[{"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","issue":"5","volume":80,"ec_funded":1,"publication_status":"published","file":[{"file_size":691245,"date_updated":"2020-07-14T12:47:54Z","creator":"system","file_name":"IST-2018-1014-v1+1_2018_Paixao_Escape.pdf","date_created":"2018-12-12T10:08:14Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4674","checksum":"7d92f5d7be81e387edeec4f06442791c"}],"language":[{"iso":"eng"}],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"1014","_id":"723","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:47:54Z","date_updated":"2023-09-11T14:11:35Z","ddc":["576"],"publisher":"Springer","quality_controlled":"1","oa":1,"page":"1604 - 1633","doi":"10.1007/s00453-017-0369-2","date_published":"2018-05-01T00:00:00Z","date_created":"2018-12-11T11:48:09Z","has_accepted_license":"1","isi":1,"year":"2018","day":"01","publication":"Algorithmica","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publist_id":"6957","author":[{"full_name":"Oliveto, Pietro","last_name":"Oliveto","first_name":"Pietro"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","last_name":"Paixao"},{"last_name":"Pérez Heredia","full_name":"Pérez Heredia, Jorge","first_name":"Jorge"},{"last_name":"Sudholt","full_name":"Sudholt, Dirk","first_name":"Dirk"},{"last_name":"Trubenova","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","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":{"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.","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.","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","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"volume":40,"issue":"5","language":[{"iso":"eng"}],"file":[{"checksum":"b19c75da06faf3291a3ca47dfa50ef63","file_id":"7835","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_IEEE_Darrell.pdf","date_created":"2020-05-14T12:50:48Z","creator":"dernst","file_size":141724,"date_updated":"2020-07-14T12:46:03Z"}],"publication_status":"published","intvolume":" 40","month":"05","scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:03Z","department":[{"_id":"ChLa"}],"ddc":["000"],"date_updated":"2023-09-11T14:07:54Z","status":"public","type":"journal_article","article_type":"original","_id":"321","date_created":"2018-12-11T11:45:48Z","doi":"10.1109/TPAMI.2018.2804998","date_published":"2018-05-01T00:00:00Z","page":"1029 - 1031","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","day":"01","year":"2018","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"IEEE","title":"Guest editors' introduction to the special section on learning with Shared information for computer vision and multimedia analysis","external_id":{"isi":["000428901200001"]},"article_processing_charge":"No","publist_id":"7544","author":[{"first_name":"Trevor","full_name":"Darrell, Trevor","last_name":"Darrell"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"},{"first_name":"Nico","full_name":"Sebe, Nico","last_name":"Sebe"},{"last_name":"Wu","full_name":"Wu, Ying","first_name":"Ying"},{"last_name":"Yan","full_name":"Yan, Yan","first_name":"Yan"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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."}},{"day":"12","year":"2018","related_material":{"record":[{"id":"448","status":"public","relation":"used_in_publication"}]},"date_published":"2018-12-12T00:00:00Z","doi":"10.5061/dryad.51d4r","date_created":"2021-08-09T13:13:48Z","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","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.51d4r"}],"oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-11T14:10:56Z","citation":{"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.","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.","mla":"Harrison, Mark C., et al. Data from: Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality. Dryad, 2018, doi:10.5061/dryad.51d4r.","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).","ieee":"M. C. Harrison et al., “Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality.” Dryad, 2018.","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","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"},"title":"Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality","department":[{"_id":"BeVi"}],"author":[{"first_name":"Mark C.","full_name":"Harrison, Mark C.","last_name":"Harrison"},{"full_name":"Jongepier, Evelien","last_name":"Jongepier","first_name":"Evelien"},{"last_name":"Robertson","full_name":"Robertson, Hugh M.","first_name":"Hugh M."},{"first_name":"Nicolas","last_name":"Arning","full_name":"Arning, Nicolas"},{"full_name":"Bitard-Feildel, Tristan","last_name":"Bitard-Feildel","first_name":"Tristan"},{"last_name":"Chao","full_name":"Chao, Hsu","first_name":"Hsu"},{"full_name":"Childers, Christopher P.","last_name":"Childers","first_name":"Christopher P."},{"last_name":"Dinh","full_name":"Dinh, Huyen","first_name":"Huyen"},{"last_name":"Doddapaneni","full_name":"Doddapaneni, Harshavardhan","first_name":"Harshavardhan"},{"first_name":"Shannon","last_name":"Dugan","full_name":"Dugan, Shannon"},{"last_name":"Gowin","full_name":"Gowin, Johannes","first_name":"Johannes"},{"last_name":"Greiner","full_name":"Greiner, Carolin","first_name":"Carolin"},{"first_name":"Yi","last_name":"Han","full_name":"Han, Yi"},{"first_name":"Haofu","last_name":"Hu","full_name":"Hu, Haofu"},{"first_name":"Daniel S. T.","last_name":"Hughes","full_name":"Hughes, Daniel S. T."},{"first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K","last_name":"Huylmans"},{"last_name":"Kemena","full_name":"Kemena, Carsten","first_name":"Carsten"},{"full_name":"Kremer, Lukas P. M.","last_name":"Kremer","first_name":"Lukas P. M."},{"full_name":"Lee, Sandra L.","last_name":"Lee","first_name":"Sandra L."},{"first_name":"Alberto","full_name":"Lopez-Ezquerra, Alberto","last_name":"Lopez-Ezquerra"},{"last_name":"Mallet","full_name":"Mallet, Ludovic","first_name":"Ludovic"},{"first_name":"Jose M.","full_name":"Monroy-Kuhn, Jose M.","last_name":"Monroy-Kuhn"},{"first_name":"Annabell","last_name":"Moser","full_name":"Moser, Annabell"},{"first_name":"Shwetha C.","last_name":"Murali","full_name":"Murali, Shwetha C."},{"last_name":"Muzny","full_name":"Muzny, Donna M.","first_name":"Donna M."},{"last_name":"Otani","full_name":"Otani, Saria","first_name":"Saria"},{"first_name":"Maria-Dolors","last_name":"Piulachs","full_name":"Piulachs, Maria-Dolors"},{"last_name":"Poelchau","full_name":"Poelchau, Monica","first_name":"Monica"},{"first_name":"Jiaxin","full_name":"Qu, Jiaxin","last_name":"Qu"},{"first_name":"Florentine","last_name":"Schaub","full_name":"Schaub, Florentine"},{"first_name":"Ayako","full_name":"Wada-Katsumata, Ayako","last_name":"Wada-Katsumata"},{"first_name":"Kim C.","last_name":"Worley","full_name":"Worley, Kim C."},{"full_name":"Xie, Qiaolin","last_name":"Xie","first_name":"Qiaolin"},{"last_name":"Ylla","full_name":"Ylla, Guillem","first_name":"Guillem"},{"first_name":"Michael","full_name":"Poulsen, Michael","last_name":"Poulsen"},{"first_name":"Richard A.","full_name":"Gibbs, Richard A.","last_name":"Gibbs"},{"first_name":"Coby","full_name":"Schal, Coby","last_name":"Schal"},{"first_name":"Stephen","full_name":"Richards, Stephen","last_name":"Richards"},{"first_name":"Xavier","last_name":"Belles","full_name":"Belles, Xavier"},{"first_name":"Judith","full_name":"Korb, Judith","last_name":"Korb"},{"last_name":"Bornberg-Bauer","full_name":"Bornberg-Bauer, Erich","first_name":"Erich"}],"article_processing_charge":"No","_id":"9841","status":"public","type":"research_data_reference"},{"date_updated":"2023-09-11T14:10:25Z","department":[{"_id":"DaAl"}],"_id":"397","conference":{"location":"Vienna, Austria","end_date":"2018-02-28","start_date":"2018-02-24","name":"PPoPP: Principles and Practice of Parallel Programming"},"type":"conference","status":"public","publication_status":"published","publication_identifier":{"isbn":["978-1-4503-4982-6"]},"language":[{"iso":"eng"}],"issue":"1","volume":53,"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"}],"oa_version":"None","alternative_title":["PPoPP"],"scopus_import":"1","intvolume":" 53","month":"02","citation":{"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","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","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.","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000446161100002"]},"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","full_name":"Brown, Trevor A","last_name":"Brown"}],"title":"Harnessing epoch-based reclamation for efficient range queries","year":"2018","isi":1,"day":"10","page":"14 - 27","date_created":"2018-12-11T11:46:14Z","doi":"10.1145/3178487.3178489","date_published":"2018-02-10T00:00:00Z","quality_controlled":"1","publisher":"ACM"},{"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"intvolume":" 25","month":"10","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"d9f74277fd57176e04732707d575cf08","file_id":"5703","creator":"dernst","date_updated":"2020-07-14T12:46:03Z","file_size":4461997,"date_created":"2018-12-17T12:42:57Z","file_name":"2018_CellReports_Chen.pdf"}],"publication_status":"published","issue":"4","volume":25,"_id":"32","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","ddc":["570"],"date_updated":"2023-09-11T14:13:32Z","file_date_updated":"2020-07-14T12:46:03Z","department":[{"_id":"SaSi"}],"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.","oa":1,"publisher":"Elsevier","quality_controlled":"1","publication":"Cell Reports","day":"23","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:44:16Z","date_published":"2018-10-23T00:00:00Z","doi":"10.1016/j.celrep.2018.09.066","page":"852 - 861.e7","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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","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."},"title":"In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2","article_processing_charge":"No","external_id":{"isi":["000448219500005"]},"author":[{"first_name":"Ting","full_name":"Chen, Ting","last_name":"Chen"},{"full_name":"Kula, Bartosz","last_name":"Kula","first_name":"Bartosz"},{"last_name":"Nagy","full_name":"Nagy, Balint","orcid":"0000-0002-4002-4686","first_name":"Balint","id":"30F830CE-02D1-11E9-9BAA-DAF4881429F2"},{"full_name":"Barzan, Ruxandra","last_name":"Barzan","first_name":"Ruxandra"},{"first_name":"Andrea","full_name":"Gall, Andrea","last_name":"Gall"},{"full_name":"Ehrlich, Ingrid","last_name":"Ehrlich","first_name":"Ingrid"},{"first_name":"Maria","last_name":"Kukley","full_name":"Kukley, Maria"}],"publist_id":"8023"},{"issue":"12","volume":215,"publication_identifier":{"issn":["00221007"]},"publication_status":"published","file":[{"file_id":"5931","checksum":"687beea1d64c213f4cb9e3c29ec11a14","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_JournalExperMed_Reversat.pdf","date_created":"2019-02-06T08:49:52Z","creator":"dernst","file_size":1216437,"date_updated":"2020-07-14T12:47:09Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"11","intvolume":" 215","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:47:09Z","date_updated":"2023-09-11T14:12:06Z","ddc":["570"],"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","_id":"5672","page":"2959-2961","date_published":"2018-11-20T00:00:00Z","doi":"10.1084/jem.20181934","date_created":"2018-12-16T22:59:18Z","has_accepted_license":"1","isi":1,"year":"2018","day":"20","publication":"Journal of Experimental Medicine","publisher":"Rockefeller University Press","quality_controlled":"1","oa":1,"author":[{"id":"35B76592-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","last_name":"Reversat","full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000451920600002"]},"title":"IgM's exit route","citation":{"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.","ama":"Reversat A, Sixt MK. IgM’s exit route. Journal of Experimental Medicine. 2018;215(12):2959-2961. doi:10.1084/jem.20181934","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"date_created":"2018-12-11T11:46:15Z","date_published":"2018-05-01T00:00:00Z","doi":"10.1016/j.wneu.2018.02.096","volume":13,"page":"e568-e578","language":[{"iso":"eng"}],"publication":"World Neurosurgery","day":"01","publication_status":"published","year":"2018","isi":1,"intvolume":" 13","month":"05","publisher":"Elsevier","quality_controlled":"1","scopus_import":"1","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"}],"department":[{"_id":"BeBi"}],"title":"Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device","external_id":{"isi":["000432942700070"]},"article_processing_charge":"No","publist_id":"7431","author":[{"last_name":"Dodier","full_name":"Dodier, Philippe","first_name":"Philippe"},{"first_name":"Josa","last_name":"Frischer","full_name":"Frischer, Josa"},{"first_name":"Wei","full_name":"Wang, Wei","last_name":"Wang"},{"orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas","last_name":"Auzinger","id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"full_name":"Mallouhi, Ammar","last_name":"Mallouhi","first_name":"Ammar"},{"full_name":"Serles, Wolfgang","last_name":"Serles","first_name":"Wolfgang"},{"full_name":"Gruber, Andreas","last_name":"Gruber","first_name":"Andreas"},{"first_name":"Engelbert","full_name":"Knosp, Engelbert","last_name":"Knosp"},{"last_name":"Bavinzski","full_name":"Bavinzski, Gerhard","first_name":"Gerhard"}],"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.","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","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","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.","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."},"status":"public","type":"journal_article","_id":"398"},{"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.","short":"A. Akopyan, A. Bobenko, Transactions of the American Mathematical Society 370 (2018) 2825–2854.","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.","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","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","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."},"title":"Incircular nets and confocal conics","publist_id":"7363","author":[{"last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"},{"last_name":"Bobenko","full_name":"Bobenko, Alexander","first_name":"Alexander"}],"article_processing_charge":"No","external_id":{"isi":["000423197800019"]},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"day":"01","publication":"Transactions of the American Mathematical Society","isi":1,"year":"2018","date_published":"2018-04-01T00:00:00Z","doi":"10.1090/tran/7292","date_created":"2018-12-11T11:46:35Z","page":"2825 - 2854","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]","publisher":"American Mathematical Society","quality_controlled":"1","oa":1,"date_updated":"2023-09-11T14:19:12Z","department":[{"_id":"HeEd"}],"_id":"458","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","issue":"4","volume":370,"ec_funded":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"}],"month":"04","intvolume":" 370","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.04637"}]},{"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","scopus_import":"1","month":"05","intvolume":" 107","publication_status":"published","language":[{"iso":"eng"}],"volume":107,"_id":"426","type":"journal_article","status":"public","date_updated":"2023-09-12T07:43:26Z","department":[{"_id":"SyCr"}],"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","quality_controlled":"1","publisher":"Elsevier","isi":1,"year":"2018","day":"01","publication":"Journal of Insect Physiology","page":"284-290","date_published":"2018-05-01T00:00:00Z","doi":"10.1016/j.jinsphys.2017.12.003","date_created":"2018-12-11T11:46:25Z","citation":{"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.","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.","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","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","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.","short":"S. Metzler, A. Schrempf, J. Heinze, Journal of Insect Physiology 107 (2018) 284–290."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7397","author":[{"last_name":"Metzler","full_name":"Metzler, Sina","orcid":"0000-0002-9547-2494","first_name":"Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexandra","last_name":"Schrempf","full_name":"Schrempf, Alexandra"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"}],"external_id":{"isi":["000434751100034"]},"article_processing_charge":"No","title":"Individual- and ejaculate-specific sperm traits in ant males"},{"volume":11316,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783030046118"],"issn":["03029743"]},"intvolume":" 11316","month":"11","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.04372"}],"alternative_title":["LNCS"],"scopus_import":"1","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"}],"department":[{"_id":"ToHe"}],"date_updated":"2023-09-12T07:44:01Z","status":"public","conference":{"name":"14th International Conference on Web and Internet Economics, WINE","start_date":"2018-12-15","end_date":"2018-12-17","location":"Oxford, UK"},"type":"conference","_id":"5788","date_created":"2018-12-30T22:59:14Z","date_published":"2018-11-21T00:00:00Z","doi":"10.1007/978-3-030-04612-5_2","page":"21-36","day":"21","year":"2018","isi":1,"oa":1,"quality_controlled":"1","publisher":"Springer","title":"Infinite-duration poorman-bidding games","article_processing_charge":"No","external_id":{"isi":["000865933000002"],"arxiv":["1804.04372"]},"author":[{"first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","short":"G. Avni, T.A. Henzinger, R. Ibsen-Jensen, in:, Springer, 2018, pp. 21–36.","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.","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","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","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.","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."},"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"},{"_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369"}]},{"abstract":[{"lang":"eng","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."}],"oa_version":"Submitted Version","pmid":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/","open_access":"1"}],"scopus_import":"1","intvolume":" 560","month":"08","publication_status":"published","publication_identifier":{"eissn":["1476-4687"]},"language":[{"iso":"eng"}],"volume":560,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-018-0505-4","relation":"erratum"}]},"issue":"7719","_id":"150","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-09-12T07:44:37Z","department":[{"_id":"FlSc"}],"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","year":"2018","isi":1,"publication":"Nature","day":"29","page":"509–512","date_created":"2018-12-11T11:44:53Z","date_published":"2018-08-29T00:00:00Z","doi":"10.1038/s41586-018-0396-4","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.","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","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000442483400046"],"pmid":["30158708"]},"article_processing_charge":"No","author":[{"first_name":"Robert","last_name":"Dick","full_name":"Dick, Robert"},{"full_name":"Zadrozny, Kaneil K","last_name":"Zadrozny","first_name":"Kaneil K"},{"full_name":"Xu, Chaoyi","last_name":"Xu","first_name":"Chaoyi"},{"first_name":"Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian","orcid":"0000-0003-4790-8078","last_name":"Schur"},{"first_name":"Terri D","full_name":"Lyddon, Terri D","last_name":"Lyddon"},{"first_name":"Clifton L","last_name":"Ricana","full_name":"Ricana, Clifton L"},{"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"},{"first_name":"Marc C","last_name":"Johnson","full_name":"Johnson, Marc C"},{"full_name":"Pornillos, Owen","last_name":"Pornillos","first_name":"Owen"},{"full_name":"Vogt, Volker","last_name":"Vogt","first_name":"Volker"}],"title":"Inositol phosphates are assembly co-factors for HIV-1"},{"volume":38,"issue":"6","language":[{"iso":"eng"}],"publication_status":"published","month":"06","intvolume":" 38","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1706.03062","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"department":[{"_id":"TaHa"}],"date_updated":"2023-09-12T07:45:37Z","status":"public","type":"journal_article","_id":"303","date_published":"2018-06-01T00:00:00Z","doi":"10.3934/dcds.2018120","date_created":"2018-12-11T11:45:43Z","page":"2827 - 2849","day":"01","publication":"Discrete and Continuous Dynamical Systems- Series A","isi":1,"year":"2018","publisher":"AIMS","quality_controlled":"1","oa":1,"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.","title":"Introduction to tropical series and wave dynamic on them","author":[{"first_name":"Nikita","full_name":"Kalinin, Nikita","last_name":"Kalinin"},{"first_name":"Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87","last_name":"Shkolnikov","full_name":"Shkolnikov, Mikhail","orcid":"0000-0002-4310-178X"}],"publist_id":"7576","external_id":{"isi":["000438818400007"],"arxiv":["1706.03062"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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","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.","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."}},{"publisher":"Neural Information Processing Systems Foundation","quality_controlled":"1","oa":1,"year":"2018","day":"06","publication":"Advances in Neural Information Processing Systems","date_published":"2018-06-06T00:00:00Z","date_created":"2023-08-22T14:15:40Z","citation":{"chicago":"Locatello, Francesco, Gideon Dresdner, Rajiv Khanna, Isabel Valera, and Gunnar Rätsch. “Boosting Black Box Variational Inference.” In Advances in Neural Information Processing Systems, Vol. 31. Neural Information Processing Systems Foundation, 2018.","ista":"Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. 2018. Boosting black box variational inference. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 31.","mla":"Locatello, Francesco, et al. “Boosting Black Box Variational Inference.” Advances in Neural Information Processing Systems, vol. 31, Neural Information Processing Systems Foundation, 2018.","apa":"Locatello, F., Dresdner, G., Khanna, R., Valera, I., & Rätsch, G. (2018). Boosting black box variational inference. In Advances in Neural Information Processing Systems (Vol. 31). Montreal, Canada: Neural Information Processing Systems Foundation.","ama":"Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. Boosting black box variational inference. In: Advances in Neural Information Processing Systems. Vol 31. Neural Information Processing Systems Foundation; 2018.","ieee":"F. Locatello, G. Dresdner, R. Khanna, I. Valera, and G. Rätsch, “Boosting black box variational inference,” in Advances in Neural Information Processing Systems, Montreal, Canada, 2018, vol. 31.","short":"F. Locatello, G. Dresdner, R. Khanna, I. Valera, G. Rätsch, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2018."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello"},{"first_name":"Gideon","full_name":"Dresdner, Gideon","last_name":"Dresdner"},{"first_name":"Rajiv","full_name":"Khanna, Rajiv","last_name":"Khanna"},{"full_name":"Valera, Isabel","last_name":"Valera","first_name":"Isabel"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"}],"article_processing_charge":"No","external_id":{"arxiv":["1806.02185"]},"title":"Boosting black box variational inference","abstract":[{"lang":"eng","text":"Approximating a probability density in a tractable manner is a central task\r\nin Bayesian statistics. Variational Inference (VI) is a popular technique that\r\nachieves tractability by choosing a relatively simple variational family.\r\nBorrowing ideas from the classic boosting framework, recent approaches attempt\r\nto \\emph{boost} VI by replacing the selection of a single density with a\r\ngreedily constructed mixture of densities. In order to guarantee convergence,\r\nprevious works impose stringent assumptions that require significant effort for\r\npractitioners. Specifically, they require a custom implementation of the greedy\r\nstep (called the LMO) for every probabilistic model with respect to an\r\nunnatural variational family of truncated distributions. Our work fixes these\r\nissues with novel theoretical and algorithmic insights. On the theoretical\r\nside, we show that boosting VI satisfies a relaxed smoothness assumption which\r\nis sufficient for the convergence of the functional Frank-Wolfe (FW) algorithm.