":"eng","text":"Non-canonical Wnt signaling plays a central role for coordinated cell polarization and directed migration in metazoan development. While spatiotemporally restricted activation of non-canonical Wnt-signaling drives cell polarization in epithelial tissues, it remains unclear whether such instructive activity is also critical for directed mesenchymal cell migration. Here, we developed a light-activated version of the non-canonical Wnt receptor Frizzled 7 (Fz7) to analyze how restricted activation of non-canonical Wnt signaling affects directed anterior axial mesendoderm (prechordal plate, ppl) cell migration within the zebrafish gastrula. We found that Fz7 signaling is required for ppl cell protrusion formation and migration and that spatiotemporally restricted ectopic activation is capable of redirecting their migration. Finally, we show that uniform activation of Fz7 signaling in ppl cells fully rescues defective directed cell migration in fz7 mutant embryos. Together, our findings reveal that in contrast to the situation in epithelial cells, non-canonical Wnt signaling functions permissively rather than instructively in directed mesenchymal cell migration during gastrulation."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Published Version","scopus_import":"1","month":"02","intvolume":" 8","publication_status":"published","file":[{"file_id":"6041","checksum":"6cb4ca6d4aa96f6f187a5983aa3e660a","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2019_elife_Capek.pdf","date_created":"2019-02-18T15:17:21Z","creator":"dernst","file_size":5500707,"date_updated":"2020-07-14T12:47:17Z"}],"language":[{"iso":"eng"}],"volume":8,"ec_funded":1,"_id":"6025","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-24T14:46:01Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:17Z","department":[{"_id":"CaHe"},{"_id":"HaJa"}],"publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2019","day":"06","publication":"eLife","doi":"10.7554/eLife.42093","date_published":"2019-02-06T00:00:00Z","date_created":"2019-02-17T22:59:22Z","article_number":"e42093","project":[{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"ista":"Capek D, Smutny M, Tichy AM, Morri M, Janovjak HL, Heisenberg C-PJ. 2019. Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. eLife. 8, e42093.","chicago":"Capek, Daniel, Michael Smutny, Alexandra Madelaine Tichy, Maurizio Morri, Harald L Janovjak, and Carl-Philipp J Heisenberg. “Light-Activated Frizzled7 Reveals a Permissive Role of Non-Canonical Wnt Signaling in Mesendoderm Cell Migration.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42093.","ama":"Capek D, Smutny M, Tichy AM, Morri M, Janovjak HL, Heisenberg C-PJ. Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. eLife. 2019;8. doi:10.7554/eLife.42093","apa":"Capek, D., Smutny, M., Tichy, A. M., Morri, M., Janovjak, H. L., & Heisenberg, C.-P. J. (2019). Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.42093","ieee":"D. Capek, M. Smutny, A. M. Tichy, M. Morri, H. L. Janovjak, and C.-P. J. Heisenberg, “Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration,” eLife, vol. 8. eLife Sciences Publications, 2019.","short":"D. Capek, M. Smutny, A.M. Tichy, M. Morri, H.L. Janovjak, C.-P.J. Heisenberg, ELife 8 (2019).","mla":"Capek, Daniel, et al. “Light-Activated Frizzled7 Reveals a Permissive Role of Non-Canonical Wnt Signaling in Mesendoderm Cell Migration.” ELife, vol. 8, e42093, eLife Sciences Publications, 2019, doi:10.7554/eLife.42093."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87","last_name":"Capek","full_name":"Capek, Daniel","orcid":"0000-0001-5199-9940"},{"first_name":"Michael","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","last_name":"Smutny","orcid":"0000-0002-5920-9090","full_name":"Smutny, Michael"},{"first_name":"Alexandra Madelaine","full_name":"Tichy, Alexandra Madelaine","last_name":"Tichy"},{"id":"4863116E-F248-11E8-B48F-1D18A9856A87","first_name":"Maurizio","last_name":"Morri","full_name":"Morri, Maurizio"},{"last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000458025300001"]},"title":"Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration"},{"scopus_import":"1","month":"02","intvolume":" 17","abstract":[{"text":"The evolution of new species is made easier when traits under divergent ecological selection are also mating cues. Such ecological mating cues are now considered more common than previously thought, but we still know little about the genetic changes underlying their evolution or more generally about the genetic basis for assortative mating behaviors. Both tight physical linkage and the existence of large-effect preference loci will strengthen genetic associations between behavioral and ecological barriers, promoting the evolution of assortative mating. The warning patterns of Heliconius melpomene and H. cydno are under disruptive selection due to increased predation of nonmimetic hybrids and are used during mate recognition. We carried out a genome-wide quantitative trait locus (QTL) analysis of preference behaviors between these species and showed that divergent male preference has a simple genetic basis. We identify three QTLs that together explain a large proportion (approximately 60%) of the difference in preference behavior observed between the parental species. One of these QTLs is just 1.2 (0-4.8) centiMorgans (cM) from the major color pattern gene optix, and, individually, all three have a large effect on the preference phenotype. Genomic divergence between H. cydno and H. melpomene is high but broadly heterogenous, and admixture is reduced at the preference-optix color pattern locus but not the other preference QTLs. The simple genetic architecture we reveal will facilitate the evolution and maintenance of new species despite ongoing gene flow by coupling behavioral and ecological aspects of reproductive isolation.","lang":"eng"}],"oa_version":"Published Version","volume":17,"issue":"2","related_material":{"record":[{"status":"public","id":"9801","relation":"research_data"}]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6036","checksum":"5f34001617ee729314ca520c049b1112","date_updated":"2020-07-14T12:47:17Z","file_size":2005949,"creator":"dernst","date_created":"2019-02-18T14:57:24Z","file_name":"2019_PLOS_Merrill.pdf"}],"language":[{"iso":"eng"}],"type":"journal_article","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","_id":"6022","file_date_updated":"2020-07-14T12:47:17Z","department":[{"_id":"NiBa"}],"date_updated":"2023-08-24T14:46:23Z","ddc":["570"],"quality_controlled":"1","publisher":"Public Library of Science","oa":1,"doi":"10.1371/journal.pbio.2005902","date_published":"2019-02-07T00:00:00Z","date_created":"2019-02-17T22:59:21Z","has_accepted_license":"1","isi":1,"year":"2019","day":"07","publication":"PLoS Biology","article_number":"e2005902","author":[{"first_name":"Richard M.","full_name":"Merrill, Richard M.","last_name":"Merrill"},{"first_name":"Pasi","last_name":"Rastas","full_name":"Rastas, Pasi"},{"last_name":"Martin","full_name":"Martin, Simon H.","first_name":"Simon H."},{"id":"386D7308-F248-11E8-B48F-1D18A9856A87","first_name":"Maria C","last_name":"Melo Hurtado","full_name":"Melo Hurtado, Maria C"},{"first_name":"Sarah","full_name":"Barker, Sarah","last_name":"Barker"},{"first_name":"John","last_name":"Davey","full_name":"Davey, John"},{"full_name":"Mcmillan, W. Owen","last_name":"Mcmillan","first_name":"W. Owen"},{"last_name":"Jiggins","full_name":"Jiggins, Chris D.","first_name":"Chris D."}],"external_id":{"isi":["000460317100001"]},"article_processing_charge":"No","title":"Genetic dissection of assortative mating behavior","citation":{"apa":"Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Genetic dissection of assortative mating behavior. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005902","ama":"Merrill RM, Rastas P, Martin SH, et al. Genetic dissection of assortative mating behavior. PLoS Biology. 2019;17(2). doi:10.1371/journal.pbio.2005902","short":"R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, PLoS Biology 17 (2019).","ieee":"R. M. Merrill et al., “Genetic dissection of assortative mating behavior,” PLoS Biology, vol. 17, no. 2. Public Library of Science, 2019.","mla":"Merrill, Richard M., et al. “Genetic Dissection of Assortative Mating Behavior.” PLoS Biology, vol. 17, no. 2, e2005902, Public Library of Science, 2019, doi:10.1371/journal.pbio.2005902.","ista":"Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Genetic dissection of assortative mating behavior. PLoS Biology. 17(2), e2005902.","chicago":"Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Genetic Dissection of Assortative Mating Behavior.” PLoS Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pbio.2005902."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"date_updated":"2023-08-24T14:46:47Z","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"_id":"6023","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","volume":5,"issue":"2","ec_funded":1,"oa_version":"Submitted Version","abstract":[{"text":"Multicellular development requires coordinated cell polarization relative to body axes, and translation to oriented cell division 1–3 . In plants, it is unknown how cell polarities are connected to organismal axes and translated to division. Here, we identify Arabidopsis SOSEKI proteins that integrate apical–basal and radial organismal axes to localize to polar cell edges. Localization does not depend on tissue context, requires cell wall integrity and is defined by a transferrable, protein-specific motif. A Domain of Unknown Function in SOSEKI proteins resembles the DIX oligomerization domain in the animal Dishevelled polarity regulator. The DIX-like domain self-interacts and is required for edge localization and for influencing division orientation, together with a second domain that defines the polar membrane domain. Our work shows that SOSEKI proteins locally interpret global polarity cues and can influence cell division orientation. Furthermore, this work reveals that, despite fundamental differences, cell polarity mechanisms in plants and animals converge on a similar protein domain.","lang":"eng"}],"month":"02","intvolume":" 5","scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/479113v1.abstract","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Yoshida S, Van Der Schuren A, Van Dop M, Van Galen L, Saiga S, Adibi M, Möller B, Ten Hove CA, Marhavý P, Smith R, Friml J, Weijers D. 2019. A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. 5(2), 160–166.","chicago":"Yoshida, Saiko, Alja Van Der Schuren, Maritza Van Dop, Luc Van Galen, Shunsuke Saiga, Milad Adibi, Barbara Möller, et al. “A SOSEKI-Based Coordinate System Interprets Global Polarity Cues in Arabidopsis.” Nature Plants. Springer Nature, 2019. https://doi.org/10.1038/s41477-019-0363-6.","apa":"Yoshida, S., Van Der Schuren, A., Van Dop, M., Van Galen, L., Saiga, S., Adibi, M., … Weijers, D. (2019). A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-019-0363-6","ama":"Yoshida S, Van Der Schuren A, Van Dop M, et al. A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. 2019;5(2):160-166. doi:10.1038/s41477-019-0363-6","short":"S. Yoshida, A. Van Der Schuren, M. Van Dop, L. Van Galen, S. Saiga, M. Adibi, B. Möller, C.A. Ten Hove, P. Marhavý, R. Smith, J. Friml, D. Weijers, Nature Plants 5 (2019) 160–166.","ieee":"S. Yoshida et al., “A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis,” Nature Plants, vol. 5, no. 2. Springer Nature, pp. 160–166, 2019.","mla":"Yoshida, Saiko, et al. “A SOSEKI-Based Coordinate System Interprets Global Polarity Cues in Arabidopsis.” Nature Plants, vol. 5, no. 2, Springer Nature, 2019, pp. 160–66, doi:10.1038/s41477-019-0363-6."},"title":"A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis","author":[{"id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko","last_name":"Yoshida","full_name":"Yoshida, Saiko"},{"first_name":"Alja","last_name":"Van Der Schuren","full_name":"Van Der Schuren, Alja"},{"last_name":"Van Dop","full_name":"Van Dop, Maritza","first_name":"Maritza"},{"first_name":"Luc","full_name":"Van Galen, Luc","last_name":"Van Galen"},{"full_name":"Saiga, Shunsuke","last_name":"Saiga","first_name":"Shunsuke"},{"last_name":"Adibi","full_name":"Adibi, Milad","first_name":"Milad"},{"last_name":"Möller","full_name":"Möller, Barbara","first_name":"Barbara"},{"last_name":"Ten Hove","full_name":"Ten Hove, Colette A.","first_name":"Colette A."},{"full_name":"Marhavy, Peter","orcid":"0000-0001-5227-5741","last_name":"Marhavy","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"first_name":"Richard","full_name":"Smith, Richard","last_name":"Smith"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"first_name":"Dolf","full_name":"Weijers, Dolf","last_name":"Weijers"}],"external_id":{"isi":["000460479600014"]},"article_processing_charge":"No","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"day":"08","publication":"Nature Plants","isi":1,"year":"2019","doi":"10.1038/s41477-019-0363-6","date_published":"2019-02-08T00:00:00Z","date_created":"2019-02-17T22:59:21Z","page":"160-166","publisher":"Springer Nature","quality_controlled":"1","oa":1},{"abstract":[{"text":"Recent technical developments in the fields of quantum electromechanics and optomechanics have spawned nanoscale mechanical transducers with the sensitivity to measure mechanical displacements at the femtometre scale and the ability to convert electromagnetic signals at the single photon level. A key challenge in this field is obtaining strong coupling between motion and electromagnetic fields without adding additional decoherence. Here we present an electromechanical transducer that integrates a high-frequency (0.42 GHz) hypersonic phononic crystal with a superconducting microwave circuit. The use of a phononic bandgap crystal enables quantum-level transduction of hypersonic mechanical motion and concurrently eliminates decoherence caused by acoustic radiation. Devices with hypersonic mechanical frequencies provide a natural pathway for integration with Josephson junction quantum circuits, a leading quantum computing technology, and nanophotonic systems capable of optical networking and distributing quantum information.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://authors.library.caltech.edu/92123/"}],"scopus_import":"1","intvolume":" 14","month":"04","publication_status":"published","publication_identifier":{"issn":["1748-3387"],"eissn":["1748-3395"]},"language":[{"iso":"eng"}],"issue":"4","volume":14,"_id":"6053","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-24T14:48:08Z","department":[{"_id":"JoFi"}],"oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2019","isi":1,"publication":"Nature Nanotechnology","day":"01","page":"334–339","date_created":"2019-02-24T22:59:21Z","date_published":"2019-04-01T00:00:00Z","doi":"10.1038/s41565-019-0377-2","citation":{"mla":"Kalaee, Mahmoud, et al. “Quantum Electromechanics of a Hypersonic Crystal.” Nature Nanotechnology, vol. 14, no. 4, Springer Nature, 2019, pp. 334–339, doi:10.1038/s41565-019-0377-2.","apa":"Kalaee, M., Mirhosseini, M., Dieterle, P. B., Peruzzo, M., Fink, J. M., & Painter, O. (2019). Quantum electromechanics of a hypersonic crystal. Nature Nanotechnology. Springer Nature. https://doi.org/10.1038/s41565-019-0377-2","ama":"Kalaee M, Mirhosseini M, Dieterle PB, Peruzzo M, Fink JM, Painter O. Quantum electromechanics of a hypersonic crystal. Nature Nanotechnology. 2019;14(4):334–339. doi:10.1038/s41565-019-0377-2","ieee":"M. Kalaee, M. Mirhosseini, P. B. Dieterle, M. Peruzzo, J. M. Fink, and O. Painter, “Quantum electromechanics of a hypersonic crystal,” Nature Nanotechnology, vol. 14, no. 4. Springer Nature, pp. 334–339, 2019.","short":"M. Kalaee, M. Mirhosseini, P.B. Dieterle, M. Peruzzo, J.M. Fink, O. Painter, Nature Nanotechnology 14 (2019) 334–339.","chicago":"Kalaee, Mahmoud, Mohammad Mirhosseini, Paul B. Dieterle, Matilda Peruzzo, Johannes M Fink, and Oskar Painter. “Quantum Electromechanics of a Hypersonic Crystal.” Nature Nanotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41565-019-0377-2.","ista":"Kalaee M, Mirhosseini M, Dieterle PB, Peruzzo M, Fink JM, Painter O. 2019. Quantum electromechanics of a hypersonic crystal. Nature Nanotechnology. 14(4), 334–339."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000463195700014"]},"article_processing_charge":"No","author":[{"first_name":"Mahmoud","last_name":"Kalaee","full_name":"Kalaee, Mahmoud"},{"first_name":"Mohammad","last_name":"Mirhosseini","full_name":"Mirhosseini, Mohammad"},{"first_name":"Paul B.","last_name":"Dieterle","full_name":"Dieterle, Paul B."},{"last_name":"Peruzzo","orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda","first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"},{"first_name":"Oskar","last_name":"Painter","full_name":"Painter, Oskar"}],"title":"Quantum electromechanics of a hypersonic crystal"},{"publication":"Proceedings of the American Mathematical Society","day":"01","year":"2019","isi":1,"date_created":"2019-02-24T22:59:19Z","date_published":"2019-01-01T00:00:00Z","doi":"10.1090/proc/14240","page":"91-102","oa":1,"publisher":"AMS","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"A. Akopyan, R. Fedorov, Proceedings of the American Mathematical Society 147 (2019) 91–102.","ieee":"A. Akopyan and R. Fedorov, “Two circles and only a straightedge,” Proceedings of the American Mathematical Society, vol. 147. AMS, pp. 91–102, 2019.","apa":"Akopyan, A., & Fedorov, R. (2019). Two circles and only a straightedge. Proceedings of the American Mathematical Society. AMS. https://doi.org/10.1090/proc/14240","ama":"Akopyan A, Fedorov R. Two circles and only a straightedge. Proceedings of the American Mathematical Society. 2019;147:91-102. doi:10.1090/proc/14240","mla":"Akopyan, Arseniy, and Roman Fedorov. “Two Circles and Only a Straightedge.” Proceedings of the American Mathematical Society, vol. 147, AMS, 2019, pp. 91–102, doi:10.1090/proc/14240.","ista":"Akopyan A, Fedorov R. 2019. Two circles and only a straightedge. Proceedings of the American Mathematical Society. 147, 91–102.","chicago":"Akopyan, Arseniy, and Roman Fedorov. “Two Circles and Only a Straightedge.” Proceedings of the American Mathematical Society. AMS, 2019. https://doi.org/10.1090/proc/14240."