[{"language":[{"iso":"eng"}],"publication_status":"published","volume":50,"oa_version":"Submitted Version","abstract":[{"text":"Conventional wisdom has it that proteins fold and assemble into definite structures, and that this defines their function. Glycosaminoglycans (GAGs) are different. In most cases the structures they form have a low degree of order, even when interacting with proteins. Here, we discuss how physical features common to all GAGs — hydrophilicity, charge, linearity and semi-flexibility — underpin the overall properties of GAG-rich matrices. By integrating soft matter physics concepts (e.g. polymer brushes and phase separation) with our molecular understanding of GAG–protein interactions, we can better comprehend how GAG-rich matrices assemble, what their properties are, and how they function. Taking perineuronal nets (PNNs) — a GAG-rich matrix enveloping neurons — as a relevant example, we propose that microphase separation determines the holey PNN anatomy that is pivotal to PNN functions.","lang":"eng"}],"intvolume":" 50","month":"06","main_file_link":[{"url":"http://eprints.whiterose.ac.uk/125524/","open_access":"1"}],"scopus_import":"1","date_updated":"2023-09-11T14:07:03Z","department":[{"_id":"MaLo"}],"_id":"555","status":"public","type":"journal_article","article_type":"original","publication":"Current Opinion in Structural Biology","day":"01","year":"2018","isi":1,"date_created":"2018-12-11T11:47:09Z","doi":"10.1016/j.sbi.2017.12.002","date_published":"2018-06-01T00:00:00Z","page":"65 - 74","acknowledgement":"This work was supported by the European Research Council [Starting Grant 306435 ‘JELLY’; to RPR], the Spanish Ministry of Competitiveness and Innovation [MAT2014-54867-R, to RPR], the EPSRC Centre for Doctoral Training in Tissue Engineering and Regenerative Medicine — Innovation in Medical and Biological Engineering [EP/L014823/1, to JCFK], the Royal Society [RG160410, to JCFK], Wings for Life [WFL-UK-008/15, to JCFK] and the European Union, the Operational Programme Research, Development and Education in the framework of the project ‘Centre of Reconstructive Neuroscience’ [CZ.02.1.01/0.0./0.0/15_003/0000419, to JCFK]. AJD would like to thank Arthritis Research UK [16539, 19489] and the MRC [76445, G0900538] for funding his work on GAG–protein interactions.\r\n","oa":1,"quality_controlled":"1","publisher":"Elsevier","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Richter R, Baranova NS, Day A, Kwok J. 2018. Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? Current Opinion in Structural Biology. 50, 65–74.","chicago":"Richter, Ralf, Natalia S. Baranova, Anthony Day, and Jessica Kwok. “Glycosaminoglycans in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal Nets?” Current Opinion in Structural Biology. Elsevier, 2018. https://doi.org/10.1016/j.sbi.2017.12.002.","ama":"Richter R, Baranova NS, Day A, Kwok J. Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? Current Opinion in Structural Biology. 2018;50:65-74. doi:10.1016/j.sbi.2017.12.002","apa":"Richter, R., Baranova, N. S., Day, A., & Kwok, J. (2018). Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2017.12.002","short":"R. Richter, N.S. Baranova, A. Day, J. Kwok, Current Opinion in Structural Biology 50 (2018) 65–74.","ieee":"R. Richter, N. S. Baranova, A. Day, and J. Kwok, “Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?,” Current Opinion in Structural Biology, vol. 50. Elsevier, pp. 65–74, 2018.","mla":"Richter, Ralf, et al. “Glycosaminoglycans in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal Nets?” Current Opinion in Structural Biology, vol. 50, Elsevier, 2018, pp. 65–74, doi:10.1016/j.sbi.2017.12.002."},"title":"Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?","external_id":{"isi":["000443661300011"]},"article_processing_charge":"No","publist_id":"7259","author":[{"last_name":"Richter","full_name":"Richter, Ralf","first_name":"Ralf"},{"first_name":"Natalia","id":"38661662-F248-11E8-B48F-1D18A9856A87","last_name":"Baranova","orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia"},{"full_name":"Day, Anthony","last_name":"Day","first_name":"Anthony"},{"last_name":"Kwok","full_name":"Kwok, Jessica","first_name":"Jessica"}]},{"date_updated":"2023-09-11T14:10:57Z","ddc":["576"],"department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:46:30Z","_id":"448","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"969","publication_status":"published","file":[{"file_id":"4731","checksum":"874953136ac125e65f37971d3cabc5b7","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:09:08Z","file_name":"IST-2018-969-v1+1_2018_Huylmans_Hemimetabolous_genomes.pdf","date_updated":"2020-07-14T12:46:30Z","file_size":3730583,"creator":"system"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"9841","relation":"research_data"}]},"issue":"3","volume":2,"abstract":[{"lang":"eng","text":"Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity."}],"oa_version":"Published Version","scopus_import":"1","month":"02","intvolume":" 2","citation":{"ista":"Harrison M, Jongepier E, Robertson H, Arning N, Bitard Feildel T, Chao H, Childers C, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu H, Hughes D, Huylmans AK, Kemena K, Kremer L, Lee S, López Ezquerra A, Mallet L, Monroy Kuhn J, Moser A, Murali S, Muzny D, Otani S, Piulachs M, Poelchau M, Qu J, Schaub F, Wada Katsumata A, Worley K, Xie Q, Ylla G, Poulsen M, Gibbs R, Schal C, Richards S, Belles X, Korb J, Bornberg Bauer E. 2018. Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology and Evolution. 2(3), 557–566.","chicago":"Harrison, Mark, Evelien Jongepier, Hugh Robertson, Nicolas Arning, Tristan Bitard Feildel, Hsu Chao, Christopher Childers, et al. “Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Nature Ecology and Evolution. Springer Nature, 2018. https://doi.org/10.1038/s41559-017-0459-1.","short":"M. Harrison, E. Jongepier, H. Robertson, N. Arning, T. Bitard Feildel, H. Chao, C. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner, Y. Han, H. Hu, D. Hughes, A.K. Huylmans, K. Kemena, L. Kremer, S. Lee, A. López Ezquerra, L. Mallet, J. Monroy Kuhn, A. Moser, S. Murali, D. Muzny, S. Otani, M. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada Katsumata, K. Worley, Q. Xie, G. Ylla, M. Poulsen, R. Gibbs, C. Schal, S. Richards, X. Belles, J. Korb, E. Bornberg Bauer, Nature Ecology and Evolution 2 (2018) 557–566.","ieee":"M. Harrison et al., “Hemimetabolous genomes reveal molecular basis of termite eusociality,” Nature Ecology and Evolution, vol. 2, no. 3. Springer Nature, pp. 557–566, 2018.","apa":"Harrison, M., Jongepier, E., Robertson, H., Arning, N., Bitard Feildel, T., Chao, H., … Bornberg Bauer, E. (2018). Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-017-0459-1","ama":"Harrison M, Jongepier E, Robertson H, et al. Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology and Evolution. 2018;2(3):557-566. doi:10.1038/s41559-017-0459-1","mla":"Harrison, Mark, et al. “Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Nature Ecology and Evolution, vol. 2, no. 3, Springer Nature, 2018, pp. 557–66, doi:10.1038/s41559-017-0459-1."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7375","author":[{"last_name":"Harrison","full_name":"Harrison, Mark","first_name":"Mark"},{"first_name":"Evelien","last_name":"Jongepier","full_name":"Jongepier, Evelien"},{"first_name":"Hugh","full_name":"Robertson, Hugh","last_name":"Robertson"},{"full_name":"Arning, Nicolas","last_name":"Arning","first_name":"Nicolas"},{"full_name":"Bitard Feildel, Tristan","last_name":"Bitard Feildel","first_name":"Tristan"},{"full_name":"Chao, Hsu","last_name":"Chao","first_name":"Hsu"},{"last_name":"Childers","full_name":"Childers, Christopher","first_name":"Christopher"},{"last_name":"Dinh","full_name":"Dinh, Huyen","first_name":"Huyen"},{"first_name":"Harshavardhan","full_name":"Doddapaneni, Harshavardhan","last_name":"Doddapaneni"},{"first_name":"Shannon","full_name":"Dugan, Shannon","last_name":"Dugan"},{"first_name":"Johannes","full_name":"Gowin, Johannes","last_name":"Gowin"},{"first_name":"Carolin","full_name":"Greiner, Carolin","last_name":"Greiner"},{"last_name":"Han","full_name":"Han, Yi","first_name":"Yi"},{"last_name":"Hu","full_name":"Hu, Haofu","first_name":"Haofu"},{"full_name":"Hughes, Daniel","last_name":"Hughes","first_name":"Daniel"},{"last_name":"Huylmans","full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kemena, Karsten","last_name":"Kemena","first_name":"Karsten"},{"first_name":"Lukas","full_name":"Kremer, Lukas","last_name":"Kremer"},{"last_name":"Lee","full_name":"Lee, Sandra","first_name":"Sandra"},{"full_name":"López Ezquerra, Alberto","last_name":"López Ezquerra","first_name":"Alberto"},{"last_name":"Mallet","full_name":"Mallet, Ludovic","first_name":"Ludovic"},{"first_name":"Jose","last_name":"Monroy Kuhn","full_name":"Monroy Kuhn, Jose"},{"full_name":"Moser, Annabell","last_name":"Moser","first_name":"Annabell"},{"first_name":"Shwetha","full_name":"Murali, Shwetha","last_name":"Murali"},{"first_name":"Donna","last_name":"Muzny","full_name":"Muzny, Donna"},{"first_name":"Saria","last_name":"Otani","full_name":"Otani, Saria"},{"first_name":"Maria","full_name":"Piulachs, Maria","last_name":"Piulachs"},{"full_name":"Poelchau, Monica","last_name":"Poelchau","first_name":"Monica"},{"full_name":"Qu, Jiaxin","last_name":"Qu","first_name":"Jiaxin"},{"full_name":"Schaub, Florentine","last_name":"Schaub","first_name":"Florentine"},{"first_name":"Ayako","full_name":"Wada Katsumata, Ayako","last_name":"Wada Katsumata"},{"first_name":"Kim","last_name":"Worley","full_name":"Worley, Kim"},{"first_name":"Qiaolin","full_name":"Xie, Qiaolin","last_name":"Xie"},{"first_name":"Guillem","last_name":"Ylla","full_name":"Ylla, Guillem"},{"full_name":"Poulsen, Michael","last_name":"Poulsen","first_name":"Michael"},{"full_name":"Gibbs, Richard","last_name":"Gibbs","first_name":"Richard"},{"full_name":"Schal, Coby","last_name":"Schal","first_name":"Coby"},{"first_name":"Stephen","full_name":"Richards, Stephen","last_name":"Richards"},{"first_name":"Xavier","last_name":"Belles","full_name":"Belles, Xavier"},{"first_name":"Judith","last_name":"Korb","full_name":"Korb, Judith"},{"first_name":"Erich","last_name":"Bornberg Bauer","full_name":"Bornberg Bauer, Erich"}],"article_processing_charge":"No","external_id":{"isi":["000426559600026"]},"title":"Hemimetabolous genomes reveal molecular basis of termite eusociality","isi":1,"has_accepted_license":"1","year":"2018","day":"05","publication":"Nature Ecology and Evolution","page":"557-566","doi":"10.1038/s41559-017-0459-1","date_published":"2018-02-05T00:00:00Z","date_created":"2018-12-11T11:46:32Z","acknowledgement":"We thank O. Niehuis for allowing use of the unpublished E. danica genome, J. Gadau and C. Smith for comments and advice on the manuscript, and J. Schmitz for assistance with analyses and proofreading the manuscript. J.K. thanks Charles Darwin University (Australia), especially S. Garnett and the Horticulture and Aquaculture team, for providing logistic support to collect C. secundus. The Parks and Wildlife Commission, Northern Territory, the Department of the Environment, Water, Heritage and the Arts gave permission to collect (Permit number 36401) and export (Permit WT2010-6997) the termites. USDA is an equal opportunity provider and employer. M.C.H. and E.J. are supported by DFG grant BO2544/11-1 to E.B.-B. J.K. is supported by University of Osnabrück and DFG grant KO1895/16-1. X.B. and M.-D.P. are supported by Spanish Ministerio de Economía y Competitividad (CGL2012-36251 and CGL2015-64727-P to X.B., and CGL2016-76011-R to M.-D.P.), including FEDER funds, and by Catalan Government (2014 SGR 619). C.S. is supported by grants from the US Department of Housing and Urban Development (NCHHU-0017-13), the National Science Foundation (IOS-1557864), the Alfred P. Sloan Foundation (2013-5-35 MBE), the National Institute of Environmental Health Sciences (P30ES025128) to the Center for Human Health and the Environment, and the Blanton J. Whitmire Endowment. M.P. is supported by a Villum Kann Rasmussen Young Investigator Fellowship (VKR10101).","publisher":"Springer Nature","quality_controlled":"1","oa":1},{"issue":"5","volume":80,"ec_funded":1,"publication_status":"published","file":[{"file_name":"IST-2018-1014-v1+1_2018_Paixao_Escape.pdf","date_created":"2018-12-12T10:08:14Z","file_size":691245,"date_updated":"2020-07-14T12:47:54Z","creator":"system","checksum":"7d92f5d7be81e387edeec4f06442791c","file_id":"4674","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 80","abstract":[{"text":"Escaping local optima is one of the major obstacles to function optimisation. Using the metaphor of a fitness landscape, local optima correspond to hills separated by fitness valleys that have to be overcome. We define a class of fitness valleys of tunable difficulty by considering their length, representing the Hamming path between the two optima and their depth, the drop in fitness. For this function class we present a runtime comparison between stochastic search algorithms using different search strategies. The (1+1) EA is a simple and well-studied evolutionary algorithm that has to jump across the valley to a point of higher fitness because it does not accept worsening moves (elitism). In contrast, the Metropolis algorithm and the Strong Selection Weak Mutation (SSWM) algorithm, a famous process in population genetics, are both able to cross the fitness valley by accepting worsening moves. We show that the runtime of the (1+1) EA depends critically on the length of the valley while the runtimes of the non-elitist algorithms depend crucially on the depth of the valley. Moreover, we show that both SSWM and Metropolis can also efficiently optimise a rugged function consisting of consecutive valleys.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:47:54Z","date_updated":"2023-09-11T14:11:35Z","ddc":["576"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"1014","_id":"723","page":"1604 - 1633","doi":"10.1007/s00453-017-0369-2","date_published":"2018-05-01T00:00:00Z","date_created":"2018-12-11T11:48:09Z","isi":1,"has_accepted_license":"1","year":"2018","day":"01","publication":"Algorithmica","quality_controlled":"1","publisher":"Springer","oa":1,"publist_id":"6957","author":[{"first_name":"Pietro","full_name":"Oliveto, Pietro","last_name":"Oliveto"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","last_name":"Paixao","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953"},{"first_name":"Jorge","full_name":"Pérez Heredia, Jorge","last_name":"Pérez Heredia"},{"first_name":"Dirk","last_name":"Sudholt","full_name":"Sudholt, Dirk"},{"orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora"}],"article_processing_charge":"No","external_id":{"isi":["000428239300010"]},"title":"How to escape local optima in black box optimisation when non elitism outperforms elitism","citation":{"chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica. Springer, 2018. https://doi.org/10.1007/s00453-017-0369-2.","ista":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2018. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 80(5), 1604–1633.","mla":"Oliveto, Pietro, et al. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica, vol. 80, no. 5, Springer, 2018, pp. 1604–33, doi:10.1007/s00453-017-0369-2.","ama":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 2018;80(5):1604-1633. doi:10.1007/s00453-017-0369-2","apa":"Oliveto, P., Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2018). How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. Springer. https://doi.org/10.1007/s00453-017-0369-2","ieee":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “How to escape local optima in black box optimisation when non elitism outperforms elitism,” Algorithmica, vol. 80, no. 5. Springer, pp. 1604–1633, 2018.","short":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 80 (2018) 1604–1633."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091"}]},{"quality_controlled":"1","publisher":"IEEE","oa":1,"has_accepted_license":"1","isi":1,"year":"2018","day":"01","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","page":"1029 - 1031","date_published":"2018-05-01T00:00:00Z","doi":"10.1109/TPAMI.2018.2804998","date_created":"2018-12-11T11:45:48Z","citation":{"mla":"Darrell, Trevor, et al. “Guest Editors’ Introduction to the Special Section on Learning with Shared Information for Computer Vision and Multimedia Analysis.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 5, IEEE, 2018, pp. 1029–31, doi:10.1109/TPAMI.2018.2804998.","ieee":"T. Darrell, C. Lampert, N. Sebe, Y. Wu, and Y. Yan, “Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 5. IEEE, pp. 1029–1031, 2018.","short":"T. Darrell, C. Lampert, N. Sebe, Y. Wu, Y. Yan, IEEE Transactions on Pattern Analysis and Machine Intelligence 40 (2018) 1029–1031.","ama":"Darrell T, Lampert C, Sebe N, Wu Y, Yan Y. Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2018;40(5):1029-1031. doi:10.1109/TPAMI.2018.2804998","apa":"Darrell, T., Lampert, C., Sebe, N., Wu, Y., & Yan, Y. (2018). Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2018.2804998","chicago":"Darrell, Trevor, Christoph Lampert, Nico Sebe, Ying Wu, and Yan Yan. “Guest Editors’ Introduction to the Special Section on Learning with Shared Information for Computer Vision and Multimedia Analysis.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2018. https://doi.org/10.1109/TPAMI.2018.2804998.","ista":"Darrell T, Lampert C, Sebe N, Wu Y, Yan Y. 2018. Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. 40(5), 1029–1031."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Trevor","full_name":"Darrell, Trevor","last_name":"Darrell"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"},{"first_name":"Nico","full_name":"Sebe, Nico","last_name":"Sebe"},{"last_name":"Wu","full_name":"Wu, Ying","first_name":"Ying"},{"full_name":"Yan, Yan","last_name":"Yan","first_name":"Yan"}],"publist_id":"7544","external_id":{"isi":["000428901200001"]},"article_processing_charge":"No","title":"Guest editors' introduction to the special section on learning with Shared information for computer vision and multimedia analysis","abstract":[{"lang":"eng","text":"The twelve papers in this special section focus on learning systems with shared information for computer vision and multimedia communication analysis. In the real world, a realistic setting for computer vision or multimedia recognition problems is that we have some classes containing lots of training data and many classes containing a small amount of training data. Therefore, how to use frequent classes to help learning rare classes for which it is harder to collect the training data is an open question. Learning with shared information is an emerging topic in machine learning, computer vision and multimedia analysis. There are different levels of components that can be shared during concept modeling and machine learning stages, such as sharing generic object parts, sharing attributes, sharing transformations, sharing regularization parameters and sharing training examples, etc. Regarding the specific methods, multi-task learning, transfer learning and deep learning can be seen as using different strategies to share information. These learning with shared information methods are very effective in solving real-world large-scale problems."}],"oa_version":"Published Version","scopus_import":"1","month":"05","intvolume":" 40","publication_status":"published","file":[{"creator":"dernst","file_size":141724,"date_updated":"2020-07-14T12:46:03Z","file_name":"2018_IEEE_Darrell.pdf","date_created":"2020-05-14T12:50:48Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7835","checksum":"b19c75da06faf3291a3ca47dfa50ef63"}],"language":[{"iso":"eng"}],"volume":40,"issue":"5","_id":"321","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-09-11T14:07:54Z","ddc":["000"],"file_date_updated":"2020-07-14T12:46:03Z","department":[{"_id":"ChLa"}]},{"_id":"9841","status":"public","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-11T14:10:56Z","citation":{"ista":"Harrison MC, Jongepier E, Robertson HM, Arning N, Bitard-Feildel T, Chao H, Childers CP, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu H, Hughes DST, Huylmans AK, Kemena C, Kremer LPM, Lee SL, Lopez-Ezquerra A, Mallet L, Monroy-Kuhn JM, Moser A, Murali SC, Muzny DM, Otani S, Piulachs M-D, Poelchau M, Qu J, Schaub F, Wada-Katsumata A, Worley KC, Xie Q, Ylla G, Poulsen M, Gibbs RA, Schal C, Richards S, Belles X, Korb J, Bornberg-Bauer E. 2018. Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality, Dryad, 10.5061/dryad.51d4r.","chicago":"Harrison, Mark C., Evelien Jongepier, Hugh M. Robertson, Nicolas Arning, Tristan Bitard-Feildel, Hsu Chao, Christopher P. Childers, et al. “Data from: Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Dryad, 2018. https://doi.org/10.5061/dryad.51d4r.","ieee":"M. C. Harrison et al., “Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality.” Dryad, 2018.","short":"M.C. Harrison, E. Jongepier, H.M. Robertson, N. Arning, T. Bitard-Feildel, H. Chao, C.P. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner, Y. Han, H. Hu, D.S.T. Hughes, A.K. Huylmans, C. Kemena, L.P.M. Kremer, S.L. Lee, A. Lopez-Ezquerra, L. Mallet, J.M. Monroy-Kuhn, A. Moser, S.C. Murali, D.M. Muzny, S. Otani, M.-D. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada-Katsumata, K.C. Worley, Q. Xie, G. Ylla, M. Poulsen, R.A. Gibbs, C. Schal, S. Richards, X. Belles, J. Korb, E. Bornberg-Bauer, (2018).","apa":"Harrison, M. C., Jongepier, E., Robertson, H. M., Arning, N., Bitard-Feildel, T., Chao, H., … Bornberg-Bauer, E. (2018). Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality. Dryad. https://doi.org/10.5061/dryad.51d4r","ama":"Harrison MC, Jongepier E, Robertson HM, et al. Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality. 2018. doi:10.5061/dryad.51d4r","mla":"Harrison, Mark C., et al. Data from: Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality. Dryad, 2018, doi:10.5061/dryad.51d4r."},"title":"Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality","department":[{"_id":"BeVi"}],"author":[{"first_name":"Mark C.","last_name":"Harrison","full_name":"Harrison, Mark C."},{"full_name":"Jongepier, Evelien","last_name":"Jongepier","first_name":"Evelien"},{"first_name":"Hugh M.","last_name":"Robertson","full_name":"Robertson, Hugh M."},{"first_name":"Nicolas","full_name":"Arning, Nicolas","last_name":"Arning"},{"last_name":"Bitard-Feildel","full_name":"Bitard-Feildel, Tristan","first_name":"Tristan"},{"full_name":"Chao, Hsu","last_name":"Chao","first_name":"Hsu"},{"full_name":"Childers, Christopher P.","last_name":"Childers","first_name":"Christopher P."},{"first_name":"Huyen","full_name":"Dinh, Huyen","last_name":"Dinh"},{"last_name":"Doddapaneni","full_name":"Doddapaneni, Harshavardhan","first_name":"Harshavardhan"},{"full_name":"Dugan, Shannon","last_name":"Dugan","first_name":"Shannon"},{"first_name":"Johannes","full_name":"Gowin, Johannes","last_name":"Gowin"},{"first_name":"Carolin","last_name":"Greiner","full_name":"Greiner, Carolin"},{"full_name":"Han, Yi","last_name":"Han","first_name":"Yi"},{"last_name":"Hu","full_name":"Hu, Haofu","first_name":"Haofu"},{"full_name":"Hughes, Daniel S. T.","last_name":"Hughes","first_name":"Daniel S. T."},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","last_name":"Huylmans","orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K"},{"last_name":"Kemena","full_name":"Kemena, Carsten","first_name":"Carsten"},{"full_name":"Kremer, Lukas P. M.","last_name":"Kremer","first_name":"Lukas P. M."},{"last_name":"Lee","full_name":"Lee, Sandra L.","first_name":"Sandra L."},{"first_name":"Alberto","last_name":"Lopez-Ezquerra","full_name":"Lopez-Ezquerra, Alberto"},{"first_name":"Ludovic","last_name":"Mallet","full_name":"Mallet, Ludovic"},{"first_name":"Jose M.","last_name":"Monroy-Kuhn","full_name":"Monroy-Kuhn, Jose M."},{"last_name":"Moser","full_name":"Moser, Annabell","first_name":"Annabell"},{"full_name":"Murali, Shwetha C.","last_name":"Murali","first_name":"Shwetha C."},{"full_name":"Muzny, Donna M.","last_name":"Muzny","first_name":"Donna M."