\r\nFurthermore, we rephrase the LMO problem and propose to maximize the Residual\r\nELBO (RELBO) which replaces the standard ELBO optimization in VI. These\r\ntheoretical enhancements allow for black box implementation of the boosting\r\nsubroutine. Finally, we present a stopping criterion drawn from the duality gap\r\nin the classic FW analyses and exhaustive experiments to illustrate the\r\nusefulness of our theoretical and algorithmic contributions."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1806.02185","open_access":"1"}],"month":"06","intvolume":" 31","publication_identifier":{"isbn":["9781510884472"],"eissn":["1049-5258"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":31,"_id":"14202","type":"conference","conference":{"name":"NeurIPS: Neural Information Processing Systems","end_date":"2018-12-08","location":"Montreal, Canada","start_date":"2018-12-03"},"status":"public","date_updated":"2023-09-13T07:38:24Z","extern":"1","department":[{"_id":"FrLo"}]},{"date_created":"2023-08-22T14:15:20Z","date_published":"2018-04-15T00:00:00Z","page":"464-472","publication":"Proceedings of the 21st International Conference on Artificial Intelligence and Statistics","day":"15","year":"2018","oa":1,"publisher":"ML Research Press","quality_controlled":"1","title":"Boosting variational inference: An optimization perspective","article_processing_charge":"No","external_id":{"arxiv":["1708.01733"]},"author":[{"last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"last_name":"Khanna","full_name":"Khanna, Rajiv","first_name":"Rajiv"},{"full_name":"Ghosh, Joydeep","last_name":"Ghosh","first_name":"Joydeep"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Locatello F, Khanna R, Ghosh J, Rätsch G. 2018. Boosting variational inference: An optimization perspective. Proceedings of the 21st International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics, PMLR, vol. 84, 464–472.","chicago":"Locatello, Francesco, Rajiv Khanna, Joydeep Ghosh, and Gunnar Rätsch. “Boosting Variational Inference: An Optimization Perspective.” In Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, 84:464–72. ML Research Press, 2018.","short":"F. Locatello, R. Khanna, J. Ghosh, G. Rätsch, in:, Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, ML Research Press, 2018, pp. 464–472.","ieee":"F. Locatello, R. Khanna, J. Ghosh, and G. Rätsch, “Boosting variational inference: An optimization perspective,” in Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, Playa Blanca, Lanzarote, 2018, vol. 84, pp. 464–472.","ama":"Locatello F, Khanna R, Ghosh J, Rätsch G. Boosting variational inference: An optimization perspective. In: Proceedings of the 21st International Conference on Artificial Intelligence and Statistics. Vol 84. ML Research Press; 2018:464-472.","apa":"Locatello, F., Khanna, R., Ghosh, J., & Rätsch, G. (2018). Boosting variational inference: An optimization perspective. In Proceedings of the 21st International Conference on Artificial Intelligence and Statistics (Vol. 84, pp. 464–472). Playa Blanca, Lanzarote: ML Research Press.","mla":"Locatello, Francesco, et al. “Boosting Variational Inference: An Optimization Perspective.” Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, vol. 84, ML Research Press, 2018, pp. 464–72."},"volume":84,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 84","month":"04","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.01733"}],"scopus_import":"1","alternative_title":["PMLR"],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Variational inference is a popular technique to approximate a possibly\r\nintractable Bayesian posterior with a more tractable one. Recently, boosting\r\nvariational inference has been proposed as a new paradigm to approximate the\r\nposterior by a mixture of densities by greedily adding components to the\r\nmixture. However, as is the case with many other variational inference\r\nalgorithms, its theoretical properties have not been studied. In the present\r\nwork, we study the convergence properties of this approach from a modern\r\noptimization viewpoint by establishing connections to the classic Frank-Wolfe\r\nalgorithm. Our analyses yields novel theoretical insights regarding the\r\nsufficient conditions for convergence, explicit rates, and algorithmic\r\nsimplifications. Since a lot of focus in previous works for variational\r\ninference has been on tractability, our work is especially important as a much\r\nneeded attempt to bridge the gap between probabilistic models and their\r\ncorresponding theoretical properties."}],"department":[{"_id":"FrLo"}],"extern":"1","date_updated":"2023-09-13T07:52:40Z","status":"public","conference":{"name":"AISTATS: Conference on Artificial Intelligence and Statistics","location":"Playa Blanca, Lanzarote","end_date":"2018-04-11","start_date":"2018-04-09"},"type":"conference","_id":"14201"},{"language":[{"iso":"eng"}],"publication":"International Conference on Learning Representations","day":"06","publication_status":"published","year":"2018","date_created":"2023-08-22T14:12:48Z","date_published":"2018-06-06T00:00:00Z","oa_version":"Preprint","abstract":[{"lang":"eng","text":"High-dimensional time series are common in many domains. Since human\r\ncognition is not optimized to work well in high-dimensional spaces, these areas\r\ncould benefit from interpretable low-dimensional representations. However, most\r\nrepresentation learning algorithms for time series data are difficult to\r\ninterpret. This is due to non-intuitive mappings from data features to salient\r\nproperties of the representation and non-smoothness over time. To address this\r\nproblem, we propose a new representation learning framework building on ideas\r\nfrom interpretable discrete dimensionality reduction and deep generative\r\nmodeling. This framework allows us to learn discrete representations of time\r\nseries, which give rise to smooth and interpretable embeddings with superior\r\nclustering performance. We introduce a new way to overcome the\r\nnon-differentiability in discrete representation learning and present a\r\ngradient-based version of the traditional self-organizing map algorithm that is\r\nmore performant than the original. Furthermore, to allow for a probabilistic\r\ninterpretation of our method, we integrate a Markov model in the representation\r\nspace. This model uncovers the temporal transition structure, improves\r\nclustering performance even further and provides additional explanatory\r\ninsights as well as a natural representation of uncertainty. We evaluate our\r\nmodel in terms of clustering performance and interpretability on static\r\n(Fashion-)MNIST data, a time series of linearly interpolated (Fashion-)MNIST\r\nimages, a chaotic Lorenz attractor system with two macro states, as well as on\r\na challenging real world medical time series application on the eICU data set.\r\nOur learned representations compare favorably with competitor methods and\r\nfacilitate downstream tasks on the real world data."}],"month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.02199"}],"oa":1,"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2023-09-13T06:35:12Z","citation":{"chicago":"Fortuin, Vincent, Matthias Hüser, Francesco Locatello, Heiko Strathmann, and Gunnar Rätsch. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” In International Conference on Learning Representations, 2018.","ista":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. 2018. SOM-VAE: Interpretable discrete representation learning on time series. International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","mla":"Fortuin, Vincent, et al. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” International Conference on Learning Representations, 2018.","short":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, G. Rätsch, in:, International Conference on Learning Representations, 2018.","ieee":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, and G. Rätsch, “SOM-VAE: Interpretable discrete representation learning on time series,” in International Conference on Learning Representations, New Orleans, LA, United States, 2018.","ama":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. SOM-VAE: Interpretable discrete representation learning on time series. In: International Conference on Learning Representations. ; 2018.","apa":"Fortuin, V., Hüser, M., Locatello, F., Strathmann, H., & Rätsch, G. (2018). SOM-VAE: Interpretable discrete representation learning on time series. In International Conference on Learning Representations. New Orleans, LA, United States."},"department":[{"_id":"FrLo"}],"title":"SOM-VAE: Interpretable discrete representation learning on time series","article_processing_charge":"No","external_id":{"arxiv":["1806.02199"]},"author":[{"full_name":"Fortuin, Vincent","last_name":"Fortuin","first_name":"Vincent"},{"full_name":"Hüser, Matthias","last_name":"Hüser","first_name":"Matthias"},{"last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"first_name":"Heiko","full_name":"Strathmann, Heiko","last_name":"Strathmann"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"}],"_id":"14198","status":"public","conference":{"name":"ICLR: International Conference on Learning Representations","start_date":"2019-05-06","end_date":"2019-05-09","location":"New Orleans, LA, United States"},"type":"conference"},{"author":[{"first_name":"Alp","last_name":"Yurtsever","full_name":"Yurtsever, Alp"},{"first_name":"Olivier","full_name":"Fercoq, Olivier","last_name":"Fercoq"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"first_name":"Volkan","full_name":"Cevher, Volkan","last_name":"Cevher"}],"external_id":{"arxiv":["1804.08544"]},"article_processing_charge":"No","title":"A conditional gradient framework for composite convex minimization with applications to semidefinite programming","citation":{"chicago":"Yurtsever, Alp, Olivier Fercoq, Francesco Locatello, and Volkan Cevher. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” In Proceedings of the 35th International Conference on Machine Learning, 80:5727–36. ML Research Press, 2018.","ista":"Yurtsever A, Fercoq O, Locatello F, Cevher V. 2018. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. Proceedings of the 35th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 80, 5727–5736.","mla":"Yurtsever, Alp, et al. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 5727–36.","apa":"Yurtsever, A., Fercoq, O., Locatello, F., & Cevher, V. (2018). A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 5727–5736). Stockholm, Sweden: ML Research Press.","ama":"Yurtsever A, Fercoq O, Locatello F, Cevher V. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:5727-5736.","ieee":"A. Yurtsever, O. Fercoq, F. Locatello, and V. Cevher, “A conditional gradient framework for composite convex minimization with applications to semidefinite programming,” in Proceedings of the 35th International Conference on Machine Learning, Stockholm, Sweden, 2018, vol. 80, pp. 5727–5736.","short":"A. Yurtsever, O. Fercoq, F. Locatello, V. Cevher, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 5727–5736."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"5727-5736","date_published":"2018-07-15T00:00:00Z","date_created":"2023-08-22T14:16:01Z","year":"2018","day":"15","publication":"Proceedings of the 35th International Conference on Machine Learning","publisher":"ML Research Press","quality_controlled":"1","oa":1,"department":[{"_id":"FrLo"}],"date_updated":"2023-09-13T08:13:39Z","extern":"1","type":"conference","conference":{"end_date":"2018-07-15","location":"Stockholm, Sweden","start_date":"2018-07-10","name":"ICML: International Conference on Machine Learning"},"status":"public","_id":"14203","volume":80,"publication_status":"published","language":[{"iso":"eng"}],"alternative_title":["PMLR"],"main_file_link":[{"url":"https://arxiv.org/abs/1804.08544","open_access":"1"}],"month":"07","intvolume":" 80","abstract":[{"text":"We propose a conditional gradient framework for a composite convex minimization template with broad applications. Our approach combines smoothing and homotopy techniques under the CGM framework, and provably achieves the optimal O(1/k−−√) convergence rate. We demonstrate that the same rate holds if the linear subproblems are solved approximately with additive or multiplicative error. In contrast with the relevant work, we are able to characterize the convergence when the non-smooth term is an indicator function. Specific applications of our framework include the non-smooth minimization, semidefinite programming, and minimization with linear inclusion constraints over a compact domain. Numerical evidence demonstrates the benefits of our framework.","lang":"eng"}],"oa_version":"Preprint"},{"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."}],"intvolume":" 209","month":"08","main_file_link":[{"url":"https://www.biorxiv.org/content/early/2017/11/30/227082","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","volume":209,"issue":"4","_id":"282","status":"public","type":"journal_article","date_updated":"2023-09-13T08:22:32Z","department":[{"_id":"NiBa"}],"oa":1,"quality_controlled":"1","publisher":"Genetics Society of America","publication":"Genetics","day":"01","year":"2018","isi":1,"date_created":"2018-12-11T11:45:36Z","doi":"10.1534/genetics.118.301018","date_published":"2018-08-01T00:00:00Z","page":"1279 - 1303","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","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","short":"H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.","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.","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."},"title":"Introgression of a block of genome under infinitesimal selection","external_id":{"isi":["000440014100020"]},"article_processing_charge":"No","publist_id":"7617","author":[{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}]},{"oa":1,"quality_controlled":"1","publisher":"IEEE","day":"16","year":"2018","isi":1,"date_created":"2018-12-11T11:44:40Z","date_published":"2018-08-16T00:00:00Z","doi":"10.1109/ISIT.2018.8437654","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,” Vol. 2018. IEEE, 2018. https://doi.org/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.","mla":"Obremski, Marciej, and Maciej Skórski. Inverted Leftover Hash Lemma. Vol. 2018, IEEE, 2018, doi:10.1109/ISIT.2018.8437654.","short":"M. Obremski, M. Skórski, in:, IEEE, 2018.","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.","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"},"title":"Inverted leftover hash lemma","article_processing_charge":"No","external_id":{"isi":["000448139300368"]},"publist_id":"7946","author":[{"first_name":"Marciej","last_name":"Obremski","full_name":"Obremski, Marciej"},{"last_name":"Skorski","full_name":"Skorski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej"}],"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"intvolume":" 2018","month":"08","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/507"}],"scopus_import":"1","alternative_title":["ISIT Proceedings"],"language":[{"iso":"eng"}],"publication_status":"published","volume":2018,"_id":"108","status":"public","conference":{"name":"ISIT: International Symposium on Information Theory","start_date":"2018-06-17 ","end_date":"2018-06-22","location":"Vail, CO, USA"},"type":"conference","date_updated":"2023-09-13T08:23:18Z","department":[{"_id":"KrPi"}]},{"date_created":"2023-08-22T14:16:25Z","date_published":"2018-07-01T00:00:00Z","page":"3198-3207","publication":"Proceedings of the 35th International Conference on Machine Learning","day":"01","year":"2018","oa":1,"publisher":"ML Research Press","quality_controlled":"1","title":"On matching pursuit and coordinate descent","external_id":{"arxiv":["1803.09539"]},"article_processing_charge":"No","author":[{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"first_name":"Anant","last_name":"Raj","full_name":"Raj, Anant"},{"last_name":"Karimireddy","full_name":"Karimireddy, Sai Praneeth","first_name":"Sai Praneeth"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"},{"full_name":"Stich, Sebastian U.","last_name":"Stich","first_name":"Sebastian U."},{"full_name":"Jaggi, Martin","last_name":"Jaggi","first_name":"Martin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"F. Locatello, A. Raj, S.P. Karimireddy, G. Rätsch, B. Schölkopf, S.U. Stich, M. Jaggi, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 3198–3207.","ieee":"F. Locatello et al., “On matching pursuit and coordinate descent,” in Proceedings of the 35th International Conference on Machine Learning, 2018, vol. 80, pp. 3198–3207.","apa":"Locatello, F., Raj, A., Karimireddy, S. P., Rätsch, G., Schölkopf, B., Stich, S. U., & Jaggi, M. (2018). On matching pursuit and coordinate descent. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 3198–3207). ML Research Press.","ama":"Locatello F, Raj A, Karimireddy SP, et al. On matching pursuit and coordinate descent. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:3198-3207.","mla":"Locatello, Francesco, et al. “On Matching Pursuit and Coordinate Descent.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 3198–207.","ista":"Locatello F, Raj A, Karimireddy SP, Rätsch G, Schölkopf B, Stich SU, Jaggi M. 2018. On matching pursuit and coordinate descent. Proceedings of the 35th International Conference on Machine Learning. , PMLR, vol. 80, 3198–3207.","chicago":"Locatello, Francesco, Anant Raj, Sai Praneeth Karimireddy, Gunnar Rätsch, Bernhard Schölkopf, Sebastian U. Stich, and Martin Jaggi. “On Matching Pursuit and Coordinate Descent.” In Proceedings of the 35th International Conference on Machine Learning, 80:3198–3207. ML Research Press, 2018."},"volume":80,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 80","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.09539"}],"alternative_title":["PMLR"],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"Two popular examples of first-order optimization methods over linear spaces are coordinate descent and matching pursuit algorithms, with their randomized variants. While the former targets the optimization by moving along coordinates, the latter considers a generalized notion of directions. Exploiting the connection between the two algorithms, we present a unified analysis of both, providing affine invariant sublinear O(1/t) rates on smooth objectives and linear convergence on strongly convex objectives. As a byproduct of our affine invariant analysis of matching pursuit, our rates for steepest coordinate descent are the tightest known. Furthermore, we show the first accelerated convergence rate O(1/t2) for matching pursuit and steepest coordinate descent on convex objectives.","lang":"eng"}],"department":[{"_id":"FrLo"}],"extern":"1","date_updated":"2023-09-13T08:19:05Z","status":"public","type":"conference","_id":"14204"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","ista":"Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided Verification, LNCS, vol. 10981, 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.","short":"B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102.","ieee":"B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV: Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.","ama":"Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102. doi:10.1007/978-3-319-96145-3_5","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"},"title":"Layered Concurrent Programs","author":[{"last_name":"Kragl","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard","first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Qadeer, Shaz","last_name":"Qadeer","first_name":"Shaz"}],"publist_id":"7761","external_id":{"isi":["000491481600005"]},"article_processing_charge":"No","project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"day":"18","isi":1,"has_accepted_license":"1","year":"2018","date_published":"2018-07-18T00:00:00Z","doi":"10.1007/978-3-319-96145-3_5","date_created":"2018-12-11T11:44:57Z","page":"79 - 102","publisher":"Springer","quality_controlled":"1","oa":1,"ddc":["000"],"date_updated":"2023-09-13T08:45:09Z","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:45:04Z","_id":"160","status":"public","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"CAV: Computer Aided Verification","end_date":"2018-07-17","location":"Oxford, UK","start_date":"2018-07-14"},"file":[{"file_id":"5705","checksum":"c64fff560fe5a7532ec10626ad1c215e","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_LNCS_Kragl.pdf","date_created":"2018-12-17T12:52:12Z","creator":"dernst","file_size":1603844,"date_updated":"2020-07-14T12:45:04Z"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"id":"8332","status":"public","relation":"dissertation_contains"}]},"volume":10981,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"07","intvolume":" 10981","alternative_title":["LNCS"],"scopus_import":"1"},{"publisher":"Nature Publishing Group","quality_controlled":"1","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.).","date_published":"2018-05-28T00:00:00Z","doi":"10.1038/s41477-018-0160-7","date_created":"2018-12-11T11:45:35Z","page":"365 - 375","day":"28","publication":"Nature Plants","isi":1,"year":"2018","title":"KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis","author":[{"first_name":"Zhen","full_name":"Gao, Zhen","last_name":"Gao"},{"full_name":"Daneva, Anna","last_name":"Daneva","first_name":"Anna"},{"first_name":"Yuliya","id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87","last_name":"Salanenka","full_name":"Salanenka, Yuliya"},{"first_name":"Matthias","last_name":"Van Durme","full_name":"Van Durme, Matthias"},{"full_name":"Huysmans, Marlies","last_name":"Huysmans","first_name":"Marlies"},{"first_name":"Zongcheng","full_name":"Lin, Zongcheng","last_name":"Lin"},{"full_name":"De Winter, Freya","last_name":"De Winter","first_name":"Freya"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"full_name":"Karimi, Mansour","last_name":"Karimi","first_name":"Mansour"},{"first_name":"Jan","full_name":"Van De Velde, Jan","last_name":"Van De Velde"},{"first_name":"Klaas","last_name":"Vandepoele","full_name":"Vandepoele, Klaas"},{"first_name":"Davy","full_name":"Van De Walle, Davy","last_name":"Van De Walle"},{"full_name":"Dewettinck, Koen","last_name":"Dewettinck","first_name":"Koen"},{"first_name":"Bart","full_name":"Lambrecht, Bart","last_name":"Lambrecht"},{"full_name":"Nowack, Moritz","last_name":"Nowack","first_name":"Moritz"}],"publist_id":"7619","external_id":{"isi":["000435571000017"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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.","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."},"month":"05","intvolume":" 4","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."}],"issue":"6","volume":4,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"280","department":[{"_id":"JiFr"}],"date_updated":"2023-09-13T08:24:17Z"},{"title":"Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains","author":[{"first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X","last_name":"Tomasek"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet"}],"publist_id":"7317","external_id":{"isi":["000425715100006"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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."},"doi":"10.1016/j.jbiotec.2018.01.008","date_published":"2018-02-20T00:00:00Z","date_created":"2018-12-11T11:46:50Z","page":"40 - 52","day":"20","publication":"Journal of Biotechnology","isi":1,"year":"2018","publisher":"Elsevier","quality_controlled":"1","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","department":[{"_id":"CaGu"}],"date_updated":"2023-09-13T08:24:51Z","status":"public","type":"journal_article","_id":"503","volume":268,"language":[{"iso":"eng"}],"publication_status":"published","month":"02","intvolume":" 268","scopus_import":"1","oa_version":"None","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."