},"title":"Two circles and only a straightedge","article_processing_charge":"No","external_id":{"arxiv":["1709.02562"],"isi":["000450363900008"]},"author":[{"last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"},{"first_name":"Roman","last_name":"Fedorov","full_name":"Fedorov, Roman"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":147,"oa_version":"Preprint","abstract":[{"text":"We answer a question of David Hilbert: given two circles it is not possible in general to construct their centers using only a straightedge. On the other hand, we give infinitely many families of pairs of circles for which such construction is possible. ","lang":"eng"}],"intvolume":" 147","month":"01","main_file_link":[{"url":"https://arxiv.org/abs/1709.02562","open_access":"1"}],"scopus_import":"1","date_updated":"2023-08-24T14:48:59Z","department":[{"_id":"HeEd"}],"_id":"6050","status":"public","type":"journal_article"},{"date_updated":"2023-08-24T14:50:27Z","ddc":["570"],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:19Z","_id":"6095","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"publication_status":"published","file":[{"file_id":"6097","checksum":"f915885756057ec0ca5912a41f46a887","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2019_MolecularEcology_Faria.pdf","date_created":"2019-03-11T16:12:54Z","creator":"dernst","file_size":1510715,"date_updated":"2020-07-14T12:47:19Z"}],"language":[{"iso":"eng"}],"issue":"6","volume":28,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9837"}]},"abstract":[{"text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 28","citation":{"ama":"Faria R, Chaube P, Morales HE, et al. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. 2019;28(6):1375-1393. doi:10.1111/mec.14972","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2019). Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14972","ieee":"R. Faria et al., “Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes,” Molecular Ecology, vol. 28, no. 6. Wiley, pp. 1375–1393, 2019.","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, Molecular Ecology 28 (2019) 1375–1393.","mla":"Faria, Rui, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Molecular Ecology, vol. 28, no. 6, Wiley, 2019, pp. 1375–93, doi:10.1111/mec.14972.","ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2019. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. 28(6), 1375–1393.","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.14972."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"full_name":"Chaube, Pragya","last_name":"Chaube","first_name":"Pragya"},{"full_name":"Morales, Hernán E.","last_name":"Morales","first_name":"Hernán E."},{"last_name":"Larsson","full_name":"Larsson, Tomas","first_name":"Tomas"},{"first_name":"Alan R.","last_name":"Lemmon","full_name":"Lemmon, Alan R."},{"last_name":"Lemmon","full_name":"Lemmon, Emily M.","first_name":"Emily M."},{"first_name":"Marina","full_name":"Rafajlović, Marina","last_name":"Rafajlović"},{"first_name":"Marina","full_name":"Panova, Marina","last_name":"Panova"},{"last_name":"Ravinet","full_name":"Ravinet, Mark","first_name":"Mark"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"article_processing_charge":"No","external_id":{"isi":["000465219200013"]},"title":"Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","isi":1,"has_accepted_license":"1","year":"2019","day":"01","publication":"Molecular Ecology","page":"1375-1393","date_published":"2019-03-01T00:00:00Z","doi":"10.1111/mec.14972","date_created":"2019-03-10T22:59:21Z","quality_controlled":"1","publisher":"Wiley","oa":1},{"date_created":"2019-02-24T22:59:19Z","doi":"10.1088/1751-8121/aaf2dd","date_published":"2019-01-07T00:00:00Z","publication":"Journal of Physics A: Mathematical and Theoretical","day":"07","year":"2019","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"IOP Publishing","title":"Feedback-induced self-oscillations in large interacting systems subjected to phase transitions","external_id":{"isi":["000455379500001"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"De Martino D. Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical. 2019;52(4). doi:10.1088/1751-8121/aaf2dd","apa":"De Martino, D. (2019). Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical. IOP Publishing. https://doi.org/10.1088/1751-8121/aaf2dd","ieee":"D. De Martino, “Feedback-induced self-oscillations in large interacting systems subjected to phase transitions,” Journal of Physics A: Mathematical and Theoretical, vol. 52, no. 4. IOP Publishing, 2019.","short":"D. De Martino, Journal of Physics A: Mathematical and Theoretical 52 (2019).","mla":"De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting Systems Subjected to Phase Transitions.” Journal of Physics A: Mathematical and Theoretical, vol. 52, no. 4, 045002, IOP Publishing, 2019, doi:10.1088/1751-8121/aaf2dd.","ista":"De Martino D. 2019. Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical. 52(4), 045002.","chicago":"De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting Systems Subjected to Phase Transitions.” Journal of Physics A: Mathematical and Theoretical. IOP Publishing, 2019. https://doi.org/10.1088/1751-8121/aaf2dd."},"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"article_number":"045002","ec_funded":1,"issue":"4","volume":52,"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"6344","checksum":"1112304ad363a6d8afaeccece36473cf","creator":"kschuh","file_size":1804557,"date_updated":"2020-07-14T12:47:17Z","file_name":"2019_IOP_DeMartino.pdf","date_created":"2019-04-19T12:18:57Z"}],"publication_status":"published","intvolume":" 52","month":"01","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"In this article it is shown that large systems with many interacting units endowing multiple phases display self-oscillations in the presence of linear feedback between the control and order parameters, where an Andronov–Hopf bifurcation takes over the phase transition. This is simply illustrated through the mean field Landau theory whose feedback dynamics turn out to be described by the Van der Pol equation and it is then validated for the fully connected Ising model following heat bath dynamics. Despite its simplicity, this theory accounts potentially for a rich range of phenomena: here it is applied to describe in a stylized way (i) excess demand-price cycles due to strong herding in a simple agent-based market model; (ii) congestion waves in queuing networks triggered by user feedback to delays in overloaded conditions; and (iii) metabolic network oscillations resulting from cell growth control in a bistable phenotypic landscape.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:17Z","department":[{"_id":"GaTk"}],"ddc":["570"],"date_updated":"2023-08-24T14:49:23Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"6049"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Henderson NT, Le Marchand SJ, Hruska M, Hippenmeyer S, Luo L, Dalva MB. 2019. Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs. eLife. 8, e41563.","chicago":"Henderson, Nathan T., Sylvain J. Le Marchand, Martin Hruska, Simon Hippenmeyer, Liqun Luo, and Matthew B. Dalva. “Ephrin-B3 Controls Excitatory Synapse Density through Cell-Cell Competition for EphBs.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.41563.","ieee":"N. T. Henderson, S. J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, and M. B. Dalva, “Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs,” eLife, vol. 8. eLife Sciences Publications, 2019.","short":"N.T. Henderson, S.J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, M.B. Dalva, ELife 8 (2019).","ama":"Henderson NT, Le Marchand SJ, Hruska M, Hippenmeyer S, Luo L, Dalva MB. Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs. eLife. 2019;8. doi:10.7554/eLife.41563","apa":"Henderson, N. T., Le Marchand, S. J., Hruska, M., Hippenmeyer, S., Luo, L., & Dalva, M. B. (2019). Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.41563","mla":"Henderson, Nathan T., et al. “Ephrin-B3 Controls Excitatory Synapse Density through Cell-Cell Competition for EphBs.” ELife, vol. 8, e41563, eLife Sciences Publications, 2019, doi:10.7554/eLife.41563."},"title":"Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs","external_id":{"isi":["000459380600001"],"pmid":["30789343"]},"article_processing_charge":"No","author":[{"first_name":"Nathan T.","last_name":"Henderson","full_name":"Henderson, Nathan T."},{"first_name":"Sylvain J.","last_name":"Le Marchand","full_name":"Le Marchand, Sylvain J."},{"first_name":"Martin","full_name":"Hruska, Martin","last_name":"Hruska"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"},{"first_name":"Liqun","full_name":"Luo, Liqun","last_name":"Luo"},{"last_name":"Dalva","full_name":"Dalva, Matthew B.","first_name":"Matthew B."}],"article_number":"e41563","publication":"eLife","day":"21","year":"2019","has_accepted_license":"1","isi":1,"date_created":"2019-03-10T22:59:20Z","date_published":"2019-02-21T00:00:00Z","doi":"10.7554/eLife.41563","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","ddc":["570"],"date_updated":"2023-08-24T14:50:50Z","file_date_updated":"2020-07-14T12:47:19Z","department":[{"_id":"SiHi"}],"_id":"6091","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","language":[{"iso":"eng"}],"file":[{"file_id":"6098","checksum":"7b0800d003f14cd06b1802dea0c52941","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2019_eLife_Henderson.pdf","date_created":"2019-03-11T16:15:37Z","creator":"dernst","file_size":7260753,"date_updated":"2020-07-14T12:47:19Z"}],"publication_status":"published","volume":8,"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Cortical networks are characterized by sparse connectivity, with synapses found at only a subset of axo-dendritic contacts. Yet within these networks, neurons can exhibit high connection probabilities, suggesting that cell-intrinsic factors, not proximity, determine connectivity. Here, we identify ephrin-B3 (eB3) as a factor that determines synapse density by mediating a cell-cell competition that requires ephrin-B-EphB signaling. In a microisland culture system designed to isolate cell-cell competition, we find that eB3 determines winning and losing neurons in a contest for synapses. In a Mosaic Analysis with Double Markers (MADM) genetic mouse model system in vivo the relative levels of eB3 control spine density in layer 5 and 6 neurons. MADM cortical neurons in vitro reveal that eB3 controls synapse density independently of action potential-driven activity. Our findings illustrate a new class of competitive mechanism mediated by trans-synaptic organizing proteins which control the number of synapses neurons receive relative to neighboring neurons."}],"intvolume":" 8","month":"02","scopus_import":"1"},{"project":[{"grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013"}],"article_number":"e8470","author":[{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","first_name":"Karin","last_name":"Mitosch","full_name":"Mitosch, Karin"},{"first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","full_name":"Rieckh, Georg","last_name":"Rieckh"},{"first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach"}],"article_processing_charge":"No","external_id":{"pmid":["30765425"],"isi":["000459628300003"]},"title":"Temporal order and precision of complex stress responses in individual bacteria","citation":{"ista":"Mitosch K, Rieckh G, Bollenbach MT. 2019. Temporal order and precision of complex stress responses in individual bacteria. Molecular systems biology. 15(2), e8470.","chicago":"Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Temporal Order and Precision of Complex Stress Responses in Individual Bacteria.” Molecular Systems Biology. Embo Press, 2019. https://doi.org/10.15252/msb.20188470.","ama":"Mitosch K, Rieckh G, Bollenbach MT. Temporal order and precision of complex stress responses in individual bacteria. Molecular systems biology. 2019;15(2). doi:10.15252/msb.20188470","apa":"Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2019). Temporal order and precision of complex stress responses in individual bacteria. Molecular Systems Biology. Embo Press. https://doi.org/10.15252/msb.20188470","short":"K. Mitosch, G. Rieckh, M.T. Bollenbach, Molecular Systems Biology 15 (2019).","ieee":"K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Temporal order and precision of complex stress responses in individual bacteria,” Molecular systems biology, vol. 15, no. 2. Embo Press, 2019.","mla":"Mitosch, Karin, et al. “Temporal Order and Precision of Complex Stress Responses in Individual Bacteria.” Molecular Systems Biology, vol. 15, no. 2, e8470, Embo Press, 2019, doi:10.15252/msb.20188470."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Embo Press","quality_controlled":"1","oa":1,"doi":"10.15252/msb.20188470","date_published":"2019-02-14T00:00:00Z","date_created":"2019-02-24T22:59:18Z","isi":1,"year":"2019","day":"14","publication":"Molecular systems biology","type":"journal_article","status":"public","_id":"6046","department":[{"_id":"GaTk"}],"date_updated":"2023-08-24T14:49:53Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30765425"}],"month":"02","intvolume":" 15","acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Sudden stress often triggers diverse, temporally structured gene expression responses in microbes, but it is largely unknown how variable in time such responses are and if genes respond in the same temporal order in every single cell. Here, we quantified timing variability of individual promoters responding to sublethal antibiotic stress using fluorescent reporters, microfluidics, and time‐lapse microscopy. We identified lower and upper bounds that put definite constraints on timing variability, which varies strongly among promoters and conditions. Timing variability can be interpreted using results from statistical kinetics, which enable us to estimate the number of rate‐limiting molecular steps underlying different responses. We found that just a few critical steps control some responses while others rely on dozens of steps. To probe connections between different stress responses, we then tracked the temporal order and response time correlations of promoter pairs in individual cells. Our results support that, when bacteria are exposed to the antibiotic nitrofurantoin, the ensuing oxidative stress and SOS responses are part of the same causal chain of molecular events. In contrast, under trimethoprim, the acid stress response and the SOS response are part of different chains of events running in parallel. Our approach reveals fundamental constraints on gene expression timing and provides new insights into the molecular events that underlie the timing of stress responses."}],"oa_version":"Submitted Version","pmid":1,"issue":"2","volume":15,"publication_status":"published","language":[{"iso":"eng"}]},{"citation":{"mla":"Kutzer, Megan, et al. “A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance.” Journal of Animal Ecology, vol. 88, no. 4, Wiley, 2019, pp. 566–78, doi:10.1111/1365-2656.12953.","ieee":"M. Kutzer, J. Kurtz, and S. A. O. Armitage, “A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance,” Journal of Animal Ecology, vol. 88, no. 4. Wiley, pp. 566–578, 2019.","short":"M. Kutzer, J. Kurtz, S.A.O. Armitage, Journal of Animal Ecology 88 (2019) 566–578.","ama":"Kutzer M, Kurtz J, Armitage SAO. A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. Journal of Animal Ecology. 2019;88(4):566-578. doi:10.1111/1365-2656.12953","apa":"Kutzer, M., Kurtz, J., & Armitage, S. A. O. (2019). A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. Journal of Animal Ecology. Wiley. https://doi.org/10.1111/1365-2656.12953","chicago":"Kutzer, Megan, Joachim Kurtz, and Sophie A.O. Armitage. “A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance.” Journal of Animal Ecology. Wiley, 2019. https://doi.org/10.1111/1365-2656.12953.","ista":"Kutzer M, Kurtz J, Armitage SAO. 2019. A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. Journal of Animal Ecology. 88(4), 566–578."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000467994800007"]},"author":[{"last_name":"Kutzer","full_name":"Kutzer, Megan","orcid":"0000-0002-8696-6978","first_name":"Megan","id":"29D0B332-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kurtz","full_name":"Kurtz, Joachim","first_name":"Joachim"},{"first_name":"Sophie A.O.","last_name":"Armitage","full_name":"Armitage, Sophie A.O."}],"title":"A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"year":"2019","isi":1,"has_accepted_license":"1","publication":"Journal of Animal Ecology","day":"01","page":"566-578","date_created":"2019-03-17T22:59:15Z","date_published":"2019-04-01T00:00:00Z","doi":"10.1111/1365-2656.12953","oa":1,"quality_controlled":"1","publisher":"Wiley","date_updated":"2023-08-25T08:04:53Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:19Z","department":[{"_id":"SyCr"}],"_id":"6105","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"eissn":["13652656"],"issn":["00218790"]},"language":[{"iso":"eng"}],"file":[{"checksum":"405cde15120de26018b3bd0dfa29986c","file_id":"6107","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2019_JournalAnimalEcology_Kutzer.pdf","date_created":"2019-03-18T07:43:06Z","creator":"dernst","file_size":1460662,"date_updated":"2020-07-14T12:47:19Z"}],"ec_funded":1,"issue":"4","volume":88,"related_material":{"record":[{"status":"public","id":"9806","relation":"research_data"}]},"abstract":[{"lang":"eng","text":" Hosts can alter their strategy towards pathogens during their lifetime; that is, they can show phenotypic plasticity in immunity or life history. Immune priming is one such example, where a previous encounter with a pathogen confers enhanced protection upon secondary challenge, resulting in reduced pathogen load (i.e., resistance) and improved host survival. However, an initial encounter might also enhance tolerance, particularly to less virulent opportunistic pathogens that establish persistent infections. In this scenario, individuals are better able to reduce the negative fecundity consequences that result from a high pathogen burden. Finally, previous exposure may also lead to life‐history adjustments, such as terminal investment into reproduction.\r\n Using different Drosophila melanogaster host genotypes and two bacterial pathogens, Lactococcus lactis and Pseudomonas entomophila, we tested whether previous exposure results in resistance or tolerance and whether it modifies immune gene expression during an acute‐phase infection (one day post‐challenge). We then asked whether previous pathogen exposure affects chronic‐phase pathogen persistence and longer‐term survival (28 days post‐challenge).\r\n We predicted that previous exposure would increase host resistance to an early stage bacterial infection while it might come at a cost to host fecundity tolerance. We reasoned that resistance would be due in part to stronger immune gene expression after challenge. We expected that previous exposure would improve long‐term survival, that it would reduce infection persistence, and we expected to find genetic variation in these responses.