},{"first_name":"Saria","last_name":"Otani","full_name":"Otani, Saria"},{"first_name":"Maria-Dolors","full_name":"Piulachs, Maria-Dolors","last_name":"Piulachs"},{"full_name":"Poelchau, Monica","last_name":"Poelchau","first_name":"Monica"},{"full_name":"Qu, Jiaxin","last_name":"Qu","first_name":"Jiaxin"},{"first_name":"Florentine","full_name":"Schaub, Florentine","last_name":"Schaub"},{"last_name":"Wada-Katsumata","full_name":"Wada-Katsumata, Ayako","first_name":"Ayako"},{"first_name":"Kim C.","full_name":"Worley, Kim C.","last_name":"Worley"},{"first_name":"Qiaolin","full_name":"Xie, Qiaolin","last_name":"Xie"},{"full_name":"Ylla, Guillem","last_name":"Ylla","first_name":"Guillem"},{"last_name":"Poulsen","full_name":"Poulsen, Michael","first_name":"Michael"},{"last_name":"Gibbs","full_name":"Gibbs, Richard A.","first_name":"Richard A."},{"last_name":"Schal","full_name":"Schal, Coby","first_name":"Coby"},{"last_name":"Richards","full_name":"Richards, Stephen","first_name":"Stephen"},{"last_name":"Belles","full_name":"Belles, Xavier","first_name":"Xavier"},{"last_name":"Korb","full_name":"Korb, Judith","first_name":"Judith"},{"full_name":"Bornberg-Bauer, Erich","last_name":"Bornberg-Bauer","first_name":"Erich"}],"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"text":"Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity.","lang":"eng"}],"month":"12","publisher":"Dryad","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.51d4r","open_access":"1"}],"day":"12","year":"2018","doi":"10.5061/dryad.51d4r","date_published":"2018-12-12T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"448","status":"public"}]},"date_created":"2021-08-09T13:13:48Z"},{"issue":"1","volume":53,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-1-4503-4982-6"]},"publication_status":"published","month":"02","intvolume":" 53","alternative_title":["PPoPP"],"scopus_import":"1","oa_version":"None","abstract":[{"text":"Concurrent sets with range query operations are highly desirable in applications such as in-memory databases. However, few set implementations offer range queries. Known techniques for augmenting data structures with range queries (or operations that can be used to build range queries) have numerous problems that limit their usefulness. For example, they impose high overhead or rely heavily on garbage collection. In this work, we show how to augment data structures with highly efficient range queries, without relying on garbage collection. We identify a property of epoch-based memory reclamation algorithms that makes them ideal for implementing range queries, and produce three algorithms, which use locks, transactional memory and lock-free techniques, respectively. Our algorithms are applicable to more data structures than previous work, and are shown to be highly efficient on a large scale Intel system. ","lang":"eng"}],"department":[{"_id":"DaAl"}],"date_updated":"2023-09-11T14:10:25Z","status":"public","type":"conference","conference":{"end_date":"2018-02-28","location":"Vienna, Austria","start_date":"2018-02-24","name":"PPoPP: Principles and Practice of Parallel Programming"},"_id":"397","doi":"10.1145/3178487.3178489","date_published":"2018-02-10T00:00:00Z","date_created":"2018-12-11T11:46:14Z","page":"14 - 27","day":"10","isi":1,"year":"2018","publisher":"ACM","quality_controlled":"1","title":"Harnessing epoch-based reclamation for efficient range queries","publist_id":"7430","author":[{"first_name":"Maya","last_name":"Arbel Raviv","full_name":"Arbel Raviv, Maya"},{"first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","full_name":"Brown, Trevor A"}],"external_id":{"isi":["000446161100002"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Arbel Raviv, Maya, and Trevor A Brown. “Harnessing Epoch-Based Reclamation for Efficient Range Queries,” 53:14–27. ACM, 2018. https://doi.org/10.1145/3178487.3178489.","ista":"Arbel Raviv M, Brown TA. 2018. Harnessing epoch-based reclamation for efficient range queries. PPoPP: Principles and Practice of Parallel Programming, PPoPP, vol. 53, 14–27.","mla":"Arbel Raviv, Maya, and Trevor A. Brown. Harnessing Epoch-Based Reclamation for Efficient Range Queries. Vol. 53, no. 1, ACM, 2018, pp. 14–27, doi:10.1145/3178487.3178489.","short":"M. Arbel Raviv, T.A. Brown, in:, ACM, 2018, pp. 14–27.","ieee":"M. Arbel Raviv and T. A. Brown, “Harnessing epoch-based reclamation for efficient range queries,” presented at the PPoPP: Principles and Practice of Parallel Programming, Vienna, Austria, 2018, vol. 53, no. 1, pp. 14–27.","apa":"Arbel Raviv, M., & Brown, T. A. (2018). Harnessing epoch-based reclamation for efficient range queries (Vol. 53, pp. 14–27). Presented at the PPoPP: Principles and Practice of Parallel Programming, Vienna, Austria: ACM. https://doi.org/10.1145/3178487.3178489","ama":"Arbel Raviv M, Brown TA. Harnessing epoch-based reclamation for efficient range queries. In: Vol 53. ACM; 2018:14-27. doi:10.1145/3178487.3178489"}},{"citation":{"chicago":"Chen, Ting, Bartosz Kula, Balint Nagy, Ruxandra Barzan, Andrea Gall, Ingrid Ehrlich, and Maria Kukley. “In Vivo Regulation of Oligodendrocyte Processor Cell Proliferation and Differentiation by the AMPA-Receptor Subunit GluA2.” Cell Reports. Elsevier, 2018. https://doi.org/10.1016/j.celrep.2018.09.066.","ista":"Chen T, Kula B, Nagy B, Barzan R, Gall A, Ehrlich I, Kukley M. 2018. In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2. Cell Reports. 25(4), 852–861.e7.","mla":"Chen, Ting, et al. “In Vivo Regulation of Oligodendrocyte Processor Cell Proliferation and Differentiation by the AMPA-Receptor Subunit GluA2.” Cell Reports, vol. 25, no. 4, Elsevier, 2018, p. 852–861.e7, doi:10.1016/j.celrep.2018.09.066.","ama":"Chen T, Kula B, Nagy B, et al. In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2. Cell Reports. 2018;25(4):852-861.e7. doi:10.1016/j.celrep.2018.09.066","apa":"Chen, T., Kula, B., Nagy, B., Barzan, R., Gall, A., Ehrlich, I., & Kukley, M. (2018). In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2018.09.066","short":"T. Chen, B. Kula, B. Nagy, R. Barzan, A. Gall, I. Ehrlich, M. Kukley, Cell Reports 25 (2018) 852–861.e7.","ieee":"T. Chen et al., “In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2,” Cell Reports, vol. 25, no. 4. Elsevier, p. 852–861.e7, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"8023","author":[{"last_name":"Chen","full_name":"Chen, Ting","first_name":"Ting"},{"full_name":"Kula, Bartosz","last_name":"Kula","first_name":"Bartosz"},{"id":"30F830CE-02D1-11E9-9BAA-DAF4881429F2","first_name":"Balint","last_name":"Nagy","orcid":"0000-0002-4002-4686","full_name":"Nagy, Balint"},{"last_name":"Barzan","full_name":"Barzan, Ruxandra","first_name":"Ruxandra"},{"last_name":"Gall","full_name":"Gall, Andrea","first_name":"Andrea"},{"last_name":"Ehrlich","full_name":"Ehrlich, Ingrid","first_name":"Ingrid"},{"last_name":"Kukley","full_name":"Kukley, Maria","first_name":"Maria"}],"article_processing_charge":"No","external_id":{"isi":["000448219500005"]},"title":"In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2","acknowledgement":"This work was supported by Deutsche Forschungsgemeinschaft (DFG) grant KU2569/1-1 (to M.K.); DFG project EXC307Centre for Integrative Neuroscience (CIN), including grant Pool Project 2011-12 (jointly to M.K. and I.E.); and the Charitable Hertie Foundation (to I.E.). CIN is an Excellence Cluster funded by the DFG within the framework of the Excellence Initiative for 2008–2018. M.K. is supported by the Tistou & Charlotte Kerstan Foundation.","publisher":"Elsevier","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2018","day":"23","publication":"Cell Reports","page":"852 - 861.e7","date_published":"2018-10-23T00:00:00Z","doi":"10.1016/j.celrep.2018.09.066","date_created":"2018-12-11T11:44:16Z","_id":"32","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","date_updated":"2023-09-11T14:13:32Z","ddc":["570"],"department":[{"_id":"SaSi"}],"file_date_updated":"2020-07-14T12:46:03Z","abstract":[{"lang":"eng","text":"The functional role of AMPA receptor (AMPAR)-mediated synaptic signaling between neurons and oligodendrocyte precursor cells (OPCs) remains enigmatic. We modified the properties of AMPARs at axon-OPC synapses in the mouse corpus callosum in vivo during the peak of myelination by targeting the GluA2 subunit. Expression of the unedited (Ca2+ permeable) or the pore-dead GluA2 subunit of AMPARs triggered proliferation of OPCs and reduced their differentiation into oligodendrocytes. Expression of the cytoplasmic C-terminal (GluA2(813-862)) of the GluA2 subunit (C-tail), a modification designed to affect the interaction between GluA2 and AMPAR-binding proteins and to perturb trafficking of GluA2-containing AMPARs, decreased the differentiation of OPCs without affecting their proliferation. These findings suggest that ionotropic and non-ionotropic properties of AMPARs in OPCs, as well as specific aspects of AMPAR-mediated signaling at axon-OPC synapses in the mouse corpus callosum, are important for balancing the response of OPCs to proliferation and differentiation cues. In the brain, oligodendrocyte precursor cells (OPCs) receive glutamatergic AMPA-receptor-mediated synaptic input from neurons. Chen et al. show that modifying AMPA-receptor properties at axon-OPC synapses alters proliferation and differentiation of OPCs. This expands the traditional view of synaptic transmission by suggesting neurons also use synapses to modulate behavior of glia."}],"oa_version":"Published Version","scopus_import":"1","month":"10","intvolume":" 25","publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"d9f74277fd57176e04732707d575cf08","file_id":"5703","date_updated":"2020-07-14T12:46:03Z","file_size":4461997,"creator":"dernst","date_created":"2018-12-17T12:42:57Z","file_name":"2018_CellReports_Chen.pdf"}],"language":[{"iso":"eng"}],"issue":"4","volume":25,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/"},{"_id":"5672","type":"journal_article","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","date_updated":"2023-09-11T14:12:06Z","ddc":["570"],"department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:47:09Z","abstract":[{"lang":"eng","text":"The release of IgM is the first line of an antibody response and precedes the generation of high affinity IgG in germinal centers. Once secreted by freshly activated plasmablasts, IgM is released into the efferent lymph of reactive lymph nodes as early as 3 d after immunization. As pentameric IgM has an enormous size of 1,000 kD, its diffusibility is low, and one might wonder how it can pass through the densely lymphocyte-packed environment of a lymph node parenchyma in order to reach its exit. In this issue of JEM, Thierry et al. show that, in order to reach the blood stream, IgM molecules take a specific micro-anatomical route via lymph node conduits."}],"oa_version":"Published Version","scopus_import":"1","month":"11","intvolume":" 215","publication_identifier":{"issn":["00221007"]},"publication_status":"published","file":[{"file_size":1216437,"date_updated":"2020-07-14T12:47:09Z","creator":"dernst","file_name":"2018_JournalExperMed_Reversat.pdf","date_created":"2019-02-06T08:49:52Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"687beea1d64c213f4cb9e3c29ec11a14","file_id":"5931"}],"language":[{"iso":"eng"}],"issue":"12","volume":215,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","citation":{"short":"A. Reversat, M.K. Sixt, Journal of Experimental Medicine 215 (2018) 2959–2961.","ieee":"A. Reversat and M. K. Sixt, “IgM’s exit route,” Journal of Experimental Medicine, vol. 215, no. 12. Rockefeller University Press, pp. 2959–2961, 2018.","apa":"Reversat, A., & Sixt, M. K. (2018). IgM’s exit route. Journal of Experimental Medicine. Rockefeller University Press. https://doi.org/10.1084/jem.20181934","ama":"Reversat A, Sixt MK. IgM’s exit route. Journal of Experimental Medicine. 2018;215(12):2959-2961. doi:10.1084/jem.20181934","mla":"Reversat, Anne, and Michael K. Sixt. “IgM’s Exit Route.” Journal of Experimental Medicine, vol. 215, no. 12, Rockefeller University Press, 2018, pp. 2959–61, doi:10.1084/jem.20181934.","ista":"Reversat A, Sixt MK. 2018. IgM’s exit route. Journal of Experimental Medicine. 215(12), 2959–2961.","chicago":"Reversat, Anne, and Michael K Sixt. “IgM’s Exit Route.” Journal of Experimental Medicine. Rockefeller University Press, 2018. https://doi.org/10.1084/jem.20181934."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87","full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928","last_name":"Reversat"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"article_processing_charge":"No","external_id":{"isi":["000451920600002"]},"title":"IgM's exit route","publisher":"Rockefeller University Press","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2018","day":"20","publication":"Journal of Experimental Medicine","page":"2959-2961","doi":"10.1084/jem.20181934","date_published":"2018-11-20T00:00:00Z","date_created":"2018-12-16T22:59:18Z"},{"day":"01","publication":"World Neurosurgery","language":[{"iso":"eng"}],"isi":1,"year":"2018","publication_status":"published","date_published":"2018-05-01T00:00:00Z","doi":"10.1016/j.wneu.2018.02.096","volume":13,"date_created":"2018-12-11T11:46:15Z","page":"e568-e578","oa_version":"None","abstract":[{"text":"Objective: To report long-term results after Pipeline Embolization Device (PED) implantation, characterize complex and standard aneurysms comprehensively, and introduce a modified flow disruption scale. Methods: We retrospectively reviewed a consecutive series of 40 patients harboring 59 aneurysms treated with 54 PEDs. Aneurysm complexity was assessed using our proposed classification. Immediate angiographic results were analyzed using previously published grading scales and our novel flow disruption scale. Results: According to our new definition, 46 (78%) aneurysms were classified as complex. Most PED interventions were performed in the paraophthalmic and cavernous internal carotid artery segments. Excellent neurologic outcome (modified Rankin Scale 0 and 1) was observed in 94% of patients. Our data showed low permanent procedure-related mortality (0%) and morbidity (3%) rates. Long-term angiographic follow-up showed complete occlusion in 81% and near-total obliteration in a further 14%. Complete obliteration after deployment of a single PED was achieved in all standard aneurysms with 1-year follow-up. Our new scale was an independent predictor of aneurysm occlusion in a multivariable analysis. All aneurysms with a high flow disruption grade showed complete occlusion at follow-up regardless of PED number or aneurysm complexity. Conclusions: Treatment with the PED should be recognized as a primary management strategy for a highly selected cohort with predominantly complex intracranial aneurysms. We further show that a priori assessment of aneurysm complexity and our new postinterventional angiographic flow disruption scale predict occlusion probability and may help to determine the adequate number of per-aneurysm devices.","lang":"eng"}],"month":"05","intvolume":" 13","publisher":"Elsevier","quality_controlled":"1","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-11T14:12:33Z","citation":{"chicago":"Dodier, Philippe, Josa Frischer, Wei Wang, Thomas Auzinger, Ammar Mallouhi, Wolfgang Serles, Andreas Gruber, Engelbert Knosp, and Gerhard Bavinzski. “Immediate Flow Disruption as a Prognostic Factor after Flow Diverter Treatment Long Term Experience with the Pipeline Embolization Device.” World Neurosurgery. Elsevier, 2018. https://doi.org/10.1016/j.wneu.2018.02.096.","ista":"Dodier P, Frischer J, Wang W, Auzinger T, Mallouhi A, Serles W, Gruber A, Knosp E, Bavinzski G. 2018. Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. 13, e568–e578.","mla":"Dodier, Philippe, et al. “Immediate Flow Disruption as a Prognostic Factor after Flow Diverter Treatment Long Term Experience with the Pipeline Embolization Device.” World Neurosurgery, vol. 13, Elsevier, 2018, pp. e568–78, doi:10.1016/j.wneu.2018.02.096.","apa":"Dodier, P., Frischer, J., Wang, W., Auzinger, T., Mallouhi, A., Serles, W., … Bavinzski, G. (2018). Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. Elsevier. https://doi.org/10.1016/j.wneu.2018.02.096","ama":"Dodier P, Frischer J, Wang W, et al. Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. 2018;13:e568-e578. doi:10.1016/j.wneu.2018.02.096","ieee":"P. Dodier et al., “Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device,” World Neurosurgery, vol. 13. Elsevier, pp. e568–e578, 2018.","short":"P. Dodier, J. Frischer, W. Wang, T. Auzinger, A. Mallouhi, W. Serles, A. Gruber, E. Knosp, G. Bavinzski, World Neurosurgery 13 (2018) e568–e578."},"title":"Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device","department":[{"_id":"BeBi"}],"publist_id":"7431","author":[{"last_name":"Dodier","full_name":"Dodier, Philippe","first_name":"Philippe"},{"last_name":"Frischer","full_name":"Frischer, Josa","first_name":"Josa"},{"last_name":"Wang","full_name":"Wang, Wei","first_name":"Wei"},{"last_name":"Auzinger","orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"first_name":"Ammar","last_name":"Mallouhi","full_name":"Mallouhi, Ammar"},{"last_name":"Serles","full_name":"Serles, Wolfgang","first_name":"Wolfgang"},{"full_name":"Gruber, Andreas","last_name":"Gruber","first_name":"Andreas"},{"last_name":"Knosp","full_name":"Knosp, Engelbert","first_name":"Engelbert"},{"last_name":"Bavinzski","full_name":"Bavinzski, Gerhard","first_name":"Gerhard"}],"article_processing_charge":"No","external_id":{"isi":["000432942700070"]},"_id":"398","status":"public","type":"journal_article"},{"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Incircular nets and confocal conics","external_id":{"isi":["000423197800019"]},"article_processing_charge":"No","author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"last_name":"Bobenko","full_name":"Bobenko, Alexander","first_name":"Alexander"}],"publist_id":"7363","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Akopyan A, Bobenko A. 2018. Incircular nets and confocal conics. Transactions of the American Mathematical Society. 370(4), 2825–2854.","chicago":"Akopyan, Arseniy, and Alexander Bobenko. “Incircular Nets and Confocal Conics.” Transactions of the American Mathematical Society. American Mathematical Society, 2018. https://doi.org/10.1090/tran/7292.","apa":"Akopyan, A., & Bobenko, A. (2018). Incircular nets and confocal conics. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/7292","ama":"Akopyan A, Bobenko A. Incircular nets and confocal conics. Transactions of the American Mathematical Society. 2018;370(4):2825-2854. doi:10.1090/tran/7292","ieee":"A. Akopyan and A. Bobenko, “Incircular nets and confocal conics,” Transactions of the American Mathematical Society, vol. 370, no. 4. American Mathematical Society, pp. 2825–2854, 2018.","short":"A. Akopyan, A. Bobenko, Transactions of the American Mathematical Society 370 (2018) 2825–2854.","mla":"Akopyan, Arseniy, and Alexander Bobenko. “Incircular Nets and Confocal Conics.” Transactions of the American Mathematical Society, vol. 370, no. 4, American Mathematical Society, 2018, pp. 2825–54, doi:10.1090/tran/7292."},"oa":1,"quality_controlled":"1","publisher":"American Mathematical Society","acknowledgement":"DFG Collaborative Research Center TRR 109 “Discretization in Geometry and Dynamics”; People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) REA grant agreement n◦[291734]","date_created":"2018-12-11T11:46:35Z","date_published":"2018-04-01T00:00:00Z","doi":"10.1090/tran/7292","page":"2825 - 2854","publication":"Transactions of the American Mathematical Society","day":"01","year":"2018","isi":1,"status":"public","type":"journal_article","_id":"458","department":[{"_id":"HeEd"}],"date_updated":"2023-09-11T14:19:12Z","intvolume":" 370","month":"04","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.04637"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"We consider congruences of straight lines in a plane with the combinatorics of the square grid, with all elementary quadrilaterals possessing an incircle. It is shown that all the vertices of such nets (we call them incircular or IC-nets) lie on confocal conics. Our main new results are on checkerboard IC-nets in the plane. These are congruences of straight lines in the plane with the combinatorics of the square grid, combinatorially colored as a checkerboard, such that all black coordinate quadrilaterals possess inscribed circles. We show how this larger class of IC-nets appears quite naturally in Laguerre geometry of oriented planes and spheres and leads to new remarkable incidence theorems. Most of our results are valid in hyperbolic and spherical geometries as well. We present also generalizations in spaces of higher dimension, called checkerboard IS-nets. The construction of these nets is based on a new 9 inspheres incidence theorem.","lang":"eng"}],"ec_funded":1,"volume":370,"issue":"4","language":[{"iso":"eng"}],"publication_status":"published"},{"volume":107,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 107","abstract":[{"text":"Sperm cells are the most morphologically diverse cells across animal taxa. Within species, sperm and ejaculate traits have been suggested to vary with the male's competitive environment, e.g., level of sperm competition, female mating status and quality, and also with male age, body mass, physiological condition, and resource availability. Most previous studies have based their conclusions on the analysis of only one or a few ejaculates per male without investigating differences among the ejaculates of the same individual. This masks potential ejaculate-specific traits. Here, we provide data on the length, quantity, and viability of sperm ejaculated by wingless males of the ant Cardiocondyla obscurior. Males of this ant species are relatively long-lived and can mate with large numbers of female sexuals throughout their lives. We analyzed all ejaculates across the individuals' lifespan and manipulated the availability of mating partners. Our study shows that both the number and size of sperm cells transferred during copulations differ among individuals and also among ejaculates of the same male. Sperm quality does not decrease with male age, but the variation in sperm number between ejaculates indicates that males need considerable time to replenish their sperm supplies. Producing many ejaculates in a short time appears to be traded-off against male longevity rather than sperm quality.","lang":"eng"}],"oa_version":"None","department":[{"_id":"SyCr"}],"date_updated":"2023-09-12T07:43:26Z","type":"journal_article","status":"public","_id":"426","page":"284-290","doi":"10.1016/j.jinsphys.2017.12.003","date_published":"2018-05-01T00:00:00Z","date_created":"2018-12-11T11:46:25Z","isi":1,"year":"2018","day":"01","publication":"Journal of Insect Physiology","publisher":"Elsevier","quality_controlled":"1","acknowledgement":"Research with C. obscurior from Brazil was permitted by Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis, IBAMA (permit no. 20324-1). We thank the German Science Foundation ( DFG ) for funding ( Schr1135/2-1 ), T. Suckert for help with sperm length measurements and A.K. Huylmans for advice concerning graphs. One referee made helpful comments on the manuscript.\r\n","publist_id":"7397","author":[{"last_name":"Metzler","orcid":"0000-0002-9547-2494","full_name":"Metzler, Sina","first_name":"Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexandra","full_name":"Schrempf, Alexandra","last_name":"Schrempf"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"}],"article_processing_charge":"No","external_id":{"isi":["000434751100034"]},"title":"Individual- and ejaculate-specific sperm traits in ant males","citation":{"mla":"Metzler, Sina, et al. “Individual- and Ejaculate-Specific Sperm Traits in Ant Males.” Journal of Insect Physiology, vol. 107, Elsevier, 2018, pp. 284–90, doi:10.1016/j.jinsphys.2017.12.003.","short":"S. Metzler, A. Schrempf, J. Heinze, Journal of Insect Physiology 107 (2018) 284–290.","ieee":"S. Metzler, A. Schrempf, and J. Heinze, “Individual- and ejaculate-specific sperm traits in ant males,” Journal of Insect Physiology, vol. 107. Elsevier, pp. 284–290, 2018.","apa":"Metzler, S., Schrempf, A., & Heinze, J. (2018). Individual- and ejaculate-specific sperm traits in ant males. Journal of Insect Physiology. Elsevier. https://doi.org/10.1016/j.jinsphys.2017.12.003","ama":"Metzler S, Schrempf A, Heinze J. Individual- and ejaculate-specific sperm traits in ant males. Journal of Insect Physiology. 