}]},{"issue":"8","volume":16,"related_material":{"record":[{"relation":"research_data","id":"9810","status":"public"}]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"527076f78265cd4ea192cd1569851587","file_id":"5706","creator":"dernst","date_updated":"2020-07-14T12:48:10Z","file_size":4007095,"date_created":"2018-12-17T12:55:31Z","file_name":"2018_Plos_Chaudhry.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"08","intvolume":" 16","abstract":[{"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.”.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:48:10Z","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","doi":"10.1371/journal.pbio.2005971","date_published":"2018-08-16T00:00:00Z","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,"author":[{"full_name":"Chaudhry, Waqas","last_name":"Chaudhry","first_name":"Waqas"},{"last_name":"Pleska","full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479","id":"4569785E-F248-11E8-B48F-1D18A9856A87","first_name":"Maros"},{"first_name":"Nilang","full_name":"Shah, Nilang","last_name":"Shah"},{"full_name":"Weiss, Howard","last_name":"Weiss","first_name":"Howard"},{"first_name":"Ingrid","full_name":"Mccall, Ingrid","last_name":"Mccall"},{"first_name":"Justin","full_name":"Meyer, Justin","last_name":"Meyer"},{"last_name":"Gupta","full_name":"Gupta, Animesh","first_name":"Animesh"},{"last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Levin, Bruce","last_name":"Levin","first_name":"Bruce"}],"publist_id":"7972","article_processing_charge":"Yes","external_id":{"isi":["000443383300024"]},"title":"Leaky resistance and the conditions for the existence of lytic bacteriophage","citation":{"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","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","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018).","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.","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"2005971"},{"publist_id":"8053","author":[{"last_name":"Umetani","full_name":"Umetani, Nobuyuki","first_name":"Nobuyuki"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385"}],"external_id":{"isi":["000448185000050"]},"article_processing_charge":"No","title":"Learning three-dimensional flow for interactive aerodynamic design","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.","ama":"Umetani N, Bickel B. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans Graph. 2018;37(4). 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","short":"N. Umetani, B. Bickel, ACM Trans. Graph. 37 (2018).","ieee":"N. Umetani and B. Bickel, “Learning three-dimensional flow for interactive aerodynamic design,” ACM Trans. Graph., vol. 37, no. 4. ACM, 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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"article_number":"89","doi":"10.1145/3197517.3201325","date_published":"2018-08-04T00:00:00Z","date_created":"2018-12-11T11:44:06Z","has_accepted_license":"1","isi":1,"year":"2018","day":"04","publication":"ACM Trans. Graph.","quality_controlled":"1","publisher":"ACM","oa":1,"department":[{"_id":"BeBi"}],"file_date_updated":"2020-07-14T12:46:22Z","date_updated":"2023-09-13T08:46:15Z","ddc":["003","004"],"type":"journal_article","status":"public","pubrep_id":"1049","_id":"4","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"}]},"volume":37,"issue":"4","ec_funded":1,"publication_status":"published","file":[{"creator":"system","file_size":22803163,"date_updated":"2020-07-14T12:46:22Z","file_name":"IST-2018-1049-v1+1_2018_sigg_Learning3DAerodynamics.pdf","date_created":"2018-12-12T10:16:28Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5216","checksum":"7a2243668f215821bc6aecad0320079a"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"08","intvolume":" 37","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"}],"oa_version":"Submitted Version"},{"title":"Localizing faults in simulink/stateflow models with STL","publist_id":"7738","author":[{"first_name":"Ezio","last_name":"Bartocci","full_name":"Bartocci, Ezio"},{"orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","last_name":"Ferrere","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"full_name":"Manjunath, Niveditha","last_name":"Manjunath","first_name":"Niveditha"},{"first_name":"Dejan","last_name":"Nickovic","full_name":"Nickovic, Dejan"}],"external_id":{"isi":["000474781600022"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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","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.","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."},"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"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":{"name":"HSCC: Hybrid Systems: Computation and Control","location":"Porto, Portugal","end_date":"2018-04-13","start_date":"2018-04-11"},"_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"}]},{"author":[{"last_name":"Alt","full_name":"Alt, Johannes","first_name":"Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös"},{"id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","last_name":"Krüger"}],"article_processing_charge":"No","external_id":{"isi":["000431721800005"],"arxiv":["1612.07776 "]},"title":"Local inhomogeneous circular law","citation":{"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.","short":"J. Alt, L. Erdös, T.H. Krüger, Annals Applied Probability 28 (2018) 148–203.","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","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":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","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,"department":[{"_id":"LaEr"}],"date_updated":"2023-09-13T08:47:52Z","type":"journal_article","article_type":"original","status":"public","_id":"566","volume":28,"related_material":{"record":[{"id":"149","status":"public","relation":"dissertation_contains"}]},"issue":"1","ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1612.07776 ","open_access":"1"}],"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"},{"citation":{"ama":"Akopyan A, Petrunin A. Long geodesics on convex surfaces. Mathematical Intelligencer. 2018;40(3):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","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.","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.","ista":"Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical Intelligencer. 40(3), 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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"arxiv":["1702.05172"],"isi":["000444141200005"]},"publist_id":"7948","author":[{"first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"first_name":"Anton","last_name":"Petrunin","full_name":"Petrunin, Anton"}],"title":"Long geodesics on convex surfaces","oa":1,"publisher":"Springer","quality_controlled":"1","year":"2018","isi":1,"publication":"Mathematical Intelligencer","day":"01","page":"26 - 31","date_created":"2018-12-11T11:44:40Z","date_published":"2018-09-01T00:00:00Z","doi":"10.1007/s00283-018-9795-5","_id":"106","type":"journal_article","status":"public","date_updated":"2023-09-13T08:49:16Z","department":[{"_id":"HeEd"}],"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."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.05172"}],"scopus_import":"1","intvolume":" 40","month":"09","publication_status":"published","language":[{"iso":"eng"}],"issue":"3","volume":40},{"publisher":"Public Library of Science","month":"08","oa_version":"Published Version","date_published":"2018-08-16T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"82"}]},"doi":"10.1371/journal.pbio.2005971.s008","date_created":"2021-08-06T12:43:44Z","year":"2018","day":"16","type":"research_data_reference","status":"public","_id":"9810","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","full_name":"Shah, Nilang","last_name":"Shah"},{"first_name":"Howard","last_name":"Weiss","full_name":"Weiss, Howard"},{"first_name":"Ingrid","full_name":"Mccall, Ingrid","last_name":"Mccall"},{"first_name":"Justin","full_name":"Meyer, Justin","last_name":"Meyer"},{"first_name":"Animesh","full_name":"Gupta, Animesh","last_name":"Gupta"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","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","department":[{"_id":"CaGu"}],"title":"Numerical data used in figures","citation":{"mla":"Chaudhry, Waqas, et al. Numerical Data Used in Figures. Public Library of Science, 2018, doi:10.1371/journal.pbio.2005971.s008.","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, (2018).","ieee":"W. Chaudhry et al., “Numerical data used in figures.” Public Library of Science, 2018.","ama":"Chaudhry W, Pleska M, Shah N, et al. Numerical data used in figures. 2018. doi: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","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.","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."},"date_updated":"2023-09-13T08:45:41Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"project":[{"_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Y 564-B12","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)"},{"call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556"}],"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.","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","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","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."},"title":"Lymphatic exosomes promote dendritic cell migration along guidance cues","external_id":{"pmid":["29650776"],"isi":["000438077800026"]},"article_processing_charge":"No","publist_id":"7627","author":[{"full_name":"Brown, Markus","last_name":"Brown","first_name":"Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Johnson, Louise","last_name":"Johnson","first_name":"Louise"},{"full_name":"Leone, Dario","last_name":"Leone","first_name":"Dario"},{"last_name":"Májek","full_name":"Májek, Peter","first_name":"Peter"},{"id":"368EE576-F248-11E8-B48F-1D18A9856A87","first_name":"Kari","last_name":"Vaahtomeri","orcid":"0000-0001-7829-3518","full_name":"Vaahtomeri, Kari"},{"full_name":"Senfter, Daniel","last_name":"Senfter","first_name":"Daniel"},{"last_name":"Bukosza","full_name":"Bukosza, Nora","first_name":"Nora"},{"last_name":"Schachner","full_name":"Schachner, Helga","first_name":"Helga"},{"first_name":"Gabriele","full_name":"Asfour, Gabriele","last_name":"Asfour"},{"first_name":"Brigitte","full_name":"Langer, Brigitte","last_name":"Langer"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"full_name":"Parapatics, Katja","last_name":"Parapatics","first_name":"Katja"},{"first_name":"Young","last_name":"Hong","full_name":"Hong, Young"},{"last_name":"Bennett","full_name":"Bennett, Keiryn","first_name":"Keiryn"},{"first_name":"Renate","full_name":"Kain, Renate","last_name":"Kain"},{"first_name":"Michael","full_name":"Detmar, Michael","last_name":"Detmar"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jackson","full_name":"Jackson, David","first_name":"David"},{"full_name":"Kerjaschki, Dontscho","last_name":"Kerjaschki","first_name":"Dontscho"}],"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,"publisher":"Rockefeller University Press","quality_controlled":"1","publication":"Journal of Cell Biology","day":"12","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:45:33Z","date_published":"2018-04-12T00:00:00Z","doi":"10.1083/jcb.201612051","page":"2205 - 2221","_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","ddc":["570"],"date_updated":"2023-09-13T08:51:29Z","file_date_updated":"2020-07-14T12:45:45Z","department":[{"_id":"MiSi"},{"_id":"Bio"}],"oa_version":"Published Version","pmid":1,"abstract":[{"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.","lang":"eng"}],"intvolume":" 217","month":"04","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"9c7eba51a35c62da8c13f98120b64df4","file_id":"5704","file_size":2252043,"date_updated":"2020-07-14T12:45:45Z","creator":"dernst","file_name":"2018_JournalCellBiology_Brown.pdf","date_created":"2018-12-17T12:50:07Z"}],"publication_status":"published","ec_funded":1,"issue":"6","volume":217},{"publication":"Nature Plants","day":"16","year":"2018","isi":1,"date_created":"2018-12-11T11:44:56Z","date_published":"2018-07-16T00:00:00Z","doi":"10.1038/s41477-018-0204-z","page":"548 - 553","acknowledgement":"This work was further supported by the Czech Science Foundation GACR (GA13-40637S) to J.F.;","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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.","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.","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","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"},"title":"Maternal auxin supply contributes to early embryo patterning in Arabidopsis","article_processing_charge":"No","external_id":{"isi":["000443861300011"],"pmid":["30013211"]},"author":[{"first_name":"Hélène","last_name":"Robert","full_name":"Robert, Hélène"},{"full_name":"Park, Chulmin","last_name":"Park","first_name":"Chulmin"},{"first_name":"Carla","last_name":"Gutièrrez","full_name":"Gutièrrez, Carla"},{"first_name":"Barbara","full_name":"Wójcikowska, Barbara","last_name":"Wójcikowska"},{"last_name":"Pěnčík","full_name":"Pěnčík, Aleš","first_name":"Aleš"},{"first_name":"Ondřej","full_name":"Novák, Ondřej","last_name":"Novák"},{"last_name":"Chen","full_name":"Chen, Junyi","first_name":"Junyi"},{"first_name":"Wim","last_name":"Grunewald","full_name":"Grunewald, Wim"},{"full_name":"Dresselhaus, Thomas","last_name":"Dresselhaus","first_name":"Thomas"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"full_name":"Laux, Thomas","last_name":"Laux","first_name":"Thomas"}],"publist_id":"7763","project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/plant-mothers-talk-to-their-embryos-via-the-hormone-auxin/","description":"News on IST Homepage"}]},"issue":"8","volume":4,"oa_version":"Submitted Version","pmid":1,"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."}],"intvolume":" 4","month":"07","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30013211","open_access":"1"}],"scopus_import":"1","date_updated":"2023-09-13T08:53:28Z","department":[{"_id":"JiFr"}],"_id":"158","status":"public","type":"journal_article"},{"year":"2018","has_accepted_license":"1","isi":1,"publication":"Trends in Cell Biology","day":"26","page":"835 - 867","date_created":"2018-12-11T11:44:54Z","doi":"10.1016/j.tcb.2018.06.006","date_published":"2018-07-26T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Elsevier","citation":{"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.","short":"K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867.","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.","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","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","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.","ista":"Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 28(10), 835–867."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000445118200007"]},"author":[{"full_name":"Fiedorczuk, Karol","last_name":"Fiedorczuk","first_name":"Karol","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0"},{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"}],"publist_id":"7769","title":"Mammalian mitochondrial complex I structure and disease causing mutations","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf","date_created":"2019-11-07T12:55:20Z","file_size":2185385,"date_updated":"2020-07-14T12:45:00Z","creator":"lsazanov","checksum":"ef6d2b4e1fd63948539639242610bfa6","file_id":"6994","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"volume":28,"issue":"10","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","scopus_import":"1","intvolume":" 28","month":"07","date_updated":"2023-09-13T08:51:56Z","ddc":["572"],"file_date_updated":"2020-07-14T12:45:00Z","department":[{"_id":"LeSa"}],"_id":"152","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","status":"public"},{"project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"citation":{"short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, ACM, 2018, pp. 2341–2356.","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.","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","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","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dvorák, Wolfgang","last_name":"Dvorák","first_name":"Wolfgang"},{"last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer","first_name":"Veronika"}],"publist_id":"7555","external_id":{"arxiv":["1711.09148"],"isi":["000483921200152"]},"article_processing_charge":"No","title":"Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter","publisher":"ACM","quality_controlled":"1","oa":1,"isi":1,"year":"2018","day":"01","page":"2341 - 2356","doi":"10.1137/1.9781611975031.151","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:45:45Z","_id":"310","type":"conference","conference":{"name":"SODA: Symposium on Discrete Algorithms","start_date":"2018-01-07","end_date":"2018-01-10","location":"New Orleans, Louisiana, United States"},"status":"public","date_updated":"2023-09-13T08:50:16Z","department":[{"_id":"KrCh"}],"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","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.09148"}],"month":"01","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1},{"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/interference-as-a-new-method-for-cooling-quantum-devices/","relation":"press_release"}]},"volume":120,"issue":"6","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"02","intvolume":" 120","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.09051"}],"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"}],"department":[{"_id":"JoFi"}],"date_updated":"2023-09-13T08:52:27Z","status":"public","type":"journal_article","_id":"436","doi":"10.1103/PhysRevLett.120.060601","date_published":"2018-02-07T00:00:00Z","date_created":"2018-12-11T11:46:28Z","day":"07","publication":"Physical Review Letters","isi":1,"year":"2018","publisher":"American Physical Society","quality_controlled":"1","oa":1,"title":"Manipulating the flow of thermal noise in quantum devices","author":[{"last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir"},{"full_name":"Aquilina, Matteo","last_name":"Aquilina","first_name":"Matteo"},{"last_name":"Xuereb","full_name":"Xuereb, André","first_name":"André"}],"publist_id":"7387","external_id":{"arxiv":["1706.09051"],"isi":["000424382100004"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","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","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.","short":"S. Barzanjeh, M. Aquilina, A. Xuereb, Physical Review Letters 120 (2018).","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.","ista":"Barzanjeh S, Aquilina M, Xuereb A. 2018. Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. 120(6), 060601."},"project":[{"_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"732894","name":"Hybrid Optomechanical Technologies"},{"_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM"}],"article_number":"060601 "},{"publication_identifier":{"issn":["17425689"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:13Z","file_size":1464288,"date_created":"2019-02-05T14:46:44Z","file_name":"2018_Interface_Hross.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5925","checksum":"56eb4308a15b7190bff938fab1f780e8"}],"language":[{"iso":"eng"}],"volume":15,"issue":"149","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":"1","month":"12","intvolume":" 15","date_updated":"2023-09-13T08:55:05Z","ddc":["570"],"department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:47:13Z","_id":"5858","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","isi":1,"has_accepted_license":"1","year":"2018","day":"05","publication":"Journal of the Royal Society Interface","doi":"10.1098/rsif.2018.0600","date_published":"2018-12-05T00:00:00Z","date_created":"2019-01-20T22:59:18Z","quality_controlled":"1","publisher":"Royal Society Publishing","oa":1,"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.","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.","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","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Hross","full_name":"Hross, Sabrina","first_name":"Sabrina"},{"full_name":"Theis, Fabian J.","last_name":"Theis","first_name":"Fabian J."},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"},{"last_name":"Hasenauer","full_name":"Hasenauer, Jan","first_name":"Jan"}],"article_processing_charge":"No","external_id":{"isi":["000456783800011"]},"title":"Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data","article_number":"20180600"},{"month":"10","intvolume":" 3","scopus_import":"1","oa_version":"Submitted Version","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."}],"volume":3,"issue":"10","ec_funded":1,"file":[{"file_id":"5043","checksum":"7fc0a2322214d1c04debef36d5bf2e8a","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-1062-v1+1_PhysRevFluids.3.103303.pdf","date_created":"2018-12-12T10:13:56Z","creator":"system","file_size":1838431,"date_updated":"2020-07-14T12:45:04Z"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","pubrep_id":"1062","type":"journal_article","article_type":"original","_id":"16","department":[{"_id":"BjHo"}],"file_date_updated":"2020-07-14T12:45:04Z","ddc":["532"],"date_updated":"2023-09-13T08:57:05Z","quality_controlled":"1","publisher":"American Physical Society","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).","date_published":"2018-10-16T00:00:00Z","doi":"10.1103/PhysRevFluids.3.103303","date_created":"2018-12-11T11:44:10Z","day":"16","publication":"Physical Review Fluids","isi":1,"has_accepted_license":"1","year":"2018","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"article_number":"103303","title":"Mixing layer instability and vorticity amplification in a creeping viscoelastic flow","publist_id":"8039","author":[{"first_name":"Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","last_name":"Varshney","full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999"},{"first_name":"Victor","last_name":"Steinberg","full_name":"Steinberg, Victor"}],"external_id":{"isi":["000447469200001"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Varshney A, Steinberg V. 2018. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 3(10), 103303.","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.","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","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.","short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","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."}},{"title":"Model of bacterial toxin-dependent pathogenesis explains infective dose","author":[{"first_name":"Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel","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","external_id":{"isi":["000447491300057"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","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.","ista":"Rybicki J, Kisdi E, Anttila J. 2018. Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. 115(42), 10690–10695."},"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_published":"2018-10-02T00:00:00Z","doi":"10.1073/pnas.1721061115","date_created":"2018-12-11T11:44:19Z","page":"10690 - 10695","day":"02","publication":"PNAS","isi":1,"has_accepted_license":"1","year":"2018","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"acknowledgement":"J.R. and J.V.A. were also supported by the Academy of Finland Grants 1273253 and 267541.","file_date_updated":"2020-07-14T12:46:26Z","department":[{"_id":"DaAl"}],"ddc":["570","577"],"date_updated":"2023-09-13T08:57:38Z","status":"public","pubrep_id":"1063","type":"journal_article","_id":"43","issue":"42","volume":115,"ec_funded":1,"file":[{"checksum":"df7ac544a587c06b75692653b9fabd18","file_id":"6258","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-04-09T08:02:50Z","file_name":"2018_PNAS_Rybicki.pdf","date_updated":"2020-07-14T12:46:26Z","file_size":4070777,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"10","intvolume":" 115","scopus_import":"1","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":" 37","month":"08","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."