\r\n We found that previous exposure to P. entomophila weakened host resistance to a second infection independent of genotype and had no effect on immune gene expression. Fecundity tolerance showed genotypic variation but was not influenced by previous exposure. However, L. lactis persisted as a chronic infection, whereas survivors cleared the more pathogenic P. entomophila infection.\r\n To our knowledge, this is the first study that addresses host tolerance to bacteria in relation to previous exposure, taking a multi‐faceted approach to address the topic. Our results suggest that previous exposure comes with transient costs to resistance during the early stage of infection in this host–pathogen system and that infection persistence may be bacterium‐specific.\r\n"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 88","month":"04"},{"title":"Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity","external_id":{"isi":["000460509600013"],"pmid":["30773315"]},"article_processing_charge":"No","author":[{"orcid":"0000-0002-5419-7756","full_name":"Xia, Peng","last_name":"Xia","first_name":"Peng","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gütl, Daniel J","last_name":"Gütl","first_name":"Daniel J","id":"381929CE-F248-11E8-B48F-1D18A9856A87"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","orcid":"0000-0002-9438-4783","full_name":"Zheden, Vanessa","last_name":"Zheden"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Xia P, Gütl DJ, Zheden V, Heisenberg C-PJ. 2019. Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity. Cell. 176(6), 1379–1392.e14.","chicago":"Xia, Peng, Daniel J Gütl, Vanessa Zheden, and Carl-Philipp J Heisenberg. “Lateral Inhibition in Cell Specification Mediated by Mechanical Signals Modulating TAZ Activity.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.01.019.","short":"P. Xia, D.J. Gütl, V. Zheden, C.-P.J. Heisenberg, Cell 176 (2019) 1379–1392.e14.","ieee":"P. Xia, D. J. Gütl, V. Zheden, and C.-P. J. Heisenberg, “Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity,” Cell, vol. 176, no. 6. Elsevier, p. 1379–1392.e14, 2019.","apa":"Xia, P., Gütl, D. J., Zheden, V., & Heisenberg, C.-P. J. (2019). Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.01.019","ama":"Xia P, Gütl DJ, Zheden V, Heisenberg C-PJ. Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity. Cell. 2019;176(6):1379-1392.e14. doi:10.1016/j.cell.2019.01.019","mla":"Xia, Peng, et al. “Lateral Inhibition in Cell Specification Mediated by Mechanical Signals Modulating TAZ Activity.” Cell, vol. 176, no. 6, Elsevier, 2019, p. 1379–1392.e14, doi:10.1016/j.cell.2019.01.019."},"project":[{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"}],"date_created":"2019-03-10T22:59:19Z","doi":"10.1016/j.cell.2019.01.019","date_published":"2019-03-07T00:00:00Z","page":"1379-1392.e14","publication":"Cell","day":"07","year":"2019","isi":1,"oa":1,"quality_controlled":"1","publisher":"Elsevier","acknowledgement":"We thank Roland Dosch, Makoto Furutani-Seiki, Brian Link, Mary Mullins, and Masazumi Tada for providing transgenic and/or mutant zebrafish lines; Alexandra Schauer, Shayan Shami-Pour, and the rest of the Heisenberg lab for technical assistance and feedback on the manuscript; and the Bioimaging, Electron Microscopy, and Zebrafish facilities of IST Austria for continuous support. This work was supported by an ERC advanced grant ( MECSPEC to C.-P.H.).","department":[{"_id":"CaHe"},{"_id":"EM-Fac"}],"date_updated":"2023-08-25T08:02:23Z","status":"public","type":"journal_article","article_type":"original","_id":"6087","ec_funded":1,"issue":"6","volume":176,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/in-zebrafish-eggs-most-rapidly-growing-cell-inhibits-its-neighbours-through-mechanical-signals/","relation":"press_release","description":"News on IST Homepage"}]},"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 176","month":"03","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2019.01.019"}],"scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Cell fate specification by lateral inhibition typically involves contact signaling through the Delta-Notch signaling pathway. However, whether this is the only signaling mode mediating lateral inhibition remains unclear. Here we show that in zebrafish oogenesis, a group of cells within the granulosa cell layer at the oocyte animal pole acquire elevated levels of the transcriptional coactivator TAZ in their nuclei. One of these cells, the future micropyle precursor cell (MPC), accumulates increasingly high levels of nuclear TAZ and grows faster than its surrounding cells, mechanically compressing those cells, which ultimately lose TAZ from their nuclei. Strikingly, relieving neighbor-cell compression by MPC ablation or aspiration restores nuclear TAZ accumulation in neighboring cells, eventually leading to MPC re-specification from these cells. Conversely, MPC specification is defective in taz−/− follicles. These findings uncover a novel mode of lateral inhibition in cell fate specification based on mechanical signals controlling TAZ activity.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}]},{"date_created":"2021-08-06T12:06:40Z","related_material":{"record":[{"relation":"used_in_publication","id":"6105","status":"public"}]},"doi":"10.5061/dryad.9kj41f0","date_published":"2019-02-05T00:00:00Z","year":"2019","day":"05","main_file_link":[{"url":"https://doi.org/10.5061/dryad.9kj41f0","open_access":"1"}],"oa":1,"publisher":"Dryad","month":"02","abstract":[{"text":"1. Hosts can alter their strategy towards pathogens during their lifetime, i.e., they can show phenotypic plasticity in immunity or life history. Immune priming is one such example, where a previous encounter with a pathogen confers enhanced protection upon secondary challenge, resulting in reduced pathogen load (i.e. resistance) and improved host survival. However, an initial encounter might also enhance tolerance, particularly to less virulent opportunistic pathogens that establish persistent infections. In this scenario, individuals are better able to reduce the negative fitness consequences that result from a high pathogen load. Finally, previous exposure may also lead to life history adjustments, such as terminal investment into reproduction. 2. Using different Drosophila melanogaster host genotypes and two bacterial pathogens, Lactococcus lactis and Pseudomonas entomophila, we tested if previous exposure results in resistance or tolerance and whether it modifies immune gene expression during an acute-phase infection (one day post-challenge). We then asked if previous pathogen exposure affects chronic-phase pathogen persistence and longer-term survival (28 days post-challenge). 3. We predicted that previous exposure would increase host resistance to an early stage bacterial infection while it might come at a cost to host fecundity tolerance. We reasoned that resistance would be due in part to stronger immune gene expression after challenge. We expected that previous exposure would improve long-term survival, that it would reduce infection persistence, and we expected to find genetic variation in these responses. 4. We found that previous exposure to P. entomophila weakened host resistance to a second infection independent of genotype and had no effect on immune gene expression. Fecundity tolerance showed genotypic variation but was not influenced by previous exposure. However, L. lactis persisted as a chronic infection, whereas survivors cleared the more pathogenic P. entomophila infection. 5. To our knowledge, this is the first study that addresses host tolerance to bacteria in relation to previous exposure, taking a multi-faceted approach to address the topic. Our results suggest that previous exposure comes with transient costs to resistance during the early stage of infection in this host-pathogen system and that infection persistence may be bacterium-specific.","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"full_name":"Kutzer, Megan","orcid":"0000-0002-8696-6978","last_name":"Kutzer","first_name":"Megan","id":"29D0B332-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"},{"first_name":"Sophie A.O.","full_name":"Armitage, Sophie A.O.","last_name":"Armitage"}],"department":[{"_id":"SyCr"}],"title":"Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance","citation":{"mla":"Kutzer, Megan, et al. Data from: A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance. Dryad, 2019, doi:10.5061/dryad.9kj41f0.","ieee":"M. Kutzer, J. Kurtz, and S. A. O. Armitage, “Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance.” Dryad, 2019.","short":"M. Kutzer, J. Kurtz, S.A.O. Armitage, (2019).","apa":"Kutzer, M., Kurtz, J., & Armitage, S. A. O. (2019). Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. Dryad. https://doi.org/10.5061/dryad.9kj41f0","ama":"Kutzer M, Kurtz J, Armitage SAO. Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. 2019. doi:10.5061/dryad.9kj41f0","chicago":"Kutzer, Megan, Joachim Kurtz, and Sophie A.O. Armitage. “Data from: A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance.” Dryad, 2019. https://doi.org/10.5061/dryad.9kj41f0.","ista":"Kutzer M, Kurtz J, Armitage SAO. 2019. Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance, Dryad, 10.5061/dryad.9kj41f0."},"date_updated":"2023-08-25T08:04:52Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9806"},{"oa":1,"publisher":"Cambridge University Press","quality_controlled":"1","publication":"Ergodic Theory and Dynamical Systems","day":"01","year":"2019","isi":1,"date_created":"2019-03-10T22:59:18Z","date_published":"2019-04-01T00:00:00Z","doi":"10.1017/etds.2017.52","page":"1082-1098","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Sadel C, Xu D. 2019. Singular analytic linear cocycles with negative infinite Lyapunov exponents. Ergodic Theory and Dynamical Systems. 39(4), 1082–1098.","chicago":"Sadel, Christian, and Disheng Xu. “Singular Analytic Linear Cocycles with Negative Infinite Lyapunov Exponents.” Ergodic Theory and Dynamical Systems. Cambridge University Press, 2019. https://doi.org/10.1017/etds.2017.52.","ieee":"C. Sadel and D. Xu, “Singular analytic linear cocycles with negative infinite Lyapunov exponents,” Ergodic Theory and Dynamical Systems, vol. 39, no. 4. Cambridge University Press, pp. 1082–1098, 2019.","short":"C. Sadel, D. Xu, Ergodic Theory and Dynamical Systems 39 (2019) 1082–1098.","ama":"Sadel C, Xu D. Singular analytic linear cocycles with negative infinite Lyapunov exponents. Ergodic Theory and Dynamical Systems. 2019;39(4):1082-1098. doi:10.1017/etds.2017.52","apa":"Sadel, C., & Xu, D. (2019). Singular analytic linear cocycles with negative infinite Lyapunov exponents. Ergodic Theory and Dynamical Systems. Cambridge University Press. https://doi.org/10.1017/etds.2017.52","mla":"Sadel, Christian, and Disheng Xu. “Singular Analytic Linear Cocycles with Negative Infinite Lyapunov Exponents.” Ergodic Theory and Dynamical Systems, vol. 39, no. 4, Cambridge University Press, 2019, pp. 1082–98, doi:10.1017/etds.2017.52."},"title":"Singular analytic linear cocycles with negative infinite Lyapunov exponents","external_id":{"arxiv":["1601.06118"],"isi":["000459725600012"]},"article_processing_charge":"No","author":[{"id":"4760E9F8-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Sadel","full_name":"Sadel, Christian","orcid":"0000-0001-8255-3968"},{"first_name":"Disheng","last_name":"Xu","full_name":"Xu, Disheng"}],"oa_version":"Preprint","abstract":[{"text":"We show that linear analytic cocycles where all Lyapunov exponents are negative infinite are nilpotent. For such one-frequency cocycles we show that they can be analytically conjugated to an upper triangular cocycle or a Jordan normal form. As a consequence, an arbitrarily small analytic perturbation leads to distinct Lyapunov exponents. Moreover, in the one-frequency case where the th Lyapunov exponent is finite and the st negative infinite, we obtain a simple criterion for domination in which case there is a splitting into a nilpotent part and an invertible part.","lang":"eng"}],"intvolume":" 39","month":"04","main_file_link":[{"url":"https://arxiv.org/abs/1601.06118","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"issue":"4","volume":39,"_id":"6086","status":"public","type":"journal_article","date_updated":"2023-08-25T08:03:30Z","department":[{"_id":"LaEr"}]},{"issue":"1","volume":8,"publication_identifier":{"issn":["20955545"],"eissn":["20477538"]},"publication_status":"published","file":[{"file_name":"2019_Light_LeFeber.pdf","date_created":"2019-03-18T08:08:22Z","file_size":1119947,"date_updated":"2020-07-14T12:47:19Z","creator":"dernst","checksum":"d71e528cff9c56f70ccc29dd7005257f","file_id":"6108","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"03","intvolume":" 8","abstract":[{"text":"Light is a union of electric and magnetic fields, and nowhere is the complex relationship between these fields more evident than in the near fields of nanophotonic structures. There, complicated electric and magnetic fields varying over subwavelength scales are generally present, which results in photonic phenomena such as extraordinary optical momentum, superchiral fields, and a complex spatial evolution of optical singularities. An understanding of such phenomena requires nanoscale measurements of the complete optical field vector. Although the sensitivity of near- field scanning optical microscopy to the complete electromagnetic field was recently demonstrated, a separation of different components required a priori knowledge of the sample. Here, we introduce a robust algorithm that can disentangle all six electric and magnetic field components from a single near-field measurement without any numerical modeling of the structure. As examples, we unravel the fields of two prototypical nanophotonic structures: a photonic crystal waveguide and a plasmonic nanowire. These results pave the way for new studies of complex photonic phenomena at the nanoscale and for the design of structures that optimize their optical behavior.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:19Z","department":[{"_id":"JoFi"}],"date_updated":"2023-08-25T08:06:10Z","ddc":["530"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"6102","date_published":"2019-03-06T00:00:00Z","doi":"10.1038/s41377-019-0124-3","date_created":"2019-03-17T22:59:13Z","isi":1,"has_accepted_license":"1","year":"2019","day":"06","publication":"Light: Science and Applications","quality_controlled":"1","publisher":"Springer Nature","oa":1,"author":[{"full_name":"Le Feber, B.","last_name":"Le Feber","first_name":"B."},{"first_name":"J. E.","last_name":"Sipe","full_name":"Sipe, J. E."},{"id":"45598606-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Wulf","full_name":"Wulf, Matthias","orcid":"0000-0001-6613-1378"},{"first_name":"L.","last_name":"Kuipers","full_name":"Kuipers, L."},{"first_name":"N.","last_name":"Rotenberg","full_name":"Rotenberg, N."}],"article_processing_charge":"No","external_id":{"arxiv":["1803.10145"],"isi":["000460470700004"]},"title":"A full vectorial mapping of nanophotonic light fields","citation":{"chicago":"Le Feber, B., J. E. Sipe, Matthias Wulf, L. Kuipers, and N. Rotenberg. “A Full Vectorial Mapping of Nanophotonic Light Fields.” Light: Science and Applications. Springer Nature, 2019. https://doi.org/10.1038/s41377-019-0124-3.","ista":"Le Feber B, Sipe JE, Wulf M, Kuipers L, Rotenberg N. 2019. A full vectorial mapping of nanophotonic light fields. Light: Science and Applications. 8(1), 28.","mla":"Le Feber, B., et al. “A Full Vectorial Mapping of Nanophotonic Light Fields.” Light: Science and Applications, vol. 8, no. 1, 28, Springer Nature, 2019, doi:10.1038/s41377-019-0124-3.","short":"B. Le Feber, J.E. Sipe, M. Wulf, L. Kuipers, N. Rotenberg, Light: Science and Applications 8 (2019).","ieee":"B. Le Feber, J. E. Sipe, M. Wulf, L. Kuipers, and N. Rotenberg, “A full vectorial mapping of nanophotonic light fields,” Light: Science and Applications, vol. 8, no. 1. Springer Nature, 2019.","apa":"Le Feber, B., Sipe, J. E., Wulf, M., Kuipers, L., & Rotenberg, N. (2019). A full vectorial mapping of nanophotonic light fields. Light: Science and Applications. Springer Nature. https://doi.org/10.1038/s41377-019-0124-3","ama":"Le Feber B, Sipe JE, Wulf M, Kuipers L, Rotenberg N. A full vectorial mapping of nanophotonic light fields. Light: Science and Applications. 2019;8(1). doi:10.1038/s41377-019-0124-3"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"28"},{"oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"19","year":"2019","has_accepted_license":"1","isi":1,"date_created":"2019-03-31T21:59:13Z","date_published":"2019-03-19T00:00:00Z","doi":"10.1073/pnas.1813255116","page":"5344-5349","project":[{"call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425","name":"Active mechano-chemical description of the cell cytoskeleton","grant_number":"P31639"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Recho, P., Hallou, A., & Hannezo, E. B. (2019). Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1813255116","ama":"Recho P, Hallou A, Hannezo EB. Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(12):5344-5349. doi:10.1073/pnas.1813255116","ieee":"P. Recho, A. Hallou, and E. B. Hannezo, “Theory of mechanochemical patterning in biphasic biological tissues,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 12. National Academy of Sciences, pp. 5344–5349, 2019.","short":"P. Recho, A. Hallou, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 5344–5349.","mla":"Recho, Pierre, et al. “Theory of Mechanochemical Patterning in Biphasic Biological Tissues.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 12, National Academy of Sciences, 2019, pp. 5344–49, doi:10.1073/pnas.1813255116.","ista":"Recho P, Hallou A, Hannezo EB. 2019. Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. 116(12), 5344–5349.","chicago":"Recho, Pierre, Adrien Hallou, and Edouard B Hannezo. “Theory of Mechanochemical Patterning in Biphasic Biological Tissues.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1813255116."