2018;107:284-290. doi:10.1016/j.jinsphys.2017.12.003","chicago":"Metzler, Sina, Alexandra Schrempf, and Jürgen Heinze. “Individual- and Ejaculate-Specific Sperm Traits in Ant Males.” Journal of Insect Physiology. Elsevier, 2018. https://doi.org/10.1016/j.jinsphys.2017.12.003.","ista":"Metzler S, Schrempf A, Heinze J. 2018. Individual- and ejaculate-specific sperm traits in ant males. Journal of Insect Physiology. 107, 284–290."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"oa_version":"Preprint","abstract":[{"text":"In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the winner or payoff of the game. Such games are central in formal verification since they model the interaction between a non-terminating system and its environment. We study bidding games in which the players bid for the right to move the token. Two bidding rules have been defined. 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. While poorman reachability games have been studied before, we present, for the first time, results on infinite-duration poorman games. A central quantity in these games is the ratio between the two players’ initial budgets. The questions we study concern a necessary and sufficient ratio with which a player can achieve a goal. For reachability objectives, such threshold ratios are known to exist for both bidding rules. We show that the properties of poorman reachability games extend to complex qualitative objectives such as parity, similarly to the Richman case. Our most interesting results concern quantitative poorman games, namely poorman mean-payoff games, where we construct optimal strategies depending on the initial ratio, by showing a connection with random-turn based games. The connection in itself is interesting, because it does not hold for reachability poorman games. We also solve the complexity problems that arise in poorman bidding games.","lang":"eng"}],"intvolume":" 11316","month":"11","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.04372"}],"alternative_title":["LNCS"],"scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783030046118"],"issn":["03029743"]},"volume":11316,"_id":"5788","status":"public","conference":{"end_date":"2018-12-17","location":"Oxford, UK","start_date":"2018-12-15","name":"14th International Conference on Web and Internet Economics, WINE"},"type":"conference","date_updated":"2023-09-12T07:44:01Z","department":[{"_id":"ToHe"}],"oa":1,"publisher":"Springer","quality_controlled":"1","day":"21","year":"2018","isi":1,"date_created":"2018-12-30T22:59:14Z","doi":"10.1007/978-3-030-04612-5_2","date_published":"2018-11-21T00:00:00Z","page":"21-36","project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Avni G, Henzinger TA, Ibsen-Jensen R. 2018. Infinite-duration poorman-bidding games. 14th International Conference on Web and Internet Economics, WINE, LNCS, vol. 11316, 21–36.","chicago":"Avni, Guy, Thomas A Henzinger, and Rasmus Ibsen-Jensen. “Infinite-Duration Poorman-Bidding Games,” 11316:21–36. Springer, 2018. https://doi.org/10.1007/978-3-030-04612-5_2.","ama":"Avni G, Henzinger TA, Ibsen-Jensen R. Infinite-duration poorman-bidding games. In: Vol 11316. Springer; 2018:21-36. doi:10.1007/978-3-030-04612-5_2","apa":"Avni, G., Henzinger, T. A., & Ibsen-Jensen, R. (2018). Infinite-duration poorman-bidding games (Vol. 11316, pp. 21–36). Presented at the 14th International Conference on Web and Internet Economics, WINE, Oxford, UK: Springer. https://doi.org/10.1007/978-3-030-04612-5_2","ieee":"G. Avni, T. A. Henzinger, and R. Ibsen-Jensen, “Infinite-duration poorman-bidding games,” presented at the 14th International Conference on Web and Internet Economics, WINE, Oxford, UK, 2018, vol. 11316, pp. 21–36.","short":"G. Avni, T.A. Henzinger, R. Ibsen-Jensen, in:, Springer, 2018, pp. 21–36.","mla":"Avni, Guy, et al. Infinite-Duration Poorman-Bidding Games. Vol. 11316, Springer, 2018, pp. 21–36, doi:10.1007/978-3-030-04612-5_2."},"title":"Infinite-duration poorman-bidding games","article_processing_charge":"No","external_id":{"arxiv":["1804.04372"],"isi":["000865933000002"]},"author":[{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","last_name":"Avni"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"}]},{"intvolume":" 560","month":"08","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/","open_access":"1"}],"scopus_import":"1","oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"A short, 14-amino-acid segment called SP1, located in the Gag structural protein1, has a critical role during the formation of the HIV-1 virus particle. During virus assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle, which holds together the Gag hexamer and facilitates the formation of a curved immature hexagonal lattice underneath the viral membrane2,3. Upon completion of assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in which the immature lattice is broken down; the liberated CA domain of Gag then re-assembles into the mature conical capsid that encloses the viral genome and associated enzymes. Folding and proteolysis of the six-helix bundle are crucial rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle is an established target of HIV-1 inhibitors4,5. Here, using a combination of structural and functional analyses, we show that inositol hexakisphosphate (InsP6, also known as IP6) facilitates the formation of the six-helix bundle and assembly of the immature HIV-1 Gag lattice. IP6 makes ionic contacts with two rings of lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks an alternative binding site, where IP6 interaction promotes the assembly of the mature capsid lattice. These studies identify IP6 as a naturally occurring small molecule that promotes both assembly and maturation of HIV-1.","lang":"eng"}],"related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-018-0505-4","relation":"erratum"}]},"volume":560,"issue":"7719","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1476-4687"]},"status":"public","article_type":"original","type":"journal_article","_id":"150","department":[{"_id":"FlSc"}],"date_updated":"2023-09-12T07:44:37Z","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","date_created":"2018-12-11T11:44:53Z","date_published":"2018-08-29T00:00:00Z","doi":"10.1038/s41586-018-0396-4","page":"509–512","publication":"Nature","day":"29","year":"2018","isi":1,"title":"Inositol phosphates are assembly co-factors for HIV-1","external_id":{"isi":["000442483400046"],"pmid":["30158708"]},"article_processing_charge":"No","author":[{"first_name":"Robert","last_name":"Dick","full_name":"Dick, Robert"},{"first_name":"Kaneil K","last_name":"Zadrozny","full_name":"Zadrozny, Kaneil K"},{"first_name":"Chaoyi","full_name":"Xu, Chaoyi","last_name":"Xu"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian","last_name":"Schur"},{"full_name":"Lyddon, Terri D","last_name":"Lyddon","first_name":"Terri D"},{"first_name":"Clifton L","full_name":"Ricana, Clifton L","last_name":"Ricana"},{"last_name":"Wagner","full_name":"Wagner, Jonathan M","first_name":"Jonathan M"},{"first_name":"Juan R","full_name":"Perilla, Juan R","last_name":"Perilla"},{"full_name":"Ganser, Pornillos Barbie K","last_name":"Ganser","first_name":"Pornillos Barbie K"},{"full_name":"Johnson, Marc C","last_name":"Johnson","first_name":"Marc C"},{"full_name":"Pornillos, Owen","last_name":"Pornillos","first_name":"Owen"},{"last_name":"Vogt","full_name":"Vogt, Volker","first_name":"Volker"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"R. Dick et al., “Inositol phosphates are assembly co-factors for HIV-1,” Nature, vol. 560, no. 7719. Nature Publishing Group, pp. 509–512, 2018.","short":"R. Dick, K.K. Zadrozny, C. Xu, F.K. Schur, T.D. Lyddon, C.L. Ricana, J.M. Wagner, J.R. Perilla, P.B.K. Ganser, M.C. Johnson, O. Pornillos, V. Vogt, Nature 560 (2018) 509–512.","apa":"Dick, R., Zadrozny, K. K., Xu, C., Schur, F. K., Lyddon, T. D., Ricana, C. L., … Vogt, V. (2018). Inositol phosphates are assembly co-factors for HIV-1. Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-018-0396-4","ama":"Dick R, Zadrozny KK, Xu C, et al. Inositol phosphates are assembly co-factors for HIV-1. Nature. 2018;560(7719):509–512. doi:10.1038/s41586-018-0396-4","mla":"Dick, Robert, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” Nature, vol. 560, no. 7719, Nature Publishing Group, 2018, pp. 509–512, doi:10.1038/s41586-018-0396-4.","ista":"Dick R, Zadrozny KK, Xu C, Schur FK, Lyddon TD, Ricana CL, Wagner JM, Perilla JR, Ganser PBK, Johnson MC, Pornillos O, Vogt V. 2018. Inositol phosphates are assembly co-factors for HIV-1. Nature. 560(7719), 509–512.","chicago":"Dick, Robert, Kaneil K Zadrozny, Chaoyi Xu, Florian KM Schur, Terri D Lyddon, Clifton L Ricana, Jonathan M Wagner, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” Nature. Nature Publishing Group, 2018. https://doi.org/10.1038/s41586-018-0396-4."}},{"year":"2018","isi":1,"publication":"Discrete and Continuous Dynamical Systems- Series A","day":"01","page":"2827 - 2849","date_created":"2018-12-11T11:45:43Z","date_published":"2018-06-01T00:00:00Z","doi":"10.3934/dcds.2018120","acknowledgement":"The first author, Nikita Kalinin, is funded by SNCF PostDoc.Mobility grant 168647. Support from the Basic Research Program of the National Research University Higher School of Economics is gratefully acknowledged. The second author, Mikhail Shkolnikov, is supported in part by the grant 159240 of the Swiss National Science Foundation as well as by the National Center of Competence in Research SwissMAP of the Swiss National Science Foundation.","oa":1,"quality_controlled":"1","publisher":"AIMS","citation":{"ista":"Kalinin N, Shkolnikov M. 2018. Introduction to tropical series and wave dynamic on them. Discrete and Continuous Dynamical Systems- Series A. 38(6), 2827–2849.","chicago":"Kalinin, Nikita, and Mikhail Shkolnikov. “Introduction to Tropical Series and Wave Dynamic on Them.” Discrete and Continuous Dynamical Systems- Series A. AIMS, 2018. https://doi.org/10.3934/dcds.2018120.","ieee":"N. Kalinin and M. Shkolnikov, “Introduction to tropical series and wave dynamic on them,” Discrete and Continuous Dynamical Systems- Series A, vol. 38, no. 6. AIMS, pp. 2827–2849, 2018.","short":"N. Kalinin, M. Shkolnikov, Discrete and Continuous Dynamical Systems- Series A 38 (2018) 2827–2849.","ama":"Kalinin N, Shkolnikov M. Introduction to tropical series and wave dynamic on them. Discrete and Continuous Dynamical Systems- Series A. 2018;38(6):2827-2849. doi:10.3934/dcds.2018120","apa":"Kalinin, N., & Shkolnikov, M. (2018). Introduction to tropical series and wave dynamic on them. Discrete and Continuous Dynamical Systems- Series A. AIMS. https://doi.org/10.3934/dcds.2018120","mla":"Kalinin, Nikita, and Mikhail Shkolnikov. “Introduction to Tropical Series and Wave Dynamic on Them.” Discrete and Continuous Dynamical Systems- Series A, vol. 38, no. 6, AIMS, 2018, pp. 2827–49, doi:10.3934/dcds.2018120."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000438818400007"],"arxiv":["1706.03062"]},"publist_id":"7576","author":[{"first_name":"Nikita","full_name":"Kalinin, Nikita","last_name":"Kalinin"},{"id":"35084A62-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Shkolnikov","full_name":"Shkolnikov, Mikhail","orcid":"0000-0002-4310-178X"}],"title":"Introduction to tropical series and wave dynamic on them","publication_status":"published","language":[{"iso":"eng"}],"volume":38,"issue":"6","abstract":[{"lang":"eng","text":"The theory of tropical series, that we develop here, firstly appeared in the study of the growth of pluriharmonic functions. Motivated by waves in sandpile models we introduce a dynamic on the set of tropical series, and it is experimentally observed that this dynamic obeys a power law. So, this paper serves as a compilation of results we need for other articles and also introduces several objects interesting by themselves."}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://arxiv.org/abs/1706.03062","open_access":"1"}],"scopus_import":"1","intvolume":" 38","month":"06","date_updated":"2023-09-12T07:45:37Z","department":[{"_id":"TaHa"}],"_id":"303","type":"journal_article","status":"public"},{"quality_controlled":"1","publisher":"Genetics Society of America","oa":1,"doi":"10.1534/genetics.118.301018","date_published":"2018-08-01T00:00:00Z","date_created":"2018-12-11T11:45:36Z","page":"1279 - 1303","day":"01","publication":"Genetics","isi":1,"year":"2018","title":"Introgression of a block of genome under infinitesimal selection","publist_id":"7617","author":[{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000440014100020"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Sachdeva, H., & Barton, N. H. (2018). Introgression of a block of genome under infinitesimal selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301018","ama":"Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal selection. Genetics. 2018;209(4):1279-1303. doi:10.1534/genetics.118.301018","ieee":"H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal selection,” Genetics, vol. 209, no. 4. Genetics Society of America, pp. 1279–1303, 2018.","short":"H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics, vol. 209, no. 4, Genetics Society of America, 2018, pp. 1279–303, doi:10.1534/genetics.118.301018.","ista":"Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 1279–1303.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301018."},"month":"08","intvolume":" 209","scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/early/2017/11/30/227082","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Adaptive introgression is common in nature and can be driven by selection acting on multiple, linked genes. We explore the effects of polygenic selection on introgression under the infinitesimal model with linkage. This model assumes that the introgressing block has an effectively infinite number of genes, each with an infinitesimal effect on the trait under selection. The block is assumed to introgress under directional selection within a native population that is genetically homogeneous. We use individual-based simulations and a branching process approximation to compute various statistics of the introgressing block, and explore how these depend on parameters such as the map length and initial trait value associated with the introgressing block, the genetic variability along the block, and the strength of selection. Our results show that the introgression dynamics of a block under infinitesimal selection is qualitatively different from the dynamics of neutral introgression. We also find that in the long run, surviving descendant blocks are likely to have intermediate lengths, and clarify how the length is shaped by the interplay between linkage and infinitesimal selection. Our results suggest that it may be difficult to distinguish introgression of single loci from that of genomic blocks with multiple, tightly linked and weakly selected loci."}],"issue":"4","volume":209,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"282","department":[{"_id":"NiBa"}],"date_updated":"2023-09-13T08:22:32Z"},{"publication_status":"published","language":[{"iso":"eng"}],"volume":2018,"abstract":[{"lang":"eng","text":"Universal hashing found a lot of applications in computer science. In cryptography the most important fact about universal families is the so called Leftover Hash Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography it states that almost universal families are good extractors. In this work we provide a somewhat surprising characterization in the opposite direction. Namely, every extractor with sufficiently good parameters yields a universal family on a noticeable fraction of its inputs. Our proof technique is based on tools from extremal graph theory applied to the \\'collision graph\\' induced by the extractor, and may be of independent interest. We discuss possible applications to the theory of randomness extractors and non-malleable codes."}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/507"}],"alternative_title":["ISIT Proceedings"],"scopus_import":"1","intvolume":" 2018","month":"08","date_updated":"2023-09-13T08:23:18Z","department":[{"_id":"KrPi"}],"_id":"108","conference":{"name":"ISIT: International Symposium on Information Theory","start_date":"2018-06-17 ","location":"Vail, CO, USA","end_date":"2018-06-22"},"type":"conference","status":"public","year":"2018","isi":1,"day":"16","date_created":"2018-12-11T11:44:40Z","doi":"10.1109/ISIT.2018.8437654","date_published":"2018-08-16T00:00:00Z","oa":1,"publisher":"IEEE","quality_controlled":"1","citation":{"apa":"Obremski, M., & Skórski, M. (2018). Inverted leftover hash lemma (Vol. 2018). Presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA: IEEE. https://doi.org/10.1109/ISIT.2018.8437654","ama":"Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018. doi:10.1109/ISIT.2018.8437654","ieee":"M. Obremski and M. Skórski, “Inverted leftover hash lemma,” presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA, 2018, vol. 2018.","short":"M. Obremski, M. Skórski, in:, IEEE, 2018.","mla":"Obremski, Marciej, and Maciej Skórski. Inverted Leftover Hash Lemma. Vol. 2018, IEEE, 2018, doi:10.1109/ISIT.2018.8437654.","ista":"Obremski M, Skórski M. 2018. Inverted leftover hash lemma. ISIT: International Symposium on Information Theory, ISIT Proceedings, vol. 2018.","chicago":"Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,” Vol. 2018. IEEE, 2018. https://doi.org/10.1109/ISIT.2018.8437654."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000448139300368"]},"publist_id":"7946","author":[{"first_name":"Marciej","last_name":"Obremski","full_name":"Obremski, Marciej"},{"first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","full_name":"Skorski, Maciej","last_name":"Skorski"}],"title":"Inverted leftover hash lemma"},{"publication_status":"published","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"c64fff560fe5a7532ec10626ad1c215e","file_id":"5705","creator":"dernst","file_size":1603844,"date_updated":"2020-07-14T12:45:04Z","file_name":"2018_LNCS_Kragl.pdf","date_created":"2018-12-17T12:52:12Z"}],"related_material":{"record":[{"id":"8332","status":"public","relation":"dissertation_contains"}]},"volume":10981,"abstract":[{"lang":"eng","text":"We present layered concurrent programs, a compact and expressive notation for specifying refinement proofs of concurrent programs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. These programs are expressed in the ordinary syntax of imperative concurrent programs using gated atomic actions, sequencing, choice, and (recursive) procedure calls. Each concurrent program is automatically extracted from the layered program. We reduce refinement to the safety of a sequence of concurrent checker programs, one each to justify the connection between every two consecutive concurrent programs. These checker programs are also automatically extracted from the layered program. Layered concurrent programs have been implemented in the CIVL verifier which has been successfully used for the verification of several complex concurrent programs."}],"oa_version":"Published Version","alternative_title":["LNCS"],"scopus_import":"1","intvolume":" 10981","month":"07","date_updated":"2023-09-13T08:45:09Z","ddc":["000"],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:45:04Z","_id":"160","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":{"end_date":"2018-07-17","location":"Oxford, UK","start_date":"2018-07-14","name":"CAV: Computer Aided Verification"},"type":"conference","status":"public","year":"2018","has_accepted_license":"1","isi":1,"day":"18","page":"79 - 102","date_created":"2018-12-11T11:44:57Z","date_published":"2018-07-18T00:00:00Z","doi":"10.1007/978-3-319-96145-3_5","oa":1,"publisher":"Springer","quality_controlled":"1","citation":{"apa":"Kragl, B., & Qadeer, S. (2018). Layered Concurrent Programs (Vol. 10981, pp. 79–102). Presented at the CAV: Computer Aided Verification, Oxford, UK: Springer. https://doi.org/10.1007/978-3-319-96145-3_5","ama":"Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102. doi:10.1007/978-3-319-96145-3_5","ieee":"B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV: Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.","short":"B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102.","mla":"Kragl, Bernhard, and Shaz Qadeer. Layered Concurrent Programs. Vol. 10981, Springer, 2018, pp. 79–102, doi:10.1007/978-3-319-96145-3_5.","ista":"Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided Verification, LNCS, vol. 10981, 79–102.","chicago":"Kragl, Bernhard, and Shaz Qadeer. “Layered Concurrent Programs,” 10981:79–102. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_5."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000491481600005"]},"article_processing_charge":"No","publist_id":"7761","author":[{"first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","last_name":"Kragl"},{"full_name":"Qadeer, Shaz","last_name":"Qadeer","first_name":"Shaz"}],"title":"Layered Concurrent Programs","project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}]},{"title":"KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis","article_processing_charge":"No","external_id":{"isi":["000435571000017"]},"publist_id":"7619","author":[{"first_name":"Zhen","last_name":"Gao","full_name":"Gao, Zhen"},{"last_name":"Daneva","full_name":"Daneva, Anna","first_name":"Anna"},{"full_name":"Salanenka, Yuliya","last_name":"Salanenka","id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87","first_name":"Yuliya"},{"first_name":"Matthias","last_name":"Van Durme","full_name":"Van Durme, Matthias"},{"full_name":"Huysmans, Marlies","last_name":"Huysmans","first_name":"Marlies"},{"last_name":"Lin","full_name":"Lin, Zongcheng","first_name":"Zongcheng"},{"full_name":"De Winter, Freya","last_name":"De Winter","first_name":"Freya"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"first_name":"Mansour","last_name":"Karimi","full_name":"Karimi, Mansour"},{"first_name":"Jan","full_name":"Van De Velde, Jan","last_name":"Van De Velde"},{"full_name":"Vandepoele, Klaas","last_name":"Vandepoele","first_name":"Klaas"},{"first_name":"Davy","last_name":"Van De Walle","full_name":"Van De Walle, Davy"},{"full_name":"Dewettinck, Koen","last_name":"Dewettinck","first_name":"Koen"},{"last_name":"Lambrecht","full_name":"Lambrecht, Bart","first_name":"Bart"},{"full_name":"Nowack, Moritz","last_name":"Nowack","first_name":"Moritz"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F, Vanneste S, Karimi M, Van De Velde J, Vandepoele K, Van De Walle D, Dewettinck K, Lambrecht B, Nowack M. 2018. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 4(6), 365–375.","chicago":"Gao, Zhen, Anna Daneva, Yuliya Salanenka, Matthias Van Durme, Marlies Huysmans, Zongcheng Lin, Freya De Winter, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0160-7.","ama":"Gao Z, Daneva A, Salanenka Y, et al. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 2018;4(6):365-375. doi:10.1038/s41477-018-0160-7","apa":"Gao, Z., Daneva, A., Salanenka, Y., Van Durme, M., Huysmans, M., Lin, Z., … Nowack, M. (2018). KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0160-7","ieee":"Z. Gao et al., “KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis,” Nature Plants, vol. 4, no. 6. Nature Publishing Group, pp. 365–375, 2018.","short":"Z. Gao, A. Daneva, Y. Salanenka, M. Van Durme, M. Huysmans, Z. Lin, F. De Winter, S. Vanneste, M. Karimi, J. Van De Velde, K. Vandepoele, D. Van De Walle, K. Dewettinck, B. Lambrecht, M. Nowack, Nature Plants 4 (2018) 365–375.","mla":"Gao, Zhen, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” Nature Plants, vol. 4, no. 6, Nature Publishing Group, 2018, pp. 365–75, doi:10.1038/s41477-018-0160-7."