}],"ec_funded":1,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/metamolds-molding-a-mold/","description":"News on IST Homepage"}]},"issue":"4","volume":37,"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:18:52Z","file_name":"IST-2018-1038-v1+1_metamolds_authorversion.pdf","creator":"system","date_updated":"2020-07-14T12:44:43Z","file_size":91939066,"file_id":"5374","checksum":"61d46273dca4de626accef1d17a0aaad","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","pubrep_id":"1038","status":"public","type":"journal_article","_id":"13","department":[{"_id":"BeBi"}],"file_date_updated":"2020-07-14T12:44:43Z","ddc":["004"],"date_updated":"2023-09-13T08:56:07Z","oa":1,"quality_controlled":"1","publisher":"ACM","date_created":"2018-12-11T11:44:09Z","doi":"10.1145/3197517.3201381","date_published":"2018-08-04T00:00:00Z","publication":"ACM Trans. Graph.","day":"04","year":"2018","has_accepted_license":"1","isi":1,"project":[{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"article_number":"136","title":"Metamolds: Computational design of silicone molds","external_id":{"isi":["000448185000097"]},"article_processing_charge":"No","author":[{"first_name":"Thomas","last_name":"Alderighi","full_name":"Alderighi, Thomas"},{"first_name":"Luigi","full_name":"Malomo, Luigi","last_name":"Malomo"},{"last_name":"Giorgi","full_name":"Giorgi, Daniela","first_name":"Daniela"},{"full_name":"Pietroni, Nico","last_name":"Pietroni","first_name":"Nico"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"},{"last_name":"Cignoni","full_name":"Cignoni, Paolo","first_name":"Paolo"}],"publist_id":"8043","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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).","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."}},{"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"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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.","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.","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.","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","apa":"Zhang, W., Herde, M., Mitchell, J., Whitfield, J., Wulff, A., Vongsouthi, V., … Henneberger, C. (2018). Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0108-2","chicago":"Zhang, William, Michel Herde, Joshua Mitchell, Jason Whitfield, Andreas Wulff, Vanessa Vongsouthi, Inmaculada Sanchez-Romero, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0108-2.","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."},"title":"Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS","article_processing_charge":"No","external_id":{"pmid":["30061718 "],"isi":["000442174500013"]},"publist_id":"7786","author":[{"first_name":"William","last_name":"Zhang","full_name":"Zhang, William"},{"first_name":"Michel","last_name":"Herde","full_name":"Herde, Michel"},{"first_name":"Joshua","last_name":"Mitchell","full_name":"Mitchell, Joshua"},{"first_name":"Jason","last_name":"Whitfield","full_name":"Whitfield, Jason"},{"first_name":"Andreas","full_name":"Wulff, Andreas","last_name":"Wulff"},{"last_name":"Vongsouthi","full_name":"Vongsouthi, Vanessa","first_name":"Vanessa"},{"last_name":"Sanchez Romero","full_name":"Sanchez Romero, Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","first_name":"Inmaculada"},{"full_name":"Gulakova, Polina","last_name":"Gulakova","first_name":"Polina"},{"first_name":"Daniel","full_name":"Minge, Daniel","last_name":"Minge"},{"first_name":"Björn","last_name":"Breithausen","full_name":"Breithausen, Björn"},{"first_name":"Susanne","full_name":"Schoch, Susanne","last_name":"Schoch"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315"},{"full_name":"Jackson, Colin","last_name":"Jackson","first_name":"Colin"},{"first_name":"Christian","last_name":"Henneberger","full_name":"Henneberger, Christian"}],"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","publication":"Nature Chemical Biology","day":"30","year":"2018","isi":1,"date_created":"2018-12-11T11:44:49Z","doi":"10.1038/s41589-018-0108-2","date_published":"2018-07-30T00:00:00Z","page":"861 - 869","_id":"137","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-09-13T08:58:05Z","department":[{"_id":"HaJa"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"Fluorescent sensors are an essential part of the experimental toolbox of the life sciences, where they are used ubiquitously to visualize intra- and extracellular signaling. In the brain, optical neurotransmitter sensors can shed light on temporal and spatial aspects of signal transmission by directly observing, for instance, neurotransmitter release and spread. Here we report the development and application of the first optical sensor for the amino acid glycine, which is both an inhibitory neurotransmitter and a co-agonist of the N-methyl-d-aspartate receptors (NMDARs) involved in synaptic plasticity. Computational design of a glycine-specific binding protein allowed us to produce the optical glycine FRET sensor (GlyFS), which can be used with single and two-photon excitation fluorescence microscopy. We took advantage of this newly developed sensor to test predictions about the uneven spatial distribution of glycine in extracellular space and to demonstrate that extracellular glycine levels are controlled by plasticity-inducing stimuli."}],"intvolume":" 14","month":"07","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30061718"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","issue":"9","volume":14},{"date_updated":"2023-09-13T08:56:35Z","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"_id":"153","status":"public","type":"book_chapter","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0091679X"]},"publication_status":"published","volume":147,"pmid":1,"oa_version":"None","abstract":[{"lang":"eng","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."}],"month":"07","intvolume":" 147","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","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","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.","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.","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."},"title":"Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments","author":[{"last_name":"Renkawitz","full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-0666-8928","full_name":"Reversat, Anne","last_name":"Reversat","first_name":"Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Leithner","orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F"},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"publist_id":"7768","article_processing_charge":"No","external_id":{"pmid":["30165964"],"isi":["000452412300006"]},"day":"27","publication":"Methods in Cell Biology","isi":1,"year":"2018","doi":"10.1016/bs.mcb.2018.07.004","date_published":"2018-07-27T00:00:00Z","date_created":"2018-12-11T11:44:54Z","page":"79 - 91","publisher":"Academic Press","quality_controlled":"1"},{"title":"Mechanical force-driven adherents junction remodeling and epithelial dynamics","article_processing_charge":"No","external_id":{"isi":["000446579900002"]},"author":[{"last_name":"Nunes Pinheiro","orcid":"0000-0003-4333-7503","full_name":"Nunes Pinheiro, Diana C","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","first_name":"Diana C"},{"full_name":"Bellaïche, Yohanns","last_name":"Bellaïche","first_name":"Yohanns"}],"publist_id":"8000","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"},"quality_controlled":"1","publisher":"Cell Press","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.","date_created":"2018-12-11T11:44:23Z","doi":"10.1016/j.devcel.2018.09.014","date_published":"2018-10-08T00:00:00Z","page":"3 - 19","publication":"Developmental Cell","day":"08","year":"2018","isi":1,"status":"public","article_type":"review","type":"journal_article","_id":"54","department":[{"_id":"CaHe"}],"date_updated":"2023-09-13T08:54:38Z","intvolume":" 47","month":"10","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2018.09.014"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"issue":"1","volume":47,"language":[{"iso":"eng"}],"publication_status":"published"},{"date_created":"2018-12-11T11:45:34Z","doi":"10.1371/journal.pone.0198330","date_published":"2018-06-07T00:00:00Z","publication":"PLoS One","day":"07","year":"2018","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Public Library of Science","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.","title":"Nano-scale microfluidics to study 3D chemotaxis at the single cell level","article_processing_charge":"No","external_id":{"isi":["000434384900031"]},"author":[{"first_name":"Corina","last_name":"Frick","full_name":"Frick, Corina"},{"first_name":"Philip","last_name":"Dettinger","full_name":"Dettinger, Philip"},{"last_name":"Renkawitz","full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jauch","full_name":"Jauch, Annaïse","first_name":"Annaïse"},{"full_name":"Berger, Christoph","last_name":"Berger","first_name":"Christoph"},{"first_name":"Mike","last_name":"Recher","full_name":"Recher, Mike"},{"first_name":"Timm","full_name":"Schroeder, Timm","last_name":"Schroeder"},{"full_name":"Mehling, Matthias","last_name":"Mehling","first_name":"Matthias"}],"publist_id":"7626","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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.","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","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","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."},"article_number":"e0198330","volume":13,"issue":"6","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:45:45Z","file_size":7682167,"date_created":"2018-12-17T14:10:32Z","file_name":"2018_Plos_Frick.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5709","checksum":"95fc5dc3938b3ad3b7697d10c83cc143"}],"publication_status":"published","intvolume":" 13","month":"06","scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"file_date_updated":"2020-07-14T12:45:45Z","department":[{"_id":"MiSi"}],"ddc":["570"],"date_updated":"2023-09-13T09:00:15Z","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","article_type":"original","_id":"276"},{"date_updated":"2023-09-13T08:59:27Z","ddc":["570"],"department":[{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:45:49Z","_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","publication_status":"published","file":[{"file_name":"2018_ScientificReports_Ceinos.pdf","date_created":"2018-12-17T13:04:46Z","file_size":1855324,"date_updated":"2020-07-14T12:45:49Z","creator":"dernst","file_id":"5707","checksum":"9c3942d772f84f3df032ffde0ed9a8ea","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"issue":"1","volume":8,"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","citation":{"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.","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.","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).","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.","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","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Ceinos, Rosa Maria","last_name":"Ceinos","first_name":"Rosa Maria"},{"first_name":"Elena","full_name":"Frigato, Elena","last_name":"Frigato"},{"full_name":"Pagano, Cristina","last_name":"Pagano","first_name":"Cristina"},{"last_name":"Frohlich","full_name":"Frohlich, Nadine","first_name":"Nadine"},{"first_name":"Pietro","full_name":"Negrini, Pietro","last_name":"Negrini"},{"last_name":"Cavallari","full_name":"Cavallari, Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola"},{"first_name":"Daniela","full_name":"Vallone, Daniela","last_name":"Vallone"},{"first_name":"Silvia","last_name":"Fuselli","full_name":"Fuselli, Silvia"},{"first_name":"Cristiano","full_name":"Bertolucci, Cristiano","last_name":"Bertolucci"},{"first_name":"Nicholas S","full_name":"Foulkes, Nicholas S","last_name":"Foulkes"}],"publist_id":"7616","article_processing_charge":"No","external_id":{"isi":["000434640800008"]},"title":"Mutations in blind cavefish target the light regulated circadian clock gene period 2","article_number":"8754","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","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1},{"oa":1,"publisher":"Springer","quality_controlled":"1","year":"2018","has_accepted_license":"1","isi":1,"day":"26","page":"53 - 70","date_created":"2018-12-11T11:44:31Z","doi":"10.1007/978-3-030-00151-3_4","date_published":"2018-08-26T00:00:00Z","project":[{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"citation":{"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.","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.","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","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000884993200004"]},"article_processing_charge":"No","publist_id":"7973","author":[{"full_name":"Elgyütt, Adrian","last_name":"Elgyütt","id":"4A2E9DBA-F248-11E8-B48F-1D18A9856A87","first_name":"Adrian"},{"last_name":"Ferrere","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"}],"title":"Monitoring temporal logic with clock variables","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","alternative_title":["LNCS"],"scopus_import":"1","intvolume":" 11022","month":"08","publication_status":"published","language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"e5d81c9b50a6bd9d8a2c16953aad7e23","file_id":"8638","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_LNCS_Elgyuett.pdf","date_created":"2020-10-09T06:24:21Z","creator":"dernst","file_size":537219,"date_updated":"2020-10-09T06:24:21Z"}],"volume":11022,"_id":"81","conference":{"end_date":"2018-09-06","location":"Beijing, China","start_date":"2018-09-04","name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"type":"conference","status":"public","date_updated":"2023-09-13T08:58:34Z","ddc":["000"],"file_date_updated":"2020-10-09T06:24:21Z","department":[{"_id":"ToHe"}]},{"publication":"Distributed Computing","day":"12","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:44:30Z","date_published":"2018-09-12T00:00:00Z","doi":"10.1007/s00446-018-0342-6","oa":1,"quality_controlled":"1","publisher":"Springer","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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","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).","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."},"title":"Near-optimal self-stabilising counting and firing squads","external_id":{"isi":["000475627800005"]},"article_processing_charge":"Yes (via OA deal)","publist_id":"7978","author":[{"first_name":"Christoph","full_name":"Lenzen, Christoph","last_name":"Lenzen"},{"full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646","last_name":"Rybicki","first_name":"Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"language":[{"iso":"eng"}],"file":[{"checksum":"872db70bba9b401500abe3c6ae2f1a61","file_id":"5711","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_DistributedComputing_Lenzen.pdf","date_created":"2018-12-17T14:21:22Z","file_size":799337,"date_updated":"2020-07-14T12:48:01Z","creator":"dernst"}],"publication_status":"published","oa_version":"Published Version","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"}],"month":"09","scopus_import":"1","ddc":["000"],"date_updated":"2023-09-13T09:01:06Z","department":[{"_id":"DaAl"}],"file_date_updated":"2020-07-14T12:48:01Z","_id":"76","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"},{"type":"journal_article","status":"public","_id":"530","file_date_updated":"2020-07-14T12:46:38Z","department":[{"_id":"HeEd"}],"date_updated":"2023-09-13T08:59:00Z","ddc":["000"],"scopus_import":"1","month":"03","intvolume":" 68","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."}],"oa_version":"Preprint","volume":68,"ec_funded":1,"publication_status":"published","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"}],"language":[{"iso":"eng"}],"project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Topological Complex Systems","grant_number":"318493"}],"publist_id":"7289","author":[{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Iglesias Ham","full_name":"Iglesias Ham, Mabel","first_name":"Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000415778300010"]},"title":"Multiple covers with balls I: Inclusion–exclusion","citation":{"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.","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.","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","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.","ista":"Edelsbrunner H, Iglesias Ham M. 2018. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 68, 119–133."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Elsevier","quality_controlled":"1","oa":1,"page":"119 - 133","date_published":"2018-03-01T00:00:00Z","doi":"10.1016/j.comgeo.2017.06.014","date_created":"2018-12-11T11:46:59Z","isi":1,"has_accepted_license":"1","year":"2018","day":"01","publication":"Computational Geometry: Theory and Applications"},{"month":"04","intvolume":" 97","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.10127"}],"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. "}],"issue":"4","volume":97,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","article_type":"original","_id":"307","department":[{"_id":"JoFi"}],"date_updated":"2023-09-13T09:00:41Z","quality_controlled":"1","publisher":"American Physical Society","oa":1,"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).","date_published":"2018-04-09T00:00:00Z","doi":"10.1103/PhysRevA.97.043812","date_created":"2018-12-11T11:45:44Z","day":"09","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","isi":1,"year":"2018","article_number":" 043812 ","title":"Nanoscopy of pairs of atoms by fluorescence in a magnetic field","author":[{"last_name":"Redchenko","full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena"},{"last_name":"Makarov","full_name":"Makarov, Alexander","first_name":"Alexander"},{"last_name":"Yudson","full_name":"Yudson, Vladimir","first_name":"Vladimir"}],"publist_id":"7572","article_processing_charge":"No","external_id":{"arxiv":["1712.10127"],"isi":["000429454000015"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","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","short":"E. Redchenko, A. Makarov, V. Yudson, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","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.","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."}},{"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 19","month":"05","publication_status":"published","language":[{"iso":"eng"}],"file":[{"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,"file_id":"5708","checksum":"f3e4922486bd9bf1483271bdbed394a7","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"ec_funded":1,"volume":19,"related_material":{"record":[{"status":"public","id":"9811","relation":"research_data"},{"relation":"research_data","status":"public","id":"9812"}]},"_id":"279","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","date_updated":"2023-09-13T09:01:32Z","ddc":["570"],"department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:45:47Z","oa":1,"quality_controlled":"1","publisher":"BioMed Central","year":"2018","has_accepted_license":"1","isi":1,"publication":"Genome Biology","day":"31","date_created":"2018-12-11T11:45:35Z","date_published":"2018-05-31T00:00:00Z","doi":"10.1186/s13059-018-1434-0","article_number":"67","project":[{"_id":"26120F5C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Systematic investigation of epistasis in molecular evolution","grant_number":"335980"}],"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).","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","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000433986200001"]},"article_processing_charge":"No","author":[{"first_name":"Luis","full_name":"Zapata, Luis","last_name":"Zapata"},{"first_name":"Oriol","full_name":"Pich, Oriol","last_name":"Pich"},{"last_name":"Serrano","full_name":"Serrano, Luis","first_name":"Luis"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"},{"first_name":"Stephan","full_name":"Ossowski, Stephan","last_name":"Ossowski"},{"full_name":"Schaefer, Martin","last_name":"Schaefer","first_name":"Martin"}],"publist_id":"7620","title":"Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome"},{"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."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 37","month":"08","publication_status":"published","publication_identifier":{"issn":["0261-4189"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"a540feb6c9af6aefc78de531461a8835","file_id":"5710","date_updated":"2020-07-14T12:44:56Z","file_size":2846470,"creator":"dernst","date_created":"2018-12-17T14:17:29Z","file_name":"2018_EMBO_Truckenbrodt.pdf"}],"issue":"15","volume":37,"_id":"145","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","status":"public","date_updated":"2023-09-13T09:02:48Z","ddc":["570"],"department":[{"_id":"JoDa"}],"file_date_updated":"2020-07-14T12:44:56Z","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","year":"2018","has_accepted_license":"1","isi":1,"publication":"The EMBO Journal","day":"01","date_created":"2018-12-11T11:44:52Z","doi":"10.15252/embj.201798044","date_published":"2018-08-01T00:00:00Z","article_number":"e98044","citation":{"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","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.","short":"S.M. Truckenbrodt, A. Viplav, S. Jähne, A. Vogts, A. Denker, H. Wildhagen, E. Fornasiero, S. Rizzoli, The EMBO Journal 37 (2018).","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"pmid":["29950309"],"isi":["000440416900005"]},"publist_id":"7778","author":[{"full_name":"Truckenbrodt, Sven M","last_name":"Truckenbrodt","first_name":"Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Viplav, Abhiyan","last_name":"Viplav","first_name":"Abhiyan"},{"first_name":"Sebsatian","full_name":"Jähne, Sebsatian","last_name":"Jähne"},{"full_name":"Vogts, Angela","last_name":"Vogts","first_name":"Angela"},{"full_name":"Denker, Annette","last_name":"Denker","first_name":"Annette"},{"first_name":"Hanna","full_name":"Wildhagen, Hanna","last_name":"Wildhagen"},{"first_name":"Eugenio","last_name":"Fornasiero","full_name":"Fornasiero, Eugenio"},{"last_name":"Rizzoli","full_name":"Rizzoli, Silvio","first_name":"Silvio"}],"title":"Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission"},{"author":[{"first_name":"Ligang","full_name":"Fan, Ligang","last_name":"Fan"},{"full_name":"Zhao, Lei","last_name":"Zhao","first_name":"Lei"},{"full_name":"Hu, Wei","last_name":"Hu","first_name":"Wei"},{"first_name":"Weina","full_name":"Li, Weina","last_name":"Li"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"first_name":"Miroslav","last_name":"Strnad","full_name":"Strnad, Miroslav"},{"full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741","last_name":"Simon","first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shen, Jinbo","last_name":"Shen","first_name":"Jinbo"},{"last_name":"Jiang","full_name":"Jiang, Liwen","first_name":"Liwen"},{"first_name":"Quan","last_name":"Qiu","full_name":"Qiu, 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":{"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.","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.","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.","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","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"850 - 864","doi":"10.1111/pce.13153","date_published":"2018-05-01T00:00:00Z","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. ","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:46:32Z","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,"publication_status":"published","file":[{"file_size":1937976,"date_updated":"2020-07-14T12:46:32Z","creator":"dernst","file_name":"2018_PlantCellEnv_Fan.pdf","date_created":"2019-11-18T16:22:22Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7042","checksum":"6a20f843565f962cb20281cdf5e40914"}],"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"}],"oa_version":"Submitted Version","pmid":1},{"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.","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","short":"S. Altmeyer, Journal of Magnetism and Magnetic Materials 452 (2018) 427–441.