},"title":"Theory of mechanochemical patterning in biphasic biological tissues","article_processing_charge":"No","external_id":{"pmid":["30819884"],"isi":["000461679000027"]},"author":[{"first_name":"Pierre","full_name":"Recho, Pierre","last_name":"Recho"},{"first_name":"Adrien","last_name":"Hallou","full_name":"Hallou, Adrien"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The formation of self-organized patterns is key to the morphogenesis of multicellular organisms, although a comprehensive theory of biological pattern formation is still lacking. Here, we propose a minimal model combining tissue mechanics with morphogen turnover and transport to explore routes to patterning. Our active description couples morphogen reaction and diffusion, which impact cell differentiation and tissue mechanics, to a two-phase poroelastic rheology, where one tissue phase consists of a poroelastic cell network and the other one of a permeating extracellular fluid, which provides a feedback by actively transporting morphogens. While this model encompasses previous theories approximating tissues to inert monophasic media, such as Turing’s reaction–diffusion model, it overcomes some of their key limitations permitting pattern formation via any two-species biochemical kinetics due to mechanically induced cross-diffusion flows. Moreover, we describe a qualitatively different advection-driven Keller–Segel instability which allows for the formation of patterns with a single morphogen and whose fundamental mode pattern robustly scales with tissue size. We discuss the potential relevance of these findings for tissue morphogenesis."}],"intvolume":" 116","month":"03","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_id":"6193","checksum":"8b67eee0ea8e5db61583e4d485215258","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2019_PNAS_Recho.pdf","date_created":"2019-04-03T14:10:30Z","creator":"dernst","file_size":3456045,"date_updated":"2020-07-14T12:47:23Z"}],"publication_status":"published","publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"volume":116,"related_material":{"link":[{"relation":"supplementary_material","url":"www.pnas.org/lookup/suppl/doi:10.1073/pnas.1813255116/-/DCSupplemental"}]},"issue":"12","_id":"6191","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["570"],"date_updated":"2023-08-25T08:57:30Z","file_date_updated":"2020-07-14T12:47:23Z","department":[{"_id":"EdHa"}]},{"date_created":"2019-03-31T21:59:12Z","doi":"10.1158/1541-7786.MCR-18-0530","date_published":"2019-03-01T00:00:00Z","page":"783-793","publication":"Molecular Cancer Research","day":"01","year":"2019","isi":1,"oa":1,"quality_controlled":"1","publisher":"AACR","title":"CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis","external_id":{"pmid":["30552233"],"isi":["000460099800012"]},"article_processing_charge":"No","author":[{"id":"3047D808-F248-11E8-B48F-1D18A9856A87","first_name":"Marko","full_name":"Roblek, Marko","orcid":"0000-0001-9588-1389","last_name":"Roblek"},{"first_name":"Darya","last_name":"Protsyuk","full_name":"Protsyuk, Darya"},{"first_name":"Paul F.","full_name":"Becker, Paul F.","last_name":"Becker"},{"first_name":"Cristina","last_name":"Stefanescu","full_name":"Stefanescu, Cristina"},{"first_name":"Christian","full_name":"Gorzelanny, Christian","last_name":"Gorzelanny"},{"full_name":"Glaus Garzon, Jesus F.","last_name":"Glaus Garzon","first_name":"Jesus F."},{"full_name":"Knopfova, Lucia","last_name":"Knopfova","first_name":"Lucia"},{"full_name":"Heikenwalder, Mathias","last_name":"Heikenwalder","first_name":"Mathias"},{"first_name":"Bruno","last_name":"Luckow","full_name":"Luckow, Bruno"},{"first_name":"Stefan W.","last_name":"Schneider","full_name":"Schneider, Stefan W."},{"first_name":"Lubor","last_name":"Borsig","full_name":"Borsig, Lubor"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Roblek, Marko, Darya Protsyuk, Paul F. Becker, Cristina Stefanescu, Christian Gorzelanny, Jesus F. Glaus Garzon, Lucia Knopfova, et al. “CCL2 Is a Vascular Permeability Factor Inducing CCR2-Dependent Endothelial Retraction during Lung Metastasis.” Molecular Cancer Research. AACR, 2019. https://doi.org/10.1158/1541-7786.MCR-18-0530.","ista":"Roblek M, Protsyuk D, Becker PF, Stefanescu C, Gorzelanny C, Glaus Garzon JF, Knopfova L, Heikenwalder M, Luckow B, Schneider SW, Borsig L. 2019. CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis. Molecular Cancer Research. 17(3), 783–793.","mla":"Roblek, Marko, et al. “CCL2 Is a Vascular Permeability Factor Inducing CCR2-Dependent Endothelial Retraction during Lung Metastasis.” Molecular Cancer Research, vol. 17, no. 3, AACR, 2019, pp. 783–93, doi:10.1158/1541-7786.MCR-18-0530.","ieee":"M. Roblek et al., “CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis,” Molecular Cancer Research, vol. 17, no. 3. AACR, pp. 783–793, 2019.","short":"M. Roblek, D. Protsyuk, P.F. Becker, C. Stefanescu, C. Gorzelanny, J.F. Glaus Garzon, L. Knopfova, M. Heikenwalder, B. Luckow, S.W. Schneider, L. Borsig, Molecular Cancer Research 17 (2019) 783–793.","apa":"Roblek, M., Protsyuk, D., Becker, P. F., Stefanescu, C., Gorzelanny, C., Glaus Garzon, J. F., … Borsig, L. (2019). CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis. Molecular Cancer Research. AACR. https://doi.org/10.1158/1541-7786.MCR-18-0530","ama":"Roblek M, Protsyuk D, Becker PF, et al. CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis. Molecular Cancer Research. 2019;17(3):783-793. doi:10.1158/1541-7786.MCR-18-0530"},"issue":"3","volume":17,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["15417786"],"eissn":["15573125"]},"intvolume":" 17","month":"03","main_file_link":[{"url":"https://doi.org/10.1158/1541-7786.MCR-18-0530","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Increased levels of the chemokine CCL2 in cancer patients are associated with poor prognosis. Experimental evidence suggests that CCL2 correlates with inflammatory monocyte recruitment and induction of vascular activation, but the functionality remains open. Here, we show that endothelial Ccr2 facilitates pulmonary metastasis using an endothelial-specific Ccr2-deficient mouse model (Ccr2ecKO). Similar levels of circulating monocytes and equal leukocyte recruitment to metastatic lesions of Ccr2ecKO and Ccr2fl/fl littermates were observed. The absence of endothelial Ccr2 strongly reduced pulmonary metastasis, while the primary tumor growth was unaffected. Despite a comparable cytokine milieu in Ccr2ecKO and Ccr2fl/fl littermates the absence of vascular permeability induction was observed only in Ccr2ecKO mice. CCL2 stimulation of pulmonary endothelial cells resulted in increased phosphorylation of MLC2, endothelial cell retraction, and vascular leakiness that was blocked by an addition of a CCR2 inhibitor. These data demonstrate that endothelial CCR2 expression is required for tumor cell extravasation and pulmonary metastasis.\r\n\r\nImplications: The findings provide mechanistic insight into how CCL2–CCR2 signaling in endothelial cells promotes their activation through myosin light chain phosphorylation, resulting in endothelial retraction and enhanced tumor cell migration and metastasis.","lang":"eng"}],"department":[{"_id":"DaSi"}],"date_updated":"2023-08-25T08:57:01Z","status":"public","type":"journal_article","article_type":"original","_id":"6190"},{"title":"Why structure matters","external_id":{"isi":["000461988300001"]},"article_processing_charge":"No","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"first_name":"Joachim","last_name":"Hermisson","full_name":"Hermisson, Joachim"},{"last_name":"Nordborg","full_name":"Nordborg, Magnus","first_name":"Magnus"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Barton NH, Hermisson J, Nordborg M. 2019. Why structure matters. eLife. 8, e45380.","chicago":"Barton, Nicholas H, Joachim Hermisson, and Magnus Nordborg. “Why Structure Matters.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.45380.","apa":"Barton, N. H., Hermisson, J., & Nordborg, M. (2019). Why structure matters. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.45380","ama":"Barton NH, Hermisson J, Nordborg M. Why structure matters. eLife. 2019;8. doi:10.7554/eLife.45380","short":"N.H. Barton, J. Hermisson, M. Nordborg, ELife 8 (2019).","ieee":"N. H. Barton, J. Hermisson, and M. Nordborg, “Why structure matters,” eLife, vol. 8. eLife Sciences Publications, 2019.","mla":"Barton, Nicholas H., et al. “Why Structure Matters.” ELife, vol. 8, e45380, eLife Sciences Publications, 2019, doi:10.7554/eLife.45380."},"article_number":"e45380","date_created":"2019-04-07T21:59:15Z","date_published":"2019-03-21T00:00:00Z","doi":"10.7554/eLife.45380","publication":"eLife","day":"21","year":"2019","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:24Z","ddc":["570"],"date_updated":"2023-08-25T08:59:38Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"6230","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/body-height-bmi-disease-risk-co/","relation":"press_release"}]},"volume":8,"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:24Z","file_size":298466,"creator":"dernst","date_created":"2019-04-11T11:43:38Z","file_name":"2019_eLife_Barton.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6293","checksum":"130d7544b57df4a6787e1263c2d7ea43"}],"publication_status":"published","publication_identifier":{"eissn":["2050084X"]},"intvolume":" 8","month":"03","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Great care is needed when interpreting claims about the genetic basis of human variation based on data from genome-wide association studies.","lang":"eng"}]},{"author":[{"id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate","last_name":"Gerencser","full_name":"Gerencser, Mate"}],"external_id":{"isi":["000459681900005"],"arxiv":["1705.05364"]},"article_processing_charge":"No","title":"Boundary regularity of stochastic PDEs","citation":{"chicago":"Gerencser, Mate. “Boundary Regularity of Stochastic PDEs.” Annals of Probability. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AOP1272.","ista":"Gerencser M. 2019. Boundary regularity of stochastic PDEs. Annals of Probability. 47(2), 804–834.","mla":"Gerencser, Mate. “Boundary Regularity of Stochastic PDEs.” Annals of Probability, vol. 47, no. 2, Institute of Mathematical Statistics, 2019, pp. 804–34, doi:10.1214/18-AOP1272.","ama":"Gerencser M. Boundary regularity of stochastic PDEs. Annals of Probability. 2019;47(2):804-834. doi:10.1214/18-AOP1272","apa":"Gerencser, M. (2019). Boundary regularity of stochastic PDEs. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AOP1272","ieee":"M. Gerencser, “Boundary regularity of stochastic PDEs,” Annals of Probability, vol. 47, no. 2. Institute of Mathematical Statistics, pp. 804–834, 2019.","short":"M. Gerencser, Annals of Probability 47 (2019) 804–834."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"804-834","date_published":"2019-03-01T00:00:00Z","doi":"10.1214/18-AOP1272","date_created":"2019-04-07T21:59:15Z","isi":1,"year":"2019","day":"01","publication":"Annals of Probability","quality_controlled":"1","publisher":"Institute of Mathematical Statistics","oa":1,"department":[{"_id":"JaMa"}],"date_updated":"2023-08-25T08:59:11Z","type":"journal_article","status":"public","_id":"6232","volume":47,"issue":"2","publication_identifier":{"issn":["00911798"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1705.05364","open_access":"1"}],"month":"03","intvolume":" 47","abstract":[{"lang":"eng","text":"The boundary behaviour of solutions of stochastic PDEs with Dirichlet boundary conditions can be surprisingly—and in a sense, arbitrarily—bad: as shown by Krylov[ SIAM J. Math. Anal.34(2003) 1167–1182], for any α>0 one can find a simple 1-dimensional constant coefficient linear equation whose solution at the boundary is not α-Hölder continuous.We obtain a positive counterpart of this: under some mild regularity assumptions on the coefficients, solutions of semilinear SPDEs on C1 domains are proved to be α-Hölder continuous up to the boundary with some α>0."}],"oa_version":"Preprint"},{"status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"6262","file_date_updated":"2020-07-14T12:47:25Z","department":[{"_id":"JiFr"}],"ddc":["580"],"date_updated":"2023-08-25T10:11:03Z","month":"06","intvolume":" 98","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Gravitropism is an adaptive response that orients plant growth parallel to the gravity vector. Asymmetric\r\ndistribution of the phytohormone auxin is a necessary prerequisite to the tropic bending both in roots and\r\nshoots. During hypocotyl gravitropic response, the PIN3 auxin transporter polarizes within gravity-sensing\r\ncells to redirect intercellular auxin fluxes. First gravity-induced PIN3 polarization to the bottom cell mem-\r\nbranes leads to the auxin accumulation at the lower side of the organ, initiating bending and, later, auxin\r\nfeedback-mediated repolarization restores symmetric auxin distribution to terminate bending. Here, we per-\r\nformed a forward genetic screen to identify regulators of both PIN3 polarization events during gravitropic\r\nresponse. We searched for mutants with defective PIN3 polarizations based on easy-to-score morphological\r\noutputs of decreased or increased gravity-induced hypocotyl bending. We identified the number of\r\nhypocotyl reduced bending (hrb) and hypocotyl hyperbending (hhb) mutants, revealing that reduced bending corre-\r\nlated typically with defective gravity-induced PIN3 relocation whereas all analyzed hhb mutants showed\r\ndefects in the second, auxin-mediated PIN3 relocation. Next-generation sequencing-aided mutation map-\r\nping identified several candidate genes, including SCARECROW and ACTIN2, revealing roles of endodermis\r\nspecification and actin cytoskeleton in the respective gravity- and auxin-induced PIN polarization events.\r\nThe hypocotyl gravitropism screen thus promises to provide novel insights into mechanisms underlying cell\r\npolarity and plant adaptive development.","lang":"eng"}],"issue":"6","volume":98,"ec_funded":1,"file":[{"file_size":1383100,"date_updated":"2020-07-14T12:47:25Z","creator":"dernst","file_name":"2019_PlantJournal_Rakusov.pdf","date_created":"2019-04-15T09:38:43Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"ad3b5e270b67ba2a45f894ce3be27920","file_id":"6304"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1365-313x"],"issn":["0960-7412"]},"publication_status":"published","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"title":"Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls","author":[{"first_name":"Hana","last_name":"Rakusová","full_name":"Rakusová, Hana"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin","last_name":"Han","full_name":"Han, Huibin"},{"first_name":"Petr","id":"3CDB6F94-F248-11E8-B48F-1D18A9856A87","full_name":"Valošek, Petr","last_name":"Valošek"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"external_id":{"pmid":["30821050"],"isi":["000473644100008"]},"article_processing_charge":"Yes (via OA deal)","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Rakusová H, Han H, Valošek P, Friml J. 2019. Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant Journal. 98(6), 1048–1059.","chicago":"Rakusová, Hana, Huibin Han, Petr Valošek, and Jiří Friml. “Genetic Screen for Factors Mediating PIN Polarization in Gravistimulated Arabidopsis Thaliana Hypocotyls.” The Plant Journal. Wiley, 2019. https://doi.org/10.1111/tpj.14301.","short":"H. Rakusová, H. Han, P. Valošek, J. Friml, The Plant Journal 98 (2019) 1048–1059.","ieee":"H. Rakusová, H. Han, P. Valošek, and J. Friml, “Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls,” The Plant Journal, vol. 98, no. 6. Wiley, pp. 1048–1059, 2019.","ama":"Rakusová H, Han H, Valošek P, Friml J. Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant Journal. 2019;98(6):1048-1059. doi:10.1111/tpj.14301","apa":"Rakusová, H., Han, H., Valošek, P., & Friml, J. (2019). Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant Journal. Wiley. https://doi.org/10.1111/tpj.14301","mla":"Rakusová, Hana, et al. “Genetic Screen for Factors Mediating PIN Polarization in Gravistimulated Arabidopsis Thaliana Hypocotyls.” The Plant Journal, vol. 98, no. 6, Wiley, 2019, pp. 1048–59, doi:10.1111/tpj.14301."},"publisher":"Wiley","quality_controlled":"1","oa":1,"date_published":"2019-06-01T00:00:00Z","doi":"10.1111/tpj.14301","date_created":"2019-04-09T08:46:44Z","page":"1048-1059","day":"01","publication":"The Plant Journal","has_accepted_license":"1","isi":1,"year":"2019"},{"status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","_id":"6297","department":[{"_id":"MaLo"}],"file_date_updated":"2020-07-14T12:47:27Z","ddc":["570"],"date_updated":"2023-08-25T10:11:28Z","month":"05","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Cell-cell and cell-glycocalyx interactions under flow are important for the behaviour of circulating cells in blood and lymphatic vessels. However, such interactions are not well understood due in part to a lack of tools to study them in defined environments. Here, we develop a versatile in vitro platform for the study of cell-glycocalyx interactions in well-defined physical and chemical settings under flow. Our approach is demonstrated with the interaction between hyaluronan (HA, a key component of the endothelial glycocalyx) and its cell receptor CD44. We generate HA brushes in situ within a microfluidic device, and demonstrate the tuning of their physical (thickness and softness) and chemical (density of CD44 binding sites) properties using characterisation with reflection interference contrast microscopy (RICM) and application of polymer theory. We highlight the interactions of HA brushes with CD44-displaying beads and cells under flow. Observations of CD44+ beads on a HA brush with RICM enabled the 3-dimensional trajectories to be generated, and revealed interactions in the form of stop and go phases with reduced rolling velocity and reduced distance between the bead and the HA brush, compared to uncoated beads. Combined RICM and bright-field microscopy of CD44+ AKR1 T-lymphocytes revealed complementary information about the dynamics of cell rolling and cell morphology, and highlighted the formation of tethers and slings, as they interacted with a HA brush under flow. This platform can readily incorporate more complex models of the glycocalyx, and should permit the study of how mechanical and biochemical factors are orchestrated to enable highly selective blood cell-vessel wall interactions under flow."}],"volume":"78-79","language":[{"iso":"eng"}],"file":[{"checksum":"790878cd78bfc54a147ddcc7c8f286a0","file_id":"7825","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-05-14T09:02:07Z","file_name":"2018_MatrixBiology_Davies.pdf","date_updated":"2020-07-14T12:47:27Z","file_size":4444339,"creator":"dernst"}],"publication_status":"published","publication_identifier":{"issn":["0945-053X"]},"title":"An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments","article_processing_charge":"No","external_id":{"isi":["000468707600005"]},"author":[{"full_name":"Davies, Heather S.","last_name":"Davies","first_name":"Heather S."