},"date_created":"2018-12-11T11:45:35Z","doi":"10.1038/s41477-018-0160-7","date_published":"2018-05-28T00:00:00Z","page":"365 - 375","publication":"Nature Plants","day":"28","year":"2018","isi":1,"quality_controlled":"1","publisher":"Nature Publishing Group","acknowledgement":"We gratefully acknowledge funding from the Chinese Scholarship Council (CSC; project number 201206910025 to Z.G.), the Fonds Wetenschappelijk Onderzoek (FWO; project number G005112N to A.D.; fellowship number 12I7417N to Z.L.), the Belgian Federal Science Policy Office (BELSPO; to Y.S.), the Agency for Innovation by Science and Technology of Belgium (IWT; fellowship number 121110 to M.V.D.), the Hercules foundation (grant AUGE-09-029 to K.D.), and the ERC StG PROCELLDEATH (project number 639234 to M.K.N.).","department":[{"_id":"JiFr"}],"date_updated":"2023-09-13T08:24:17Z","status":"public","type":"journal_article","_id":"280","volume":4,"issue":"6","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 4","month":"05","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"Flowers have a species-specific functional life span that determines the time window in which pollination, fertilization and seed set can occur. The stigma tissue plays a key role in flower receptivity by intercepting pollen and initiating pollen tube growth toward the ovary. In this article, we show that a developmentally controlled cell death programme terminates the functional life span of stigma cells in Arabidopsis. We identified the leaf senescence regulator ORESARA1 (also known as ANAC092) and the previously uncharacterized KIRA1 (also known as ANAC074) as partially redundant transcription factors that modulate stigma longevity by controlling the expression of programmed cell death-associated genes. KIRA1 expression is sufficient to induce cell death and terminate floral receptivity, whereas lack of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly, the extension of stigma longevity is accompanied by only a moderate extension of flower receptivity, suggesting that additional processes participate in the control of the flower's receptive life span."}]},{"citation":{"short":"K. Tomasek, T. Bergmiller, C.C. Guet, Journal of Biotechnology 268 (2018) 40–52.","ieee":"K. Tomasek, T. Bergmiller, and C. C. Guet, “Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains,” Journal of Biotechnology, vol. 268. Elsevier, pp. 40–52, 2018.","apa":"Tomasek, K., Bergmiller, T., & Guet, C. C. (2018). Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. Elsevier. https://doi.org/10.1016/j.jbiotec.2018.01.008","ama":"Tomasek K, Bergmiller T, Guet CC. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 2018;268:40-52. doi:10.1016/j.jbiotec.2018.01.008","mla":"Tomasek, Kathrin, et al. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” Journal of Biotechnology, vol. 268, Elsevier, 2018, pp. 40–52, doi:10.1016/j.jbiotec.2018.01.008.","ista":"Tomasek K, Bergmiller T, Guet CC. 2018. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 268, 40–52.","chicago":"Tomasek, Kathrin, Tobias Bergmiller, and Calin C Guet. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” Journal of Biotechnology. Elsevier, 2018. https://doi.org/10.1016/j.jbiotec.2018.01.008."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000425715100006"]},"article_processing_charge":"No","publist_id":"7317","author":[{"last_name":"Tomasek","full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin"},{"first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","last_name":"Bergmiller"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"title":"Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains","year":"2018","isi":1,"publication":"Journal of Biotechnology","day":"20","page":"40 - 52","date_created":"2018-12-11T11:46:50Z","date_published":"2018-02-20T00:00:00Z","doi":"10.1016/j.jbiotec.2018.01.008","acknowledgement":"We thank R Chait and M Lagator for sharing Bacillus subtilis CR_Y1 and pZS*_2R-cIPtet-Venus-Prm, respectively. We are grateful to T Pilizota and all members of the Guet lab for critically reading the manuscript. We also thank the Bioimaging facility at IST Austria for assistance using the FACSAria III system.\r\n\r\n","publisher":"Elsevier","quality_controlled":"1","date_updated":"2023-09-13T08:24:51Z","department":[{"_id":"CaGu"}],"_id":"503","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":268,"acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Buffers are essential for diluting bacterial cultures for flow cytometry analysis in order to study bacterial physiology and gene expression parameters based on fluorescence signals. Using a variety of constitutively expressed fluorescent proteins in Escherichia coli K-12 strain MG1655, we found strong artifactual changes in fluorescence levels after dilution into the commonly used flow cytometry buffer phosphate-buffered saline (PBS) and two other buffer solutions, Tris-HCl and M9 salts. These changes appeared very rapidly after dilution, and were linked to increased membrane permeability and loss in cell viability. We observed buffer-related effects in several different E. coli strains, K-12, C and W, but not E. coli B, which can be partially explained by differences in lipopolysaccharide (LPS) and outer membrane composition. Supplementing the buffers with divalent cations responsible for outer membrane stability, Mg2+ and Ca2+, preserved fluorescence signals, membrane integrity and viability of E. coli. Thus, stabilizing the bacterial outer membrane is essential for precise and unbiased measurements of fluorescence parameters using flow cytometry."}],"oa_version":"None","scopus_import":"1","intvolume":" 268","month":"02"},{"issue":"8","volume":16,"related_material":{"record":[{"id":"9810","status":"public","relation":"research_data"}]},"publication_status":"published","file":[{"date_updated":"2020-07-14T12:48:10Z","file_size":4007095,"creator":"dernst","date_created":"2018-12-17T12:55:31Z","file_name":"2018_Plos_Chaudhry.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5706","checksum":"527076f78265cd4ea192cd1569851587"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"08","intvolume":" 16","abstract":[{"lang":"eng","text":"In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage, bacterial cells resistant to the phage commonly emerge and become the dominant population of bacteria. Following the ascent of resistant mutants, the densities of bacteria in these simple communities become limited by resources rather than the phage. Despite the evolution of resistant hosts, upon which the phage cannot replicate, the lytic phage population is most commonly maintained in an apparently stable state with the resistant bacteria. Several mechanisms have been put forward to account for this result. Here we report the results of population dynamic/evolution experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli in serial transfer cultures. We show that, following the ascent of λVIR-resistant bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal media and in all cases in nutrient-rich broth. Using mathematical models and experiments, we show that the dominant mechanism responsible for maintenance of λVIRin these resource-limited populations dominated by resistant E. coli is a high rate of either phenotypic or genetic transition from resistance to susceptibility—a hitherto undemonstrated mechanism we term "leaky resistance." We discuss the implications of leaky resistance to our understanding of the conditions for the maintenance of phage in populations of bacteria—their “existence conditions.”."}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:10Z","department":[{"_id":"CaGu"}],"date_updated":"2023-09-13T08:45:41Z","ddc":["570"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"82","date_published":"2018-08-16T00:00:00Z","doi":"10.1371/journal.pbio.2005971","date_created":"2018-12-11T11:44:32Z","isi":1,"has_accepted_license":"1","year":"2018","day":"16","publication":"PLoS Biology","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"publist_id":"7972","author":[{"last_name":"Chaudhry","full_name":"Chaudhry, Waqas","first_name":"Waqas"},{"id":"4569785E-F248-11E8-B48F-1D18A9856A87","first_name":"Maros","last_name":"Pleska","full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479"},{"last_name":"Shah","full_name":"Shah, Nilang","first_name":"Nilang"},{"first_name":"Howard","last_name":"Weiss","full_name":"Weiss, Howard"},{"last_name":"Mccall","full_name":"Mccall, Ingrid","first_name":"Ingrid"},{"full_name":"Meyer, Justin","last_name":"Meyer","first_name":"Justin"},{"last_name":"Gupta","full_name":"Gupta, Animesh","first_name":"Animesh"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet"},{"last_name":"Levin","full_name":"Levin, Bruce","first_name":"Bruce"}],"external_id":{"isi":["000443383300024"]},"article_processing_charge":"Yes","title":"Leaky resistance and the conditions for the existence of lytic bacteriophage","citation":{"mla":"Chaudhry, Waqas, et al. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology, vol. 16, no. 8, 2005971, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005971.","ieee":"W. Chaudhry et al., “Leaky resistance and the conditions for the existence of lytic bacteriophage,” PLoS Biology, vol. 16, no. 8. Public Library of Science, 2018.","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018).","ama":"Chaudhry W, Pleska M, Shah N, et al. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 2018;16(8). doi:10.1371/journal.pbio.2005971","apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971","chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.","ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 16(8), 2005971."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"2005971"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive Aerodynamic Design.” ACM Trans. Graph., vol. 37, no. 4, 89, ACM, 2018, doi:10.1145/3197517.3201325.","apa":"Umetani, N., & Bickel, B. (2018). Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201325","ama":"Umetani N, Bickel B. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201325","ieee":"N. Umetani and B. Bickel, “Learning three-dimensional flow for interactive aerodynamic design,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.","short":"N. Umetani, B. Bickel, ACM Trans. Graph. 37 (2018).","chicago":"Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive Aerodynamic Design.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201325.","ista":"Umetani N, Bickel B. 2018. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. 37(4), 89."},"title":"Learning three-dimensional flow for interactive aerodynamic design","publist_id":"8053","author":[{"first_name":"Nobuyuki","last_name":"Umetani","full_name":"Umetani, Nobuyuki"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel"}],"article_processing_charge":"No","external_id":{"isi":["000448185000050"]},"article_number":"89","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"day":"04","publication":"ACM Trans. Graph.","isi":1,"has_accepted_license":"1","year":"2018","doi":"10.1145/3197517.3201325","date_published":"2018-08-04T00:00:00Z","date_created":"2018-12-11T11:44:06Z","publisher":"ACM","quality_controlled":"1","oa":1,"ddc":["003","004"],"date_updated":"2023-09-13T08:46:15Z","department":[{"_id":"BeBi"}],"file_date_updated":"2020-07-14T12:46:22Z","_id":"4","status":"public","pubrep_id":"1049","type":"journal_article","file":[{"creator":"system","date_updated":"2020-07-14T12:46:22Z","file_size":22803163,"date_created":"2018-12-12T10:16:28Z","file_name":"IST-2018-1049-v1+1_2018_sigg_Learning3DAerodynamics.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5216","checksum":"7a2243668f215821bc6aecad0320079a"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-interactive-machine-learning-tool-makes-car-designs-more-aerodynamic/","relation":"press_release"}]},"issue":"4","volume":37,"ec_funded":1,"oa_version":"Submitted Version","abstract":[{"text":"We present a data-driven technique to instantly predict how fluid flows around various three-dimensional objects. Such simulation is useful for computational fabrication and engineering, but is usually computationally expensive since it requires solving the Navier-Stokes equation for many time steps. To accelerate the process, we propose a machine learning framework which predicts aerodynamic forces and velocity and pressure fields given a threedimensional shape input. Handling detailed free-form three-dimensional shapes in a data-driven framework is challenging because machine learning approaches usually require a consistent parametrization of input and output. We present a novel PolyCube maps-based parametrization that can be computed for three-dimensional shapes at interactive rates. This allows us to efficiently learn the nonlinear response of the flow using a Gaussian process regression. We demonstrate the effectiveness of our approach for the interactive design and optimization of a car body.","lang":"eng"}],"month":"08","intvolume":" 37","scopus_import":"1"},{"title":"Localizing faults in simulink/stateflow models with STL","author":[{"first_name":"Ezio","last_name":"Bartocci","full_name":"Bartocci, Ezio"},{"full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","last_name":"Ferrere","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Niveditha","last_name":"Manjunath","full_name":"Manjunath, Niveditha"},{"last_name":"Nickovic","full_name":"Nickovic, Dejan","first_name":"Dejan"}],"publist_id":"7738","external_id":{"isi":["000474781600022"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Bartocci, E., Ferrere, T., Manjunath, N., & Nickovic, D. (2018). Localizing faults in simulink/stateflow models with STL (pp. 197–206). Presented at the HSCC: Hybrid Systems: Computation and Control, Porto, Portugal: Association for Computing Machinery, Inc. https://doi.org/10.1145/3178126.3178131","ama":"Bartocci E, Ferrere T, Manjunath N, Nickovic D. Localizing faults in simulink/stateflow models with STL. In: Association for Computing Machinery, Inc; 2018:197-206. doi:10.1145/3178126.3178131","ieee":"E. Bartocci, T. Ferrere, N. Manjunath, and D. Nickovic, “Localizing faults in simulink/stateflow models with STL,” presented at the HSCC: Hybrid Systems: Computation and Control, Porto, Portugal, 2018, pp. 197–206.","short":"E. Bartocci, T. Ferrere, N. Manjunath, D. Nickovic, in:, Association for Computing Machinery, Inc, 2018, pp. 197–206.","mla":"Bartocci, Ezio, et al. Localizing Faults in Simulink/Stateflow Models with STL. Association for Computing Machinery, Inc, 2018, pp. 197–206, doi:10.1145/3178126.3178131.","ista":"Bartocci E, Ferrere T, Manjunath N, Nickovic D. 2018. Localizing faults in simulink/stateflow models with STL. HSCC: Hybrid Systems: Computation and Control, HSCC Proceedings, , 197–206.","chicago":"Bartocci, Ezio, Thomas Ferrere, Niveditha Manjunath, and Dejan Nickovic. “Localizing Faults in Simulink/Stateflow Models with STL,” 197–206. Association for Computing Machinery, Inc, 2018. https://doi.org/10.1145/3178126.3178131."},"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"date_published":"2018-04-11T00:00:00Z","doi":"10.1145/3178126.3178131","date_created":"2018-12-11T11:45:04Z","page":"197 - 206","day":"11","isi":1,"year":"2018","quality_controlled":"1","publisher":"Association for Computing Machinery, Inc","acknowledgement":"This work was partially supported by the Austrian Science Fund (FWF) under grants S11402-N23 and S11405-N23 (RiSE/SHiNE), the CPS/IoT project (HRSM), the EU ICT COST Action IC1402 on Run-time Verification beyond Monitoring (ARVI), the AMASS project (ECSEL 692474), and the ENABLE-S3 project (ECSEL 692455). The CPS/IoT project receives support from the Austrian government through the Federal Ministry of Science, Research and Economy (BMWFW) in the funding program Hochschulraum-Strukturmittel (HRSM) 2016. The ECSEL Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and Austria, Denmark, Germany, Finland, Czech Republic, Italy, Spain, Portugal, Poland, Ireland, Belgium, France, Netherlands, United Kingdom, Slovakia, Norway.","department":[{"_id":"ToHe"}],"date_updated":"2023-09-13T08:48:46Z","status":"public","type":"conference","conference":{"location":"Porto, Portugal","end_date":"2018-04-13","start_date":"2018-04-11","name":"HSCC: Hybrid Systems: Computation and Control"},"_id":"183","language":[{"iso":"eng"}],"publication_status":"published","month":"04","alternative_title":["HSCC Proceedings"],"scopus_import":"1","oa_version":"None","abstract":[{"text":"Fault-localization is considered to be a very tedious and time-consuming activity in the design of complex Cyber-Physical Systems (CPS). This laborious task essentially requires expert knowledge of the system in order to discover the cause of the fault. In this context, we propose a new procedure that AIDS designers in debugging Simulink/Stateflow hybrid system models, guided by Signal Temporal Logic (STL) specifications. The proposed method relies on three main ingredients: (1) a monitoring and a trace diagnostics procedure that checks whether a tested behavior satisfies or violates an STL specification, localizes time segments and interfaces variables contributing to the property violations; (2) a slicing procedure that maps these observable behavior segments to the internal states and transitions of the Simulink model; and (3) a spectrum-based fault-localization method that combines the previous analysis from multiple tests to identify the internal states and/or transitions that are the most likely to explain the fault. We demonstrate the applicability of our approach on two Simulink models from the automotive and the avionics domain.","lang":"eng"}]},{"department":[{"_id":"LaEr"}],"date_updated":"2023-09-13T08:47:52Z","article_type":"original","type":"journal_article","status":"public","_id":"566","issue":"1","related_material":{"record":[{"id":"149","status":"public","relation":"dissertation_contains"}]},"volume":28,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1612.07776 "}],"month":"03","intvolume":" 28","abstract":[{"text":"We consider large random matrices X with centered, independent entries which have comparable but not necessarily identical variances. Girko's circular law asserts that the spectrum is supported in a disk and in case of identical variances, the limiting density is uniform. In this special case, the local circular law by Bourgade et. al. [11,12] shows that the empirical density converges even locally on scales slightly above the typical eigenvalue spacing. In the general case, the limiting density is typically inhomogeneous and it is obtained via solving a system of deterministic equations. Our main result is the local inhomogeneous circular law in the bulk spectrum on the optimal scale for a general variance profile of the entries of X. \r\n\r\n","lang":"eng"}],"oa_version":"Preprint","author":[{"last_name":"Alt","full_name":"Alt, Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes"},{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"last_name":"Krüger","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["1612.07776 "],"isi":["000431721800005"]},"title":"Local inhomogeneous circular law","citation":{"ama":"Alt J, Erdös L, Krüger TH. Local inhomogeneous circular law. Annals Applied Probability . 2018;28(1):148-203. doi:10.1214/17-AAP1302","apa":"Alt, J., Erdös, L., & Krüger, T. H. (2018). Local inhomogeneous circular law. Annals Applied Probability . Institute of Mathematical Statistics. https://doi.org/10.1214/17-AAP1302","short":"J. Alt, L. Erdös, T.H. Krüger, Annals Applied Probability 28 (2018) 148–203.","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “Local inhomogeneous circular law,” Annals Applied Probability , vol. 28, no. 1. Institute of Mathematical Statistics, pp. 148–203, 2018.","mla":"Alt, Johannes, et al. “Local Inhomogeneous Circular Law.” Annals Applied Probability , vol. 28, no. 1, Institute of Mathematical Statistics, 2018, pp. 148–203, doi:10.1214/17-AAP1302.","ista":"Alt J, Erdös L, Krüger TH. 2018. Local inhomogeneous circular law. Annals Applied Probability . 28(1), 148–203.","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “Local Inhomogeneous Circular Law.” Annals Applied Probability . Institute of Mathematical Statistics, 2018. https://doi.org/10.1214/17-AAP1302."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}],"page":"148-203","doi":"10.1214/17-AAP1302","date_published":"2018-03-03T00:00:00Z","date_created":"2018-12-11T11:47:13Z","isi":1,"year":"2018","day":"03","publication":"Annals Applied Probability ","publisher":"Institute of Mathematical Statistics","quality_controlled":"1","oa":1},{"title":"Long geodesics on convex surfaces","external_id":{"arxiv":["1702.05172"],"isi":["000444141200005"]},"article_processing_charge":"No","publist_id":"7948","author":[{"last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"},{"last_name":"Petrunin","full_name":"Petrunin, Anton","first_name":"Anton"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” Mathematical Intelligencer, vol. 40, no. 3, Springer, 2018, pp. 26–31, doi:10.1007/s00283-018-9795-5.","apa":"Akopyan, A., & Petrunin, A. (2018). Long geodesics on convex surfaces. Mathematical Intelligencer. Springer. https://doi.org/10.1007/s00283-018-9795-5","ama":"Akopyan A, Petrunin A. Long geodesics on convex surfaces. Mathematical Intelligencer. 2018;40(3):26-31. doi:10.1007/s00283-018-9795-5","ieee":"A. Akopyan and A. Petrunin, “Long geodesics on convex surfaces,” Mathematical Intelligencer, vol. 40, no. 3. Springer, pp. 26–31, 2018.","short":"A. Akopyan, A. Petrunin, Mathematical Intelligencer 40 (2018) 26–31.","chicago":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” Mathematical Intelligencer. Springer, 2018. https://doi.org/10.1007/s00283-018-9795-5.","ista":"Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical Intelligencer. 40(3), 26–31."},"oa":1,"publisher":"Springer","quality_controlled":"1","date_created":"2018-12-11T11:44:40Z","doi":"10.1007/s00283-018-9795-5","date_published":"2018-09-01T00:00:00Z","page":"26 - 31","publication":"Mathematical Intelligencer","day":"01","year":"2018","isi":1,"status":"public","type":"journal_article","_id":"106","department":[{"_id":"HeEd"}],"date_updated":"2023-09-13T08:49:16Z","intvolume":" 40","month":"09","main_file_link":[{"url":"https://arxiv.org/abs/1702.05172","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"The goal of this article is to introduce the reader to the theory of intrinsic geometry of convex surfaces. We illustrate the power of the tools by proving a theorem on convex surfaces containing an arbitrarily long closed simple geodesic. Let us remind ourselves that a curve in a surface is called geodesic if every sufficiently short arc of the curve is length minimizing; if, in addition, it has no self-intersections, we call it simple geodesic. A tetrahedron with equal opposite edges is called isosceles. The axiomatic method of Alexandrov geometry allows us to work with the metrics of convex surfaces directly, without approximating it first by a smooth or polyhedral metric. Such approximations destroy the closed geodesics on the surface; therefore it is difficult (if at all possible) to apply approximations in the proof of our theorem. On the other hand, a proof in the smooth or polyhedral case usually admits a translation into Alexandrov’s language; such translation makes the result more general. In fact, our proof resembles a translation of the proof given by Protasov. Note that the main theorem implies in particular that a smooth convex surface does not have arbitrarily long simple closed geodesics. However we do not know a proof of this corollary that is essentially simpler than the one presented below."}],"issue":"3","volume":40,"language":[{"iso":"eng"}],"publication_status":"published"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-13T08:45:41Z","citation":{"ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Numerical data used in figures, Public Library of Science, 10.1371/journal.pbio.2005971.s008.","chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Numerical Data Used in Figures.” Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.s008.","apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Numerical data used in figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971.s008","ama":"Chaudhry W, Pleska M, Shah N, et al. Numerical data used in figures. 2018. doi:10.1371/journal.pbio.2005971.s008","ieee":"W. Chaudhry et al., “Numerical data used in figures.” Public Library of Science, 2018.","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, (2018).","mla":"Chaudhry, Waqas, et al. Numerical Data Used in Figures. Public Library of Science, 2018, doi:10.1371/journal.pbio.2005971.s008."},"title":"Numerical data used in figures","department":[{"_id":"CaGu"}],"author":[{"last_name":"Chaudhry","full_name":"Chaudhry, Waqas","first_name":"Waqas"},{"orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros","last_name":"Pleska","id":"4569785E-F248-11E8-B48F-1D18A9856A87","first_name":"Maros"},{"first_name":"Nilang","last_name":"Shah","full_name":"Shah, Nilang"},{"last_name":"Weiss","full_name":"Weiss, Howard","first_name":"Howard"},{"first_name":"Ingrid","last_name":"Mccall","full_name":"Mccall, Ingrid"},{"first_name":"Justin","full_name":"Meyer, Justin","last_name":"Meyer"},{"full_name":"Gupta, Animesh","last_name":"Gupta","first_name":"Animesh"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"},{"first_name":"Bruce","full_name":"Levin, Bruce","last_name":"Levin"}],"article_processing_charge":"No","_id":"9810","status":"public","type":"research_data_reference","day":"16","year":"2018","date_published":"2018-08-16T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"82","status":"public"}]},"doi":"10.1371/journal.pbio.2005971.s008","date_created":"2021-08-06T12:43:44Z","oa_version":"Published Version","month":"08","publisher":"Public Library of Science"},{"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"9c7eba51a35c62da8c13f98120b64df4","file_id":"5704","creator":"dernst","file_size":2252043,"date_updated":"2020-07-14T12:45:45Z","file_name":"2018_JournalCellBiology_Brown.pdf","date_created":"2018-12-17T12:50:07Z"}],"publication_status":"published","ec_funded":1,"issue":"6","volume":217,"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Lymphatic endothelial cells (LECs) release extracellular chemokines to guide the migration of dendritic cells. In this study, we report that LECs also release basolateral exosome-rich endothelial vesicles (EEVs) that are secreted in greater numbers in the presence of inflammatory cytokines and accumulate in the perivascular stroma of small lymphatic vessels in human chronic inflammatory diseases. Proteomic analyses of EEV fractions identified > 1,700 cargo proteins and revealed a dominant motility-promoting protein signature. In vitro and ex vivo EEV fractions augmented cellular protrusion formation in a CX3CL1/fractalkine-dependent fashion and enhanced the directional migratory response of human dendritic cells along guidance cues. We conclude that perilymphatic LEC exosomes enhance exploratory behavior and thus promote directional migration of CX3CR1-expressing cells in complex tissue environments."}],"intvolume":" 217","month":"04","scopus_import":"1","ddc":["570"],"date_updated":"2023-09-13T08:51:29Z","department":[{"_id":"MiSi"},{"_id":"Bio"}],"file_date_updated":"2020-07-14T12:45:45Z","_id":"275","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","publication":"Journal of Cell Biology","day":"12","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:45:33Z","doi":"10.1083/jcb.201612051","date_published":"2018-04-12T00:00:00Z","page":"2205 - 2221","acknowledgement":"M. Brown was supported by the Cell Communication in Health and Disease Graduate Study Program of the Austrian Science Fund and Medizinische Universität Wien, M. Sixt by the European Research Council (ERC GA 281556) and an Austrian Science Fund START award, K.L. Bennett by the Austrian Academy of Sciences, D.G. Jackson and L.A. Johnson by Unit Funding (MC_UU_12010/2) and project grants from the Medical Research Council (G1100134 and MR/L008610/1), and M. Detmar by the Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung and Advanced European Research Council grant LYVICAM. K. Vaahtomeri was supported by an Academy of Finland postdoctoral research grant (287853). This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 668036 (RELENT).","oa":1,"quality_controlled":"1","publisher":"Rockefeller University Press","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Brown, Markus, Louise Johnson, Dario Leone, Peter Májek, Kari Vaahtomeri, Daniel Senfter, Nora Bukosza, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” Journal of Cell Biology. Rockefeller University Press, 2018. https://doi.org/10.1083/jcb.201612051.","ista":"Brown M, Johnson L, Leone D, Májek P, Vaahtomeri K, Senfter D, Bukosza N, Schachner H, Asfour G, Langer B, Hauschild R, Parapatics K, Hong Y, Bennett K, Kain R, Detmar M, Sixt MK, Jackson D, Kerjaschki D. 2018. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 217(6), 2205–2221.","mla":"Brown, Markus, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” Journal of Cell Biology, vol. 217, no. 6, Rockefeller University Press, 2018, pp. 2205–21, doi:10.1083/jcb.201612051.","ieee":"M. Brown et al., “Lymphatic exosomes promote dendritic cell migration along guidance cues,” Journal of Cell Biology, vol. 217, no. 6. Rockefeller University Press, pp. 2205–2221, 2018.","short":"M. Brown, L. Johnson, D. Leone, P. Májek, K. Vaahtomeri, D. Senfter, N. Bukosza, H. Schachner, G. Asfour, B. Langer, R. Hauschild, K. Parapatics, Y. Hong, K. Bennett, R. Kain, M. Detmar, M.K. Sixt, D. Jackson, D. Kerjaschki, Journal of Cell Biology 217 (2018) 2205–2221.","apa":"Brown, M., Johnson, L., Leone, D., Májek, P., Vaahtomeri, K., Senfter, D., … Kerjaschki, D. (2018). Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201612051","ama":"Brown M, Johnson L, Leone D, et al. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 2018;217(6):2205-2221. doi:10.1083/jcb.201612051"},"title":"Lymphatic exosomes promote dendritic cell migration along guidance cues","external_id":{"isi":["000438077800026"],"pmid":["29650776"]},"article_processing_charge":"No","author":[{"first_name":"Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Markus","last_name":"Brown"},{"last_name":"Johnson","full_name":"Johnson, Louise","first_name":"Louise"},{"full_name":"Leone, Dario","last_name":"Leone","first_name":"Dario"},{"first_name":"Peter","full_name":"Májek, Peter","last_name":"Májek"},{"first_name":"Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87","full_name":"Vaahtomeri, Kari","orcid":"0000-0001-7829-3518","last_name":"Vaahtomeri"},{"full_name":"Senfter, Daniel","last_name":"Senfter","first_name":"Daniel"},{"first_name":"Nora","last_name":"Bukosza","full_name":"Bukosza, Nora"},{"first_name":"Helga","full_name":"Schachner, Helga","last_name":"Schachner"},{"last_name":"Asfour","full_name":"Asfour, Gabriele","first_name":"Gabriele"},{"first_name":"Brigitte","last_name":"Langer","full_name":"Langer, Brigitte"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"last_name":"Parapatics","full_name":"Parapatics, Katja","first_name":"Katja"},{"full_name":"Hong, Young","last_name":"Hong","first_name":"Young"},{"last_name":"Bennett","full_name":"Bennett, Keiryn","first_name":"Keiryn"},{"full_name":"Kain, Renate","last_name":"Kain","first_name":"Renate"},{"last_name":"Detmar","full_name":"Detmar, Michael","first_name":"Michael"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"},{"first_name":"David","full_name":"Jackson, David","last_name":"Jackson"},{"first_name":"Dontscho","full_name":"Kerjaschki, Dontscho","last_name":"Kerjaschki"}],"publist_id":"7627","project":[{"grant_number":"Y 564-B12","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"},{"grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425"}]},{"status":"public","type":"journal_article","_id":"158","department":[{"_id":"JiFr"}],"date_updated":"2023-09-13T08:53:28Z","month":"07","intvolume":" 4","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30013211"}],"pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The angiosperm seed is composed of three genetically distinct tissues: the diploid embryo that originates from the fertilized egg cell, the triploid endosperm that is produced from the fertilized central cell, and the maternal sporophytic integuments that develop into the seed coat1. At the onset of embryo development in Arabidopsis thaliana, the zygote divides asymmetrically, producing a small apical embryonic cell and a larger basal cell that connects the embryo to the maternal tissue2. The coordinated and synchronous development of the embryo and the surrounding integuments, and the alignment of their growth axes, suggest communication between maternal tissues and the embryo. In contrast to animals, however, where a network of maternal factors that direct embryo patterning have been identified3,4, only a few maternal mutations have been described to affect embryo development in plants5–7. Early embryo patterning in Arabidopsis requires accumulation of the phytohormone auxin in the apical cell by directed transport from the suspensor8–10. However, the origin of this auxin has remained obscure. Here we investigate the source of auxin for early embryogenesis and provide evidence that the mother plant coordinates seed development by supplying auxin to the early embryo from the integuments of the ovule. We show that auxin response increases in ovules after fertilization, due to upregulated auxin biosynthesis in the integuments, and this maternally produced auxin is required for correct embryo development."}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/plant-mothers-talk-to-their-embryos-via-the-hormone-auxin/"}]},"volume":4,"issue":"8","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"title":"Maternal auxin supply contributes to early embryo patterning in Arabidopsis","author":[{"full_name":"Robert, Hélène","last_name":"Robert","first_name":"Hélène"},{"first_name":"Chulmin","full_name":"Park, Chulmin","last_name":"Park"},{"first_name":"Carla","full_name":"Gutièrrez, Carla","last_name":"Gutièrrez"},{"last_name":"Wójcikowska","full_name":"Wójcikowska, Barbara","first_name":"Barbara"},{"first_name":"Aleš","last_name":"Pěnčík","full_name":"Pěnčík, Aleš"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"full_name":"Chen, Junyi","last_name":"Chen","first_name":"Junyi"},{"first_name":"Wim","last_name":"Grunewald","full_name":"Grunewald, Wim"},{"last_name":"Dresselhaus","full_name":"Dresselhaus, Thomas","first_name":"Thomas"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Laux, Thomas","last_name":"Laux","first_name":"Thomas"}],"publist_id":"7763","article_processing_charge":"No","external_id":{"pmid":["30013211"],"isi":["000443861300011"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Robert, Hélène, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” Nature Plants, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 548–53, doi:10.1038/s41477-018-0204-z.","apa":"Robert, H., Park, C., Gutièrrez, C., Wójcikowska, B., Pěnčík, A., Novák, O., … Laux, T. (2018). Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0204-z","ama":"Robert H, Park C, Gutièrrez C, et al. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. 2018;4(8):548-553. doi:10.1038/s41477-018-0204-z","short":"H. Robert, C. Park, C. Gutièrrez, B. Wójcikowska, A. Pěnčík, O. Novák, J. Chen, W. Grunewald, T. Dresselhaus, J. Friml, T. Laux, Nature Plants 4 (2018) 548–553.","ieee":"H. Robert et al., “Maternal auxin supply contributes to early embryo patterning in Arabidopsis,” Nature Plants, vol. 4, no. 8. Nature Publishing Group, pp. 548–553, 2018.","chicago":"Robert, Hélène, Chulmin Park, Carla Gutièrrez, Barbara Wójcikowska, Aleš Pěnčík, Ondřej Novák, Junyi Chen, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0204-z.","ista":"Robert H, Park C, Gutièrrez C, Wójcikowska B, Pěnčík A, Novák O, Chen J, Grunewald W, Dresselhaus T, Friml J, Laux T. 2018. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. 4(8), 548–553."},"quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"acknowledgement":"This work was further supported by the Czech Science Foundation GACR (GA13-40637S) to J.F.;","date_published":"2018-07-16T00:00:00Z","doi":"10.1038/s41477-018-0204-z","date_created":"2018-12-11T11:44:56Z","page":"548 - 553","day":"16","publication":"Nature Plants","isi":1,"year":"2018"},{"volume":28,"issue":"10","publication_status":"published","file":[{"file_id":"6994","checksum":"ef6d2b4e1fd63948539639242610bfa6","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf","date_created":"2019-11-07T12:55:20Z","creator":"lsazanov","file_size":2185385,"date_updated":"2020-07-14T12:45:00Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"07","intvolume":" 28","abstract":[{"text":"Complex I has an essential role in ATP production by coupling electron transfer from NADH to quinone with translocation of protons across the inner mitochondrial membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative conditions. Until recently, the understanding of complex I deficiency on the molecular level was limited due to the lack of high-resolution structures of the enzyme. However, due to developments in single particle cryo-electron microscopy (cryo-EM), recent studies have reported nearly atomic resolution maps and models of mitochondrial complex I. These structures significantly add to our understanding of complex I mechanism and assembly. The disease-causing mutations are discussed here in their structural context.","lang":"eng"}],"oa_version":"Submitted Version","file_date_updated":"2020-07-14T12:45:00Z","department":[{"_id":"LeSa"}],"date_updated":"2023-09-13T08:51:56Z","ddc":["572"],"article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"152","page":"835 - 867","date_published":"2018-07-26T00:00:00Z","doi":"10.1016/j.tcb.2018.06.006","date_created":"2018-12-11T11:44:54Z","has_accepted_license":"1","isi":1,"year":"2018","day":"26","publication":"Trends in Cell Biology","publisher":"Elsevier","quality_controlled":"1","oa":1,"author":[{"full_name":"Fiedorczuk, Karol","last_name":"Fiedorczuk","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","first_name":"Karol"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov"}],"publist_id":"7769","external_id":{"isi":["000445118200007"]},"article_processing_charge":"No","title":"Mammalian mitochondrial complex I structure and disease causing mutations","citation":{"ista":"Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 28(10), 835–867.","chicago":"Fiedorczuk, Karol, and Leonid A Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” Trends in Cell Biology. Elsevier, 2018. https://doi.org/10.1016/j.tcb.2018.06.006.","apa":"Fiedorczuk, K., & Sazanov, L. A. (2018). Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. Elsevier. https://doi.org/10.1016/j.tcb.2018.06.006","ama":"Fiedorczuk K, Sazanov LA. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 2018;28(10):835-867. doi:10.1016/j.tcb.2018.06.006","ieee":"K. Fiedorczuk and L. A. Sazanov, “Mammalian mitochondrial complex I structure and disease causing mutations,” Trends in Cell Biology, vol. 28, no. 10. Elsevier, pp. 835–867, 2018.","short":"K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867.","mla":"Fiedorczuk, Karol, and Leonid A. Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” Trends in Cell Biology, vol. 28, no. 10, Elsevier, 2018, pp. 835–67, doi:10.1016/j.tcb.2018.06.006."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"date_updated":"2023-09-13T08:50:16Z","department":[{"_id":"KrCh"}],"_id":"310","conference":{"name":"SODA: Symposium on Discrete Algorithms","location":"New Orleans, Louisiana, United States","end_date":"2018-01-10","start_date":"2018-01-07"},"type":"conference","status":"public","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"abstract":[{"text":"A model of computation that is widely used in the formal analysis of reactive systems is symbolic algorithms. In this model the access to the input graph is restricted to consist of symbolic operations, which are expensive in comparison to the standard RAM operations. We give lower bounds on the number of symbolic operations for basic graph problems such as the computation of the strongly connected components and of the approximate diameter as well as for fundamental problems in model checking such as safety, liveness, and coliveness. Our lower bounds are linear in the number of vertices of the graph, even for constant-diameter graphs. For none of these problems lower bounds on the number of symbolic operations were known before. The lower bounds show an interesting separation of these problems from the reachability problem, which can be solved with O(D) symbolic operations, where D is the diameter of the graph. Additionally we present an approximation algorithm for the graph diameter which requires Õ(n/D) symbolic steps to achieve a (1 +ϵ)-approximation for any constant > 0. This compares to O(n/D) symbolic steps for the (naive) exact algorithm and O(D) symbolic steps for a 2-approximation. Finally we also give a refined analysis of the strongly connected components algorithms of [15], showing that it uses an optimal number of symbolic steps that is proportional to the sum of the diameters of the strongly connected components.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.09148"}],"scopus_import":"1","month":"01","citation":{"chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Veronika Loitzenbauer. “Lower Bounds for Symbolic Computation on Graphs: Strongly Connected Components, Liveness, Safety, and Diameter,” 2341–56. ACM, 2018. https://doi.org/10.1137/1.9781611975031.151.","ista":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2018. Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter. SODA: Symposium on Discrete Algorithms, 2341–2356.","mla":"Chatterjee, Krishnendu, et al. Lower Bounds for Symbolic Computation on Graphs: Strongly Connected Components, Liveness, Safety, and Diameter. ACM, 2018, pp. 2341–56, doi:10.1137/1.9781611975031.151.","ama":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter. In: ACM; 2018:2341-2356. doi:10.1137/1.9781611975031.151","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., & Loitzenbauer, V. (2018). Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter (pp. 2341–2356). Presented at the SODA: Symposium on Discrete Algorithms, New Orleans, Louisiana, United States: ACM. https://doi.org/10.1137/1.9781611975031.151","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter,” presented at the SODA: Symposium on Discrete Algorithms, New Orleans, Louisiana, United States, 2018, pp. 2341–2356.","short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, ACM, 2018, pp. 2341–2356."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000483921200152"],"arxiv":["1711.09148"]},"publist_id":"7555","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Dvorák, Wolfgang","last_name":"Dvorák","first_name":"Wolfgang"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger"},{"first_name":"Veronika","last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika"}],"title":"Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"year":"2018","isi":1,"day":"01","page":"2341 - 2356","date_created":"2018-12-11T11:45:45Z","doi":"10.1137/1.9781611975031.151","date_published":"2018-01-01T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"ACM"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Barzanjeh S, Aquilina M, Xuereb A. Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. 2018;120(6). doi:10.1103/PhysRevLett.120.060601","apa":"Barzanjeh, S., Aquilina, M., & Xuereb, A. (2018). Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.120.060601","short":"S. Barzanjeh, M. Aquilina, A. Xuereb, Physical Review Letters 120 (2018).","ieee":"S. Barzanjeh, M. Aquilina, and A. Xuereb, “Manipulating the flow of thermal noise in quantum devices,” Physical Review Letters, vol. 120, no. 6. American Physical Society, 2018.","mla":"Barzanjeh, Shabir, et al. “Manipulating the Flow of Thermal Noise in Quantum Devices.” Physical Review Letters, vol. 120, no. 6, 060601, American Physical Society, 2018, doi:10.1103/PhysRevLett.120.060601.","ista":"Barzanjeh S, Aquilina M, Xuereb A. 2018. Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. 120(6), 060601.","chicago":"Barzanjeh, Shabir, Matteo Aquilina, and André Xuereb. “Manipulating the Flow of Thermal Noise in Quantum Devices.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.120.060601."},"title":"Manipulating the flow of thermal noise in quantum devices","article_processing_charge":"No","external_id":{"isi":["000424382100004"],"arxiv":["1706.09051"]},"publist_id":"7387","author":[{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir","last_name":"Barzanjeh","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir"},{"first_name":"Matteo","full_name":"Aquilina, Matteo","last_name":"Aquilina"},{"full_name":"Xuereb, André","last_name":"Xuereb","first_name":"André"}],"article_number":"060601 ","project":[{"name":"Hybrid Optomechanical Technologies","grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","grant_number":"707438","call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425"}],"publication":"Physical Review Letters","day":"07","year":"2018","isi":1,"date_created":"2018-12-11T11:46:28Z","doi":"10.1103/PhysRevLett.120.060601","date_published":"2018-02-07T00:00:00Z","oa":1,"publisher":"American Physical Society","quality_controlled":"1","date_updated":"2023-09-13T08:52:27Z","department":[{"_id":"JoFi"}],"_id":"436","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/interference-as-a-new-method-for-cooling-quantum-devices/","description":"News on IST Homepage"}]},"volume":120,"issue":"6","oa_version":"Preprint","abstract":[{"text":"There has been significant interest recently in using complex quantum systems to create effective nonreciprocal dynamics. Proposals have been put forward for the realization of artificial magnetic fields for photons and phonons; experimental progress is fast making these proposals a reality. Much work has concentrated on the use of such systems for controlling the flow of signals, e.g., to create isolators or directional amplifiers for optical signals. In this Letter, we build on this work but move in a different direction. We develop the theory of and discuss a potential realization for the controllable flow of thermal noise in quantum systems. We demonstrate theoretically that the unidirectional flow of thermal noise is possible within quantum cascaded systems. Viewing an optomechanical platform as a cascaded system we show here that one can ultimately control the direction of the flow of thermal noise. By appropriately engineering the mechanical resonator, which acts as an artificial reservoir, the flow of thermal noise can be constrained to a desired direction, yielding a thermal rectifier. The proposed quantum thermal noise rectifier could potentially be used to develop devices such as a thermal modulator, a thermal router, and a thermal amplifier for nanoelectronic devices and superconducting circuits.","lang":"eng"}],"intvolume":" 120","month":"02","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.09051"}],"scopus_import":"1"},{"file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"MiSi"}],"ddc":["570"],"date_updated":"2023-09-13T08:55:05Z","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":"5858","issue":"149","volume":15,"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:13Z","file_size":1464288,"creator":"dernst","date_created":"2019-02-05T14:46:44Z","file_name":"2018_Interface_Hross.