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000425547700061"]},"publist_id":"7297","author":[{"id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Altmeyer","orcid":"0000-0001-5964-0203","full_name":"Altmeyer, Sebastian"}],"title":"Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow","acknowledgement":"S.Altmeyer is a Serra Húnter Fellow","oa":1,"publisher":"Elsevier","quality_controlled":"1","year":"2018","isi":1,"has_accepted_license":"1","publication":"Journal of Magnetism and Magnetic Materials","day":"15","page":"427 - 441","date_created":"2018-12-11T11:46:56Z","doi":"10.1016/j.jmmm.2017.12.073","date_published":"2018-04-15T00:00:00Z","_id":"519","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-13T09:03:44Z","ddc":["530"],"department":[{"_id":"BjHo"}],"file_date_updated":"2020-07-14T12:46:37Z","abstract":[{"lang":"eng","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. "}],"oa_version":"Submitted Version","scopus_import":"1","intvolume":" 452","month":"04","publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"431f5cd4a628d7ca21161f82b14ccb4f","file_id":"7838","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_Magnetism_Altmeyer.pdf","date_created":"2020-05-14T14:41:17Z","file_size":17309535,"date_updated":"2020-07-14T12:46:37Z","creator":"dernst"}],"volume":452},{"volume":11275,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["03029743"],"isbn":["9783030027674"]},"intvolume":" 11275","month":"12","main_file_link":[{"url":"http://arxiv.org/abs/1806.06683","open_access":"1"}],"scopus_import":"1","alternative_title":["LNCS"],"oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"department":[{"_id":"KrCh"}],"date_updated":"2023-09-13T09:02:22Z","status":"public","conference":{"start_date":"2018-12-02","location":"Wellington, New Zealand","end_date":"2018-12-06","name":"16th Asian Symposium on Programming Languages and Systems, APLAS"},"type":"conference","_id":"5679","date_created":"2018-12-16T22:59:20Z","date_published":"2018-12-01T00:00:00Z","doi":"10.1007/978-3-030-02768-1_11","page":"181-201","day":"01","year":"2018","isi":1,"oa":1,"quality_controlled":"1","publisher":"Springer","title":"New approaches for almost-sure termination of probabilistic programs","editor":[{"first_name":"Sukyoung","last_name":"Ryu","full_name":"Ryu, Sukyoung"}],"external_id":{"isi":["000916310900011"],"arxiv":["1806.06683"]},"article_processing_charge":"No","author":[{"last_name":"Huang","full_name":"Huang, Mingzhang","first_name":"Mingzhang"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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.","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."},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}]},{"_id":"546","type":"journal_article","status":"public","date_updated":"2023-09-13T09:01:56Z","department":[{"_id":"GaNo"}],"abstract":[{"lang":"eng","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."}],"oa_version":"None","scopus_import":"1","intvolume":" 48","month":"02","publication_status":"published","language":[{"iso":"eng"}],"issue":"2","volume":48,"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.","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","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.","short":"R. Sacco, E. Cacci, G. Novarino, Current Opinion in Neurobiology 48 (2018) 131–138."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000427101600018"]},"article_processing_charge":"No","publist_id":"7268","author":[{"id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","first_name":"Roberto","last_name":"Sacco","full_name":"Sacco, Roberto"},{"full_name":"Cacci, Emanuele","last_name":"Cacci","first_name":"Emanuele"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"title":"Neural stem cells in neuropsychiatric disorders","quality_controlled":"1","publisher":"Elsevier","year":"2018","isi":1,"publication":"Current Opinion in Neurobiology","day":"01","page":"131 - 138","date_created":"2018-12-11T11:47:06Z","doi":"10.1016/j.conb.2017.12.005","date_published":"2018-02-01T00:00:00Z"},{"_id":"9812","status":"public","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","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.","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).","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","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","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."},"date_updated":"2023-09-13T09:01:31Z","title":"Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","department":[{"_id":"FyKo"}],"article_processing_charge":"No","author":[{"full_name":"Zapata, Luis","last_name":"Zapata","first_name":"Luis"},{"first_name":"Oriol","full_name":"Pich, Oriol","last_name":"Pich"},{"first_name":"Luis","full_name":"Serrano, Luis","last_name":"Serrano"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"},{"first_name":"Stephan","last_name":"Ossowski","full_name":"Ossowski, Stephan"},{"first_name":"Martin","full_name":"Schaefer, Martin","last_name":"Schaefer"}],"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","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.6401414.v1"}],"oa":1,"publisher":"Springer Nature","day":"31","year":"2018","date_created":"2021-08-06T12:58:25Z","related_material":{"record":[{"relation":"used_in_publication","id":"279","status":"public"}]},"date_published":"2018-05-31T00:00:00Z","doi":"10.6084/m9.figshare.6401414.v1"},{"date_created":"2021-08-06T12:53:49Z","related_material":{"record":[{"status":"public","id":"279","relation":"used_in_publication"}]},"date_published":"2018-05-31T00:00:00Z","doi":"10.6084/m9.figshare.6401390.v1","year":"2018","day":"31","oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.6401390.v1","open_access":"1"}],"publisher":"Springer Nature","month":"05","abstract":[{"lang":"eng","text":"This document contains additional supporting evidence presented as supplemental tables. (XLSX 50Â kb)"}],"oa_version":"Preprint","article_processing_charge":"No","author":[{"full_name":"Zapata, Luis","last_name":"Zapata","first_name":"Luis"},{"first_name":"Oriol","last_name":"Pich","full_name":"Pich, Oriol"},{"last_name":"Serrano","full_name":"Serrano, Luis","first_name":"Luis"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"last_name":"Ossowski","full_name":"Ossowski, Stephan","first_name":"Stephan"},{"full_name":"Schaefer, Martin","last_name":"Schaefer","first_name":"Martin"}],"department":[{"_id":"FyKo"}],"title":"Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","date_updated":"2023-09-13T09:01:31Z","citation":{"mla":"Zapata, Luis, et al. Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401390.v1.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401390.v1","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401390.v1","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 1: 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).","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 1: 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.6401390.v1.","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401390.v1."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9811"},{"language":[{"iso":"eng"}],"file":[{"file_name":"2018_BMCGenomics_Higareda.pdf","date_created":"2018-12-17T14:52:57Z","file_size":4629784,"date_updated":"2020-07-14T12:45:23Z","creator":"dernst","checksum":"a56516e734dab589dc7f3e1915973b4d","file_id":"5712","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"issn":["1471-2164"]},"volume":19,"issue":"1","related_material":{"record":[{"id":"9807","status":"public","relation":"research_data"},{"id":"9808","status":"public","relation":"research_data"}]},"oa_version":"Published Version","abstract":[{"text":"Background: Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level. Results: We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation. In addition, we identified a transcriptional regulatory network with IEGs as master regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover, a functional enrichment analysis and gene clustering into functional modules suggest a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether, our network biology approach explores for the first time the immediate-early systems level response of human adipocytes to acute sympathetic activation, thereby providing a first network basis of early cell fate programs and crosstalks between metabolic and transcriptional networks required for proper WAT function.","lang":"eng"}],"intvolume":" 19","month":"11","scopus_import":"1","ddc":["570"],"date_updated":"2023-09-13T09:10:47Z","file_date_updated":"2020-07-14T12:45:23Z","department":[{"_id":"SiHi"}],"_id":"20","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","publication":"BMC Genomics","day":"03","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:44:12Z","doi":"10.1186/s12864-018-5173-0","date_published":"2018-11-03T00:00:00Z","acknowledgement":"This work was funded by the German Centre for Diabetes Research (DZD) and the Austrian Science Fund (FWF, P25729-B19).","oa":1,"quality_controlled":"1","publisher":"BioMed Central","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 19(1).","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics. BioMed Central, 2018. https://doi.org/10.1186/s12864-018-5173-0.","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-018-5173-0","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 2018;19(1). doi:10.1186/s12864-018-5173-0","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, BMC Genomics 19 (2018).","ieee":"J. Higareda Almaraz et al., “Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes,” BMC Genomics, vol. 19, no. 1. BioMed Central, 2018.","mla":"Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics, vol. 19, no. 1, BioMed Central, 2018, doi:10.1186/s12864-018-5173-0."},"title":"Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","article_processing_charge":"No","external_id":{"isi":["000450976700002"]},"publist_id":"8035","author":[{"first_name":"Juan","full_name":"Higareda Almaraz, Juan","last_name":"Higareda Almaraz"},{"last_name":"Karbiener","full_name":"Karbiener, Michael","first_name":"Michael"},{"last_name":"Giroud","full_name":"Giroud, Maude","first_name":"Maude"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pauler","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian"},{"first_name":"Teresa","last_name":"Gerhalter","full_name":"Gerhalter, Teresa"},{"full_name":"Herzig, Stephan","last_name":"Herzig","first_name":"Stephan"},{"first_name":"Marcel","full_name":"Scheideler, Marcel","last_name":"Scheideler"}]},{"publist_id":"7947","author":[{"full_name":"Dziembowski, Stefan","last_name":"Dziembowski","first_name":"Stefan"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"},{"first_name":"Daniel","full_name":"Wichs, Daniel","last_name":"Wichs"}],"external_id":{"isi":["000442938200004"]},"article_processing_charge":"No","title":"Non-malleable codes","citation":{"ista":"Dziembowski S, Pietrzak KZ, Wichs D. 2018. Non-malleable codes. Journal of the ACM. 65(4), 20.","chicago":"Dziembowski, Stefan, Krzysztof Z Pietrzak, and Daniel Wichs. “Non-Malleable Codes.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3178432.","apa":"Dziembowski, S., Pietrzak, K. Z., & Wichs, D. (2018). Non-malleable codes. Journal of the ACM. ACM. https://doi.org/10.1145/3178432","ama":"Dziembowski S, Pietrzak KZ, Wichs D. Non-malleable codes. Journal of the ACM. 2018;65(4). doi:10.1145/3178432","short":"S. Dziembowski, K.Z. Pietrzak, D. Wichs, Journal of the ACM 65 (2018).","ieee":"S. Dziembowski, K. Z. Pietrzak, and D. Wichs, “Non-malleable codes,” Journal of the ACM, vol. 65, no. 4. ACM, 2018.","mla":"Dziembowski, Stefan, et al. “Non-Malleable Codes.” Journal of the ACM, vol. 65, no. 4, 20, ACM, 2018, doi:10.1145/3178432."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815"},{"grant_number":"259668","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"20","doi":"10.1145/3178432","date_published":"2018-08-01T00:00:00Z","date_created":"2018-12-11T11:44:40Z","isi":1,"year":"2018","day":"01","publication":"Journal of the ACM","publisher":"ACM","quality_controlled":"1","oa":1,"department":[{"_id":"KrPi"}],"date_updated":"2023-09-13T09:05:17Z","type":"journal_article","article_type":"original","status":"public","_id":"107","issue":"4","volume":65,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2009/608"}],"month":"08","intvolume":" 65","abstract":[{"lang":"eng","text":"We introduce the notion of “non-malleable codes” which relaxes the notion of error correction and error detection. Informally, a code is non-malleable if the message contained in a modified codeword is either the original message, or a completely unrelated value. In contrast to error correction and error detection, non-malleability can be achieved for very rich classes of modifications. We construct an efficient code that is non-malleable with respect to modifications that affect each bit of the codeword arbitrarily (i.e., leave it untouched, flip it, or set it to either 0 or 1), but independently of the value of the other bits of the codeword. Using the probabilistic method, we also show a very strong and general statement: there exists a non-malleable code for every “small enough” family F of functions via which codewords can be modified. Although this probabilistic method argument does not directly yield efficient constructions, it gives us efficient non-malleable codes in the random-oracle model for very general classes of tampering functions—e.g., functions where every bit in the tampered codeword can depend arbitrarily on any 99% of the bits in the original codeword. As an application of non-malleable codes, we show that they provide an elegant algorithmic solution to the task of protecting functionalities implemented in hardware (e.g., signature cards) against “tampering attacks.” In such attacks, the secret state of a physical system is tampered, in the hopes that future interaction with the modified system will reveal some secret information. This problem was previously studied in the work of Gennaro et al. in 2004 under the name “algorithmic tamper proof security” (ATP). We show that non-malleable codes can be used to achieve important improvements over the prior work. In particular, we show that any functionality can be made secure against a large class of tampering attacks, simply by encoding the secret state with a non-malleable code while it is stored in memory."}],"oa_version":"Preprint"},{"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"title":"Occluding junctions as novel regulators of tissue mechanics during wound repair","external_id":{"pmid":["30228162 "],"isi":["000451960800018"]},"article_processing_charge":"No","author":[{"last_name":"Carvalho","full_name":"Carvalho, Lara","first_name":"Lara"},{"last_name":"Patricio","full_name":"Patricio, Pedro","first_name":"Pedro"},{"first_name":"Susana","last_name":"Ponte","full_name":"Ponte, Susana"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"first_name":"Luis","full_name":"Almeida, Luis","last_name":"Almeida"},{"first_name":"André S.","full_name":"Nunes, André S.","last_name":"Nunes"},{"first_name":"Nuno A.M.","last_name":"Araújo","full_name":"Araújo, Nuno A.M."},{"last_name":"Jacinto","full_name":"Jacinto, Antonio","first_name":"Antonio"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Carvalho, Lara, et al. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” Journal of Cell Biology, vol. 217, no. 12, Rockefeller University Press, 2018, pp. 4267–83, doi:10.1083/jcb.201804048.","short":"L. Carvalho, P. Patricio, S. Ponte, C.-P.J. Heisenberg, L. Almeida, A.S. Nunes, N.A.M. Araújo, A. Jacinto, Journal of Cell Biology 217 (2018) 4267–4283.","ieee":"L. Carvalho et al., “Occluding junctions as novel regulators of tissue mechanics during wound repair,” Journal of Cell Biology, vol. 217, no. 12. Rockefeller University Press, pp. 4267–4283, 2018.","ama":"Carvalho L, Patricio P, Ponte S, et al. Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. 2018;217(12):4267-4283. doi:10.1083/jcb.201804048","apa":"Carvalho, L., Patricio, P., Ponte, S., Heisenberg, C.-P. J., Almeida, L., Nunes, A. S., … Jacinto, A. (2018). Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201804048","chicago":"Carvalho, Lara, Pedro Patricio, Susana Ponte, Carl-Philipp J Heisenberg, Luis Almeida, André S. Nunes, Nuno A.M. Araújo, and Antonio Jacinto. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” Journal of Cell Biology. Rockefeller University Press, 2018. https://doi.org/10.1083/jcb.201804048.","ista":"Carvalho L, Patricio P, Ponte S, Heisenberg C-PJ, Almeida L, Nunes AS, Araújo NAM, Jacinto A. 2018. Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. 217(12), 4267–4283."},"oa":1,"publisher":"Rockefeller University Press","quality_controlled":"1","date_created":"2018-12-16T22:59:19Z","date_published":"2018-12-01T00:00:00Z","doi":"10.1083/jcb.201804048","page":"4267-4283","publication":"Journal of Cell Biology","day":"01","year":"2018","isi":1,"status":"public","type":"journal_article","_id":"5676","department":[{"_id":"CaHe"}],"date_updated":"2023-09-13T09:11:17Z","intvolume":" 217","month":"12","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30228162","open_access":"1"}],"scopus_import":"1","pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"In epithelial tissues, cells tightly connect to each other through cell–cell junctions, but they also present the remarkable capacity of reorganizing themselves without compromising tissue integrity. Upon injury, simple epithelia efficiently resolve small lesions through the action of actin cytoskeleton contractile structures at the wound edge and cellular rearrangements. However, the underlying mechanisms and how they cooperate are still poorly understood. In this study, we combine live imaging and theoretical modeling to reveal a novel and indispensable role for occluding junctions (OJs) in this process. We demonstrate that OJ loss of function leads to defects in wound-closure dynamics: instead of contracting, wounds dramatically increase their area. OJ mutants exhibit phenotypes in cell shape, cellular rearrangements, and mechanical properties as well as in actin cytoskeleton dynamics at the wound edge. We propose that OJs are essential for wound closure by impacting on epithelial mechanics at the tissue level, which in turn is crucial for correct regulation of the cellular events occurring at the wound edge."}],"ec_funded":1,"issue":"12","volume":217,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00219525"]}},{"status":"public","conference":{"name":"International Conference on Machine Learning","start_date":"2018-04-30","location":"Vancouver, Canada","end_date":"2018-05-03"},"type":"conference","_id":"14224","title":"Clustering meets implicit generative models","department":[{"_id":"FrLo"}],"article_processing_charge":"No","external_id":{"arxiv":["1804.11130"]},"author":[{"last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"},{"last_name":"Vincent","full_name":"Vincent, Damien","first_name":"Damien"},{"first_name":"Ilya","full_name":"Tolstikhin, Ilya","last_name":"Tolstikhin"},{"full_name":"Ratsch, Gunnar","last_name":"Ratsch","first_name":"Gunnar"},{"first_name":"Sylvain","last_name":"Gelly","full_name":"Gelly, Sylvain"},{"last_name":"Scholkopf","full_name":"Scholkopf, Bernhard","first_name":"Bernhard"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"mla":"Locatello, Francesco, et al. “Clustering Meets Implicit Generative Models.” 6th International Conference on Learning Representations, 2018.","apa":"Locatello, F., Vincent, D., Tolstikhin, I., Ratsch, G., Gelly, S., & Scholkopf, B. (2018). Clustering meets implicit generative models. In 6th International Conference on Learning Representations. Vancouver, Canada.","ama":"Locatello F, Vincent D, Tolstikhin I, Ratsch G, Gelly S, Scholkopf B. Clustering meets implicit generative models. In: 6th International Conference on Learning Representations. ; 2018.","ieee":"F. Locatello, D. Vincent, I. Tolstikhin, G. Ratsch, S. Gelly, and B. Scholkopf, “Clustering meets implicit generative models,” in 6th International Conference on Learning Representations, Vancouver, Canada, 2018.","short":"F. Locatello, D. Vincent, I. Tolstikhin, G. Ratsch, S. Gelly, B. Scholkopf, in:, 6th International Conference on Learning Representations, 2018.","chicago":"Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Ratsch, Sylvain Gelly, and Bernhard Scholkopf. “Clustering Meets Implicit Generative Models.” In 6th International Conference on Learning Representations, 2018.","ista":"Locatello F, Vincent D, Tolstikhin I, Ratsch G, Gelly S, Scholkopf B. 2018. Clustering meets implicit generative models. 6th International Conference on Learning Representations. International Conference on Machine Learning."},"date_updated":"2023-09-13T09:08:24Z","month":"05","main_file_link":[{"url":"https://arxiv.org/abs/1804.11130","open_access":"1"}],"oa":1,"scopus_import":"1","quality_controlled":"1","oa_version":"Preprint","abstract":[{"text":"Clustering is a cornerstone of unsupervised learning which can be thought as disentangling multiple generative mechanisms underlying the data. In this paper we introduce an algorithmic framework to train mixtures of implicit generative models which we particularize for variational autoencoders. Relying on an additional set of discriminators, we propose a competitive procedure in which the models only need to approximate the portion of the data distribution from which they can produce realistic samples. As a byproduct, each model is simpler to train, and a clustering interpretation arises naturally from the partitioning of the training points among the models. We empirically show that our approach splits the training distribution in a reasonable way and increases the quality of the generated samples.","lang":"eng"}],"date_created":"2023-08-22T14:25:34Z","date_published":"2018-05-01T00:00:00Z","publication":"6th International Conference on Learning Representations","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2018"},{"day":"03","year":"2018","date_created":"2021-08-06T12:26:53Z","date_published":"2018-11-03T00:00:00Z","doi":"10.6084/m9.figshare.7295339.v1","related_material":{"record":[{"id":"20","status":"public","relation":"used_in_publication"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Table S1. Genes with highest betweenness. Table S2. Local and Master regulators up-regulated. Table S3. Local and Master regulators down-regulated (XLSX 23 kb)."}],"month":"11","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.7295339.v1"}],"oa":1,"publisher":"Springer Nature","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-13T09:10:47Z","citation":{"mla":"Higareda Almaraz, Juan, et al. Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes. Springer Nature, 2018, doi:10.6084/m9.figshare.7295339.v1.","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:10.6084/m9.figshare.7295339.v1","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295339.v1","ieee":"J. Higareda Almaraz et al., “Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018).","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295339.v1.","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, 10.6084/m9.figshare.7295339.v1."