},{"first_name":"Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia S.","last_name":"Baranova"},{"last_name":"El Amri","full_name":"El Amri, Nouha","first_name":"Nouha"},{"first_name":"Liliane","last_name":"Coche-Guérente","full_name":"Coche-Guérente, Liliane"},{"first_name":"Claude","last_name":"Verdier","full_name":"Verdier, Claude"},{"first_name":"Lionel","last_name":"Bureau","full_name":"Bureau, Lionel"},{"first_name":"Ralf P.","full_name":"Richter, Ralf P.","last_name":"Richter"},{"last_name":"Débarre","full_name":"Débarre, Delphine","first_name":"Delphine"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente, Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.” Matrix Biology. Elsevier, 2019. https://doi.org/10.1016/j.matbio.2018.12.002.","ista":"Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L, Richter RP, Débarre D. 2019. An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. Matrix Biology. 78–79, 47–59.","mla":"Davies, Heather S., et al. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.” Matrix Biology, vol. 78–79, Elsevier, 2019, pp. 47–59, doi:10.1016/j.matbio.2018.12.002.","apa":"Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C., Bureau, L., … Débarre, D. (2019). An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. Matrix Biology. Elsevier. https://doi.org/10.1016/j.matbio.2018.12.002","ama":"Davies HS, Baranova NS, El Amri N, et al. An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. Matrix Biology. 2019;78-79:47-59. doi:10.1016/j.matbio.2018.12.002","ieee":"H. S. Davies et al., “An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments,” Matrix Biology, vol. 78–79. Elsevier, pp. 47–59, 2019.","short":"H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L. Bureau, R.P. Richter, D. Débarre, Matrix Biology 78–79 (2019) 47–59."},"oa":1,"quality_controlled":"1","publisher":"Elsevier","date_created":"2019-04-11T20:55:01Z","date_published":"2019-05-01T00:00:00Z","doi":"10.1016/j.matbio.2018.12.002","page":"47-59","publication":"Matrix Biology","day":"01","year":"2019","has_accepted_license":"1","isi":1},{"department":[{"_id":"TiBr"}],"file_date_updated":"2020-07-14T12:47:27Z","date_updated":"2023-08-25T10:11:55Z","ddc":["512"],"type":"journal_article","status":"public","_id":"6310","volume":349,"publication_identifier":{"issn":["00018708"],"eissn":["10902082"]},"publication_status":"published","file":[{"date_created":"2019-04-16T09:12:20Z","file_name":"wliqun.pdf","creator":"tbrownin","date_updated":"2020-07-14T12:47:27Z","file_size":379158,"file_id":"6311","checksum":"a63594a3a91b4ba6e2a1b78b0720b3d0","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"06","intvolume":" 349","abstract":[{"lang":"eng","text":"An asymptotic formula is established for the number of rational points of bounded anticanonical height which lie on a certain Zariskiopen subset of an arbitrary smooth biquadratic hypersurface in sufficiently many variables. The proof uses the Hardy–Littlewood circle method."}],"oa_version":"Submitted Version","author":[{"first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning"},{"last_name":"Hu","full_name":"Hu, L.Q.","first_name":"L.Q."}],"article_processing_charge":"No","external_id":{"arxiv":["1810.08426"],"isi":["000468857300025"]},"title":"Counting rational points on biquadratic hypersurfaces","citation":{"mla":"Browning, Timothy D., and L. Q. Hu. “Counting Rational Points on Biquadratic Hypersurfaces.” Advances in Mathematics, vol. 349, Elsevier, 2019, pp. 920–40, doi:10.1016/j.aim.2019.04.031.","apa":"Browning, T. D., & Hu, L. Q. (2019). Counting rational points on biquadratic hypersurfaces. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2019.04.031","ama":"Browning TD, Hu LQ. Counting rational points on biquadratic hypersurfaces. Advances in Mathematics. 2019;349:920-940. doi:10.1016/j.aim.2019.04.031","short":"T.D. Browning, L.Q. Hu, Advances in Mathematics 349 (2019) 920–940.","ieee":"T. D. Browning and L. Q. Hu, “Counting rational points on biquadratic hypersurfaces,” Advances in Mathematics, vol. 349. Elsevier, pp. 920–940, 2019.","chicago":"Browning, Timothy D, and L.Q. Hu. “Counting Rational Points on Biquadratic Hypersurfaces.” Advances in Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.aim.2019.04.031.","ista":"Browning TD, Hu LQ. 2019. Counting rational points on biquadratic hypersurfaces. Advances in Mathematics. 349, 920–940."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"920-940","date_published":"2019-06-20T00:00:00Z","doi":"10.1016/j.aim.2019.04.031","date_created":"2019-04-16T09:13:25Z","isi":1,"has_accepted_license":"1","year":"2019","day":"20","publication":"Advances in Mathematics","quality_controlled":"1","publisher":"Elsevier","oa":1},{"intvolume":" 180","month":"05","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1104/pp.18.01305"}],"scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Nitrate regulation of root stem cell activity is auxin-dependent.","lang":"eng"}],"volume":180,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"status":"public","type":"journal_article","article_type":"letter_note","_id":"6261","department":[{"_id":"JiFr"}],"date_updated":"2023-08-25T10:10:23Z","oa":1,"quality_controlled":"1","publisher":"ASPB","date_created":"2019-04-09T08:46:17Z","date_published":"2019-05-01T00:00:00Z","doi":"10.1104/pp.18.01305","page":"22-25","publication":"Plant Physiology","day":"01","year":"2019","isi":1,"title":"Nitrate modulates the differentiation of root distal stem cells","external_id":{"pmid":["30787134"],"isi":["000466860800010"]},"article_processing_charge":"No","author":[{"first_name":"Y","full_name":"Wang, Y","last_name":"Wang"},{"first_name":"Z","full_name":"Gong, Z","last_name":"Gong"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"J","last_name":"Zhang","full_name":"Zhang, J"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Wang Y, Gong Z, Friml J, Zhang J. 2019. Nitrate modulates the differentiation of root distal stem cells. Plant Physiology. 180(1), 22–25.","chicago":"Wang, Y, Z Gong, Jiří Friml, and J Zhang. “Nitrate Modulates the Differentiation of Root Distal Stem Cells.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.18.01305.","short":"Y. Wang, Z. Gong, J. Friml, J. Zhang, Plant Physiology 180 (2019) 22–25.","ieee":"Y. Wang, Z. Gong, J. Friml, and J. Zhang, “Nitrate modulates the differentiation of root distal stem cells,” Plant Physiology, vol. 180, no. 1. ASPB, pp. 22–25, 2019.","ama":"Wang Y, Gong Z, Friml J, Zhang J. Nitrate modulates the differentiation of root distal stem cells. Plant Physiology. 2019;180(1):22-25. doi:10.1104/pp.18.01305","apa":"Wang, Y., Gong, Z., Friml, J., & Zhang, J. (2019). Nitrate modulates the differentiation of root distal stem cells. Plant Physiology. ASPB. https://doi.org/10.1104/pp.18.01305","mla":"Wang, Y., et al. “Nitrate Modulates the Differentiation of Root Distal Stem Cells.” Plant Physiology, vol. 180, no. 1, ASPB, 2019, pp. 22–25, doi:10.1104/pp.18.01305."}},{"citation":{"mla":"Temnov, Andrey Alexandrovich, et al. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” Molecular Biology Reports, Springer, 2019, doi:10.1007/s11033-019-04765-z.","ama":"Temnov AA, Rogov KA, Sklifas AN, et al. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports. 2019. doi:10.1007/s11033-019-04765-z","apa":"Temnov, A. A., Rogov, K. A., Sklifas, A. N., Klychnikova, E. V., Hartl, M., Djinovic-Carugo, K., & Charnagalov, A. (2019). Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports. Springer. https://doi.org/10.1007/s11033-019-04765-z","short":"A.A. Temnov, K.A. Rogov, A.N. Sklifas, E.V. Klychnikova, M. Hartl, K. Djinovic-Carugo, A. Charnagalov, Molecular Biology Reports (2019).","ieee":"A. A. Temnov et al., “Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure,” Molecular Biology Reports. Springer, 2019.","chicago":"Temnov, Andrey Alexandrovich, Konstantin Arkadevich Rogov, Alla Nikolaevna Sklifas, Elena Valerievna Klychnikova, Markus Hartl, Kristina Djinovic-Carugo, and Alexej Charnagalov. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” Molecular Biology Reports. Springer, 2019. https://doi.org/10.1007/s11033-019-04765-z.","ista":"Temnov AA, Rogov KA, Sklifas AN, Klychnikova EV, Hartl M, Djinovic-Carugo K, Charnagalov A. 2019. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Andrey Alexandrovich","full_name":"Temnov, Andrey Alexandrovich","last_name":"Temnov"},{"first_name":"Konstantin Arkadevich","full_name":"Rogov, Konstantin Arkadevich","last_name":"Rogov"},{"first_name":"Alla Nikolaevna","last_name":"Sklifas","full_name":"Sklifas, Alla Nikolaevna"},{"first_name":"Elena Valerievna","full_name":"Klychnikova, Elena Valerievna","last_name":"Klychnikova"},{"full_name":"Hartl, Markus","last_name":"Hartl","first_name":"Markus"},{"first_name":"Kristina","last_name":"Djinovic-Carugo","full_name":"Djinovic-Carugo, Kristina"},{"full_name":"Charnagalov, Alexej","last_name":"Charnagalov","first_name":"Alexej","id":"49F06DBA-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000470332600049"]},"article_processing_charge":"Yes (via OA deal)","title":"Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure","acknowledgement":"The studies were supported by the Austrian Federal Ministry of Economy, Family and Youth through the initiative “Laura Bassi Centres of Expertise” funding the Center of Optimized Structural Stud-ies, grant No. 253275","quality_controlled":"1","publisher":"Springer","oa":1,"has_accepted_license":"1","isi":1,"year":"2019","day":"12","publication":"Molecular Biology Reports","date_published":"2019-04-12T00:00:00Z","doi":"10.1007/s11033-019-04765-z","date_created":"2019-04-28T21:59:14Z","_id":"6352","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-25T10:14:26Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:28Z","department":[{"_id":"LeSa"}],"abstract":[{"lang":"eng","text":"Chronic overuse of common pharmaceuticals, e.g. acetaminophen (paracetamol), often leads to the development of acute liver failure (ALF). This study aimed to elucidate the effect of cultured mesenchymal stem cells (MSCs) proteome on the onset of liver damage and regeneration dynamics in animals with ALF induced by acetaminophen, to test the liver protective efficacy of MSCs proteome depending on the oxygen tension in cell culture, and to blueprint protein components responsible for the effect. Protein compositions prepared from MSCs cultured in mild hypoxic (5% and 10% O2) and normal (21% O2) conditions were used to treat ALF induced in mice by injection of acetaminophen. To test the effect of reduced oxygen tension in cell culture on resulting MSCs proteome content we applied a combination of high performance liquid chromatography and mass-spectrometry (LC–MS/MS) for the identification of proteins in lysates of MSCs cultured at different O2 levels. The treatment of acetaminophen-administered animals with proteins released from cultured MSCs resulted in the inhibition of inflammatory reactions in damaged liver; the area of hepatocyte necrosis being reduced in the first 24 h. Compositions obtained from MSCs cultured at lower O2 level were shown to be more potent than a composition prepared from normoxic cells. A comparative characterization of protein pattern and identification of individual components done by a cytokine assay and proteomics analysis of protein compositions revealed that even moderate hypoxia produces discrete changes in the expression of various subsets of proteins responsible for intracellular respiration and cell signaling. The application of proteins prepared from MSCs grown in vitro at reduced oxygen tension significantly accelerates healing process in damaged liver tissue. The proteomics data obtained for different preparations offer new information about the potential candidates in the MSCs protein repertoire sensitive to oxygen tension in culture medium, which can be involved in the generalized mechanisms the cells use to respond to acute liver failure."}],"oa_version":"Published Version","scopus_import":"1","month":"04","publication_identifier":{"issn":["03014851"],"eissn":["15734978"]},"publication_status":"published","file":[{"file_id":"6362","checksum":"45bf040bbce1cea274f6013fa18ba21b","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2019_MolecularBioReport_Temnov.pdf","date_created":"2019-04-30T09:52:36Z","file_size":1948014,"date_updated":"2020-07-14T12:47:28Z","creator":"dernst"}],"language":[{"iso":"eng"}]},{"_id":"6348","type":"journal_article","status":"public","date_updated":"2023-08-25T10:15:25Z","department":[{"_id":"JoFi"}],"abstract":[{"lang":"eng","text":"High-speed optical telecommunication is enabled by wavelength-division multiplexing, whereby hundreds of individually stabilized lasers encode information within a single-mode optical fibre. Higher bandwidths require higher total optical power, but the power sent into the fibre is limited by optical nonlinearities within the fibre, and energy consumption by the light sources starts to become a substantial cost factor1. Optical frequency combs have been suggested to remedy this problem by generating numerous discrete, equidistant laser lines within a monolithic device; however, at present their stability and coherence allow them to operate only within small parameter ranges2,3,4. Here we show that a broadband frequency comb realized through the electro-optic effect within a high-quality whispering-gallery-mode resonator can operate at low microwave and optical powers. Unlike the usual third-order Kerr nonlinear optical frequency combs, our combs rely on the second-order nonlinear effect, which is much more efficient. Our result uses a fixed microwave signal that is mixed with an optical-pump signal to generate a coherent frequency comb with a precisely determined carrier separation. The resonant enhancement enables us to work with microwave powers that are three orders of magnitude lower than those in commercially available devices. We emphasize the practical relevance of our results to high rates of data communication. To circumvent the limitations imposed by nonlinear effects in optical communication fibres, one has to solve two problems: to provide a compact and fully integrated, yet high-quality and coherent, frequency comb generator; and to calculate nonlinear signal propagation in real time5. We report a solution to the first problem."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.10608"}],"scopus_import":"1","intvolume":" 568","month":"04","publication_status":"published","publication_identifier":{"eissn":["14764687"],"issn":["00280836"]},"language":[{"iso":"eng"}],"issue":"7752","related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-019-1220-5","relation":"erratum"}]},"volume":568,"citation":{"mla":"Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb.” Nature, vol. 568, no. 7752, Springer Nature, 2019, pp. 378–81, doi:10.1038/s41586-019-1110-x.","short":"A.R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, H.G.L. Schwefel, Nature 568 (2019) 378–381.","ieee":"A. R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, and H. G. L. Schwefel, “Resonant electro-optic frequency comb,” Nature, vol. 568, no. 7752. Springer Nature, pp. 378–381, 2019.","apa":"Rueda Sanchez, A. R., Sedlmeir, F., Kumari, M., Leuchs, G., & Schwefel, H. G. L. (2019). Resonant electro-optic frequency comb. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1110-x","ama":"Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. Resonant electro-optic frequency comb. Nature. 2019;568(7752):378-381. doi:10.1038/s41586-019-1110-x","chicago":"Rueda Sanchez, Alfredo R, Florian Sedlmeir, Madhuri Kumari, Gerd Leuchs, and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1110-x.","ista":"Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. 2019. Resonant electro-optic frequency comb. Nature. 568(7752), 378–381."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000464950700053"],"arxiv":["1808.10608"]},"article_processing_charge":"No","author":[{"first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860"},{"first_name":"Florian","last_name":"Sedlmeir","full_name":"Sedlmeir, Florian"},{"first_name":"Madhuri","last_name":"Kumari","full_name":"Kumari, Madhuri"},{"first_name":"Gerd","last_name":"Leuchs","full_name":"Leuchs, Gerd"},{"first_name":"Harald G.L.","full_name":"Schwefel, Harald G.L.","last_name":"Schwefel"}],"title":"Resonant electro-optic frequency comb","oa":1,"quality_controlled":"1","publisher":"Springer Nature","year":"2019","isi":1,"publication":"Nature","day":"18","page":"378-381","date_created":"2019-04-28T21:59:13Z","doi":"10.1038/s41586-019-1110-x","date_published":"2019-04-18T00:00:00Z"},{"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2019.01.052","open_access":"1"}],"month":"04","intvolume":" 102","abstract":[{"text":"Hippocampal activity patterns representing movement trajectories are reactivated in immobility and sleep periods, a process associated with memory recall, consolidation, and decision making. It is thought that only fixed, behaviorally relevant patterns can be reactivated, which are stored across hippocampal synaptic connections. To test whether some generalized rules govern reactivation, we examined trajectory reactivation following non-stereotypical exploration of familiar open-field environments. We found that random trajectories of varying lengths and timescales were reactivated, resembling that of Brownian motion of particles. The animals’ behavioral trajectory did not follow Brownian diffusion demonstrating that the exact behavioral experience is not reactivated. Therefore, hippocampal circuits are able to generate random trajectories of any recently active map by following diffusion dynamics. This ability of hippocampal circuits to generate representations of all behavioral outcome combinations, experienced or not, may underlie a wide variety of hippocampal-dependent cognitive functions such as learning, generalization, and planning.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/memories-of-movement-are-replayed-randomly-during-sleep/"}]},"volume":102,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"6338","department":[{"_id":"JoCs"}],"date_updated":"2023-08-25T10:13:07Z","publisher":"Elsevier","quality_controlled":"1","oa":1,"page":"450-461","date_published":"2019-04-17T00:00:00Z","doi":"10.1016/j.neuron.2019.01.052","date_created":"2019-04-17T08:28:59Z","isi":1,"year":"2019","day":"17","publication":"Neuron","project":[{"grant_number":"281511","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"I03713","name":"Interneuro Plasticity During Spatial Learning","_id":"2654F984-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"author":[{"last_name":"Stella","orcid":"0000-0001-9439-3148","full_name":"Stella, Federico","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","first_name":"Federico"},{"last_name":"Baracskay","full_name":"Baracskay, Peter","first_name":"Peter","id":"361CC00E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"O'Neill","full_name":"O'Neill, Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","first_name":"Joseph"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L"}],"external_id":{"isi":["000465169700017"],"pmid":["30819547"]},"article_processing_charge":"No","title":"Hippocampal reactivation of random trajectories resembling Brownian diffusion","citation":{"mla":"Stella, Federico, et al. “Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.” Neuron, vol. 102, Elsevier, 2019, pp. 450–61, doi:10.1016/j.neuron.2019.01.052.","short":"F. Stella, P. Baracskay, J. O’Neill, J.L. Csicsvari, Neuron 102 (2019) 450–461.","ieee":"F. Stella, P. Baracskay, J. O’Neill, and J. L. Csicsvari, “Hippocampal reactivation of random trajectories resembling Brownian diffusion,” Neuron, vol. 102. Elsevier, pp. 450–461, 2019.","ama":"Stella F, Baracskay P, O’Neill J, Csicsvari JL. Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. 2019;102:450-461. doi:10.1016/j.neuron.2019.01.052","apa":"Stella, F., Baracskay, P., O’Neill, J., & Csicsvari, J. L. (2019). Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.01.052","chicago":"Stella, Federico, Peter Baracskay, Joseph O’Neill, and Jozsef L Csicsvari. “Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.01.052.","ista":"Stella F, Baracskay P, O’Neill J, Csicsvari JL. 2019. Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. 102, 450–461."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"publication":"Chaos: An Interdisciplinary Journal of Nonlinear Science","day":"22","year":"2019","isi":1,"date_created":"2019-01-23T08:35:09Z","date_published":"2019-01-22T00:00:00Z","doi":"10.1063/1.5058279","oa":1,"publisher":"AIP Publishing","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Budanur NB, Fleury M. State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. 2019;29(1). doi:10.1063/1.5058279","apa":"Budanur, N. B., & Fleury, M. (2019). State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing. https://doi.org/10.1063/1.5058279","ieee":"N. B. Budanur and M. Fleury, “State space geometry of the chaotic pilot-wave hydrodynamics,” Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 29, no. 1. AIP Publishing, 2019.","short":"N.B. Budanur, M. Fleury, Chaos: An Interdisciplinary Journal of Nonlinear Science 29 (2019).","mla":"Budanur, Nazmi B., and Marc Fleury. “State Space Geometry of the Chaotic Pilot-Wave Hydrodynamics.” Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 29, no. 1, 013122, AIP Publishing, 2019, doi:10.1063/1.5058279.","ista":"Budanur NB, Fleury M. 2019. State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. 29(1), 013122.","chicago":"Budanur, Nazmi B, and Marc Fleury. “State Space Geometry of the Chaotic Pilot-Wave Hydrodynamics.” Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing, 2019. https://doi.org/10.1063/1.5058279."},"title":"State space geometry of the chaotic pilot-wave hydrodynamics","external_id":{"isi":["000457409100028"],"arxiv":["1812.09011"]},"article_processing_charge":"No","author":[{"last_name":"Budanur","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B"},{"first_name":"Marc","last_name":"Fleury","full_name":"Fleury, Marc"}],"article_number":"013122","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1089-7682"],"issn":["1054-1500"]},"issue":"1","related_material":{"link":[{"url":"https://aip.scitation.org/doi/abs/10.1063/1.5097157","relation":"erratum"}]},"volume":29,"oa_version":"Preprint","abstract":[{"text":"We consider the motion of a droplet bouncing on a vibrating bath of the same fluid in the presence of a central potential. We formulate a rotation symmetry-reduced description of this system, which allows for the straightforward application of dynamical systems theory tools. As an illustration of the utility of the symmetry reduction, we apply it to a model of the pilot-wave system with a central harmonic force. We begin our analysis by identifying local bifurcations and the onset of chaos. We then describe the emergence of chaotic regions and their merging bifurcations, which lead to the formation of a global attractor. In this final regime, the droplet’s angular momentum spontaneously changes its sign as observed in the experiments of Perrard et al.","lang":"eng"}],"intvolume":" 29","month":"01","main_file_link":[{"url":"https://arxiv.org/abs/1812.09011","open_access":"1"}],"scopus_import":"1","date_updated":"2023-08-25T10:16:11Z","department":[{"_id":"BjHo"}],"_id":"5878","status":"public","type":"journal_article","article_type":"original"},{"ddc":["000"],"date_updated":"2023-08-25T10:19:23Z","department":[{"_id":"ToHe"}],"file_date_updated":"2020-10-08T17:25:45Z","_id":"6428","status":"public","conference":{"location":"Montreal, Canada","end_date":"2019-04-18","start_date":"2019-04-16","name":"HSCC: Hybrid Systems Computation and Control"},"type":"conference","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"b8e967081e051d1c55ca5d18fb187890","file_id":"8633","creator":"dernst","file_size":1055421,"date_updated":"2020-10-08T17:25:45Z","file_name":"2019_ACM_Ferrere.pdf","date_created":"2020-10-08T17:25:45Z"}],"publication_status":"published","publication_identifier":{"isbn":["9781450362825"]},"oa_version":"Submitted Version","abstract":[{"text":"Safety and security are major concerns in the development of Cyber-Physical Systems (CPS). Signal temporal logic (STL) was proposedas a language to specify and monitor the correctness of CPS relativeto formalized requirements. Incorporating STL into a developmentprocess enables designers to automatically monitor and diagnosetraces, compute robustness estimates based on requirements, andperform requirement falsification, leading to productivity gains inverification and validation activities; however, in its current formSTL is agnostic to the input/output classification of signals, andthis negatively impacts the relevance of the analysis results.In this paper we propose to make the interface explicit in theSTL language by introducing input/output signal declarations. Wethen define new measures of input vacuity and output robustnessthat better reflect the nature of the system and the specification in-tent. The resulting framework, which we call interface-aware signaltemporal logic (IA-STL), aids verification and validation activities.We demonstrate the benefits of IA-STL on several CPS analysisactivities: (1) robustness-driven sensitivity analysis, (2) falsificationand (3) fault localization. We describe an implementation of our en-hancement to STL and associated notions of robustness and vacuityin a prototype extension of Breach, a MATLAB®/Simulink®toolboxfor CPS verification and validation. We explore these methodologi-cal improvements and evaluate our results on two examples fromthe automotive domain: a benchmark powertrain control systemand a hydrogen fuel cell system.","lang":"eng"}],"month":"04","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. 2019. Interface-aware signal temporal logic. Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems Computation and Control, 57–66.","chicago":"Ferrere, Thomas, Dejan Nickovic, Alexandre Donzé, Hisahiro Ito, and James Kapinski. “Interface-Aware Signal Temporal Logic.” In Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, 57–66. ACM, 2019. https://doi.org/10.1145/3302504.3311800.","ieee":"T. Ferrere, D. Nickovic, A. Donzé, H. Ito, and J. Kapinski, “Interface-aware signal temporal logic,” in Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, Montreal, Canada, 2019, pp. 57–66.","short":"T. Ferrere, D. Nickovic, A. Donzé, H. Ito, J. Kapinski, in:, Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 57–66.","ama":"Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. Interface-aware signal temporal logic. In: Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control. ACM; 2019:57-66. doi:10.1145/3302504.3311800","apa":"Ferrere, T., Nickovic, D., Donzé, A., Ito, H., & Kapinski, J. (2019). Interface-aware signal temporal logic. In Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control (pp. 57–66). Montreal, Canada: ACM. https://doi.org/10.1145/3302504.3311800","mla":"Ferrere, Thomas, et al. “Interface-Aware Signal Temporal Logic.” Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 57–66, doi:10.1145/3302504.3311800."},"title":"Interface-aware signal temporal logic","external_id":{"isi":["000516713900007"]},"article_processing_charge":"No","author":[{"last_name":"Ferrere","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"full_name":"Nickovic, Dejan","last_name":"Nickovic","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","first_name":"Dejan"},{"full_name":"Donzé, Alexandre","last_name":"Donzé","first_name":"Alexandre"},{"full_name":"Ito, Hisahiro","last_name":"Ito","first_name":"Hisahiro"},{"last_name":"Kapinski","full_name":"Kapinski, James","first_name":"James"}],"project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"publication":"Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control","day":"16","year":"2019","has_accepted_license":"1","isi":1,"date_created":"2019-05-13T08:13:46Z","date_published":"2019-04-16T00:00:00Z","doi":"10.1145/3302504.3311800","page":"57-66","oa":1,"quality_controlled":"1","publisher":"ACM"},{"oa":1,"publisher":"ACM","quality_controlled":"1","year":"2019","has_accepted_license":"1","isi":1,"publication":"ACM Transactions on Graphics","day":"01","date_created":"2019-05-14T07:04:06Z","doi":"10.1145/3306346.3323002","date_published":"2019-07-01T00:00:00Z","article_number":"130","project":[{"grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425"},{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"citation":{"mla":"Schreck, Camille, et al. “Fundamental Solutions for Water Wave Animation.” ACM Transactions on Graphics, vol. 38, no. 4, 130, ACM, 2019, doi:10.1145/3306346.3323002.","ama":"Schreck C, Hafner C, Wojtan C. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3323002","apa":"Schreck, C., Hafner, C., & Wojtan, C. (2019). Fundamental solutions for water wave animation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3323002","ieee":"C. Schreck, C. Hafner, and C. Wojtan, “Fundamental solutions for water wave animation,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.","short":"C. Schreck, C. Hafner, C. Wojtan, ACM Transactions on Graphics 38 (2019).","chicago":"Schreck, Camille, Christian Hafner, and Chris Wojtan. “Fundamental Solutions for Water Wave Animation.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3323002.","ista":"Schreck C, Hafner C, Wojtan C. 2019. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 38(4), 130."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000475740600104"]},"author":[{"first_name":"Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","last_name":"Schreck","full_name":"Schreck, Camille"},{"first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","full_name":"Hafner, Christian","last_name":"Hafner"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"title":"Fundamental solutions for water wave animation","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"This paper investigates the use of fundamental solutions for animating detailed linear water surface waves. We first propose an analytical solution for efficiently animating circular ripples in closed form. We then show how to adapt the method of fundamental solutions (MFS) to create ambient waves interacting with complex obstacles. Subsequently, we present a novel wavelet-based discretization which outperforms the state of the art MFS approach for simulating time-varying water surface waves with moving obstacles. Our results feature high-resolution spatial details, interactions with complex boundaries, and large open ocean domains. Our method compares favorably with previous work as well as known analytical solutions. We also present comparisons between our method and real world examples.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","intvolume":" 38","month":"07","publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:30Z","file_size":44328918,"date_created":"2019-05-14T07:03:55Z","file_name":"2019_ACM_Schreck.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"6443","checksum":"1b737dfe3e051aba8f3f4ab1dceda673"}],"ec_funded":1,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/new-method-makes-realistic-water-wave-animations-more-efficient/"}]},"issue":"4","volume":38,"_id":"6442","type":"journal_article","status":"public","date_updated":"2023-08-25T10:18:46Z","ddc":["000","005"],"department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:47:30Z"},{"date_created":"2019-05-13T07:58:35Z","date_published":"2019-08-01T00:00:00Z","doi":"10.1016/j.ijmultiphaseflow.2019.04.027","page":"14-24","publication":"International Journal of Multiphase Flow","day":"01","year":"2019","isi":1,"oa":1,"quality_controlled":"1","publisher":"Elsevier","title":"Phase-field simulation of core-annular pipe flow","external_id":{"arxiv":["1902.07351"],"isi":["000474496000002"]},"article_processing_charge":"No","author":[{"last_name":"Song","full_name":"Song, Baofang","first_name":"Baofang"},{"last_name":"Plana","full_name":"Plana, Carlos","first_name":"Carlos"},{"orcid":"0000-0002-0384-2022","full_name":"Lopez Alonso, Jose M","last_name":"Lopez Alonso","id":"40770848-F248-11E8-B48F-1D18A9856A87","first_name":"Jose M"},{"last_name":"Avila","full_name":"Avila, Marc","first_name":"Marc"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Song B, Plana C, Lopez Alonso JM, Avila M. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 2019;117:14-24. doi:10.1016/j.ijmultiphaseflow.2019.04.027","apa":"Song, B., Plana, C., Lopez Alonso, J. M., & Avila, M. (2019). Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. Elsevier. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027","short":"B. Song, C. Plana, J.M. Lopez Alonso, M. Avila, International Journal of Multiphase Flow 117 (2019) 14–24.","ieee":"B. Song, C. Plana, J. M. Lopez Alonso, and M. Avila, “Phase-field simulation of core-annular pipe flow,” International Journal of Multiphase Flow, vol. 117. Elsevier, pp. 14–24, 2019.","mla":"Song, Baofang, et al. “Phase-Field Simulation of Core-Annular Pipe Flow.” International Journal of Multiphase Flow, vol. 117, Elsevier, 2019, pp. 14–24, doi:10.1016/j.ijmultiphaseflow.2019.04.027.","ista":"Song B, Plana C, Lopez Alonso JM, Avila M. 2019. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 117, 14–24.","chicago":"Song, Baofang, Carlos Plana, Jose M Lopez Alonso, and Marc Avila. “Phase-Field Simulation of Core-Annular Pipe Flow.” International Journal of Multiphase Flow. Elsevier, 2019. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027."},"volume":117,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["03019322"]},"intvolume":" 117","month":"08","main_file_link":[{"url":"https://arxiv.org/abs/1902.07351","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Phase-field methods have long been used to model the flow of immiscible fluids. Their ability to naturally capture interface topological changes is widely recognized, but their accuracy in simulating flows of real fluids in practical geometries is not established. We here quantitatively investigate the convergence of the phase-field method to the sharp-interface limit with simulations of two-phase pipe flow. We focus on core-annular flows, in which a highly viscous fluid is lubricated by a less viscous fluid, and validate our simulations with an analytic laminar solution, a formal linear stability analysis and also in the fully nonlinear regime. We demonstrate the ability of the phase-field method to accurately deal with non-rectangular geometry, strong advection, unsteady fluctuations and large viscosity contrast. We argue that phase-field methods are very promising for quantitatively studying moderately turbulent flows, especially at high concentrations of the disperse phase."}],"department":[{"_id":"BjHo"}],"date_updated":"2023-08-25T10:19:55Z","status":"public","type":"journal_article","article_type":"original","_id":"6413"},{"publisher":"Public Library of Science","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2019","day":"10","publication":"PLoS Genetics","doi":"10.1371/journal.pgen.1008079","date_published":"2019-04-10T00:00:00Z","date_created":"2019-05-13T07:58:38Z","article_number":"e1008079","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"citation":{"short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, PLoS Genetics 15 (2019).","ieee":"V. Pokusaeva et al., “An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape,” PLoS Genetics, vol. 15, no. 4. Public Library of Science, 2019.","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 2019;15(4). doi:10.1371/journal.pgen.1008079","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079","mla":"Pokusaeva, Victoria, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics, vol. 15, no. 4, e1008079, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 15(4), e1008079.","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics. Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"orcid":"0000-0001-7660-444X","full_name":"Pokusaeva, Victoria","last_name":"Pokusaeva","first_name":"Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dinara R.","full_name":"Usmanova, Dinara R.","last_name":"Usmanova"},{"full_name":"Putintseva, Ekaterina V.","last_name":"Putintseva","first_name":"Ekaterina V."},{"first_name":"Lorena","last_name":"Espinar","full_name":"Espinar, Lorena"},{"last_name":"Sarkisyan","orcid":"0000-0002-5375-6341","full_name":"Sarkisyan, Karen","first_name":"Karen","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander S.","full_name":"Mishin, Alexander S.","last_name":"Mishin"},{"last_name":"Bogatyreva","full_name":"Bogatyreva, Natalya S.","first_name":"Natalya S."},{"id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry","last_name":"Ivankov","full_name":"Ivankov, Dmitry"},{"last_name":"Akopyan","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"},{"first_name":"Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","last_name":"Avvakumov","full_name":"Avvakumov, Sergey"},{"first_name":"Inna S.","last_name":"Povolotskaya","full_name":"Povolotskaya, Inna S."},{"first_name":"Guillaume J.","last_name":"Filion","full_name":"Filion, Guillaume J."},{"last_name":"Carey","full_name":"Carey, Lucas B.","first_name":"Lucas B."},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"}],"external_id":{"isi":["000466866000029"]},"article_processing_charge":"No","title":"An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape","abstract":[{"text":"Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. Just 15% of amino acids found in yeast His3 orthologues were always neutral while the impact on fitness of the remaining 85% depended on the genetic background. Furthermore, at 67% of sites, amino acid replacements were under sign epistasis, having both strongly positive and negative effect in different genetic backgrounds. 