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5925","checksum":"56eb4308a15b7190bff938fab1f780e8"}],"publication_status":"published","publication_identifier":{"issn":["17425689"]},"intvolume":" 15","month":"12","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Spatial patterns are ubiquitous on the subcellular, cellular and tissue level, and can be studied using imaging techniques such as light and fluorescence microscopy. Imaging data provide quantitative information about biological systems; however, mechanisms causing spatial patterning often remain elusive. In recent years, spatio-temporal mathematical modelling has helped to overcome this problem. Yet, outliers and structured noise limit modelling of whole imaging data, and models often consider spatial summary statistics. Here, we introduce an integrated data-driven modelling approach that can cope with measurement artefacts and whole imaging data. Our approach combines mechanistic models of the biological processes with robust statistical models of the measurement process. The parameters of the integrated model are calibrated using a maximum-likelihood approach. We used this integrated modelling approach to study in vivo gradients of the chemokine (C-C motif) ligand 21 (CCL21). CCL21 gradients guide dendritic cells and are important in the adaptive immune response. Using artificial data, we verified that the integrated modelling approach provides reliable parameter estimates in the presence of measurement noise and that bias and variance of these estimates are reduced compared to conventional approaches. The application to experimental data allowed the parametrization and subsequent refinement of the model using additional mechanisms. Among other results, model-based hypothesis testing predicted lymphatic vessel-dependent concentration of heparan sulfate, the binding partner of CCL21. The selected model provided an accurate description of the experimental data and was partially validated using published data. Our findings demonstrate that integrated statistical modelling of whole imaging data is computationally feasible and can provide novel biological insights.","lang":"eng"}],"title":"Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data","external_id":{"isi":["000456783800011"]},"article_processing_charge":"No","author":[{"last_name":"Hross","full_name":"Hross, Sabrina","first_name":"Sabrina"},{"first_name":"Fabian J.","last_name":"Theis","full_name":"Theis, Fabian J."},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"first_name":"Jan","last_name":"Hasenauer","full_name":"Hasenauer, Jan"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Hross, Sabrina, et al. “Mechanistic Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal Society Interface, vol. 15, no. 149, 20180600, Royal Society Publishing, 2018, doi:10.1098/rsif.2018.0600.","apa":"Hross, S., Theis, F. J., Sixt, M. K., & Hasenauer, J. (2018). Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. Royal Society Publishing. https://doi.org/10.1098/rsif.2018.0600","ama":"Hross S, Theis FJ, Sixt MK, Hasenauer J. Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0600","short":"S. Hross, F.J. Theis, M.K. Sixt, J. Hasenauer, Journal of the Royal Society Interface 15 (2018).","ieee":"S. Hross, F. J. Theis, M. K. Sixt, and J. Hasenauer, “Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data,” Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society Publishing, 2018.","chicago":"Hross, Sabrina, Fabian J. Theis, Michael K Sixt, and Jan Hasenauer. “Mechanistic Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal Society Interface. Royal Society Publishing, 2018. https://doi.org/10.1098/rsif.2018.0600.","ista":"Hross S, Theis FJ, Sixt MK, Hasenauer J. 2018. Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. 15(149), 20180600."},"article_number":"20180600","date_created":"2019-01-20T22:59:18Z","date_published":"2018-12-05T00:00:00Z","doi":"10.1098/rsif.2018.0600","publication":"Journal of the Royal Society Interface","day":"05","year":"2018","isi":1,"has_accepted_license":"1","oa":1,"publisher":"Royal Society Publishing","quality_controlled":"1"},{"scopus_import":"1","month":"10","intvolume":" 3","abstract":[{"lang":"eng","text":"We report quantitative evidence of mixing-layer elastic instability in a viscoelastic fluid flow between two widely spaced obstacles hindering a channel flow at Re 1 and Wi 1. Two mixing layers with nonuniform shear velocity profiles are formed in the region between the obstacles. The mixing-layer instability arises in the vicinity of an inflection point on the shear velocity profile with a steep variation in the elastic stress. The instability results in an intermittent appearance of small vortices in the mixing layers and an amplification of spatiotemporal averaged vorticity in the elastic turbulence regime. The latter is characterized through scaling of friction factor with Wi and both pressure and velocity spectra. Furthermore, the observations reported provide improved understanding of the stability of the mixing layer in a viscoelastic fluid at large elasticity, i.e., Wi 1 and Re 1 and oppose the current view of suppression of vorticity solely by polymer additives."}],"oa_version":"Submitted Version","volume":3,"issue":"10","ec_funded":1,"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"7fc0a2322214d1c04debef36d5bf2e8a","file_id":"5043","creator":"system","file_size":1838431,"date_updated":"2020-07-14T12:45:04Z","file_name":"IST-2018-1062-v1+1_PhysRevFluids.3.103303.pdf","date_created":"2018-12-12T10:13:56Z"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","pubrep_id":"1062","_id":"16","file_date_updated":"2020-07-14T12:45:04Z","department":[{"_id":"BjHo"}],"date_updated":"2023-09-13T08:57:05Z","ddc":["532"],"publisher":"American Physical Society","quality_controlled":"1","oa":1,"acknowledgement":"This work was partially supported by the Israel Science Foundation (ISF; Grant No. 882/15) and the Binational USA-Israel Foundation (BSF; Grant No. 2016145).","doi":"10.1103/PhysRevFluids.3.103303","date_published":"2018-10-16T00:00:00Z","date_created":"2018-12-11T11:44:10Z","isi":1,"has_accepted_license":"1","year":"2018","day":"16","publication":"Physical Review Fluids","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"103303","author":[{"full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","last_name":"Varshney","first_name":"Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Victor","last_name":"Steinberg","full_name":"Steinberg, Victor"}],"publist_id":"8039","external_id":{"isi":["000447469200001"]},"article_processing_charge":"No","title":"Mixing layer instability and vorticity amplification in a creeping viscoelastic flow","citation":{"chicago":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.103303.","ista":"Varshney A, Steinberg V. 2018. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 3(10), 103303.","mla":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids, vol. 3, no. 10, 103303, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.103303.","apa":"Varshney, A., & Steinberg, V. (2018). Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.103303","ama":"Varshney A, Steinberg V. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 2018;3(10). doi:10.1103/PhysRevFluids.3.103303","short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","ieee":"A. Varshney and V. Steinberg, “Mixing layer instability and vorticity amplification in a creeping viscoelastic flow,” Physical Review Fluids, vol. 3, no. 10. American Physical Society, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"publication":"PNAS","day":"02","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:44:19Z","date_published":"2018-10-02T00:00:00Z","doi":"10.1073/pnas.1721061115","page":"10690 - 10695","acknowledgement":"J.R. and J.V.A. were also supported by the Academy of Finland Grants 1273253 and 267541.","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"J. Rybicki, E. Kisdi, and J. Anttila, “Model of bacterial toxin-dependent pathogenesis explains infective dose,” PNAS, vol. 115, no. 42. National Academy of Sciences, pp. 10690–10695, 2018.","short":"J. Rybicki, E. Kisdi, J. Anttila, PNAS 115 (2018) 10690–10695.","ama":"Rybicki J, Kisdi E, Anttila J. Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. 2018;115(42):10690-10695. doi:10.1073/pnas.1721061115","apa":"Rybicki, J., Kisdi, E., & Anttila, J. (2018). Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1721061115","mla":"Rybicki, Joel, et al. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” PNAS, vol. 115, no. 42, National Academy of Sciences, 2018, pp. 10690–95, doi:10.1073/pnas.1721061115.","ista":"Rybicki J, Kisdi E, Anttila J. 2018. Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. 115(42), 10690–10695.","chicago":"Rybicki, Joel, Eva Kisdi, and Jani Anttila. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1721061115."},"title":"Model of bacterial toxin-dependent pathogenesis explains infective dose","external_id":{"isi":["000447491300057"]},"article_processing_charge":"No","author":[{"first_name":"Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646","last_name":"Rybicki"},{"first_name":"Eva","last_name":"Kisdi","full_name":"Kisdi, Eva"},{"full_name":"Anttila, Jani","last_name":"Anttila","first_name":"Jani"}],"publist_id":"8011","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"6258","checksum":"df7ac544a587c06b75692653b9fabd18","file_size":4070777,"date_updated":"2020-07-14T12:46:26Z","creator":"dernst","file_name":"2018_PNAS_Rybicki.pdf","date_created":"2019-04-09T08:02:50Z"}],"publication_status":"published","ec_funded":1,"volume":115,"issue":"42","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The initial amount of pathogens required to start an infection within a susceptible host is called the infective dose and is known to vary to a large extent between different pathogen species. We investigate the hypothesis that the differences in infective doses are explained by the mode of action in the underlying mechanism of pathogenesis: Pathogens with locally acting mechanisms tend to have smaller infective doses than pathogens with distantly acting mechanisms. While empirical evidence tends to support the hypothesis, a formal theoretical explanation has been lacking. We give simple analytical models to gain insight into this phenomenon and also investigate a stochastic, spatially explicit, mechanistic within-host model for toxin-dependent bacterial infections. The model shows that pathogens secreting locally acting toxins have smaller infective doses than pathogens secreting diffusive toxins, as hypothesized. While local pathogenetic mechanisms require smaller infective doses, pathogens with distantly acting toxins tend to spread faster and may cause more damage to the host. The proposed model can serve as a basis for the spatially explicit analysis of various virulence factors also in the context of other problems in infection dynamics."}],"intvolume":" 115","month":"10","scopus_import":"1","ddc":["570","577"],"date_updated":"2023-09-13T08:57:38Z","file_date_updated":"2020-07-14T12:46:26Z","department":[{"_id":"DaAl"}],"_id":"43","pubrep_id":"1063","status":"public","type":"journal_article"},{"file_date_updated":"2020-07-14T12:44:43Z","department":[{"_id":"BeBi"}],"ddc":["004"],"date_updated":"2023-09-13T08:56:07Z","status":"public","pubrep_id":"1038","type":"journal_article","_id":"13","volume":37,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/metamolds-molding-a-mold/","relation":"press_release"}]},"issue":"4","ec_funded":1,"file":[{"date_updated":"2020-07-14T12:44:43Z","file_size":91939066,"creator":"system","date_created":"2018-12-12T10:18:52Z","file_name":"IST-2018-1038-v1+1_metamolds_authorversion.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"61d46273dca4de626accef1d17a0aaad","file_id":"5374"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"08","intvolume":" 37","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We propose a new method for fabricating digital objects through reusable silicone molds. Molds are generated by casting liquid silicone into custom 3D printed containers called metamolds. Metamolds automatically define the cuts that are needed to extract the cast object from the silicone mold. The shape of metamolds is designed through a novel segmentation technique, which takes into account both geometric and topological constraints involved in the process of mold casting. Our technique is simple, does not require changing the shape or topology of the input objects, and only requires off-the- shelf materials and technologies. We successfully tested our method on a set of challenging examples with complex shapes and rich geometric detail. © 2018 Association for Computing Machinery."}],"title":"Metamolds: Computational design of silicone molds","author":[{"last_name":"Alderighi","full_name":"Alderighi, Thomas","first_name":"Thomas"},{"first_name":"Luigi","last_name":"Malomo","full_name":"Malomo, Luigi"},{"last_name":"Giorgi","full_name":"Giorgi, Daniela","first_name":"Daniela"},{"first_name":"Nico","last_name":"Pietroni","full_name":"Pietroni, Nico"},{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Paolo","full_name":"Cignoni, Paolo","last_name":"Cignoni"}],"publist_id":"8043","external_id":{"isi":["000448185000097"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “Metamolds: Computational Design of Silicone Molds.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201381.","ista":"Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. 2018. Metamolds: Computational design of silicone molds. ACM Trans. Graph. 37(4), 136.","mla":"Alderighi, Thomas, et al. “Metamolds: Computational Design of Silicone Molds.” ACM Trans. Graph., vol. 37, no. 4, 136, ACM, 2018, doi:10.1145/3197517.3201381.","ama":"Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. Metamolds: Computational design of silicone molds. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201381","apa":"Alderighi, T., Malomo, L., Giorgi, D., Pietroni, N., Bickel, B., & Cignoni, P. (2018). Metamolds: Computational design of silicone molds. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201381","ieee":"T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, and P. Cignoni, “Metamolds: Computational design of silicone molds,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.","short":"T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, P. Cignoni, ACM Trans. Graph. 37 (2018)."},"project":[{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"article_number":"136","date_published":"2018-08-04T00:00:00Z","doi":"10.1145/3197517.3201381","date_created":"2018-12-11T11:44:09Z","day":"04","publication":"ACM Trans. Graph.","isi":1,"has_accepted_license":"1","year":"2018","publisher":"ACM","quality_controlled":"1","oa":1},{"project":[{"name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","grant_number":"RGY0084/2012","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"}],"author":[{"first_name":"William","last_name":"Zhang","full_name":"Zhang, William"},{"first_name":"Michel","full_name":"Herde, Michel","last_name":"Herde"},{"full_name":"Mitchell, Joshua","last_name":"Mitchell","first_name":"Joshua"},{"first_name":"Jason","full_name":"Whitfield, Jason","last_name":"Whitfield"},{"first_name":"Andreas","full_name":"Wulff, Andreas","last_name":"Wulff"},{"full_name":"Vongsouthi, Vanessa","last_name":"Vongsouthi","first_name":"Vanessa"},{"first_name":"Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","full_name":"Sanchez Romero, Inmaculada","last_name":"Sanchez Romero"},{"full_name":"Gulakova, Polina","last_name":"Gulakova","first_name":"Polina"},{"full_name":"Minge, Daniel","last_name":"Minge","first_name":"Daniel"},{"first_name":"Björn","full_name":"Breithausen, Björn","last_name":"Breithausen"},{"last_name":"Schoch","full_name":"Schoch, Susanne","first_name":"Susanne"},{"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":"Jackson, Colin","last_name":"Jackson","first_name":"Colin"},{"first_name":"Christian","last_name":"Henneberger","full_name":"Henneberger, Christian"}],"publist_id":"7786","external_id":{"isi":["000442174500013"],"pmid":["30061718 "]},"article_processing_charge":"No","title":"Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS","citation":{"mla":"Zhang, William, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical Biology, vol. 14, no. 9, Nature Publishing Group, 2018, pp. 861–69, doi:10.1038/s41589-018-0108-2.","apa":"Zhang, W., Herde, M., Mitchell, J., Whitfield, J., Wulff, A., Vongsouthi, V., … Henneberger, C. (2018). Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0108-2","ama":"Zhang W, Herde M, Mitchell J, et al. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. 2018;14(9):861-869. doi:10.1038/s41589-018-0108-2","short":"W. Zhang, M. Herde, J. Mitchell, J. Whitfield, A. Wulff, V. Vongsouthi, I. Sanchez-Romero, P. Gulakova, D. Minge, B. Breithausen, S. Schoch, H.L. Janovjak, C. Jackson, C. Henneberger, Nature Chemical Biology 14 (2018) 861–869.","ieee":"W. Zhang et al., “Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS,” Nature Chemical Biology, vol. 14, no. 9. Nature Publishing Group, pp. 861–869, 2018.","chicago":"Zhang, William, Michel Herde, Joshua Mitchell, Jason Whitfield, Andreas Wulff, Vanessa Vongsouthi, Inmaculada Sanchez-Romero, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0108-2.","ista":"Zhang W, Herde M, Mitchell J, Whitfield J, Wulff A, Vongsouthi V, Sanchez-Romero I, Gulakova P, Minge D, Breithausen B, Schoch S, Janovjak HL, Jackson C, Henneberger C. 2018. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. 14(9), 861–869."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"page":"861 - 869","date_published":"2018-07-30T00:00:00Z","doi":"10.1038/s41589-018-0108-2","date_created":"2018-12-11T11:44:49Z","isi":1,"year":"2018","day":"30","publication":"Nature Chemical Biology","article_type":"original","type":"journal_article","status":"public","_id":"137","department":[{"_id":"HaJa"}],"date_updated":"2023-09-13T08:58:05Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30061718"}],"month":"07","intvolume":" 14","abstract":[{"text":"Fluorescent sensors are an essential part of the experimental toolbox of the life sciences, where they are used ubiquitously to visualize intra- and extracellular signaling. In the brain, optical neurotransmitter sensors can shed light on temporal and spatial aspects of signal transmission by directly observing, for instance, neurotransmitter release and spread. Here we report the development and application of the first optical sensor for the amino acid glycine, which is both an inhibitory neurotransmitter and a co-agonist of the N-methyl-d-aspartate receptors (NMDARs) involved in synaptic plasticity. Computational design of a glycine-specific binding protein allowed us to produce the optical glycine FRET sensor (GlyFS), which can be used with single and two-photon excitation fluorescence microscopy. We took advantage of this newly developed sensor to test predictions about the uneven spatial distribution of glycine in extracellular space and to demonstrate that extracellular glycine levels are controlled by plasticity-inducing stimuli.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","volume":14,"issue":"9","publication_status":"published","language":[{"iso":"eng"}]},{"date_updated":"2023-09-13T08:56:35Z","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"_id":"153","type":"book_chapter","status":"public","publication_status":"published","publication_identifier":{"issn":["0091679X"]},"language":[{"iso":"eng"}],"volume":147,"abstract":[{"text":"Cells migrating in multicellular organisms steadily traverse complex three-dimensional (3D) environments. To decipher the underlying cell biology, current experimental setups either use simplified 2D, tissue-mimetic 3D (e.g., collagen matrices) or in vivo environments. While only in vivo experiments are truly physiological, they do not allow for precise manipulation of environmental parameters. 2D in vitro experiments do allow mechanical and chemical manipulations, but increasing evidence demonstrates substantial differences of migratory mechanisms in 2D and 3D. Here, we describe simple, robust, and versatile “pillar forests” to investigate cell migration in complex but fully controllable 3D environments. Pillar forests are polydimethylsiloxane-based setups, in which two closely adjacent surfaces are interconnected by arrays of micrometer-sized pillars. Changing the pillar shape, size, height and the inter-pillar distance precisely manipulates microenvironmental parameters (e.g., pore sizes, micro-geometry, micro-topology), while being easily combined with chemotactic cues, surface coatings, diverse cell types and advanced imaging techniques. Thus, pillar forests combine the advantages of 2D cell migration assays with the precise definition of 3D environmental parameters.","lang":"eng"}],"pmid":1,"oa_version":"None","scopus_import":"1","intvolume":" 147","month":"07","citation":{"ama":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: Methods in Cell Biology. Vol 147. Academic Press; 2018:79-91. doi:10.1016/bs.mcb.2018.07.004","apa":"Renkawitz, J., Reversat, A., Leithner, A. F., Merrin, J., & Sixt, M. K. (2018). Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In Methods in Cell Biology (Vol. 147, pp. 79–91). Academic Press. https://doi.org/10.1016/bs.mcb.2018.07.004","short":"J. Renkawitz, A. Reversat, A.F. Leithner, J. Merrin, M.K. Sixt, in:, Methods in Cell Biology, Academic Press, 2018, pp. 79–91.","ieee":"J. Renkawitz, A. Reversat, A. F. Leithner, J. Merrin, and M. K. Sixt, “Micro-engineered ‘pillar forests’ to study cell migration in complex but controlled 3D environments,” in Methods in Cell Biology, vol. 147, Academic Press, 2018, pp. 79–91.","mla":"Renkawitz, Jörg, et al. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” Methods in Cell Biology, vol. 147, Academic Press, 2018, pp. 79–91, doi:10.1016/bs.mcb.2018.07.004.","ista":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. 2018.Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: Methods in Cell Biology. vol. 147, 79–91.","chicago":"Renkawitz, Jörg, Anne Reversat, Alexander F Leithner, Jack Merrin, and Michael K Sixt. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” In Methods in Cell Biology, 147:79–91. Academic Press, 2018. https://doi.org/10.1016/bs.mcb.2018.07.004."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"pmid":["30165964"],"isi":["000452412300006"]},"publist_id":"7768","author":[{"first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz","orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg"},{"first_name":"Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87","last_name":"Reversat","full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928"},{"first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","last_name":"Leithner"},{"last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"title":"Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments","year":"2018","isi":1,"publication":"Methods in Cell Biology","day":"27","page":"79 - 91","date_created":"2018-12-11T11:44:54Z","doi":"10.1016/bs.mcb.2018.07.004","date_published":"2018-07-27T00:00:00Z","publisher":"Academic Press","quality_controlled":"1"},{"date_published":"2018-10-08T00:00:00Z","doi":"10.1016/j.devcel.2018.09.014","date_created":"2018-12-11T11:44:23Z","page":"3 - 19","day":"08","publication":"Developmental Cell","isi":1,"year":"2018","publisher":"Cell Press","quality_controlled":"1","acknowledgement":"Research in the Bellaïche laboratory is supported by the European Research Council (ERC Advanced, TiMoprh, 340784), the Fondation ARC pour la Recherche sur le Cancer (SL220130607097), the Agence Nationale de la Recherche (ANR lLabex DEEP; 11-LBX-0044, ANR-10-IDEX-0001-02), the Centre National de la Recherche Scientifique, the Institut National de la Santé et de la Recherche Médicale, and Institut Curie and PSL Research University funding or grants.","title":"Mechanical force-driven adherents junction remodeling and epithelial dynamics","author":[{"id":"2E839F16-F248-11E8-B48F-1D18A9856A87","first_name":"Diana C","orcid":"0000-0003-4333-7503","full_name":"Nunes Pinheiro, Diana C","last_name":"Nunes Pinheiro"},{"full_name":"Bellaïche, Yohanns","last_name":"Bellaïche","first_name":"Yohanns"}],"publist_id":"8000","external_id":{"isi":["000446579900002"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Nunes Pinheiro, Diana C, and Yohanns Bellaïche. “Mechanical Force-Driven Adherents Junction Remodeling and Epithelial Dynamics.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.09.014.","ista":"Nunes Pinheiro DC, Bellaïche Y. 2018. Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. 47(1), 3–19.","mla":"Nunes Pinheiro, Diana C., and Yohanns Bellaïche. “Mechanical Force-Driven Adherents Junction Remodeling and Epithelial Dynamics.” Developmental Cell, vol. 47, no. 1, Cell Press, 2018, pp. 3–19, doi:10.1016/j.devcel.2018.09.014.","ieee":"D. C. Nunes Pinheiro and Y. Bellaïche, “Mechanical force-driven adherents junction remodeling and epithelial dynamics,” Developmental Cell, vol. 47, no. 1. Cell Press, pp. 3–19, 2018.","short":"D.C. Nunes Pinheiro, Y. Bellaïche, Developmental Cell 47 (2018) 3–19.","apa":"Nunes Pinheiro, D. C., & Bellaïche, Y. (2018). Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.09.014","ama":"Nunes Pinheiro DC, Bellaïche Y. Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. 2018;47(1):3-19. doi:10.1016/j.devcel.2018.09.014"},"issue":"1","volume":47,"language":[{"iso":"eng"}],"publication_status":"published","month":"10","intvolume":" 47","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2018.09.014"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"During epithelial tissue development, repair, and homeostasis, adherens junctions (AJs) ensure intercellular adhesion and tissue integrity while allowing for cell and tissue dynamics. Mechanical forces play critical roles in AJs’ composition and dynamics. Recent findings highlight that beyond a well-established role in reinforcing cell-cell adhesion, AJ mechanosensitivity promotes junctional remodeling and polarization, thereby regulating critical processes such as cell intercalation, division, and collective migration. Here, we provide an integrated view of mechanosensing mechanisms that regulate cell-cell contact composition, geometry, and integrity under tension and highlight pivotal roles for mechanosensitive AJ remodeling in preserving epithelial integrity and sustaining tissue dynamics."}],"department":[{"_id":"CaHe"}],"date_updated":"2023-09-13T08:54:38Z","status":"public","article_type":"review","type":"journal_article","_id":"54"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Frick, Corina, Philip Dettinger, Jörg Renkawitz, Annaïse Jauch, Christoph Berger, Mike Recher, Timm Schroeder, and Matthias Mehling. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” PLoS One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0198330.","ista":"Frick C, Dettinger P, Renkawitz J, Jauch A, Berger C, Recher M, Schroeder T, Mehling M. 2018. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. 13(6), e0198330.","mla":"Frick, Corina, et al. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” PLoS One, vol. 13, no. 6, e0198330, Public Library of Science, 2018, doi:10.1371/journal.pone.0198330.","ama":"Frick C, Dettinger P, Renkawitz J, et al. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. 2018;13(6). doi:10.1371/journal.pone.0198330","apa":"Frick, C., Dettinger, P., Renkawitz, J., Jauch, A., Berger, C., Recher, M., … Mehling, M. (2018). Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0198330","short":"C. Frick, P. Dettinger, J. Renkawitz, A. Jauch, C. Berger, M. Recher, T. Schroeder, M. Mehling, PLoS One 13 (2018).","ieee":"C. Frick et al., “Nano-scale microfluidics to study 3D chemotaxis at the single cell level,” PLoS One, vol. 13, no. 6. Public Library of Science, 2018."},"title":"Nano-scale microfluidics to study 3D chemotaxis at the single cell level","publist_id":"7626","author":[{"full_name":"Frick, Corina","last_name":"Frick","first_name":"Corina"},{"full_name":"Dettinger, Philip","last_name":"Dettinger","first_name":"Philip"},{"full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","first_name":"Jörg"},{"first_name":"Annaïse","full_name":"Jauch, Annaïse","last_name":"Jauch"},{"last_name":"Berger","full_name":"Berger, Christoph","first_name":"Christoph"},{"first_name":"Mike","full_name":"Recher, Mike","last_name":"Recher"},{"first_name":"Timm","last_name":"Schroeder","full_name":"Schroeder, Timm"},{"last_name":"Mehling","full_name":"Mehling, Matthias","first_name":"Matthias"}],"external_id":{"isi":["000434384900031"]},"article_processing_charge":"No","article_number":"e0198330","day":"07","publication":"PLoS One","has_accepted_license":"1","isi":1,"year":"2018","doi":"10.1371/journal.pone.0198330","date_published":"2018-06-07T00:00:00Z","date_created":"2018-12-11T11:45:34Z","acknowledgement":"This work was supported by the Swiss National Science Foundation (MD-PhD fellowships, 323530_164221 to C.F.; and 323630_151483 to A.J.; grant PZ00P3_144863 to M.R, grant 31003A_156431 to T.S.; PZ00P3_148000 to C.T.B.; PZ00P3_154733 to M.M.), a Novartis “FreeNovation” grant to M.M. and T.S. and an EMBO long-term fellowship (ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409) to J.R.. M.R. was supported by the Gebert Rüf Foundation (GRS 058/14). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"ddc":["570"],"date_updated":"2023-09-13T09:00:15Z","department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:45:45Z","_id":"276","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","file_size":7682167,"date_updated":"2020-07-14T12:45:45Z","file_name":"2018_Plos_Frick.pdf","date_created":"2018-12-17T14:10:32Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5709","checksum":"95fc5dc3938b3ad3b7697d10c83cc143"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":13,"issue":"6","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Directed migration of cells relies on their ability to sense directional guidance cues and to interact with pericellular structures in order to transduce contractile cytoskeletal- into mechanical forces. These biomechanical processes depend highly on microenvironmental factors such as exposure to 2D surfaces or 3D matrices. In vivo, the majority of cells are exposed to 3D environments. Data on 3D cell migration are mostly derived from intravital microscopy or collagen-based in vitro assays. Both approaches offer only limited controlla-bility of experimental conditions. Here, we developed an automated microfluidic system that allows positioning of cells in 3D microenvironments containing highly controlled diffusion-based chemokine gradients. Tracking migration in such gradients was feasible in real time at the single cell level. Moreover, the setup allowed on-chip immunocytochemistry and thus linking of functional with phenotypical properties in individual cells. Spatially defined retrieval of cells from the device allows down-stream off-chip analysis. Using dendritic cells as a model, our setup specifically allowed us for the first time to quantitate key migration characteristics of cells exposed to identical gradients of the chemokine CCL19 yet placed on 2D vs in 3D environments. Migration properties between 2D and 3D migration were distinct. Morphological features of cells migrating in an in vitro 3D environment were similar to those of cells migrating in animal tissues, but different from cells migrating on a surface. Our system thus offers a highly controllable in vitro-mimic of a 3D environment that cells traffic in vivo."}],"month":"06","intvolume":" 13","scopus_import":"1"},{"publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2018","day":"08","publication":"Scientific Reports","doi":"10.1038/s41598-018-27080-2","date_published":"2018-06-08T00:00:00Z","date_created":"2018-12-11T11:45:36Z","article_number":"8754","citation":{"mla":"Ceinos, Rosa Maria, et al. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” Scientific Reports, vol. 8, no. 1, 8754, Nature Publishing Group, 2018, doi:10.1038/s41598-018-27080-2.","ama":"Ceinos RM, Frigato E, Pagano C, et al. Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-27080-2","apa":"Ceinos, R. M., Frigato, E., Pagano, C., Frohlich, N., Negrini, P., Cavallari, N., … Foulkes, N. S. (2018). Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-27080-2","ieee":"R. M. Ceinos et al., “Mutations in blind cavefish target the light regulated circadian clock gene period 2,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","short":"R.M. Ceinos, E. Frigato, C. Pagano, N. Frohlich, P. Negrini, N. Cavallari, D. Vallone, S. Fuselli, C. Bertolucci, N.S. Foulkes, Scientific Reports 8 (2018).","chicago":"Ceinos, Rosa Maria, Elena Frigato, Cristina Pagano, Nadine Frohlich, Pietro Negrini, Nicola Cavallari, Daniela Vallone, Silvia Fuselli, Cristiano Bertolucci, and Nicholas S Foulkes. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-27080-2.","ista":"Ceinos RM, Frigato E, Pagano C, Frohlich N, Negrini P, Cavallari N, Vallone D, Fuselli S, Bertolucci C, Foulkes NS. 2018. Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. 8(1), 8754."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Ceinos","full_name":"Ceinos, Rosa Maria","first_name":"Rosa Maria"},{"last_name":"Frigato","full_name":"Frigato, Elena","first_name":"Elena"},{"last_name":"Pagano","full_name":"Pagano, Cristina","first_name":"Cristina"},{"full_name":"Frohlich, Nadine","last_name":"Frohlich","first_name":"Nadine"},{"last_name":"Negrini","full_name":"Negrini, Pietro","first_name":"Pietro"},{"id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola","last_name":"Cavallari","full_name":"Cavallari, Nicola"},{"full_name":"Vallone, Daniela","last_name":"Vallone","first_name":"Daniela"},{"first_name":"Silvia","last_name":"Fuselli","full_name":"Fuselli, Silvia"},{"first_name":"Cristiano","last_name":"Bertolucci","full_name":"Bertolucci, Cristiano"},{"first_name":"Nicholas S","full_name":"Foulkes, Nicholas S","last_name":"Foulkes"}],"publist_id":"7616","external_id":{"isi":["000434640800008"]},"article_processing_charge":"No","title":"Mutations in blind cavefish target the light regulated circadian clock gene period 2","abstract":[{"text":"Light represents the principal signal driving circadian clock entrainment. However, how light influences the evolution of the clock remains poorly understood. The cavefish Phreatichthys andruzzii represents a fascinating model to explore how evolution under extreme aphotic conditions shapes the circadian clock, since in this species the clock is unresponsive to light. We have previously demonstrated that loss-of-function mutations targeting non-visual opsins contribute in part to this blind clock phenotype. Here, we have compared orthologs of two core clock genes that play a key role in photic entrainment, cry1a and per2, in both zebrafish and P. andruzzii. We encountered aberrantly spliced variants for the P. andruzzii per2 transcript. The most abundant transcript encodes a truncated protein lacking the C-terminal Cry binding domain and incorporating an intronic, transposon-derived coding sequence. We demonstrate that the transposon insertion leads to a predominantly cytoplasmic localization of the cavefish Per2 protein in contrast to the zebrafish ortholog which is distributed in both the nucleus and cytoplasm. Thus, it seems that during evolution in complete darkness, the photic entrainment pathway of the circadian clock has been subject to mutation at multiple levels, extending from opsin photoreceptors to nuclear effectors.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"06","intvolume":" 8","publication_status":"published","file":[{"file_id":"5707","checksum":"9c3942d772f84f3df032ffde0ed9a8ea","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-17T13:04:46Z","file_name":"2018_ScientificReports_Ceinos.pdf","date_updated":"2020-07-14T12:45:49Z","file_size":1855324,"creator":"dernst"}],"language":[{"iso":"eng"}],"issue":"1","volume":8,"_id":"283","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":"2023-09-13T08:59:27Z","ddc":["570"],"department":[{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:45:49Z"},{"project":[{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"}],"publist_id":"7973","author":[{"last_name":"Elgyütt","full_name":"Elgyütt, Adrian","first_name":"Adrian","id":"4A2E9DBA-F248-11E8-B48F-1D18A9856A87"},{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ferrere","full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"}],"external_id":{"isi":["000884993200004"]},"article_processing_charge":"No","title":"Monitoring temporal logic with clock variables","citation":{"mla":"Elgyütt, Adrian, et al. Monitoring Temporal Logic with Clock Variables. Vol. 11022, Springer, 2018, pp. 53–70, doi:10.1007/978-3-030-00151-3_4.","apa":"Elgyütt, A., Ferrere, T., & Henzinger, T. A. (2018). Monitoring temporal logic with clock variables (Vol. 11022, pp. 53–70). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_4","ama":"Elgyütt A, Ferrere T, Henzinger TA. Monitoring temporal logic with clock variables. In: Vol 11022. Springer; 2018:53-70. doi:10.1007/978-3-030-00151-3_4","short":"A. Elgyütt, T. Ferrere, T.A. Henzinger, in:, Springer, 2018, pp. 53–70.","ieee":"A. Elgyütt, T. Ferrere, and T. A. Henzinger, “Monitoring temporal logic with clock variables,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China, 2018, vol. 11022, pp. 53–70.","chicago":"Elgyütt, Adrian, Thomas Ferrere, and Thomas A Henzinger. “Monitoring Temporal Logic with Clock Variables,” 11022:53–70. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_4.","ista":"Elgyütt A, Ferrere T, Henzinger TA. 2018. Monitoring temporal logic with clock variables. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 53–70."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer","quality_controlled":"1","oa":1,"page":"53 - 70","date_published":"2018-08-26T00:00:00Z","doi":"10.1007/978-3-030-00151-3_4","date_created":"2018-12-11T11:44:31Z","has_accepted_license":"1","isi":1,"year":"2018","day":"26","type":"conference","conference":{"start_date":"2018-09-04","end_date":"2018-09-06","location":"Beijing, China","name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"status":"public","_id":"81","department":[{"_id":"ToHe"}],"file_date_updated":"2020-10-09T06:24:21Z","date_updated":"2023-09-13T08:58:34Z","ddc":["000"],"scopus_import":"1","alternative_title":["LNCS"],"month":"08","intvolume":" 11022","abstract":[{"text":"We solve the offline monitoring problem for timed propositional temporal logic (TPTL), interpreted over dense-time Boolean signals. The variant of TPTL we consider extends linear temporal logic (LTL) with clock variables and reset quantifiers, providing a mechanism to specify real-time constraints. We first describe a general monitoring algorithm based on an exhaustive computation of the set of satisfying clock assignments as a finite union of zones. We then propose a specialized monitoring algorithm for the one-variable case using a partition of the time domain based on the notion of region equivalence, whose complexity is linear in the length of the signal, thereby generalizing a known result regarding the monitoring of metric temporal logic (MTL). The region and zone representations of time constraints are known from timed automata verification and can also be used in the discrete-time case. Our prototype implementation appears to outperform previous discrete-time implementations of TPTL monitoring,","lang":"eng"}],"oa_version":"Submitted Version","volume":11022,"publication_status":"published","file":[{"date_created":"2020-10-09T06:24:21Z","file_name":"2018_LNCS_Elgyuett.pdf","creator":"dernst","date_updated":"2020-10-09T06:24:21Z","file_size":537219,"file_id":"8638","checksum":"e5d81c9b50a6bd9d8a2c16953aad7e23","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}]},{"department":[{"_id":"DaAl"}],"file_date_updated":"2020-07-14T12:48:01Z","date_updated":"2023-09-13T09:01:06Z","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","status":"public","_id":"76","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-17T14:21:22Z","file_name":"2018_DistributedComputing_Lenzen.pdf","date_updated":"2020-07-14T12:48:01Z","file_size":799337,"creator":"dernst","checksum":"872db70bba9b401500abe3c6ae2f1a61","file_id":"5711","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"scopus_import":"1","month":"09","abstract":[{"text":"Consider a fully-connected synchronous distributed system consisting of n nodes, where up to f nodes may be faulty and every node starts in an arbitrary initial state. In the synchronous C-counting problem, all nodes need to eventually agree on a counter that is increased by one modulo C in each round for given C>1. In the self-stabilising firing squad problem, the task is to eventually guarantee that all non-faulty nodes have simultaneous responses to external inputs: if a subset of the correct nodes receive an external “go” signal as input, then all correct nodes should agree on a round (in the not-too-distant future) in which to jointly output a “fire” signal. Moreover, no node should generate a “fire” signal without some correct node having previously received a “go” signal as input. We present a framework reducing both tasks to binary consensus at very small cost. For example, we obtain a deterministic algorithm for self-stabilising Byzantine firing squads with optimal resilience f<n/3, asymptotically optimal stabilisation and response time O(f), and message size O(log f). As our framework does not restrict the type of consensus routines used, we also obtain efficient randomised solutions.","lang":"eng"}],"oa_version":"Published Version","external_id":{"isi":["000475627800005"]},"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Lenzen, Christoph","last_name":"Lenzen","first_name":"Christoph"},{"orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel"}],"publist_id":"7978","title":"Near-optimal self-stabilising counting and firing squads","citation":{"ieee":"C. Lenzen and J. Rybicki, “Near-optimal self-stabilising counting and firing squads,” Distributed Computing. Springer, 2018.","short":"C. Lenzen, J. Rybicki, Distributed Computing (2018).","ama":"Lenzen C, Rybicki J. Near-optimal self-stabilising counting and firing squads. Distributed Computing. 2018. doi:10.1007/s00446-018-0342-6","apa":"Lenzen, C., & Rybicki, J. (2018). Near-optimal self-stabilising counting and firing squads. Distributed Computing. Springer. https://doi.org/10.1007/s00446-018-0342-6","mla":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing, Springer, 2018, doi:10.1007/s00446-018-0342-6.","ista":"Lenzen C, Rybicki J. 2018. Near-optimal self-stabilising counting and firing squads. Distributed Computing.","chicago":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-018-0342-6."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"date_created":"2018-12-11T11:44:30Z","doi":"10.1007/s00446-018-0342-6","date_published":"2018-09-12T00:00:00Z","year":"2018","has_accepted_license":"1","isi":1,"publication":"Distributed Computing","day":"12","oa":1,"publisher":"Springer","quality_controlled":"1"},{"publication":"Computational Geometry: Theory and Applications","day":"01","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:46:59Z","date_published":"2018-03-01T00:00:00Z","doi":"10.1016/j.comgeo.2017.06.014","page":"119 - 133","oa":1,"publisher":"Elsevier","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Edelsbrunner H, Iglesias Ham M. 2018. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 68, 119–133.","chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications. Elsevier, 2018. https://doi.org/10.1016/j.comgeo.2017.06.014.","apa":"Edelsbrunner, H., & Iglesias Ham, M. (2018). Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2017.06.014","ama":"Edelsbrunner H, Iglesias Ham M. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 2018;68:119-133. doi:10.1016/j.comgeo.2017.06.014","short":"H. Edelsbrunner, M. Iglesias Ham, Computational Geometry: Theory and Applications 68 (2018) 119–133.","ieee":"H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls I: Inclusion–exclusion,” Computational Geometry: Theory and Applications, vol. 68. Elsevier, pp. 119–133, 2018.","mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications, vol. 68, Elsevier, 2018, pp. 119–33, doi:10.1016/j.comgeo.2017.06.014."},"title":"Multiple covers with balls I: Inclusion–exclusion","article_processing_charge":"No","external_id":{"isi":["000415778300010"]},"publist_id":"7289","author":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"first_name":"Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","full_name":"Iglesias Ham, Mabel","last_name":"Iglesias Ham"}],"project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"318493","name":"Topological Complex Systems"}],"language":[{"iso":"eng"}],"file":[{"file_id":"5953","checksum":"1c8d58cd489a66cd3e2064c1141c8c5e","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_Edelsbrunner.pdf","date_created":"2019-02-12T06:47:52Z","file_size":708357,"date_updated":"2020-07-14T12:46:38Z","creator":"dernst"}],"publication_status":"published","ec_funded":1,"volume":68,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Inclusion–exclusion is an effective method for computing the volume of a union of measurable sets. We extend it to multiple coverings, proving short inclusion–exclusion formulas for the subset of Rn covered by at least k balls in a finite set. We implement two of the formulas in dimension n=3 and report on results obtained with our software."}],"intvolume":" 68","month":"03","scopus_import":"1","ddc":["000"],"date_updated":"2023-09-13T08:59:00Z","department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:46:38Z","_id":"530","status":"public","type":"journal_article"},{"acknowledgement":"The work was partially supported by Russian Foundation for Basic Research (Grant No. 15-02-05657a) and by the Basic research program of Higher School of Economics (HSE).","publisher":"American Physical Society","quality_controlled":"1","oa":1,"day":"09","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","isi":1,"year":"2018","doi":"10.1103/PhysRevA.97.043812","date_published":"2018-04-09T00:00:00Z","date_created":"2018-12-11T11:45:44Z","article_number":" 043812 ","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"E. Redchenko, A. Makarov, and V. Yudson, “Nanoscopy of pairs of atoms by fluorescence in a magnetic field,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4. American Physical Society, 2018.","short":"E. Redchenko, A. Makarov, V. Yudson, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","ama":"Redchenko E, Makarov A, Yudson V. Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(4). doi:10.1103/PhysRevA.97.043812","apa":"Redchenko, E., Makarov, A., & Yudson, V. (2018). Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.043812","mla":"Redchenko, Elena, et al. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4, 043812, American Physical Society, 2018, doi:10.1103/PhysRevA.97.043812.","ista":"Redchenko E, Makarov A, Yudson V. 2018. Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. 97(4), 043812.","chicago":"Redchenko, Elena, Alexander Makarov, and Vladimir Yudson. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.043812."},"title":"Nanoscopy of pairs of atoms by fluorescence in a magnetic field","author":[{"first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena","last_name":"Redchenko"},{"first_name":"Alexander","last_name":"Makarov","full_name":"Makarov, Alexander"},{"first_name":"Vladimir","last_name":"Yudson","full_name":"Yudson, Vladimir"}],"publist_id":"7572","external_id":{"arxiv":["1712.10127"],"isi":["000429454000015"]},"article_processing_charge":"No","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Spontaneous emission spectra of two initially excited closely spaced identical atoms are very sensitive to the strength and the direction of the applied magnetic field. We consider the relevant schemes that ensure the determination of the mutual spatial orientation of the atoms and the distance between them by entirely optical means. A corresponding theoretical description is given accounting for the dipole-dipole interaction between the two atoms in the presence of a magnetic field and for polarizations of the quantum field interacting with magnetic sublevels of the two-atom system. "}],"month":"04","intvolume":" 97","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.10127"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"4","volume":97,"_id":"307","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-09-13T09:00:41Z","department":[{"_id":"JoFi"}]},{"article_number":"67","project":[{"_id":"26120F5C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"335980","name":"Systematic investigation of epistasis in molecular evolution"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 19, 67.","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology. BioMed Central, 2018. https://doi.org/10.1186/s13059-018-1434-0.","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” Genome Biology, vol. 19. BioMed Central, 2018.