},"department":[{"_id":"SiHi"}],"title":"Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","article_processing_charge":"No","author":[{"first_name":"Juan","full_name":"Higareda Almaraz, Juan","last_name":"Higareda Almaraz"},{"first_name":"Michael","full_name":"Karbiener, Michael","last_name":"Karbiener"},{"first_name":"Maude","last_name":"Giroud","full_name":"Giroud, Maude"},{"full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"full_name":"Gerhalter, Teresa","last_name":"Gerhalter","first_name":"Teresa"},{"last_name":"Herzig","full_name":"Herzig, Stephan","first_name":"Stephan"},{"first_name":"Marcel","full_name":"Scheideler, Marcel","last_name":"Scheideler"}],"_id":"9807","status":"public","type":"research_data_reference"},{"status":"public","type":"research_data_reference","_id":"9808","department":[{"_id":"SiHi"}],"title":"Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","author":[{"full_name":"Higareda Almaraz, Juan","last_name":"Higareda Almaraz","first_name":"Juan"},{"last_name":"Karbiener","full_name":"Karbiener, Michael","first_name":"Michael"},{"first_name":"Maude","full_name":"Giroud, Maude","last_name":"Giroud"},{"last_name":"Pauler","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Teresa","full_name":"Gerhalter, Teresa","last_name":"Gerhalter"},{"first_name":"Stephan","full_name":"Herzig, Stephan","last_name":"Herzig"},{"last_name":"Scheideler","full_name":"Scheideler, Marcel","first_name":"Marcel"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-13T09:10:47Z","citation":{"ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, 10.6084/m9.figshare.7295369.v1.","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295369.v1.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018).","ieee":"J. Higareda Almaraz et al., “Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295369.v1","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:10.6084/m9.figshare.7295369.v1","mla":"Higareda Almaraz, Juan, et al. Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes. Springer Nature, 2018, doi:10.6084/m9.figshare.7295369.v1."},"month":"11","publisher":"Springer Nature","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.7295369.v1"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb)."}],"date_published":"2018-11-03T00:00:00Z","doi":"10.6084/m9.figshare.7295369.v1","related_material":{"record":[{"relation":"used_in_publication","id":"20","status":"public"}]},"date_created":"2021-08-06T12:31:57Z","day":"03","year":"2018"},{"page":"51 - 65","doi":"10.1145/3196494.3196534","date_published":"2018-06-01T00:00:00Z","date_created":"2018-12-11T11:45:07Z","isi":1,"year":"2018","day":"01","publication":"Proceedings of the 2018 on Asia Conference on Computer and Communication Security","quality_controlled":"1","publisher":"ACM","oa":1,"acknowledgement":"Leonid Reyzin was supported in part by IST Austria and by US NSF grants 1012910, 1012798, and 1422965; this research was performed while he was visiting IST Austria.","publist_id":"7723","author":[{"full_name":"Alwen, Joel F","last_name":"Alwen","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter","full_name":"Gazi, Peter","last_name":"Gazi"},{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","last_name":"Kamath Hosdurg","full_name":"Kamath Hosdurg, Chethan"},{"last_name":"Klein","full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen"},{"first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang","full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"},{"first_name":"Lenoid","full_name":"Reyzin, Lenoid","last_name":"Reyzin"},{"full_name":"Rolinek, Michal","last_name":"Rolinek","first_name":"Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87"},{"id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","last_name":"Rybar","full_name":"Rybar, Michal"}],"article_processing_charge":"No","external_id":{"isi":["000516620100005"]},"title":"On the memory hardness of data independent password hashing functions","citation":{"chicago":"Alwen, Joel F, Peter Gazi, Chethan Kamath Hosdurg, Karen Klein, Georg F Osang, Krzysztof Z Pietrzak, Lenoid Reyzin, Michal Rolinek, and Michal Rybar. “On the Memory Hardness of Data Independent Password Hashing Functions.” In Proceedings of the 2018 on Asia Conference on Computer and Communication Security, 51–65. ACM, 2018. https://doi.org/10.1145/3196494.3196534.","ista":"Alwen JF, Gazi P, Kamath Hosdurg C, Klein K, Osang GF, Pietrzak KZ, Reyzin L, Rolinek M, Rybar M. 2018. On the memory hardness of data independent password hashing functions. Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ASIACCS: Asia Conference on Computer and Communications Security , 51–65.","mla":"Alwen, Joel F., et al. “On the Memory Hardness of Data Independent Password Hashing Functions.” Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65, doi:10.1145/3196494.3196534.","ama":"Alwen JF, Gazi P, Kamath Hosdurg C, et al. On the memory hardness of data independent password hashing functions. In: Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ACM; 2018:51-65. doi:10.1145/3196494.3196534","apa":"Alwen, J. F., Gazi, P., Kamath Hosdurg, C., Klein, K., Osang, G. F., Pietrzak, K. Z., … Rybar, M. (2018). On the memory hardness of data independent password hashing functions. In Proceedings of the 2018 on Asia Conference on Computer and Communication Security (pp. 51–65). Incheon, Republic of Korea: ACM. https://doi.org/10.1145/3196494.3196534","short":"J.F. Alwen, P. Gazi, C. Kamath Hosdurg, K. Klein, G.F. Osang, K.Z. Pietrzak, L. Reyzin, M. Rolinek, M. Rybar, in:, Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65.","ieee":"J. F. Alwen et al., “On the memory hardness of data independent password hashing functions,” in Proceedings of the 2018 on Asia Conference on Computer and Communication Security, Incheon, Republic of Korea, 2018, pp. 51–65."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice"},{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://eprint.iacr.org/2016/783","open_access":"1"}],"month":"06","abstract":[{"text":"We show attacks on five data-independent memory-hard functions (iMHF) that were submitted to the password hashing competition (PHC). Informally, an MHF is a function which cannot be evaluated on dedicated hardware, like ASICs, at significantly lower hardware and/or energy cost than evaluating a single instance on a standard single-core architecture. Data-independent means the memory access pattern of the function is independent of the input; this makes iMHFs harder to construct than data-dependent ones, but the latter can be attacked by various side-channel attacks. Following [Alwen-Blocki'16], we capture the evaluation of an iMHF as a directed acyclic graph (DAG). The cumulative parallel pebbling complexity of this DAG is a measure for the hardware cost of evaluating the iMHF on an ASIC. Ideally, one would like the complexity of a DAG underlying an iMHF to be as close to quadratic in the number of nodes of the graph as possible. Instead, we show that (the DAGs underlying) the following iMHFs are far from this bound: Rig.v2, TwoCats and Gambit each having an exponent no more than 1.75. Moreover, we show that the complexity of the iMHF modes of the PHC finalists Pomelo and Lyra2 have exponents at most 1.83 and 1.67 respectively. To show this we investigate a combinatorial property of each underlying DAG (called its depth-robustness. By establishing upper bounds on this property we are then able to apply the general technique of [Alwen-Block'16] for analyzing the hardware costs of an iMHF.","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"KrPi"},{"_id":"HeEd"},{"_id":"VlKo"}],"date_updated":"2023-09-13T09:13:12Z","type":"conference","conference":{"name":"ASIACCS: Asia Conference on Computer and Communications Security ","end_date":"2018-06-08","location":"Incheon, Republic of Korea","start_date":"2018-06-04"},"status":"public","_id":"193"},{"day":"31","year":"2018","isi":1,"date_created":"2018-12-11T11:45:42Z","doi":"10.1007/978-3-319-78381-9_1","date_published":"2018-03-31T00:00:00Z","page":"3 - 28","acknowledgement":"Research supported in part by the Defense Advanced Research Projects Agency (DARPA) and the U.S. Army Research Office under the SafeWare program. Opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views, position or policy of the Government. The second author was also supported by the European Research Council, ERC consolidator grant (682815 - TOCNeT).","oa":1,"publisher":"Springer","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Micciancio D, Walter M. 2018. On the bit security of cryptographic primitives. Eurocrypt: Advances in Cryptology, LNCS, vol. 10820, 3–28.","chicago":"Micciancio, Daniele, and Michael Walter. “On the Bit Security of Cryptographic Primitives,” 10820:3–28. Springer, 2018. https://doi.org/10.1007/978-3-319-78381-9_1.","ama":"Micciancio D, Walter M. On the bit security of cryptographic primitives. In: Vol 10820. Springer; 2018:3-28. doi:10.1007/978-3-319-78381-9_1","apa":"Micciancio, D., & Walter, M. (2018). On the bit security of cryptographic primitives (Vol. 10820, pp. 3–28). Presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78381-9_1","short":"D. Micciancio, M. Walter, in:, Springer, 2018, pp. 3–28.","ieee":"D. Micciancio and M. Walter, “On the bit security of cryptographic primitives,” presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10820, pp. 3–28.","mla":"Micciancio, Daniele, and Michael Walter. On the Bit Security of Cryptographic Primitives. Vol. 10820, Springer, 2018, pp. 3–28, doi:10.1007/978-3-319-78381-9_1."},"title":"On the bit security of cryptographic primitives","article_processing_charge":"No","external_id":{"isi":["000517097500001"]},"publist_id":"7581","author":[{"full_name":"Micciancio, Daniele","last_name":"Micciancio","first_name":"Daniele"},{"first_name":"Michael","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3186-2482","full_name":"Walter, Michael","last_name":"Walter"}],"project":[{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":10820,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We introduce a formal quantitative notion of “bit security” for a general type of cryptographic games (capturing both decision and search problems), aimed at capturing the intuition that a cryptographic primitive with k-bit security is as hard to break as an ideal cryptographic function requiring a brute force attack on a k-bit key space. Our new definition matches the notion of bit security commonly used by cryptographers and cryptanalysts when studying search (e.g., key recovery) problems, where the use of the traditional definition is well established. However, it produces a quantitatively different metric in the case of decision (indistinguishability) problems, where the use of (a straightforward generalization of) the traditional definition is more problematic and leads to a number of paradoxical situations or mismatches between theoretical/provable security and practical/common sense intuition. Key to our new definition is to consider adversaries that may explicitly declare failure of the attack. We support and justify the new definition by proving a number of technical results, including tight reductions between several standard cryptographic problems, a new hybrid theorem that preserves bit security, and an application to the security analysis of indistinguishability primitives making use of (approximate) floating point numbers. This is the first result showing that (standard precision) 53-bit floating point numbers can be used to achieve 100-bit security in the context of cryptographic primitives with general indistinguishability-based security definitions. Previous results of this type applied only to search problems, or special types of decision problems."}],"intvolume":" 10820","month":"03","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2018/077"}],"alternative_title":["LNCS"],"scopus_import":"1","date_updated":"2023-09-13T09:12:04Z","department":[{"_id":"KrPi"}],"_id":"300","status":"public","conference":{"location":"Tel Aviv, Israel","end_date":"2018-05-03","start_date":"2018-04-29","name":"Eurocrypt: Advances in Cryptology"},"type":"conference"},{"day":"29","publication":"SIAM J Discrete Math","isi":1,"year":"2018","doi":"10.1137/16M1097201","date_published":"2018-03-29T00:00:00Z","date_created":"2018-12-11T11:45:46Z","page":"750 - 782","acknowledgement":"This work was partially supported by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics,” through grant I02979-N35 of the Austrian Science Fund (FWF).","quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics ","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"H. Edelsbrunner, M. Iglesias Ham, SIAM J Discrete Math 32 (2018) 750–782.","ieee":"H. Edelsbrunner and M. Iglesias Ham, “On the optimality of the FCC lattice for soft sphere packing,” SIAM J Discrete Math, vol. 32, no. 1. Society for Industrial and Applied Mathematics , pp. 750–782, 2018.","ama":"Edelsbrunner H, Iglesias Ham M. On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. 2018;32(1):750-782. doi:10.1137/16M1097201","apa":"Edelsbrunner, H., & Iglesias Ham, M. (2018). On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M1097201","mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “On the Optimality of the FCC Lattice for Soft Sphere Packing.” SIAM J Discrete Math, vol. 32, no. 1, Society for Industrial and Applied Mathematics , 2018, pp. 750–82, doi:10.1137/16M1097201.","ista":"Edelsbrunner H, Iglesias Ham M. 2018. On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. 32(1), 750–782.","chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “On the Optimality of the FCC Lattice for Soft Sphere Packing.” SIAM J Discrete Math. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M1097201."},"title":"On the optimality of the FCC lattice for soft sphere packing","author":[{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Iglesias Ham","full_name":"Iglesias Ham, Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","first_name":"Mabel"}],"publist_id":"7553","external_id":{"isi":["000428958900038"]},"article_processing_charge":"No","project":[{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["08954801"]},"publication_status":"published","issue":"1","volume":32,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Motivated by biological questions, we study configurations of equal spheres that neither pack nor cover. Placing their centers on a lattice, we define the soft density of the configuration by penalizing multiple overlaps. Considering the 1-parameter family of diagonally distorted 3-dimensional integer lattices, we show that the soft density is maximized at the FCC lattice."}],"month":"03","intvolume":" 32","scopus_import":"1","main_file_link":[{"url":"http://pdfs.semanticscholar.org/d2d5/6da00fbc674e6a8b1bb9d857167e54200dc6.pdf","open_access":"1"}],"date_updated":"2023-09-13T09:34:38Z","department":[{"_id":"HeEd"}],"_id":"312","status":"public","type":"journal_article","article_type":"original"},{"citation":{"ieee":"A. Akopyan, “On the number of non-hexagons in a planar tiling,” Comptes Rendus Mathematique, vol. 356, no. 4. Elsevier, pp. 412–414, 2018.","short":"A. Akopyan, Comptes Rendus Mathematique 356 (2018) 412–414.","apa":"Akopyan, A. (2018). On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. Elsevier. https://doi.org/10.1016/j.crma.2018.03.005","ama":"Akopyan A. On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. 2018;356(4):412-414. doi:10.1016/j.crma.2018.03.005","mla":"Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes Rendus Mathematique, vol. 356, no. 4, Elsevier, 2018, pp. 412–14, doi:10.1016/j.crma.2018.03.005.","ista":"Akopyan A. 2018. On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. 356(4), 412–414.","chicago":"Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes Rendus Mathematique. Elsevier, 2018. https://doi.org/10.1016/j.crma.2018.03.005."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000430402700009"],"arxiv":["1805.01652"]},"publist_id":"7420","author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan"}],"title":"On the number of non-hexagons in a planar tiling","year":"2018","isi":1,"publication":"Comptes Rendus Mathematique","day":"01","page":"412-414","date_created":"2018-12-11T11:46:19Z","doi":"10.1016/j.crma.2018.03.005","date_published":"2018-04-01T00:00:00Z","oa":1,"publisher":"Elsevier","quality_controlled":"1","date_updated":"2023-09-13T09:34:12Z","department":[{"_id":"HeEd"}],"_id":"409","type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"issn":["1631073X"]},"language":[{"iso":"eng"}],"volume":356,"issue":"4","abstract":[{"text":"We give a simple proof of T. Stehling's result [4], whereby in any normal tiling of the plane with convex polygons with number of sides not less than six, all tiles except a finite number are hexagons.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1805.01652","open_access":"1"}],"scopus_import":"1","intvolume":" 356","month":"04"},{"title":"Partners and rivals in direct reciprocity","external_id":{"isi":["000446612000016"]},"article_processing_charge":"No","publist_id":"7404","author":[{"orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Hilbe, Christian, et al. “Partners and Rivals in Direct Reciprocity.” Nature Human Behaviour, vol. 2, Nature Publishing Group, 2018, pp. 469–477, doi:10.1038/s41562-018-0320-9.","ieee":"C. Hilbe, K. Chatterjee, and M. Nowak, “Partners and rivals in direct reciprocity,” Nature Human Behaviour, vol. 2. Nature Publishing Group, pp. 469–477, 2018.","short":"C. Hilbe, K. Chatterjee, M. Nowak, Nature Human Behaviour 2 (2018) 469–477.","ama":"Hilbe C, Chatterjee K, Nowak M. Partners and rivals in direct reciprocity. Nature Human Behaviour. 2018;2:469–477. doi:10.1038/s41562-018-0320-9","apa":"Hilbe, C., Chatterjee, K., & Nowak, M. (2018). Partners and rivals in direct reciprocity. Nature Human Behaviour. Nature Publishing Group. https://doi.org/10.1038/s41562-018-0320-9","chicago":"Hilbe, Christian, Krishnendu Chatterjee, and Martin Nowak. “Partners and Rivals in Direct Reciprocity.” Nature Human Behaviour. Nature Publishing Group, 2018. https://doi.org/10.1038/s41562-018-0320-9.","ista":"Hilbe C, Chatterjee K, Nowak M. 2018. Partners and rivals in direct reciprocity. Nature Human Behaviour. 2, 469–477."},"project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_created":"2018-12-11T11:46:22Z","date_published":"2018-03-19T00:00:00Z","doi":"10.1038/s41562-018-0320-9","page":"469–477","publication":"Nature Human Behaviour","day":"19","year":"2018","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:46:25Z","ddc":["000"],"date_updated":"2023-09-13T09:38:54Z","status":"public","article_type":"review","type":"journal_article","_id":"419","ec_funded":1,"related_material":{"link":[{"relation":"erratum","url":"http://doi.org/10.1038/s41562-018-0342-3"}]},"volume":2,"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":598033,"date_updated":"2020-07-14T12:46:25Z","file_name":"2018_NatureHumanBeh_Hilbe.pdf","date_created":"2019-11-19T08:19:51Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7052","checksum":"571b8cc0ba14e8d5d8b18e439a9835eb"}],"publication_status":"published","intvolume":" 2","month":"03","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"Reciprocity is a major factor in human social life and accounts for a large part of cooperation in our communities. Direct reciprocity arises when repeated interactions occur between the same individuals. The framework of iterated games formalizes this phenomenon. Despite being introduced more than five decades ago, the concept keeps offering beautiful surprises. Recent theoretical research driven by new mathematical tools has proposed a remarkable dichotomy among the crucial strategies: successful individuals either act as partners or as rivals. Rivals strive for unilateral advantages by applying selfish or extortionate strategies. Partners aim to share the payoff for mutual cooperation, but are ready to fight back when being exploited. Which of these behaviours evolves depends on the environment. Whereas small population sizes and a limited number of rounds favour rivalry, partner strategies are selected when populations are large and relationships stable. Only partners allow for evolution of cooperation, while the rivals’ attempt to put themselves first leads to defection. Hilbe et al. synthesize recent theoretical work on zero-determinant and ‘rival’ versus ‘partner’ strategies in social dilemmas. They describe the environments under which these contrasting selfish or cooperative strategies emerge in evolution.","lang":"eng"}]},{"oa_version":"Submitted Version","abstract":[{"text":"We provide a procedure for detecting the sub-segments of an incrementally observed Boolean signal ω that match a given temporal pattern ϕ. As a pattern specification language, we use timed regular expressions, a formalism well-suited for expressing properties of concurrent asynchronous behaviors embedded in metric time. We construct a timed automaton accepting the timed language denoted by ϕ and modify it slightly for the purpose of matching. We then apply zone-based reachability computation to this automaton while it reads ω, and retrieve all the matching segments from the results. Since the procedure is automaton based, it can be applied to patterns specified by other formalisms such as timed temporal logics reducible to timed automata or directly encoded as timed automata. The procedure has been implemented and its performance on synthetic examples is demonstrated.","lang":"eng"}],"month":"08","intvolume":" 11022","alternative_title":["LNCS"],"scopus_import":"1","file":[{"date_created":"2020-05-14T11:34:34Z","file_name":"2018_LNCS_Bakhirkin.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:03Z","file_size":374851,"checksum":"436b7574934324cfa7d1d3986fddc65b","file_id":"7831","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-030-00150-6"]},"publication_status":"published","volume":11022,"_id":"78","status":"public","type":"conference","conference":{"location":"Bejing, China","end_date":"2018-09-06","start_date":"2018-09-04","name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"ddc":["000"],"date_updated":"2023-09-13T09:35:46Z","file_date_updated":"2020-07-14T12:48:03Z","department":[{"_id":"ToHe"}],"publisher":"Springer","quality_controlled":"1","oa":1,"day":"26","has_accepted_license":"1","isi":1,"year":"2018","date_published":"2018-08-26T00:00:00Z","doi":"10.1007/978-3-030-00151-3_13","date_created":"2018-12-11T11:44:31Z","page":"215 - 232","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. Online timed pattern matching using automata. In: Vol 11022. Springer; 2018:215-232. doi:10.1007/978-3-030-00151-3_13","apa":"Bakhirkin, A., Ferrere, T., Nickovic, D., Maler, O., & Asarin, E. (2018). Online timed pattern matching using automata (Vol. 11022, pp. 215–232). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_13","short":"A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, E. Asarin, in:, Springer, 2018, pp. 215–232.","ieee":"A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, and E. Asarin, “Online timed pattern matching using automata,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China, 2018, vol. 11022, pp. 215–232.","mla":"Bakhirkin, Alexey, et al. Online Timed Pattern Matching Using Automata. Vol. 11022, Springer, 2018, pp. 215–32, doi:10.1007/978-3-030-00151-3_13.","ista":"Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. 2018. Online timed pattern matching using automata. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 215–232.","chicago":"Bakhirkin, Alexey, Thomas Ferrere, Dejan Nickovic, Oded Maler, and Eugene Asarin. “Online Timed Pattern Matching Using Automata,” 11022:215–32. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_13."