46% of sites were under reciprocal sign epistasis. The fitness impact of amino acid replacements was influenced by only a few genetic backgrounds but involved interaction of multiple sites, shaping a rugged fitness landscape in which many of the shortest paths between highly fit genotypes are inaccessible.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 15","publication_identifier":{"eissn":["15537404"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:30Z","file_size":3726017,"date_created":"2019-05-14T08:26:08Z","file_name":"2019_PLOSGenetics_Pokusaeva.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"6445","checksum":"cf3889c8a8a16053dacf9c3776cbe217"}],"language":[{"iso":"eng"}],"issue":"4","related_material":{"record":[{"status":"public","id":"9789","relation":"research_data"},{"relation":"research_data","id":"9790","status":"public"},{"id":"9797","status":"public","relation":"research_data"}]},"volume":15,"ec_funded":1,"_id":"6419","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-25T10:30:37Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:30Z","department":[{"_id":"FyKo"}]},{"article_number":"1931","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O. 2019. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 10(1), 1931.","chicago":"Moussa, Hagar F., Daniel Bsteh, Ramesh Yelagandula, Carina Pribitzer, Karin Stecher, Katarina Bartalska, Luca Michetti, et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09628-6.","apa":"Moussa, H. F., Bsteh, D., Yelagandula, R., Pribitzer, C., Stecher, K., Bartalska, K., … Bell, O. (2019). Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09628-6","ama":"Moussa HF, Bsteh D, Yelagandula R, et al. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-09628-6","ieee":"H. F. Moussa et al., “Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019.","short":"H.F. Moussa, D. Bsteh, R. Yelagandula, C. Pribitzer, K. Stecher, K. Bartalska, L. Michetti, J. Wang, J.A. Zepeda-Martinez, U. Elling, J.I. Stuckey, L.I. James, S.V. Frye, O. Bell, Nature Communications 10 (2019).","mla":"Moussa, Hagar F., et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications, vol. 10, no. 1, 1931, Springer Nature, 2019, doi:10.1038/s41467-019-09628-6."},"title":"Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing","author":[{"last_name":"Moussa","full_name":"Moussa, Hagar F.","first_name":"Hagar F."},{"first_name":"Daniel","full_name":"Bsteh, Daniel","last_name":"Bsteh"},{"full_name":"Yelagandula, Ramesh","last_name":"Yelagandula","first_name":"Ramesh"},{"last_name":"Pribitzer","full_name":"Pribitzer, Carina","first_name":"Carina"},{"full_name":"Stecher, Karin","last_name":"Stecher","first_name":"Karin"},{"full_name":"Bartalska, Katarina","last_name":"Bartalska","id":"4D883232-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina"},{"first_name":"Luca","full_name":"Michetti, Luca","last_name":"Michetti"},{"full_name":"Wang, Jingkui","last_name":"Wang","first_name":"Jingkui"},{"last_name":"Zepeda-Martinez","full_name":"Zepeda-Martinez, Jorge A.","first_name":"Jorge A."},{"first_name":"Ulrich","last_name":"Elling","full_name":"Elling, Ulrich"},{"first_name":"Jacob I.","last_name":"Stuckey","full_name":"Stuckey, Jacob I."},{"full_name":"James, Lindsey I.","last_name":"James","first_name":"Lindsey I."},{"full_name":"Frye, Stephen V.","last_name":"Frye","first_name":"Stephen V."},{"last_name":"Bell","full_name":"Bell, Oliver","first_name":"Oliver"}],"article_processing_charge":"No","external_id":{"isi":["000466118700002"]},"quality_controlled":"1","publisher":"Springer Nature","oa":1,"day":"29","publication":"Nature Communications","isi":1,"has_accepted_license":"1","year":"2019","doi":"10.1038/s41467-019-09628-6","date_published":"2019-04-29T00:00:00Z","date_created":"2019-05-13T07:58:35Z","_id":"6412","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-08-25T10:31:56Z","file_date_updated":"2020-07-14T12:47:29Z","department":[{"_id":"SaSi"}],"oa_version":"Published Version","abstract":[{"text":"Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates.","lang":"eng"}],"month":"04","intvolume":" 10","scopus_import":"1","file":[{"checksum":"6550a328335396c856db4cbdda7d2994","file_id":"6448","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-05-14T08:45:51Z","file_name":"2019_NatureComm_Moussa.pdf","date_updated":"2020-07-14T12:47:29Z","file_size":1223647,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20411723"]},"publication_status":"published","issue":"1","volume":10},{"title":"Run-time optimization for learned controllers through quantitative games","author":[{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy","last_name":"Avni","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287"},{"full_name":"Bloem, Roderick","last_name":"Bloem","first_name":"Roderick"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Bettina","full_name":"Konighofer, Bettina","last_name":"Konighofer"},{"last_name":"Pranger","full_name":"Pranger, Stefan","first_name":"Stefan"}],"article_processing_charge":"No","external_id":{"isi":["000491468000036"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Avni, Guy, Roderick Bloem, Krishnendu Chatterjee, Thomas A Henzinger, Bettina Konighofer, and Stefan Pranger. “Run-Time Optimization for Learned Controllers through Quantitative Games.” In 31st International Conference on Computer-Aided Verification, 11561:630–49. Springer, 2019. https://doi.org/10.1007/978-3-030-25540-4_36.","ista":"Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. 2019. Run-time optimization for learned controllers through quantitative games. 31st International Conference on Computer-Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 11561, 630–649.","mla":"Avni, Guy, et al. “Run-Time Optimization for Learned Controllers through Quantitative Games.” 31st International Conference on Computer-Aided Verification, vol. 11561, Springer, 2019, pp. 630–49, doi:10.1007/978-3-030-25540-4_36.","ama":"Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. Run-time optimization for learned controllers through quantitative games. In: 31st International Conference on Computer-Aided Verification. Vol 11561. Springer; 2019:630-649. doi:10.1007/978-3-030-25540-4_36","apa":"Avni, G., Bloem, R., Chatterjee, K., Henzinger, T. A., Konighofer, B., & Pranger, S. (2019). Run-time optimization for learned controllers through quantitative games. In 31st International Conference on Computer-Aided Verification (Vol. 11561, pp. 630–649). New York, NY, United States: Springer. https://doi.org/10.1007/978-3-030-25540-4_36","ieee":"G. Avni, R. Bloem, K. Chatterjee, T. A. Henzinger, B. Konighofer, and S. Pranger, “Run-time optimization for learned controllers through quantitative games,” in 31st International Conference on Computer-Aided Verification, New York, NY, United States, 2019, vol. 11561, pp. 630–649.","short":"G. Avni, R. Bloem, K. Chatterjee, T.A. Henzinger, B. Konighofer, S. Pranger, in:, 31st International Conference on Computer-Aided Verification, Springer, 2019, pp. 630–649."},"project":[{"name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"date_published":"2019-07-12T00:00:00Z","doi":"10.1007/978-3-030-25540-4_36","date_created":"2019-05-16T11:22:30Z","page":"630-649","day":"12","publication":"31st International Conference on Computer-Aided Verification","has_accepted_license":"1","isi":1,"year":"2019","quality_controlled":"1","publisher":"Springer","oa":1,"file_date_updated":"2020-07-14T12:47:31Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"ddc":["000"],"date_updated":"2023-08-25T10:33:27Z","status":"public","type":"conference","conference":{"end_date":"2019-07-18","location":"New York, NY, United States","start_date":"2019-07-13","name":"CAV: Computer Aided Verification"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"6462","volume":11561,"file":[{"file_id":"6816","checksum":"c231579f2485c6fd4df17c9443a4d80b","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2019_CAV_Avni.pdf","date_created":"2019-08-14T09:35:24Z","file_size":659766,"date_updated":"2020-07-14T12:47:31Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783030255398"],"issn":["0302-9743"]},"publication_status":"published","month":"07","intvolume":" 11561","alternative_title":["LNCS"],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"A controller is a device that interacts with a plant. At each time point,it reads the plant’s state and issues commands with the goal that the plant oper-ates optimally. Constructing optimal controllers is a fundamental and challengingproblem. Machine learning techniques have recently been successfully applied totrain controllers, yet they have limitations. Learned controllers are monolithic andhard to reason about. In particular, it is difficult to add features without retraining,to guarantee any level of performance, and to achieve acceptable performancewhen encountering untrained scenarios. These limitations can be addressed bydeploying quantitative run-timeshieldsthat serve as a proxy for the controller.At each time point, the shield reads the command issued by the controller andmay choose to alter it before passing it on to the plant. We show how optimalshields that interfere as little as possible while guaranteeing a desired level ofcontroller performance, can be generated systematically and automatically usingreactive synthesis. First, we abstract the plant by building a stochastic model.Second, we consider the learned controller to be a black box. Third, we mea-surecontroller performanceandshield interferenceby two quantitative run-timemeasures that are formally defined using weighted automata. Then, the problemof constructing a shield that guarantees maximal performance with minimal inter-ference is the problem of finding an optimal strategy in a stochastic2-player game“controller versus shield” played on the abstract state space of the plant with aquantitative objective obtained from combining the performance and interferencemeasures. We illustrate the effectiveness of our approach by automatically con-structing lightweight shields for learned traffic-light controllers in various roadnetworks. The shields we generate avoid liveness bugs, improve controller per-formance in untrained and changing traffic situations, and add features to learnedcontrollers, such as giving priority to emergency vehicles.","lang":"eng"}]},{"oa_version":"Published Version","abstract":[{"text":"Thermalizing quantum systems are conventionallydescribed by statistical mechanics at equilib-rium. However, not all systems fall into this category, with many-body localization providinga generic mechanism for thermalization to fail in strongly disordered systems. Many-bodylocalized (MBL) systems remain perfect insulators at nonzero temperature, which do notthermalize and therefore cannot be describedusing statistical mechanics. This Colloquiumreviews recent theoretical and experimental advances in studies of MBL systems, focusing onthe new perspective provided by entanglement and nonequilibrium experimental probes suchas quantum quenches. Theoretically, MBL systems exhibit a new kind of robust integrability: anextensive set of quasilocal integrals of motion emerges, which provides an intuitive explanationof the breakdown of thermalization. A description based on quasilocal integrals of motion isused to predict dynamical properties of MBL systems, such as the spreading of quantumentanglement, the behavior of local observables, and the response to external dissipativeprocesses. Furthermore, MBL systems can exhibit eigenstate transitions and quantum ordersforbidden in thermodynamic equilibrium. An outline isgiven of the current theoretical under-standing of the quantum-to-classical transitionbetween many-body localized and ergodic phasesand anomalous transport in the vicinity of that transition. Experimentally, synthetic quantumsystems, which are well isolated from an external thermal reservoir, provide natural platforms forrealizing the MBL phase. Recent experiments with ultracold atoms, trapped ions, superconductingqubits, and quantum materials, in which different signatures of many-body localization have beenobserved, are reviewed. This Colloquium concludes by listing outstanding challenges andpromising future research directions.","lang":"eng"}],"intvolume":" 91","month":"05","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2019-05-23T07:39:05Z","file_name":"RevModPhys.91.021001.pdf","date_updated":"2020-07-14T12:47:31Z","file_size":1695677,"creator":"mserbyn","file_id":"6478","checksum":"4aec0e6662b09f6e0f828cd30ff2c3a6","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"eissn":["0034-6861"],"issn":["1539-0756"]},"volume":91,"issue":"2","_id":"6477","status":"public","type":"journal_article","article_type":"original","ddc":["530"],"date_updated":"2023-08-25T10:37:56Z","file_date_updated":"2020-07-14T12:47:31Z","department":[{"_id":"MaSe"}],"oa":1,"quality_controlled":"1","publisher":"American Physical Society","publication":"Reviews of Modern Physics","day":"22","year":"2019","isi":1,"has_accepted_license":"1","date_created":"2019-05-23T07:38:43Z","date_published":"2019-05-22T00:00:00Z","doi":"10.1103/revmodphys.91.021001","article_number":"021001","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Abanin DA, Altman E, Bloch I, Serbyn M. 2019. Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. 91(2), 021001.","chicago":"Abanin, Dmitry A., Ehud Altman, Immanuel Bloch, and Maksym Serbyn. “Colloquium: Many-Body Localization, Thermalization, and Entanglement.” Reviews of Modern Physics. American Physical Society, 2019. https://doi.org/10.1103/revmodphys.91.021001.","short":"D.A. Abanin, E. Altman, I. Bloch, M. Serbyn, Reviews of Modern Physics 91 (2019).","ieee":"D. A. Abanin, E. Altman, I. Bloch, and M. Serbyn, “Colloquium: Many-body localization, thermalization, and entanglement,” Reviews of Modern Physics, vol. 91, no. 2. American Physical Society, 2019.","apa":"Abanin, D. A., Altman, E., Bloch, I., & Serbyn, M. (2019). Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. American Physical Society. https://doi.org/10.1103/revmodphys.91.021001","ama":"Abanin DA, Altman E, Bloch I, Serbyn M. Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. 2019;91(2). doi:10.1103/revmodphys.91.021001","mla":"Abanin, Dmitry A., et al. “Colloquium: Many-Body Localization, Thermalization, and Entanglement.” Reviews of Modern Physics, vol. 91, no. 2, 021001, American Physical Society, 2019, doi:10.1103/revmodphys.91.021001."},"title":"Colloquium: Many-body localization, thermalization, and entanglement","article_processing_charge":"No","external_id":{"isi":["000469046900001"],"arxiv":["1804.11065"]},"author":[{"first_name":"Dmitry A.","full_name":"Abanin, Dmitry A.","last_name":"Abanin"},{"first_name":"Ehud","full_name":"Altman, Ehud","last_name":"Altman"},{"last_name":"Bloch","full_name":"Bloch, Immanuel","first_name":"Immanuel"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn"}]},{"date_updated":"2023-08-25T10:37:30Z","ddc":["580","576"],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:31Z","_id":"6466","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["1365294X"]},"language":[{"iso":"eng"}],"file":[{"file_size":367711,"date_updated":"2020-07-14T12:47:31Z","creator":"dernst","file_name":"2019_MolecularEcology_Field.pdf","date_created":"2019-05-20T11:49:06Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"521e3aff3e9263ddf2ffbfe0b6157715","file_id":"6472"}],"volume":28,"issue":"7","abstract":[{"lang":"eng","text":"One of the most striking and consistent results in speciation genomics is the heterogeneous divergence observed across the genomes of closely related species. This pattern was initially attributed to different levels of gene exchange—with divergence preserved at loci generating a barrier to gene flow but homogenized at unlinked neutral loci. Although there is evidence to support this model, it is now recognized that interpreting patterns of divergence across genomes is not so straightforward. One \r\nproblem is that heterogenous divergence between populations can also be generated by other processes (e.g. recurrent selective sweeps or background selection) without any involvement of differential gene flow. Thus, integrated studies that identify which loci are likely subject to divergent selection are required to shed light on the interplay between selection and gene flow during the early phases of speciation. In this issue of Molecular Ecology, Rifkin et al. (2019) confront this challenge using a pair of sister morning glory species. They wisely design their sampling to take the geographic context of individuals into account, including geographically isolated (allopatric) and co‐occurring (sympatric) populations. This enabled them to show that individuals are phenotypically less differentiated in sympatry. They also found that the loci that resist introgression are enriched for those most differentiated in allopatry and loci that exhibit signals of divergent selection. One great strength of the \r\nstudy is the combination of methods from population genetics and molecular evolution, including the development of a model to simultaneously infer admixture proportions and selfing rates."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 28","month":"04","citation":{"ista":"Field D, Fraisse C. 2019. Breaking down barriers in morning glories. Molecular ecology. 28(7), 1579–1581.","chicago":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.15048.","ama":"Field D, Fraisse C. Breaking down barriers in morning glories. Molecular ecology. 2019;28(7):1579-1581. doi:10.1111/mec.15048","apa":"Field, D., & Fraisse, C. (2019). Breaking down barriers in morning glories. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15048","ieee":"D. Field and C. Fraisse, “Breaking down barriers in morning glories,” Molecular ecology, vol. 28, no. 7. Wiley, pp. 1579–1581, 2019.","short":"D. Field, C. Fraisse, Molecular Ecology 28 (2019) 1579–1581.","mla":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” Molecular Ecology, vol. 28, no. 7, Wiley, 2019, pp. 1579–81, doi:10.1111/mec.15048."