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018).","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 2018;19. doi:10.1186/s13059-018-1434-0","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1434-0","mla":"Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology, vol. 19, 67, BioMed Central, 2018, doi:10.1186/s13059-018-1434-0."},"title":"Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","author":[{"full_name":"Zapata, Luis","last_name":"Zapata","first_name":"Luis"},{"first_name":"Oriol","full_name":"Pich, Oriol","last_name":"Pich"},{"full_name":"Serrano, Luis","last_name":"Serrano","first_name":"Luis"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"last_name":"Ossowski","full_name":"Ossowski, Stephan","first_name":"Stephan"},{"first_name":"Martin","last_name":"Schaefer","full_name":"Schaefer, Martin"}],"publist_id":"7620","external_id":{"isi":["000433986200001"]},"article_processing_charge":"No","publisher":"BioMed Central","quality_controlled":"1","oa":1,"day":"31","publication":"Genome Biology","isi":1,"has_accepted_license":"1","year":"2018","doi":"10.1186/s13059-018-1434-0","date_published":"2018-05-31T00:00:00Z","date_created":"2018-12-11T11:45:35Z","_id":"279","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":"2023-09-13T09:01:32Z","file_date_updated":"2020-07-14T12:45:47Z","department":[{"_id":"FyKo"}],"oa_version":"Published Version","abstract":[{"text":"Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions: In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments.","lang":"eng"}],"month":"05","intvolume":" 19","scopus_import":"1","file":[{"file_id":"5708","checksum":"f3e4922486bd9bf1483271bdbed394a7","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-17T14:05:01Z","file_name":"2018_GenomeBiology_Zapata.pdf","creator":"dernst","date_updated":"2020-07-14T12:45:47Z","file_size":1414722}],"language":[{"iso":"eng"}],"publication_status":"published","volume":19,"related_material":{"record":[{"id":"9811","status":"public","relation":"research_data"},{"status":"public","id":"9812","relation":"research_data"}]},"ec_funded":1},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"S.M. Truckenbrodt, A. Viplav, S. Jähne, A. Vogts, A. Denker, H. Wildhagen, E. Fornasiero, S. Rizzoli, The EMBO Journal 37 (2018).","ieee":"S. M. Truckenbrodt et al., “Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission,” The EMBO Journal, vol. 37, no. 15. Wiley, 2018.","apa":"Truckenbrodt, S. M., Viplav, A., Jähne, S., Vogts, A., Denker, A., Wildhagen, H., … Rizzoli, S. (2018). Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. Wiley. https://doi.org/10.15252/embj.201798044","ama":"Truckenbrodt SM, Viplav A, Jähne S, et al. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 2018;37(15). doi:10.15252/embj.201798044","mla":"Truckenbrodt, Sven M., et al. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” The EMBO Journal, vol. 37, no. 15, e98044, Wiley, 2018, doi:10.15252/embj.201798044.","ista":"Truckenbrodt SM, Viplav A, Jähne S, Vogts A, Denker A, Wildhagen H, Fornasiero E, Rizzoli S. 2018. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 37(15), e98044.","chicago":"Truckenbrodt, Sven M, Abhiyan Viplav, Sebsatian Jähne, Angela Vogts, Annette Denker, Hanna Wildhagen, Eugenio Fornasiero, and Silvio Rizzoli. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” The EMBO Journal. Wiley, 2018. https://doi.org/10.15252/embj.201798044."},"title":"Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission","external_id":{"isi":["000440416900005"],"pmid":["29950309"]},"article_processing_charge":"No","author":[{"full_name":"Truckenbrodt, Sven M","last_name":"Truckenbrodt","first_name":"Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Abhiyan","full_name":"Viplav, Abhiyan","last_name":"Viplav"},{"last_name":"Jähne","full_name":"Jähne, Sebsatian","first_name":"Sebsatian"},{"last_name":"Vogts","full_name":"Vogts, Angela","first_name":"Angela"},{"first_name":"Annette","last_name":"Denker","full_name":"Denker, Annette"},{"full_name":"Wildhagen, Hanna","last_name":"Wildhagen","first_name":"Hanna"},{"first_name":"Eugenio","last_name":"Fornasiero","full_name":"Fornasiero, Eugenio"},{"first_name":"Silvio","last_name":"Rizzoli","full_name":"Rizzoli, Silvio"}],"publist_id":"7778","article_number":"e98044","publication":"The EMBO Journal","day":"01","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:44:52Z","doi":"10.15252/embj.201798044","date_published":"2018-08-01T00:00:00Z","acknowledgement":"We thank Reinhard Jahn for providing a plasmid for YFP-SNAP25. We thank Erwin Neher for help with the development of the mathematical model of the synaptic vesicle life cycle. We thank Martin Meschkat, Andreas Höbartner, Annedore Punge, and Peer Hoopmann for help with the experiments. We thank Burkhard Rammner for providing the illustrations of synaptic vesicle and protein dynamics. We thank Manuel Maidorn, Martin Helm, and Katharina N. Richter for critically reading the manuscript. S.T. was supported by an Excellence Stipend of the Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (GGNB). E.F.F. is a recipient of long-term fellowships from the European Molecular Biology Organization (ALTF_797-2012) and from the Human Frontier Science Program (HFSP_LT000830/2013). The work was supported by grants to S.O.R. from the European Research Council (ERC-2013-CoG NeuroMolAnatomy) and from the Deutsche Forschungsgemeinschaft (Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, SFB1190/P09, SFB889/A05, and SFB1286/A03, and DFG RI 1967 7/1). The nanoSIMS instrument was funded by the German Federal Ministry of Education and Research (03F0626A).","oa":1,"quality_controlled":"1","publisher":"Wiley","ddc":["570"],"date_updated":"2023-09-13T09:02:48Z","file_date_updated":"2020-07-14T12:44:56Z","department":[{"_id":"JoDa"}],"_id":"145","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","language":[{"iso":"eng"}],"file":[{"file_name":"2018_EMBO_Truckenbrodt.pdf","date_created":"2018-12-17T14:17:29Z","file_size":2846470,"date_updated":"2020-07-14T12:44:56Z","creator":"dernst","file_id":"5710","checksum":"a540feb6c9af6aefc78de531461a8835","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"issn":["0261-4189"]},"issue":"15","volume":37,"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Aged proteins can become hazardous to cellular function, by accumulating molecular damage. This implies that cells should preferentially rely on newly produced ones. We tested this hypothesis in cultured hippocampal neurons, focusing on synaptic transmission. We found that newly synthesized vesicle proteins were incorporated in the actively recycling pool of vesicles responsible for all neurotransmitter release during physiological activity. We observed this for the calcium sensor Synaptotagmin 1, for the neurotransmitter transporter VGAT, and for the fusion protein VAMP2 (Synaptobrevin 2). Metabolic labeling of proteins and visualization by secondary ion mass spectrometry enabled us to query the entire protein makeup of the actively recycling vesicles, which we found to be younger than that of non-recycling vesicles. The young vesicle proteins remained in use for up to ~ 24 h, during which they participated in recycling a few hundred times. They were afterward reluctant to release and were degraded after an additional ~ 24–48 h. We suggest that the recycling pool of synaptic vesicles relies on newly synthesized proteins, while the inactive reserve pool contains older proteins."}],"intvolume":" 37","month":"08","scopus_import":"1"},{"file_date_updated":"2020-07-14T12:46:32Z","department":[{"_id":"JiFr"}],"date_updated":"2023-09-13T09:03:18Z","ddc":["580"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","_id":"462","volume":41,"license":"https://creativecommons.org/licenses/by-nc/4.0/","publication_status":"published","file":[{"checksum":"6a20f843565f962cb20281cdf5e40914","file_id":"7042","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_PlantCellEnv_Fan.pdf","date_created":"2019-11-18T16:22:22Z","file_size":1937976,"date_updated":"2020-07-14T12:46:32Z","creator":"dernst"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 41","abstract":[{"text":"AtNHX5 and AtNHX6 are endosomal Na+,K+/H+ antiporters that are critical for growth and development in Arabidopsis, but the mechanism behind their action remains unknown. Here, we report that AtNHX5 and AtNHX6, functioning as H+ leak, control auxin homeostasis and auxin-mediated development. We found that nhx5 nhx6 exhibited growth variations of auxin-related defects. We further showed that nhx5 nhx6 was affected in auxin homeostasis. Genetic analysis showed that AtNHX5 and AtNHX6 were required for the function of the ER-localized auxin transporter PIN5. Although AtNHX5 and AtNHX6 were co-localized with PIN5 at ER, they did not interact directly. Instead, the conserved acidic residues in AtNHX5 and AtNHX6, which are essential for exchange activity, were required for PIN5 function. AtNHX5 and AtNHX6 regulated the pH in ER. Overall, AtNHX5 and AtNHX6 may regulate auxin transport across the ER via the pH gradient created by their transport activity. H+-leak pathway provides a fine-tuning mechanism that controls cellular auxin fluxes. ","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","author":[{"last_name":"Fan","full_name":"Fan, Ligang","first_name":"Ligang"},{"first_name":"Lei","full_name":"Zhao, Lei","last_name":"Zhao"},{"full_name":"Hu, Wei","last_name":"Hu","first_name":"Wei"},{"last_name":"Li","full_name":"Li, Weina","first_name":"Weina"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"full_name":"Strnad, Miroslav","last_name":"Strnad","first_name":"Miroslav"},{"last_name":"Simon","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"first_name":"Jinbo","last_name":"Shen","full_name":"Shen, Jinbo"},{"first_name":"Liwen","last_name":"Jiang","full_name":"Jiang, Liwen"},{"full_name":"Qiu, Quan","last_name":"Qiu","first_name":"Quan"}],"publist_id":"7359","external_id":{"pmid":["29360148"],"isi":["000426870500012"]},"article_processing_charge":"No","title":"NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development","citation":{"ista":"Fan L, Zhao L, Hu W, Li W, Novák O, Strnad M, Simon S, Friml J, Shen J, Jiang L, Qiu Q. 2018. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 41, 850–864.","chicago":"Fan, Ligang, Lei Zhao, Wei Hu, Weina Li, Ondřej Novák, Miroslav Strnad, Sibu Simon, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment. Wiley-Blackwell, 2018. https://doi.org/10.1111/pce.13153.","ama":"Fan L, Zhao L, Hu W, et al. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 2018;41:850-864. doi:10.1111/pce.13153","apa":"Fan, L., Zhao, L., Hu, W., Li, W., Novák, O., Strnad, M., … Qiu, Q. (2018). NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. Wiley-Blackwell. https://doi.org/10.1111/pce.13153","short":"L. Fan, L. Zhao, W. Hu, W. Li, O. Novák, M. Strnad, S. Simon, J. Friml, J. Shen, L. Jiang, Q. Qiu, Plant, Cell and Environment 41 (2018) 850–864.","ieee":"L. Fan et al., “NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development,” Plant, Cell and Environment, vol. 41. Wiley-Blackwell, pp. 850–864, 2018.","mla":"Fan, Ligang, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment, vol. 41, Wiley-Blackwell, 2018, pp. 850–64, doi:10.1111/pce.13153."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"850 - 864","date_published":"2018-05-01T00:00:00Z","doi":"10.1111/pce.13153","date_created":"2018-12-11T11:46:36Z","has_accepted_license":"1","isi":1,"year":"2018","day":"01","publication":"Plant, Cell and Environment","publisher":"Wiley-Blackwell","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by the National Natural Science Foundation of China (31571464, 31371438 and 31070222 to Q.S.Q.), the National Basic Research Program of China (973 project, 2013CB429904 to Q.S.Q.), the Research Fund for the Doctoral Program of Higher Education of China (20130211110001 to Q.S.Q.), the Ministry of Education, Youth and Sports of the Czech Republic (the National Program for Sustainability I, LO1204), and The Czech Science Foundation GAČR (GA13–40637S) to JF. We thank Dr. Tom J. Guilfoyle for DR5::GUS line and Dr. Jia Li for pBIB‐RFP vector and DR5::GFP line. We thank Liping Guan and Yang Zhao for their help with the confocal microscope assay. "},{"day":"15","publication":"Journal of Magnetism and Magnetic Materials","has_accepted_license":"1","isi":1,"year":"2018","doi":"10.1016/j.jmmm.2017.12.073","date_published":"2018-04-15T00:00:00Z","date_created":"2018-12-11T11:46:56Z","page":"427 - 441","acknowledgement":"S.Altmeyer is a Serra Húnter Fellow","publisher":"Elsevier","quality_controlled":"1","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Altmeyer S. 2018. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 452, 427–441.","chicago":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials. Elsevier, 2018. https://doi.org/10.1016/j.jmmm.2017.12.073.","ieee":"S. Altmeyer, “Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow,” Journal of Magnetism and Magnetic Materials, vol. 452. Elsevier, pp. 427–441, 2018.","short":"S. Altmeyer, Journal of Magnetism and Magnetic Materials 452 (2018) 427–441.","ama":"Altmeyer S. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 2018;452:427-441. doi:10.1016/j.jmmm.2017.12.073","apa":"Altmeyer, S. (2018). Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. Elsevier. https://doi.org/10.1016/j.jmmm.2017.12.073","mla":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials, vol. 452, Elsevier, 2018, pp. 427–41, doi:10.1016/j.jmmm.2017.12.073."},"title":"Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow","publist_id":"7297","author":[{"orcid":"0000-0001-5964-0203","full_name":"Altmeyer, Sebastian","last_name":"Altmeyer","first_name":"Sebastian","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000425547700061"]},"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"431f5cd4a628d7ca21161f82b14ccb4f","file_id":"7838","date_updated":"2020-07-14T12:46:37Z","file_size":17309535,"creator":"dernst","date_created":"2020-05-14T14:41:17Z","file_name":"2018_Magnetism_Altmeyer.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":452,"oa_version":"Submitted Version","abstract":[{"text":"This study treats with the influence of a symmetry-breaking transversal magnetic field on the nonlinear dynamics of ferrofluidic Taylor-Couette flow – flow confined between two concentric independently rotating cylinders. We detected alternating ‘flip’ solutions which are flow states featuring typical characteristics of slow-fast-dynamics in dynamical systems. The flip corresponds to a temporal change in the axial wavenumber and we find them to appear either as pure 2-fold axisymmetric (due to the symmetry-breaking nature of the applied transversal magnetic field) or involving non-axisymmetric, helical modes in its interim solution. The latter ones show features of typical ribbon solutions. In any case the flip solutions have a preferential first axial wavenumber which corresponds to the more stable state (slow dynamics) and second axial wavenumber, corresponding to the short appearing more unstable state (fast dynamics). However, in both cases the flip time grows exponential with increasing the magnetic field strength before the flip solutions, living on 2-tori invariant manifolds, cease to exist, with lifetime going to infinity. Further we show that ferrofluidic flow turbulence differ from the classical, ordinary (usually at high Reynolds number) turbulence. The applied magnetic field hinders the free motion of ferrofluid partials and therefore smoothen typical turbulent quantities and features so that speaking of mildly chaotic dynamics seems to be a more appropriate expression for the observed motion. ","lang":"eng"}],"month":"04","intvolume":" 452","scopus_import":"1","ddc":["530"],"date_updated":"2023-09-13T09:03:44Z","department":[{"_id":"BjHo"}],"file_date_updated":"2020-07-14T12:46:37Z","_id":"519","status":"public","type":"journal_article","article_type":"original"},{"date_updated":"2023-09-13T09:02:22Z","department":[{"_id":"KrCh"}],"_id":"5679","conference":{"name":"16th Asian Symposium on Programming Languages and Systems, APLAS","start_date":"2018-12-02","end_date":"2018-12-06","location":"Wellington, New Zealand"},"type":"conference","status":"public","publication_identifier":{"isbn":["9783030027674"],"issn":["03029743"]},"language":[{"iso":"eng"}],"volume":11275,"abstract":[{"text":"We study the almost-sure termination problem for probabilistic programs. First, we show that supermartingales with lower bounds on conditional absolute difference provide a sound approach for the almost-sure termination problem. Moreover, using this approach we can obtain explicit optimal bounds on tail probabilities of non-termination within a given number of steps. Second, we present a new approach based on Central Limit Theorem for the almost-sure termination problem, and show that this approach can establish almost-sure termination of programs which none of the existing approaches can handle. Finally, we discuss algorithmic approaches for the two above methods that lead to automated analysis techniques for almost-sure termination of probabilistic programs.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1806.06683"}],"scopus_import":"1","alternative_title":["LNCS"],"intvolume":" 11275","month":"12","citation":{"mla":"Huang, Mingzhang, et al. New Approaches for Almost-Sure Termination of Probabilistic Programs. Edited by Sukyoung Ryu, vol. 11275, Springer, 2018, pp. 181–201, doi:10.1007/978-3-030-02768-1_11.","ama":"Huang M, Fu H, Chatterjee K. New approaches for almost-sure termination of probabilistic programs. In: Ryu S, ed. Vol 11275. Springer; 2018:181-201. doi:10.1007/978-3-030-02768-1_11","apa":"Huang, M., Fu, H., & Chatterjee, K. (2018). New approaches for almost-sure termination of probabilistic programs. In S. Ryu (Ed.) (Vol. 11275, pp. 181–201). Presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand: Springer. https://doi.org/10.1007/978-3-030-02768-1_11","ieee":"M. Huang, H. Fu, and K. Chatterjee, “New approaches for almost-sure termination of probabilistic programs,” presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand, 2018, vol. 11275, pp. 181–201.","short":"M. Huang, H. Fu, K. Chatterjee, in:, S. Ryu (Ed.), Springer, 2018, pp. 181–201.","chicago":"Huang, Mingzhang, Hongfei Fu, and Krishnendu Chatterjee. “New Approaches for Almost-Sure Termination of Probabilistic Programs.” edited by Sukyoung Ryu, 11275:181–201. Springer, 2018. https://doi.org/10.1007/978-3-030-02768-1_11.","ista":"Huang M, Fu H, Chatterjee K. 2018. New approaches for almost-sure termination of probabilistic programs. 16th Asian Symposium on Programming Languages and Systems, APLAS, LNCS, vol. 11275, 181–201."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000916310900011"],"arxiv":["1806.06683"]},"article_processing_charge":"No","author":[{"first_name":"Mingzhang","last_name":"Huang","full_name":"Huang, Mingzhang"},{"first_name":"Hongfei","full_name":"Fu, Hongfei","last_name":"Fu"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"title":"New approaches for almost-sure termination of probabilistic programs","editor":[{"first_name":"Sukyoung","last_name":"Ryu","full_name":"Ryu, Sukyoung"}],"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"year":"2018","isi":1,"day":"01","page":"181-201","date_created":"2018-12-16T22:59:20Z","doi":"10.1007/978-3-030-02768-1_11","date_published":"2018-12-01T00:00:00Z","oa":1,"publisher":"Springer","quality_controlled":"1"},{"publisher":"Elsevier","quality_controlled":"1","year":"2018","isi":1,"publication":"Current Opinion in Neurobiology","day":"01","page":"131 - 138","date_created":"2018-12-11T11:47:06Z","date_published":"2018-02-01T00:00:00Z","doi":"10.1016/j.conb.2017.12.005","citation":{"chicago":"Sacco, Roberto, Emanuele Cacci, and Gaia Novarino. “Neural Stem Cells in Neuropsychiatric Disorders.” Current Opinion in Neurobiology. Elsevier, 2018. https://doi.org/10.1016/j.conb.2017.12.005.","ista":"Sacco R, Cacci E, Novarino G. 2018. Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. 48(2), 131–138.","mla":"Sacco, Roberto, et al. “Neural Stem Cells in Neuropsychiatric Disorders.” Current Opinion in Neurobiology, vol. 48, no. 2, Elsevier, 2018, pp. 131–38, doi:10.1016/j.conb.2017.12.005.","short":"R. Sacco, E. Cacci, G. Novarino, Current Opinion in Neurobiology 48 (2018) 131–138.","ieee":"R. Sacco, E. Cacci, and G. Novarino, “Neural stem cells in neuropsychiatric disorders,” Current Opinion in Neurobiology, vol. 48, no. 2. Elsevier, pp. 131–138, 2018.","ama":"Sacco R, Cacci E, Novarino G. Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. 2018;48(2):131-138. doi:10.1016/j.conb.2017.12.005","apa":"Sacco, R., Cacci, E., & Novarino, G. (2018). Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2017.12.005"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000427101600018"]},"author":[{"full_name":"Sacco, Roberto","last_name":"Sacco","first_name":"Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cacci","full_name":"Cacci, Emanuele","first_name":"Emanuele"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino"}],"publist_id":"7268","title":"Neural stem cells in neuropsychiatric disorders","abstract":[{"text":"The precise control of neural stem cell (NSC) proliferation and differentiation is crucial for the development and function of the human brain. Here, we review the emerging links between the alteration of embryonic and adult neurogenesis and the etiology of neuropsychiatric disorders (NPDs) such as autism spectrum disorders (ASDs) and schizophrenia (SCZ), as well as the advances in stem cell-based modeling and the novel therapeutic targets derived from these studies.","lang":"eng"}],"oa_version":"None","scopus_import":"1","intvolume":" 48","month":"02","publication_status":"published","language":[{"iso":"eng"}],"issue":"2","volume":48,"_id":"546","type":"journal_article","status":"public","date_updated":"2023-09-13T09:01:56Z","department":[{"_id":"GaNo"}]},{"day":"31","year":"2018","related_material":{"record":[{"id":"279","status":"public","relation":"used_in_publication"}]},"doi":"10.6084/m9.figshare.6401414.v1","date_published":"2018-05-31T00:00:00Z","date_created":"2021-08-06T12:58:25Z","oa_version":"Published Version","abstract":[{"text":"This document contains the full list of genes with their respective significance and dN/dS values. (TXT 4499Â kb)","lang":"eng"}],"month":"05","publisher":"Springer Nature","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.6401414.v1","open_access":"1"}],"oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-13T09:01:31Z","citation":{"ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401414.v1.","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401414.v1.","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401414.v1","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401414.v1","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","mla":"Zapata, Luis, et al. Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401414.v1."},"department":[{"_id":"FyKo"}],"title":"Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","author":[{"first_name":"Luis","last_name":"Zapata","full_name":"Zapata, Luis"},{"first_name":"Oriol","last_name":"Pich","full_name":"Pich, Oriol"},{"first_name":"Luis","full_name":"Serrano, Luis","last_name":"Serrano"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"},{"full_name":"Ossowski, Stephan","last_name":"Ossowski","first_name":"Stephan"},{"last_name":"Schaefer","full_name":"Schaefer, Martin","first_name":"Martin"}],"article_processing_charge":"No","_id":"9812","status":"public","type":"research_data_reference"}]