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000474808300001"]},"author":[{"last_name":"Field","orcid":"0000-0002-4014-8478","full_name":"Field, David","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"}],"title":"Breaking down barriers in morning glories","year":"2019","isi":1,"has_accepted_license":"1","publication":"Molecular ecology","day":"01","page":"1579-1581","date_created":"2019-05-19T21:59:15Z","date_published":"2019-04-01T00:00:00Z","doi":"10.1111/mec.15048","oa":1,"publisher":"Wiley","quality_controlled":"1"},{"article_number":"2013","title":"A modular degron library for synthetic circuits in mammalian cells","article_processing_charge":"No","external_id":{"isi":["000466338600006"]},"author":[{"first_name":"Hélène","full_name":"Chassin, Hélène","last_name":"Chassin"},{"first_name":"Marius","last_name":"Müller","full_name":"Müller, Marius"},{"last_name":"Tigges","full_name":"Tigges, Marcel","first_name":"Marcel"},{"full_name":"Scheller, Leo","last_name":"Scheller","first_name":"Leo"},{"last_name":"Lang","full_name":"Lang, Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","first_name":"Moritz"},{"last_name":"Fussenegger","full_name":"Fussenegger, Martin","first_name":"Martin"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Chassin H, Müller M, Tigges M, Scheller L, Lang M, Fussenegger M. 2019. A modular degron library for synthetic circuits in mammalian cells. Nature Communications. 10(1), 2013.","chicago":"Chassin, Hélène, Marius Müller, Marcel Tigges, Leo Scheller, Moritz Lang, and Martin Fussenegger. “A Modular Degron Library for Synthetic Circuits in Mammalian Cells.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09974-5.","ama":"Chassin H, Müller M, Tigges M, Scheller L, Lang M, Fussenegger M. A modular degron library for synthetic circuits in mammalian cells. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-09974-5","apa":"Chassin, H., Müller, M., Tigges, M., Scheller, L., Lang, M., & Fussenegger, M. (2019). A modular degron library for synthetic circuits in mammalian cells. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09974-5","short":"H. Chassin, M. Müller, M. Tigges, L. Scheller, M. Lang, M. Fussenegger, Nature Communications 10 (2019).","ieee":"H. Chassin, M. Müller, M. Tigges, L. Scheller, M. Lang, and M. Fussenegger, “A modular degron library for synthetic circuits in mammalian cells,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019.","mla":"Chassin, Hélène, et al. “A Modular Degron Library for Synthetic Circuits in Mammalian Cells.” Nature Communications, vol. 10, no. 1, 2013, Springer Nature, 2019, doi:10.1038/s41467-019-09974-5."},"oa":1,"quality_controlled":"1","publisher":"Springer Nature","date_created":"2019-05-19T21:59:14Z","date_published":"2019-05-01T00:00:00Z","doi":"10.1038/s41467-019-09974-5","publication":"Nature Communications","day":"01","year":"2019","isi":1,"has_accepted_license":"1","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"6465","file_date_updated":"2020-07-14T12:47:31Z","department":[{"_id":"CaGu"}],"ddc":["570"],"date_updated":"2023-08-25T10:33:51Z","intvolume":" 10","month":"05","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Tight control over protein degradation is a fundamental requirement for cells to respond rapidly to various stimuli and adapt to a fluctuating environment. Here we develop a versatile, easy-to-handle library of destabilizing tags (degrons) for the precise regulation of protein expression profiles in mammalian cells by modulating target protein half-lives in a predictable manner. Using the well-established tetracycline gene-regulation system as a model, we show that the dynamics of protein expression can be tuned by fusing appropriate degron tags to gene regulators. Next, we apply this degron library to tune a synthetic pulse-generating circuit in mammalian cells. With this toolbox we establish a set of pulse generators with tailored pulse lengths and magnitudes of protein expression. This methodology will prove useful in the functional roles of essential proteins, fine-tuning of gene-expression systems, and enabling a higher complexity in the design of synthetic biological systems in mammalian cells."}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-023-36111-0"}]},"volume":10,"issue":"1","language":[{"iso":"eng"}],"file":[{"checksum":"e214d3e4f8c81e35981583c4569b51b8","file_id":"6471","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-05-20T07:33:54Z","file_name":"2019_NatureComm_Chassin.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:31Z","file_size":1191827}],"publication_status":"published","publication_identifier":{"eissn":["20411723"]}},{"intvolume":" 15","month":"04","main_file_link":[{"url":"https://doi.org/10.1098/rsbl.2018.0881","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations.","lang":"eng"}],"ec_funded":1,"volume":15,"issue":"4","related_material":{"record":[{"relation":"research_data","id":"9798","status":"public"},{"id":"9799","status":"public","relation":"research_data"}],"link":[{"relation":"supplementary_material","url":"https://dx.doi.org/10.6084/m9.figshare.c.4461008"}]},"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["17449561"],"eissn":["1744957X"]},"status":"public","type":"journal_article","article_type":"original","_id":"6467","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_updated":"2023-08-25T10:34:41Z","oa":1,"quality_controlled":"1","publisher":"Royal Society of London","date_created":"2019-05-19T21:59:15Z","date_published":"2019-04-03T00:00:00Z","doi":"10.1098/rsbl.2018.0881","publication":"Biology Letters","day":"03","year":"2019","isi":1,"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"article_number":"0881","title":"The distribution of epistasis on simple fitness landscapes","article_processing_charge":"No","external_id":{"isi":["000465405300010"],"pmid":["31014191"]},"author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse"},{"first_name":"John J.","last_name":"Welch","full_name":"Welch, John J."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters, vol. 15, no. 4, 0881, Royal Society of London, 2019, doi:10.1098/rsbl.2018.0881.","ama":"Fraisse C, Welch JJ. The distribution of epistasis on simple fitness landscapes. Biology Letters. 2019;15(4). doi:10.1098/rsbl.2018.0881","apa":"Fraisse, C., & Welch, J. J. (2019). The distribution of epistasis on simple fitness landscapes. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2018.0881","short":"C. Fraisse, J.J. Welch, Biology Letters 15 (2019).","ieee":"C. Fraisse and J. J. Welch, “The distribution of epistasis on simple fitness landscapes,” Biology Letters, vol. 15, no. 4. Royal Society of London, 2019.","chicago":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters. Royal Society of London, 2019. https://doi.org/10.1098/rsbl.2018.0881.","ista":"Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness landscapes. Biology Letters. 15(4), 0881."}},{"publication_identifier":{"issn":["00223751"],"eissn":["14697793"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"11","volume":597,"abstract":[{"text":"Investigating neuronal activity using genetically encoded Ca2+ indicators in behaving animals is hampered by inaccuracies in spike inference from fluorescent tracers. Here we combine two‐photon [Ca2+] imaging with cell‐attached recordings, followed by post hoc determination of the expression level of GCaMP6f, to explore how it affects the amplitude, kinetics and temporal summation of somatic [Ca2+] transients in mouse hippocampal pyramidal cells (PCs). The amplitude of unitary [Ca2+] transients (evoked by a single action potential) negatively correlates with GCaMP6f expression, but displays large variability even among PCs with similarly low expression levels. The summation of fluorescence signals is frequency‐dependent, supralinear and also shows remarkable cell‐to‐cell variability. We performed experimental data‐based simulations and found that spike inference error rates using MLspike depend strongly on unitary peak amplitudes and GCaMP6f expression levels. We provide simple methods for estimating the unitary [Ca2+] transients in individual weakly GCaMP6f‐expressing PCs, with which we achieve spike inference error rates of ∼5%. ","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1113/JP277681","open_access":"1"}],"month":"06","intvolume":" 597","date_updated":"2023-08-25T10:34:15Z","department":[{"_id":"GaNo"}],"_id":"6470","article_type":"original","type":"journal_article","status":"public","isi":1,"year":"2019","day":"01","publication":"Journal of Physiology","page":"2925–2947","date_published":"2019-06-01T00:00:00Z","doi":"10.1113/JP277681","date_created":"2019-05-19T21:59:17Z","publisher":"Wiley","quality_controlled":"1","oa":1,"citation":{"chicago":"Éltes, Tímea, Miklos Szoboszlay, Margit Katalin Szigeti, and Zoltan Nusser. “Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” Journal of Physiology. Wiley, 2019. https://doi.org/10.1113/JP277681.","ista":"Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. 2019. Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. 597(11), 2925–2947.","mla":"Éltes, Tímea, et al. “Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” Journal of Physiology, vol. 597, no. 11, Wiley, 2019, pp. 2925–2947, doi:10.1113/JP277681.","ieee":"T. Éltes, M. Szoboszlay, M. K. Szigeti, and Z. Nusser, “Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells,” Journal of Physiology, vol. 597, no. 11. Wiley, pp. 2925–2947, 2019.","short":"T. Éltes, M. Szoboszlay, M.K. Szigeti, Z. Nusser, Journal of Physiology 597 (2019) 2925–2947.","ama":"Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. 2019;597(11):2925–2947. doi:10.1113/JP277681","apa":"Éltes, T., Szoboszlay, M., Szigeti, M. K., & Nusser, Z. (2019). Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. Wiley. https://doi.org/10.1113/JP277681"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Tímea","full_name":"Éltes, Tímea","last_name":"Éltes"},{"first_name":"Miklos","full_name":"Szoboszlay, Miklos","last_name":"Szoboszlay"},{"full_name":"Szigeti, Margit Katalin","orcid":"0000-0001-9500-8758","last_name":"Szigeti","first_name":"Margit Katalin","id":"44F4BDC0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Zoltan","full_name":"Nusser, Zoltan","last_name":"Nusser"}],"external_id":{"pmid":["31006863"],"isi":["000470780400013"]},"article_processing_charge":"No","title":"Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells"},{"intvolume":" 11561","month":"07","alternative_title":["LNCS"],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We present two algorithmic approaches for synthesizing linear hybrid automata from experimental data. Unlike previous approaches, our algorithms work without a template and generate an automaton with nondeterministic guards and invariants, and with an arbitrary number and topology of modes. They thus construct a succinct model from the data and provide formal guarantees. In particular, (1) the generated automaton can reproduce the data up to a specified tolerance and (2) the automaton is tight, given the first guarantee. Our first approach encodes the synthesis problem as a logical formula in the theory of linear arithmetic, which can then be solved by an SMT solver. This approach minimizes the number of modes in the resulting model but is only feasible for limited data sets. To address scalability, we propose a second approach that does not enforce to find a minimal model. The algorithm constructs an initial automaton and then iteratively extends the automaton based on processing new data. Therefore the algorithm is well-suited for online and synthesis-in-the-loop applications. The core of the algorithm is a membership query that checks whether, within the specified tolerance, a given data set can result from the execution of a given automaton. We solve this membership problem for linear hybrid automata by repeated reachability computations. We demonstrate the effectiveness of the algorithm on synthetic data sets and on cardiac-cell measurements.","lang":"eng"}],"ec_funded":1,"volume":11561,"language":[{"iso":"eng"}],"file":[{"file_id":"6817","checksum":"1f1d61b83a151031745ef70a501da3d6","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2019_CAV_GarciaSoto.pdf","date_created":"2019-08-14T11:05:30Z","file_size":674795,"date_updated":"2020-07-14T12:47:32Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"issn":["0302-9743"],"isbn":["9783030255398"]},"keyword":["Synthesis","Linear hybrid automaton","Membership"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"CAV: Computer-Aided Verification","start_date":"2019-07-15","end_date":"2019-07-18","location":"New York City, NY, USA"},"type":"conference","_id":"6493","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:32Z","ddc":["000"],"date_updated":"2023-08-25T10:40:41Z","oa":1,"publisher":"Springer","quality_controlled":"1","date_created":"2019-05-27T07:09:53Z","date_published":"2019-07-12T00:00:00Z","doi":"10.1007/978-3-030-25540-4_16","page":"297-314","publication":"31st International Conference on Computer-Aided Verification","day":"12","year":"2019","has_accepted_license":"1","isi":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"}],"title":"Membership-based synthesis of linear hybrid automata","article_processing_charge":"No","external_id":{"isi":["000491468000016"]},"author":[{"orcid":"0000−0003−2936−5719","full_name":"Garcia Soto, Miriam","last_name":"Garcia Soto","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian","last_name":"Schilling"},{"first_name":"Luka","id":"3ADCA2E4-F248-11E8-B48F-1D18A9856A87","full_name":"Zeleznik, Luka","last_name":"Zeleznik"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Garcia Soto, Miriam, et al. “Membership-Based Synthesis of Linear Hybrid Automata.” 31st International Conference on Computer-Aided Verification, vol. 11561, Springer, 2019, pp. 297–314, doi:10.1007/978-3-030-25540-4_16.","short":"M. Garcia Soto, T.A. Henzinger, C. Schilling, L. Zeleznik, in:, 31st International Conference on Computer-Aided Verification, Springer, 2019, pp. 297–314.","ieee":"M. Garcia Soto, T. A. Henzinger, C. Schilling, and L. Zeleznik, “Membership-based synthesis of linear hybrid automata,” in 31st International Conference on Computer-Aided Verification, New York City, NY, USA, 2019, vol. 11561, pp. 297–314.","apa":"Garcia Soto, M., Henzinger, T. A., Schilling, C., & Zeleznik, L. (2019). Membership-based synthesis of linear hybrid automata. In 31st International Conference on Computer-Aided Verification (Vol. 11561, pp. 297–314). New York City, NY, USA: Springer. https://doi.org/10.1007/978-3-030-25540-4_16","ama":"Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. Membership-based synthesis of linear hybrid automata. In: 31st International Conference on Computer-Aided Verification. Vol 11561. Springer; 2019:297-314. doi:10.1007/978-3-030-25540-4_16","chicago":"Garcia Soto, Miriam, Thomas A Henzinger, Christian Schilling, and Luka Zeleznik. “Membership-Based Synthesis of Linear Hybrid Automata.” In 31st International Conference on Computer-Aided Verification, 11561:297–314. Springer, 2019. https://doi.org/10.1007/978-3-030-25540-4_16.","ista":"Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. 2019. Membership-based synthesis of linear hybrid automata. 31st International Conference on Computer-Aided Verification. CAV: Computer-Aided Verification, LNCS, vol. 11561, 297–314."}},{"quality_controlled":"1","publisher":"Wiley","oa":1,"has_accepted_license":"1","isi":1,"year":"2019","day":"01","publication":"New Phytologist","page":"761-774","doi":"10.1111/nph.15932","date_published":"2019-10-01T00:00:00Z","date_created":"2019-05-28T14:33:26Z","citation":{"short":"Y. Zhang, P. He, X. Ma, Z. Yang, C. Pang, J. Yu, G. Wang, J. Friml, G. Xiao, New Phytologist 224 (2019) 761–774.","ieee":"Y. Zhang et al., “Auxin-mediated statolith production for root gravitropism,” New Phytologist, vol. 224, no. 2. Wiley, pp. 761–774, 2019.","ama":"Zhang Y, He P, Ma X, et al. Auxin-mediated statolith production for root gravitropism. New Phytologist. 2019;224(2):761-774. doi:10.1111/nph.15932","apa":"Zhang, Y., He, P., Ma, X., Yang, Z., Pang, C., Yu, J., … Xiao, G. (2019). Auxin-mediated statolith production for root gravitropism. New Phytologist. Wiley. https://doi.org/10.1111/nph.15932","mla":"Zhang, Yuzhou, et al. “Auxin-Mediated Statolith Production for Root Gravitropism.” New Phytologist, vol. 224, no. 2, Wiley, 2019, pp. 761–74, doi:10.1111/nph.15932.","ista":"Zhang Y, He P, Ma X, Yang Z, Pang C, Yu J, Wang G, Friml J, Xiao G. 2019. Auxin-mediated statolith production for root gravitropism. New Phytologist. 224(2), 761–774.","chicago":"Zhang, Yuzhou, P He, X Ma, Z Yang, C Pang, J Yu, G Wang, Jiří Friml, and G Xiao. “Auxin-Mediated Statolith Production for Root Gravitropism.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.15932."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","last_name":"Zhang"},{"full_name":"He, P","last_name":"He","first_name":"P"},{"first_name":"X","last_name":"Ma","full_name":"Ma, X"},{"last_name":"Yang","full_name":"Yang, Z","first_name":"Z"},{"last_name":"Pang","full_name":"Pang, C","first_name":"C"},{"first_name":"J","full_name":"Yu, J","last_name":"Yu"},{"last_name":"Wang","full_name":"Wang, G","first_name":"G"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Xiao","full_name":"Xiao, G","first_name":"G"}],"external_id":{"isi":["000487184200024"],"pmid":["31111487"]},"article_processing_charge":"No","title":"Auxin-mediated statolith production for root gravitropism","abstract":[{"text":"Root gravitropism is one of the most important processes allowing plant adaptation to the land environment. Auxin plays a central role in mediating root gravitropism, but how auxin contributes to gravitational perception and the subsequent response is still unclear.\r\n\r\nHere, we showed that the local auxin maximum/gradient within the root apex, which is generated by the PIN directional auxin transporters, regulates the expression of three key starch granule synthesis genes, SS4, PGM and ADG1, which in turn influence the accumulation of starch granules that serve as a statolith perceiving gravity.\r\n\r\nMoreover, using the cvxIAA‐ccvTIR1 system, we also showed that TIR1‐mediated auxin signaling is required for starch granule formation and gravitropic response within root tips. In addition, axr3 mutants showed reduced auxin‐mediated starch granule accumulation and disruption of gravitropism within the root apex.\r\n\r\nOur results indicate that auxin‐mediated statolith production relies on the TIR1/AFB‐AXR3‐mediated auxin signaling pathway. In summary, we propose a dual role for auxin in gravitropism: the regulation of both gravity perception and response.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","scopus_import":"1","month":"10","intvolume":" 224","publication_identifier":{"issn":["0028-646x"],"eissn":["1469-8137"]},"publication_status":"published","file":[{"success":1,"checksum":"6488243334538f5c39099a701cbf76b9","file_id":"8661","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2019_NewPhytologist_Zhang_accepted.pdf","date_created":"2020-10-14T08:59:33Z","creator":"dernst","file_size":1099061,"date_updated":"2020-10-14T08:59:33Z"}],"language":[{"iso":"eng"}],"issue":"2","volume":224,"_id":"6504","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-28T08:40:13Z","ddc":["580"],"file_date_updated":"2020-10-14T08:59:33Z","department":[{"_id":"JiFr"}]}]