},"title":"Online timed pattern matching using automata","publist_id":"7976","author":[{"first_name":"Alexey","full_name":"Bakhirkin, Alexey","last_name":"Bakhirkin"},{"orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","last_name":"Ferrere","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"first_name":"Dejan","full_name":"Nickovic, Dejan","last_name":"Nickovic"},{"first_name":"Oded","full_name":"Maler, Oded","last_name":"Maler"},{"first_name":"Eugene","full_name":"Asarin, Eugene","last_name":"Asarin"}],"external_id":{"isi":["000884993200013"]},"article_processing_charge":"No"},{"issue":"1","volume":8,"publication_status":"published","file":[{"file_id":"5256","checksum":"20af238ca4ba6491b77270be8d826bf5","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2018-1016-v1+1_2018_Brauns_Palladium_gates.pdf","date_created":"2018-12-12T10:17:04Z","file_size":1850530,"date_updated":"2020-07-14T12:46:02Z","creator":"system"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"04","intvolume":" 8","abstract":[{"lang":"eng","text":"We replace the established aluminium gates for the formation of quantum dots in silicon with gates made from palladium. We study the morphology of both aluminium and palladium gates with transmission electron microscopy. The native aluminium oxide is found to be formed all around the aluminium gates, which could lead to the formation of unintentional dots. Therefore, we report on a novel fabrication route that replaces aluminium and its native oxide by palladium with atomic-layer-deposition-grown aluminium oxide. Using this approach, we show the formation of low-disorder gate-defined quantum dots, which are reproducibly fabricated. Furthermore, palladium enables us to further shrink the gate design, allowing us to perform electron transport measurements in the few-electron regime in devices comprising only two gate layers, a major technological advancement. It remains to be seen, whether the introduction of palladium gates can improve the excellent results on electron and nuclear spin qubits defined with an aluminium gate stack."}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:46:02Z","department":[{"_id":"GeKa"}],"date_updated":"2023-09-13T09:38:00Z","ddc":["539"],"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":"1016","_id":"317","date_published":"2018-04-09T00:00:00Z","doi":"10.1038/s41598-018-24004-y","date_created":"2018-12-11T11:45:47Z","has_accepted_license":"1","isi":1,"year":"2018","day":"09","publication":"Scientific Reports","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"author":[{"full_name":"Brauns, Matthias","last_name":"Brauns","id":"33F94E3C-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"first_name":"Sergey","last_name":"Amitonov","full_name":"Amitonov, Sergey"},{"last_name":"Spruijtenburg","full_name":"Spruijtenburg, Paul","first_name":"Paul"},{"last_name":"Zwanenburg","full_name":"Zwanenburg, Floris","first_name":"Floris"}],"publist_id":"7548","external_id":{"isi":["000429404300013"]},"article_processing_charge":"No","title":"Palladium gates for reproducible quantum dots in silicon","citation":{"ista":"Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. 2018. Palladium gates for reproducible quantum dots in silicon. Scientific Reports. 8(1), 5690.","chicago":"Brauns, Matthias, Sergey Amitonov, Paul Spruijtenburg, and Floris Zwanenburg. “Palladium Gates for Reproducible Quantum Dots in Silicon.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-24004-y.","short":"M. Brauns, S. Amitonov, P. Spruijtenburg, F. Zwanenburg, Scientific Reports 8 (2018).","ieee":"M. Brauns, S. Amitonov, P. Spruijtenburg, and F. Zwanenburg, “Palladium gates for reproducible quantum dots in silicon,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","ama":"Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. Palladium gates for reproducible quantum dots in silicon. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-24004-y","apa":"Brauns, M., Amitonov, S., Spruijtenburg, P., & Zwanenburg, F. (2018). Palladium gates for reproducible quantum dots in silicon. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-24004-y","mla":"Brauns, Matthias, et al. “Palladium Gates for Reproducible Quantum Dots in Silicon.” Scientific Reports, vol. 8, no. 1, 5690, Nature Publishing Group, 2018, doi:10.1038/s41598-018-24004-y."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"5690"},{"quality_controlled":"1","publisher":"FASEB","oa":1,"isi":1,"year":"2018","day":"29","publication":"The FASEB Journal","page":"6808-6821","doi":"10.1096/fj.201800443","date_published":"2018-11-29T00:00:00Z","date_created":"2018-12-11T11:45:08Z","project":[{"_id":"25E3D34E-B435-11E9-9278-68D0E5697425","name":"Individual function and social role of oxytocin-like neuropeptides in ants"}],"citation":{"mla":"Liutkeviciute, Zita, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” The FASEB Journal, vol. 32, no. 12, FASEB, 2018, pp. 6808–21, doi:10.1096/fj.201800443.","apa":"Liutkeviciute, Z., Gil Mansilla, E., Eder, T., Casillas Perez, B. E., Giulia Di Giglio, M., Muratspahić, E., … Gruber, C. (2018). Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. FASEB. https://doi.org/10.1096/fj.201800443","ama":"Liutkeviciute Z, Gil Mansilla E, Eder T, et al. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 2018;32(12):6808-6821. doi:10.1096/fj.201800443","ieee":"Z. Liutkeviciute et al., “Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity,” The FASEB Journal, vol. 32, no. 12. FASEB, pp. 6808–6821, 2018.","short":"Z. Liutkeviciute, E. Gil Mansilla, T. Eder, B.E. Casillas Perez, M. Giulia Di Giglio, E. Muratspahić, F. Grebien, T. Rattei, M. Muttenthaler, S. Cremer, C. Gruber, The FASEB Journal 32 (2018) 6808–6821.","chicago":"Liutkeviciute, Zita, Esther Gil Mansilla, Thomas Eder, Barbara E Casillas Perez, Maria Giulia Di Giglio, Edin Muratspahić, Florian Grebien, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” The FASEB Journal. FASEB, 2018. https://doi.org/10.1096/fj.201800443.","ista":"Liutkeviciute Z, Gil Mansilla E, Eder T, Casillas Perez BE, Giulia Di Giglio M, Muratspahić E, Grebien F, Rattei T, Muttenthaler M, Cremer S, Gruber C. 2018. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 32(12), 6808–6821."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7721","author":[{"first_name":"Zita","last_name":"Liutkeviciute","full_name":"Liutkeviciute, Zita"},{"last_name":"Gil Mansilla","full_name":"Gil Mansilla, Esther","first_name":"Esther"},{"first_name":"Thomas","full_name":"Eder, Thomas","last_name":"Eder"},{"full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maria","full_name":"Giulia Di Giglio, Maria","last_name":"Giulia Di Giglio"},{"full_name":"Muratspahić, Edin","last_name":"Muratspahić","first_name":"Edin"},{"first_name":"Florian","last_name":"Grebien","full_name":"Grebien, Florian"},{"first_name":"Thomas","last_name":"Rattei","full_name":"Rattei, Thomas"},{"first_name":"Markus","last_name":"Muttenthaler","full_name":"Muttenthaler, Markus"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"},{"first_name":"Christian","full_name":"Gruber, Christian","last_name":"Gruber"}],"article_processing_charge":"No","external_id":{"pmid":["29939785"],"isi":["000449359700035"]},"title":"Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity","abstract":[{"text":"Ants are emerging model systems to study cellular signaling because distinct castes possess different physiologic phenotypes within the same colony. Here we studied the functionality of inotocin signaling, an insect ortholog of mammalian oxytocin (OT), which was recently discovered in ants. In Lasius ants, we determined that specialization within the colony, seasonal factors, and physiologic conditions down-regulated the expression of the OT-like signaling system. Given this natural variation, we interrogated its function using RNAi knockdowns. Next-generation RNA sequencing of OT-like precursor knock-down ants highlighted its role in the regulation of genes involved in metabolism. Knock-down ants exhibited higher walking activity and increased self-grooming in the brood chamber. We propose that OT-like signaling in ants is important for regulating metabolic processes and locomotion.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"url":" https://doi.org/10.1096/fj.201800443","open_access":"1"}],"month":"11","intvolume":" 32","publication_identifier":{"issn":["08926638"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":32,"issue":"12","_id":"194","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-13T09:37:32Z","department":[{"_id":"SyCr"}]},{"publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"page":"764 - 767","date_published":"2018-07-16T00:00:00Z","doi":"10.1038/s41589-018-0090-8","date_created":"2018-12-11T11:44:56Z","isi":1,"has_accepted_license":"1","year":"2018","day":"16","publication":"Nature Chemical Biology","publist_id":"7762","author":[{"full_name":"Fehrentz, Timm","last_name":"Fehrentz","first_name":"Timm"},{"first_name":"Florian","last_name":"Huber","full_name":"Huber, Florian"},{"first_name":"Nina","full_name":"Hartrampf, Nina","last_name":"Hartrampf"},{"full_name":"Bruegmann, Tobias","last_name":"Bruegmann","first_name":"Tobias"},{"first_name":"James","full_name":"Frank, James","last_name":"Frank"},{"full_name":"Fine, Nicholas","last_name":"Fine","first_name":"Nicholas"},{"first_name":"Daniela","full_name":"Malan, Daniela","last_name":"Malan"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"},{"first_name":"Denis","full_name":"Tikhonov, Denis","last_name":"Tikhonov"},{"first_name":"Maritn","last_name":"Sumser","full_name":"Sumser, Maritn"},{"first_name":"Philipp","last_name":"Sasse","full_name":"Sasse, Philipp"},{"full_name":"Hodson, David","last_name":"Hodson","first_name":"David"},{"last_name":"Zhorov","full_name":"Zhorov, Boris","first_name":"Boris"},{"first_name":"Nikolaj","last_name":"Klocker","full_name":"Klocker, Nikolaj"},{"full_name":"Trauner, Dirk","last_name":"Trauner","first_name":"Dirk"}],"article_processing_charge":"No","external_id":{"isi":["000438970200010"]},"title":"Optical control of L-type Ca2+ channels using a diltiazem photoswitch","citation":{"mla":"Fehrentz, Timm, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” Nature Chemical Biology, vol. 14, no. 8, Nature Publishing Group, 2018, pp. 764–67, doi:10.1038/s41589-018-0090-8.","ieee":"T. Fehrentz et al., “Optical control of L-type Ca2+ channels using a diltiazem photoswitch,” Nature Chemical Biology, vol. 14, no. 8. Nature Publishing Group, pp. 764–767, 2018.","short":"T. Fehrentz, F. Huber, N. Hartrampf, T. Bruegmann, J. Frank, N. Fine, D. Malan, J.G. Danzl, D. Tikhonov, M. Sumser, P. Sasse, D. Hodson, B. Zhorov, N. Klocker, D. Trauner, Nature Chemical Biology 14 (2018) 764–767.","ama":"Fehrentz T, Huber F, Hartrampf N, et al. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 2018;14(8):764-767. doi:10.1038/s41589-018-0090-8","apa":"Fehrentz, T., Huber, F., Hartrampf, N., Bruegmann, T., Frank, J., Fine, N., … Trauner, D. (2018). Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0090-8","chicago":"Fehrentz, Timm, Florian Huber, Nina Hartrampf, Tobias Bruegmann, James Frank, Nicholas Fine, Daniela Malan, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” Nature Chemical Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0090-8.","ista":"Fehrentz T, Huber F, Hartrampf N, Bruegmann T, Frank J, Fine N, Malan D, Danzl JG, Tikhonov D, Sumser M, Sasse P, Hodson D, Zhorov B, Klocker N, Trauner D. 2018. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 14(8), 764–767."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","month":"07","intvolume":" 14","abstract":[{"lang":"eng","text":"L-type Ca2+ channels (LTCCs) play a crucial role in excitation-contraction coupling and release of hormones from secretory cells. They are targets of antihypertensive and antiarrhythmic drugs such as diltiazem. Here, we present a photoswitchable diltiazem, FHU-779, which can be used to reversibly block endogenous LTCCs by light. FHU-779 is as potent as diltiazem and can be used to place pancreatic β-cell function and cardiac activity under optical control."}],"oa_version":"Submitted Version","related_material":{"link":[{"url":"https://doi.org/10.1038/s41589-021-00744-3","relation":"erratum"}]},"issue":"8","volume":14,"publication_status":"published","file":[{"date_updated":"2020-07-14T12:45:03Z","file_size":6321000,"creator":"dernst","date_created":"2020-05-14T12:14:09Z","file_name":"2018_NatureChemicalBiology_Fehrentz.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"d42935094ec845f54a0688bf12986d62","file_id":"7832"}],"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"159","file_date_updated":"2020-07-14T12:45:03Z","department":[{"_id":"JoDa"}],"date_updated":"2023-09-13T09:36:35Z","ddc":["570"]},{"publisher":"Springer","quality_controlled":"1","oa":1,"isi":1,"year":"2018","day":"15","page":"53-70","date_published":"2018-08-15T00:00:00Z","doi":"10.1007/978-3-319-99154-2_4","date_created":"2018-12-11T11:44:31Z","citation":{"ama":"Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. Parameter-independent strategies for pMDPs via POMDPs. In: Vol 11024. Springer; 2018:53-70. doi:10.1007/978-3-319-99154-2_4","apa":"Arming, S., Bartocci, E., Chatterjee, K., Katoen, J. P., & Sokolova, A. (2018). Parameter-independent strategies for pMDPs via POMDPs (Vol. 11024, pp. 53–70). Presented at the QEST: Quantitative Evaluation of Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-319-99154-2_4","short":"S. Arming, E. Bartocci, K. Chatterjee, J.P. Katoen, A. Sokolova, in:, Springer, 2018, pp. 53–70.","ieee":"S. Arming, E. Bartocci, K. Chatterjee, J. P. Katoen, and A. Sokolova, “Parameter-independent strategies for pMDPs via POMDPs,” presented at the QEST: Quantitative Evaluation of Systems, Beijing, China, 2018, vol. 11024, pp. 53–70.","mla":"Arming, Sebastian, et al. Parameter-Independent Strategies for PMDPs via POMDPs. Vol. 11024, Springer, 2018, pp. 53–70, doi:10.1007/978-3-319-99154-2_4.","ista":"Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. 2018. Parameter-independent strategies for pMDPs via POMDPs. QEST: Quantitative Evaluation of Systems, LNCS, vol. 11024, 53–70.","chicago":"Arming, Sebastian, Ezio Bartocci, Krishnendu Chatterjee, Joost P Katoen, and Ana Sokolova. “Parameter-Independent Strategies for PMDPs via POMDPs,” 11024:53–70. Springer, 2018. https://doi.org/10.1007/978-3-319-99154-2_4."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Sebastian","last_name":"Arming","full_name":"Arming, Sebastian"},{"last_name":"Bartocci","full_name":"Bartocci, Ezio","first_name":"Ezio"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Katoen, Joost P","last_name":"Katoen","id":"4524F760-F248-11E8-B48F-1D18A9856A87","first_name":"Joost P"},{"full_name":"Sokolova, Ana","last_name":"Sokolova","first_name":"Ana"}],"publist_id":"7975","article_processing_charge":"No","external_id":{"arxiv":["1806.05126"],"isi":["000548912200004"]},"title":"Parameter-independent strategies for pMDPs via POMDPs","abstract":[{"lang":"eng","text":"Markov Decision Processes (MDPs) are a popular class of models suitable for solving control decision problems in probabilistic reactive systems. We consider parametric MDPs (pMDPs) that include parameters in some of the transition probabilities to account for stochastic uncertainties of the environment such as noise or input disturbances. We study pMDPs with reachability objectives where the parameter values are unknown and impossible to measure directly during execution, but there is a probability distribution known over the parameter values. We study for the first time computing parameter-independent strategies that are expectation optimal, i.e., optimize the expected reachability probability under the probability distribution over the parameters. We present an encoding of our problem to partially observable MDPs (POMDPs), i.e., a reduction of our problem to computing optimal strategies in POMDPs. We evaluate our method experimentally on several benchmarks: a motivating (repeated) learner model; a series of benchmarks of varying configurations of a robot moving on a grid; and a consensus protocol."}],"oa_version":"Preprint","scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.05126"}],"month":"08","intvolume":" 11024","publication_status":"published","language":[{"iso":"eng"}],"volume":11024,"_id":"79","type":"conference","conference":{"location":"Beijing, China","end_date":"2018-09-07","start_date":"2018-09-04","name":"QEST: Quantitative Evaluation of Systems"},"status":"public","date_updated":"2023-09-13T09:38:28Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}]},{"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1804.11130","open_access":"1"}],"month":"04","abstract":[{"lang":"eng","text":"A common assumption in causal modeling posits that the data is generated by a\r\nset of independent mechanisms, and algorithms should aim to recover this\r\nstructure. Standard unsupervised learning, however, is often concerned with\r\ntraining a single model to capture the overall distribution or aspects thereof.\r\nInspired by clustering approaches, we consider mixtures of implicit generative\r\nmodels that ``disentangle'' the independent generative mechanisms underlying\r\nthe data. Relying on an additional set of discriminators, we propose a\r\ncompetitive training procedure in which the models only need to capture the\r\nportion of the data distribution from which they can produce realistic samples.\r\nAs a by-product, each model is simpler and faster to train. We empirically show\r\nthat our approach splits the training distribution in a sensible way and\r\nincreases the quality of the generated samples."}],"oa_version":"Preprint","date_created":"2023-09-13T12:20:49Z","doi":"10.48550/arXiv.1804.11130","date_published":"2018-04-30T00:00:00Z","publication_status":"submitted","year":"2018","publication":"arXiv","language":[{"iso":"eng"}],"day":"30","type":"preprint","status":"public","_id":"14327","article_number":"1804.11130","external_id":{"arxiv":["1804.11130"]},"article_processing_charge":"No","author":[{"last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"},{"first_name":"Damien","full_name":"Vincent, Damien","last_name":"Vincent"},{"first_name":"Ilya","last_name":"Tolstikhin","full_name":"Tolstikhin, Ilya"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"},{"full_name":"Gelly, Sylvain","last_name":"Gelly","first_name":"Sylvain"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"}],"title":"Competitive training of mixtures of independent deep generative models","department":[{"_id":"FrLo"}],"date_updated":"2023-09-13T12:23:03Z","citation":{"ama":"Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive training of mixtures of independent deep generative models. arXiv. doi:10.48550/arXiv.1804.11130","apa":"Locatello, F., Vincent, D., Tolstikhin, I., Rätsch, G., Gelly, S., & Schölkopf, B. (n.d.). Competitive training of mixtures of independent deep generative models. arXiv. https://doi.org/10.48550/arXiv.1804.11130","ieee":"F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, and B. Schölkopf, “Competitive training of mixtures of independent deep generative models,” arXiv. .","short":"F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, B. Schölkopf, ArXiv (n.d.).","mla":"Locatello, Francesco, et al. “Competitive Training of Mixtures of Independent Deep Generative Models.” ArXiv, 1804.11130, doi:10.48550/arXiv.1804.11130.","ista":"Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive training of mixtures of independent deep generative models. arXiv, 1804.11130.","chicago":"Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Rätsch, Sylvain Gelly, and Bernhard Schölkopf. “Competitive Training of Mixtures of Independent Deep Generative Models.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1804.11130."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1"},{"project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"title":"Persistence of translational symmetry in the BCS model with radial pair interaction","author":[{"full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746","last_name":"Deuchert","first_name":"Andreas","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Geisinge, Alissa","last_name":"Geisinge","first_name":"Alissa"},{"last_name":"Hainzl","full_name":"Hainzl, Christian","first_name":"Christian"},{"first_name":"Michael","full_name":"Loss, Michael","last_name":"Loss"}],"publist_id":"7429","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000429799900008"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Deuchert A, Geisinge A, Hainzl C, Loss M. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 2018;19(5):1507-1527. doi:10.1007/s00023-018-0665-7","apa":"Deuchert, A., Geisinge, A., Hainzl, C., & Loss, M. (2018). Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. Springer. https://doi.org/10.1007/s00023-018-0665-7","short":"A. Deuchert, A. Geisinge, C. Hainzl, M. Loss, Annales Henri Poincare 19 (2018) 1507–1527.","ieee":"A. Deuchert, A. Geisinge, C. Hainzl, and M. Loss, “Persistence of translational symmetry in the BCS model with radial pair interaction,” Annales Henri Poincare, vol. 19, no. 5. Springer, pp. 1507–1527, 2018.","mla":"Deuchert, Andreas, et al. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare, vol. 19, no. 5, Springer, 2018, pp. 1507–27, doi:10.1007/s00023-018-0665-7.","ista":"Deuchert A, Geisinge A, Hainzl C, Loss M. 2018. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 19(5), 1507–1527.","chicago":"Deuchert, Andreas, Alissa Geisinge, Christian Hainzl, and Michael Loss. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare. Springer, 2018. https://doi.org/10.1007/s00023-018-0665-7."},"quality_controlled":"1","publisher":"Springer","oa":1,"date_published":"2018-05-01T00:00:00Z","doi":"10.1007/s00023-018-0665-7","date_created":"2018-12-11T11:46:15Z","page":"1507 - 1527","day":"01","publication":"Annales Henri Poincare","isi":1,"has_accepted_license":"1","year":"2018","status":"public","pubrep_id":"1011","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"400","department":[{"_id":"RoSe"}],"file_date_updated":"2020-07-14T12:46:22Z","ddc":["510"],"date_updated":"2023-09-15T12:04:15Z","month":"05","intvolume":" 19","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We consider the two-dimensional BCS functional with a radial pair interaction. We show that the translational symmetry is not broken in a certain temperature interval below the critical temperature. In the case of vanishing angular momentum, our results carry over to the three-dimensional case.","lang":"eng"}],"volume":19,"issue":"5","ec_funded":1,"file":[{"file_size":582680,"date_updated":"2020-07-14T12:46:22Z","creator":"system","file_name":"IST-2018-1011-v1+1_2018_Deuchert_Persistence.pdf","date_created":"2018-12-12T10:12:47Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"04d2c9bd7cbf3ca1d7acaaf4e7dca3e5","file_id":"4966"}],"language":[{"iso":"eng"}],"publication_status":"published"},{"oa":1,"quality_controlled":"1","publisher":"Public Library of Science","acknowledgement":"This work was supported by the Human Frontier Science Program RGP0065/2012 (GT, ES).","date_created":"2018-12-11T11:46:18Z","date_published":"2018-03-07T00:00:00Z","doi":"10.1371/journal.pone.0193049","year":"2018","has_accepted_license":"1","isi":1,"publication":"PLoS One","day":"07","project":[{"grant_number":"RGP0065/2012","name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000426896800032"]},"article_processing_charge":"Yes","author":[{"first_name":"Katarína","full_name":"Bod’Ová, Katarína","last_name":"Bod’Ová"},{"full_name":"Mitchell, Gabriel","last_name":"Mitchell","first_name":"Gabriel","id":"315BCD80-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roy","full_name":"Harpaz, Roy","last_name":"Harpaz"},{"last_name":"Schneidman","full_name":"Schneidman, Elad","first_name":"Elad"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"}],"publist_id":"7423","title":"Probabilistic models of individual and collective animal behavior","citation":{"apa":"Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018). Probabilistic models of individual and collective animal behavior. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049","ama":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Probabilistic models of individual and collective animal behavior. PLoS One. 2018;13(3). doi:10.1371/journal.pone.0193049","short":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, PLoS One 13 (2018).","ieee":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Probabilistic models of individual and collective animal behavior,” PLoS One, vol. 13, no. 3. Public Library of Science, 2018.","mla":"Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One, vol. 13, no. 3, Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.","ista":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Probabilistic models of individual and collective animal behavior. PLoS One. 13(3).","chicago":"Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","intvolume":" 13","month":"03","abstract":[{"lang":"eng","text":"Recent developments in automated tracking allow uninterrupted, high-resolution recording of animal trajectories, sometimes coupled with the identification of stereotyped changes of body pose or other behaviors of interest. Analysis and interpretation of such data represents a challenge: the timing of animal behaviors may be stochastic and modulated by kinematic variables, by the interaction with the environment or with the conspecifics within the animal group, and dependent on internal cognitive or behavioral state of the individual. Existing models for collective motion typically fail to incorporate the discrete, stochastic, and internal-state-dependent aspects of behavior, while models focusing on individual animal behavior typically ignore the spatial aspects of the problem. Here we propose a probabilistic modeling framework to address this gap. Each animal can switch stochastically between different behavioral states, with each state resulting in a possibly different law of motion through space. Switching rates for behavioral transitions can depend in a very general way, which we seek to identify from data, on the effects of the environment as well as the interaction between the animals. We represent the switching dynamics as a Generalized Linear Model and show that: (i) forward simulation of multiple interacting animals is possible using a variant of the Gillespie’s Stochastic Simulation Algorithm; (ii) formulated properly, the maximum likelihood inference of switching rate functions is tractably solvable by gradient descent; (iii) model selection can be used to identify factors that modulate behavioral state switching and to appropriately adjust model complexity to data. To illustrate our framework, we apply it to two synthetic models of animal motion and to real zebrafish tracking data. "}],"oa_version":"Submitted Version","volume":13,"issue":"3","related_material":{"record":[{"relation":"research_data","id":"9831","status":"public"}]},"publication_status":"published","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"684229493db75b43e98a46cd922da497","file_id":"5165","creator":"system","file_size":6887358,"date_updated":"2020-07-14T12:46:22Z","file_name":"IST-2018-995-v1+1_2018_Bodova_Probabilistic.pdf","date_created":"2018-12-12T10:15:43Z"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"995","status":"public","_id":"406","department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:46:22Z","date_updated":"2023-09-15T12:06:19Z","ddc":["530","571"]},{"_id":"457","type":"journal_article","status":"public","date_updated":"2023-09-15T12:04:57Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"abstract":[{"lang":"eng","text":"Temperate bacteriophages integrate in bacterial genomes as prophages and represent an important source of genetic variation for bacterial evolution, frequently transmitting fitness-augmenting genes such as toxins responsible for virulence of major pathogens. However, only a fraction of bacteriophage infections are lysogenic and lead to prophage acquisition, whereas the majority are lytic and kill the infected bacteria. Unless able to discriminate lytic from lysogenic infections, mechanisms of immunity to bacteriophages are expected to act as a double-edged sword and increase the odds of survival at the cost of depriving bacteria of potentially beneficial prophages. We show that although restriction-modification systems as mechanisms of innate immunity prevent both lytic and lysogenic infections indiscriminately in individual bacteria, they increase the number of prophage-acquiring individuals at the population level. We find that this counterintuitive result is a consequence of phage-host population dynamics, in which restriction-modification systems delay infection onset until bacteria reach densities at which the probability of lysogeny increases. These results underscore the importance of population-level dynamics as a key factor modulating costs and benefits of immunity to temperate bacteriophages"}],"oa_version":"None","scopus_import":"1","intvolume":" 2","month":"02","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"issue":"2","volume":2,"related_material":{"record":[{"id":"202","status":"public","relation":"dissertation_contains"}]},"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems (HFSP Young investigators' grant)","grant_number":"RGY0079/2011","_id":"251BCBEC-B435-11E9-9278-68D0E5697425"},{"name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)","grant_number":"24210","_id":"251D65D8-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Pleska, Maros, et al. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” Nature Ecology and Evolution, vol. 2, no. 2, Springer Nature, 2018, pp. 359–66, doi:10.1038/s41559-017-0424-z.","apa":"Pleska, M., Lang, M., Refardt, D., Levin, B., & Guet, C. C. (2018). Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-017-0424-z","ama":"Pleska M, Lang M, Refardt D, Levin B, Guet CC. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. 2018;2(2):359-366. doi:10.1038/s41559-017-0424-z","short":"M. Pleska, M. Lang, D. Refardt, B. Levin, C.C. Guet, Nature Ecology and Evolution 2 (2018) 359–366.","ieee":"M. Pleska, M. Lang, D. Refardt, B. Levin, and C. C. Guet, “Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity,” Nature Ecology and Evolution, vol. 2, no. 2. Springer Nature, pp. 359–366, 2018.","chicago":"Pleska, Maros, Moritz Lang, Dominik Refardt, Bruce Levin, and Calin C Guet. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” Nature Ecology and Evolution. Springer Nature, 2018. https://doi.org/10.1038/s41559-017-0424-z.","ista":"Pleska M, Lang M, Refardt D, Levin B, Guet CC. 2018. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. 2(2), 359–366."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000426516400027"]},"article_processing_charge":"No","publist_id":"7364","author":[{"first_name":"Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros","last_name":"Pleska"},{"first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz","last_name":"Lang"},{"full_name":"Refardt, Dominik","last_name":"Refardt","first_name":"Dominik"},{"last_name":"Levin","full_name":"Levin, Bruce","first_name":"Bruce"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"title":"Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity","publisher":"Springer Nature","quality_controlled":"1","year":"2018","isi":1,"publication":"Nature Ecology and Evolution","day":"01","page":"359 - 366","date_created":"2018-12-11T11:46:35Z","doi":"10.1038/s41559-017-0424-z","date_published":"2018-02-01T00:00:00Z"},{"month":"10","intvolume":" 28","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2018.08.063"}],"oa_version":"Published Version","abstract":[{"text":"Many animals use antimicrobials to prevent or cure disease [1,2]. For example, some animals will ingest plants with medicinal properties, both prophylactically to prevent infection and therapeutically to self-medicate when sick. Antimicrobial substances are also used as topical disinfectants, to prevent infection, protect offspring and to sanitise their surroundings [1,2]. Social insects (ants, bees, wasps and termites) build nests in environments with a high abundance and diversity of pathogenic microorganisms — such as soil and rotting wood — and colonies are often densely crowded, creating conditions that favour disease outbreaks. Consequently, social insects have evolved collective disease defences to protect their colonies from epidemics. These traits can be seen as functionally analogous to the immune system of individual organisms [3,4]. This ‘social immunity’ utilises antimicrobials to prevent and eradicate infections, and to keep the brood and nest clean. However, these antimicrobial compounds can be harmful to the insects themselves, and it is unknown how colonies prevent collateral damage when using them. Here, we demonstrate that antimicrobial acids, produced by workers to disinfect the colony, are harmful to the delicate pupal brood stage, but that the pupae are protected from the acids by the presence of a silk cocoon. Garden ants spray their nests with an antimicrobial poison to sanitize contaminated nestmates and brood. Here, Pull et al show that they also prophylactically sanitise their colonies, and that the silk cocoon serves as a barrier to protect developing pupae, thus preventing collateral damage during nest sanitation.","lang":"eng"}],"issue":"19","volume":28,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","article_type":"original","_id":"55","department":[{"_id":"SyCr"}],"date_updated":"2023-09-15T12:06:46Z","publisher":"Cell Press","quality_controlled":"1","oa":1,"date_published":"2018-10-08T00:00:00Z","doi":"10.1016/j.cub.2018.08.063","date_created":"2018-12-11T11:44:23Z","page":"R1139 - R1140","day":"08","publication":"Current Biology","isi":1,"year":"2018","title":"Protection against the lethal side effects of social immunity in ants","author":[{"first_name":"Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982","full_name":"Pull, Christopher","last_name":"Pull"},{"full_name":"Metzler, Sina","orcid":"0000-0002-9547-2494","last_name":"Metzler","first_name":"Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Naderlinger","full_name":"Naderlinger, Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87","first_name":"Elisabeth"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer"}],"publist_id":"7999","external_id":{"isi":["000446693400008"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Pull, Christopher, Sina Metzler, Elisabeth Naderlinger, and Sylvia Cremer. “Protection against the Lethal Side Effects of Social Immunity in Ants.” Current Biology. Cell Press, 2018. https://doi.org/10.1016/j.cub.2018.08.063.","ista":"Pull C, Metzler S, Naderlinger E, Cremer S. 2018. Protection against the lethal side effects of social immunity in ants. Current Biology. 28(19), R1139–R1140.","mla":"Pull, Christopher, et al. “Protection against the Lethal Side Effects of Social Immunity in Ants.” Current Biology, vol. 28, no. 19, Cell Press, 2018, pp. R1139–40, doi:10.1016/j.cub.2018.08.063.","ieee":"C. Pull, S. Metzler, E. Naderlinger, and S. Cremer, “Protection against the lethal side effects of social immunity in ants,” Current Biology, vol. 28, no. 19. Cell Press, pp. R1139–R1140, 2018.","short":"C. Pull, S. Metzler, E. Naderlinger, S. Cremer, Current Biology 28 (2018) R1139–R1140.","apa":"Pull, C., Metzler, S., Naderlinger, E., & Cremer, S. (2018). Protection against the lethal side effects of social immunity in ants. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2018.08.063","ama":"Pull C, Metzler S, Naderlinger E, Cremer S. Protection against the lethal side effects of social immunity in ants. Current Biology. 2018;28(19):R1139-R1140. doi:10.1016/j.cub.2018.08.063"}},{"type":"journal_article","status":"public","_id":"181","department":[{"_id":"LaEr"}],"date_updated":"2023-09-15T12:05:52Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.01546"}],"month":"01","intvolume":" 50","abstract":[{"lang":"eng","text":"We consider large random matrices X with centered, independent entries but possibly di erent variances. We compute the normalized trace of f(X)g(X∗) for f, g functions analytic on the spectrum of X. We use these results to compute the long time asymptotics for systems of coupled di erential equations with random coe cients. We show that when the coupling is critical, the norm squared of the solution decays like t−1/2."}],"oa_version":"Published Version","issue":"3","volume":50,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"_id":"258F40A4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02080","name":"Structured Non-Hermitian Random Matrices"}],"publist_id":"7740","author":[{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"last_name":"Krüger","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H"},{"last_name":"Renfrew","full_name":"Renfrew, David T","orcid":"0000-0003-3493-121X","first_name":"David T","id":"4845BF6A-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["1708.01546"],"isi":["000437018500032"]},"title":"Power law decay for systems of randomly coupled differential equations","citation":{"chicago":"Erdös, László, Torben H Krüger, and David T Renfrew. “Power Law Decay for Systems of Randomly Coupled Differential Equations.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/17M1143125.","ista":"Erdös L, Krüger TH, Renfrew DT. 2018. Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. 50(3), 3271–3290.","mla":"Erdös, László, et al. “Power Law Decay for Systems of Randomly Coupled Differential Equations.” SIAM Journal on Mathematical Analysis, vol. 50, no. 3, Society for Industrial and Applied Mathematics , 2018, pp. 3271–90, doi:10.1137/17M1143125.","ama":"Erdös L, Krüger TH, Renfrew DT. Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. 2018;50(3):3271-3290. doi:10.1137/17M1143125","apa":"Erdös, L., Krüger, T. H., & Renfrew, D. T. (2018). Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/17M1143125","ieee":"L. Erdös, T. H. Krüger, and D. T. Renfrew, “Power law decay for systems of randomly coupled differential equations,” SIAM Journal on Mathematical Analysis, vol. 50, no. 3. Society for Industrial and Applied Mathematics , pp. 3271–3290, 2018.","short":"L. Erdös, T.H. Krüger, D.T. Renfrew, SIAM Journal on Mathematical Analysis 50 (2018) 3271–3290."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics ","oa":1,"acknowledgement":"The work of the second author was also partially supported by the Hausdorff Center of Mathematics.","page":"3271 - 3290","doi":"10.1137/17M1143125","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:45:03Z","isi":1,"year":"2018","day":"01","publication":"SIAM Journal on Mathematical Analysis"},{"intvolume":" 506","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1412.7211"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"We construct quantizations of multiplicative hypertoric varieties using an algebra of q-difference operators on affine space, where q is a root of unity in C. The quantization defines a matrix bundle (i.e. Azumaya algebra) over the multiplicative hypertoric variety and admits an explicit finite étale splitting. The global sections of this Azumaya algebra is a hypertoric quantum group, and we prove a localization theorem. We introduce a general framework of Frobenius quantum moment maps and their Hamiltonian reductions; our results shed light on an instance of this framework.","lang":"eng"}],"ec_funded":1,"volume":506,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"322","department":[{"_id":"TaHa"}],"date_updated":"2023-09-15T12:08:38Z","oa":1,"publisher":"World Scientific Publishing","quality_controlled":"1","acknowledgement":"National Science Foundation: Graduate Research Fellowship and grant No.0932078000; ERC Advanced Grant “Arithmetic and Physics of Higgs moduli spaces” No. 320593 \r\nThe author is grateful to David Jordan for suggesting this project and providing guidance throughout, particularly for the formulation of Frobenius quantum moment maps and key ideas in the proofs of Theorems 3.12 and 4.8. Special thanks to David Ben-Zvi (the author's PhD advisor) for numerous discussions and constant encouragement, and for suggesting the term ‘hypertoric quantum group.’ Many results appearing in the current paper were proven independently by Nicholas Cooney; the author is grateful to Nicholas for sharing his insight on various topics, including Proposition 3.8. The author also thanks Nicholas Proudfoot for relating the definition of multiplicative hypertoric varieties, as well as the content of Remark 2.14. The author also benefited immensely from the close reading and detailed comments of an anonymous referee, and from conversations with Justin Hilburn, Kobi Kremnitzer, Michael McBreen, Tom Nevins, Travis Schedler, and Ben Webster. \r\n\r\n\r\n\r\n","date_created":"2018-12-11T11:45:49Z","doi":"10.1016/j.jalgebra.2018.03.015","date_published":"2018-07-15T00:00:00Z","page":"92 - 128","publication":"Journal of Algebra","day":"15","year":"2018","isi":1,"project":[{"grant_number":"320593","name":"Arithmetic and physics of Higgs moduli spaces","call_identifier":"FP7","_id":"25E549F4-B435-11E9-9278-68D0E5697425"}],"title":"Quantizations of multiplicative hypertoric varieties at a root of unity","article_processing_charge":"No","external_id":{"isi":["000433270600005"],"arxiv":["1412.7211"]},"author":[{"id":"447491B8-F248-11E8-B48F-1D18A9856A87","first_name":"Iordan V","last_name":"Ganev","full_name":"Ganev, Iordan V"}],"publist_id":"7543","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties at a Root of Unity.” Journal of Algebra. World Scientific Publishing, 2018. https://doi.org/10.1016/j.jalgebra.2018.03.015.","ista":"Ganev IV. 2018. Quantizations of multiplicative hypertoric varieties at a root of unity. Journal of Algebra. 506, 92–128.","mla":"Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties at a Root of Unity.” Journal of Algebra, vol. 506, World Scientific Publishing, 2018, pp. 92–128, doi:10.1016/j.jalgebra.2018.03.015.","apa":"Ganev, I. V. (2018). Quantizations of multiplicative hypertoric varieties at a root of unity. Journal of Algebra. World Scientific Publishing. https://doi.org/10.1016/j.jalgebra.2018.03.015","ama":"Ganev IV. Quantizations of multiplicative hypertoric varieties at a root of unity. Journal of Algebra. 2018;506:92-128. doi:10.1016/j.jalgebra.2018.03.015","ieee":"I. V. Ganev, “Quantizations of multiplicative hypertoric varieties at a root of unity,” Journal of Algebra, vol. 506. World Scientific Publishing, pp. 92–128, 2018.","short":"I.V. Ganev, Journal of Algebra 506 (2018) 92–128."}},{"status":"public","type":"research_data_reference","_id":"9831","title":"Implementation of the inference method in Matlab","department":[{"_id":"GaTk"}],"article_processing_charge":"No","author":[{"first_name":"Katarína","full_name":"Bod’Ová, Katarína","last_name":"Bod’Ová"},{"last_name":"Mitchell","full_name":"Mitchell, Gabriel","id":"315BCD80-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel"},{"first_name":"Roy","full_name":"Harpaz, Roy","last_name":"Harpaz"},{"first_name":"Elad","last_name":"Schneidman","full_name":"Schneidman, Elad"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-15T12:06:18Z","citation":{"chicago":"Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Implementation of the Inference Method in Matlab.” Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049.s001.","ista":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Implementation of the inference method in Matlab, Public Library of Science, 10.1371/journal.pone.0193049.s001.","mla":"Bod’Ová, Katarína, et al. Implementation of the Inference Method in Matlab. Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.s001.","short":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).","ieee":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Implementation of the inference method in Matlab.” Public Library of Science, 2018.","ama":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Implementation of the inference method in Matlab. 2018. doi:10.1371/journal.pone.0193049.s001","apa":"Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018). Implementation of the inference method in Matlab. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049.s001"},"month":"03","publisher":"Public Library of Science","oa_version":"Published Version","abstract":[{"text":"Implementation of the inference method in Matlab, including three applications of the method: The first one for the model of ant motion, the second one for bacterial chemotaxis, and the third one for the motion of fish.","lang":"eng"}],"date_created":"2021-08-09T07:01:24Z","doi":"10.1371/journal.pone.0193049.s001","date_published":"2018-03-07T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"406","status":"public"}]},"day":"07","year":"2018"},{"status":"public","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"CAV: Computer Aided Verification","start_date":"2018-07-14","end_date":"2018-07-17","location":"Oxford, United Kingdom"},"_id":"142","file_date_updated":"2020-07-14T12:44:53Z","department":[{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2023-09-15T12:12:08Z","month":"07","intvolume":" 10981","scopus_import":"1","alternative_title":["LNCS"],"oa_version":"Published Version","abstract":[{"text":"We address the problem of analyzing the reachable set of a polynomial nonlinear continuous system by over-approximating the flowpipe of its dynamics. The common approach to tackle this problem is to perform a numerical integration over a given time horizon based on Taylor expansion and interval arithmetic. However, this method results to be very conservative when there is a large difference in speed between trajectories as time progresses. In this paper, we propose to use combinations of barrier functions, which we call piecewise barrier tube (PBT), to over-approximate flowpipe. The basic idea of PBT is that for each segment of a flowpipe, a coarse box which is big enough to contain the segment is constructed using sampled simulation and then in the box we compute by linear programming a set of barrier functions (called barrier tube or BT for short) which work together to form a tube surrounding the flowpipe. The benefit of using PBT is that (1) BT is independent of time and hence can avoid being stretched and deformed by time; and (2) a small number of BTs can form a tight over-approximation for the flowpipe, which means that the computation required to decide whether the BTs intersect the unsafe set can be reduced significantly. We implemented a prototype called PBTS in C++. Experiments on some benchmark systems show that our approach is effective.","lang":"eng"}],"volume":10981,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5718","checksum":"fd95e8026deacef3dc752a733bb9355f","file_size":5591566,"date_updated":"2020-07-14T12:44:53Z","creator":"dernst","file_name":"2018_LNCS_Kong.pdf","date_created":"2018-12-17T15:57:06Z"}],"language":[{"iso":"eng"}],"publication_status":"published","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"}],"title":"Reachable set over-approximation for nonlinear systems using piecewise barrier tubes","author":[{"first_name":"Hui","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3066-6941","full_name":"Kong, Hui","last_name":"Kong"},{"first_name":"Ezio","last_name":"Bartocci","full_name":"Bartocci, Ezio"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"publist_id":"7781","external_id":{"isi":["000491481600024"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"H. Kong, E. Bartocci, T.A. Henzinger, in:, Springer, 2018, pp. 449–467.","ieee":"H. Kong, E. Bartocci, and T. A. Henzinger, “Reachable set over-approximation for nonlinear systems using piecewise barrier tubes,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 449–467.","apa":"Kong, H., Bartocci, E., & Henzinger, T. A. (2018). Reachable set over-approximation for nonlinear systems using piecewise barrier tubes (Vol. 10981, pp. 449–467). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96145-3_24","ama":"Kong H, Bartocci E, Henzinger TA. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. In: Vol 10981. Springer; 2018:449-467. doi:10.1007/978-3-319-96145-3_24","mla":"Kong, Hui, et al. Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes. Vol. 10981, Springer, 2018, pp. 449–67, doi:10.1007/978-3-319-96145-3_24.","ista":"Kong H, Bartocci E, Henzinger TA. 2018. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. CAV: Computer Aided Verification, LNCS, vol. 10981, 449–467.","chicago":"Kong, Hui, Ezio Bartocci, and Thomas A Henzinger. “Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes,” 10981:449–67. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_24."},"quality_controlled":"1","publisher":"Springer","oa":1,"acknowledgement":"Austrian Science Fund FWF: S11402-N23, S11405-N23, Z211-N32","doi":"10.1007/978-3-319-96145-3_24","date_published":"2018-07-18T00:00:00Z","date_created":"2018-12-11T11:44:51Z","page":"449 - 467","day":"18","isi":1,"has_accepted_license":"1","year":"2018"},{"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"022510","title":"Quantum interference in laser spectroscopy of highly charged lithiumlike ions","article_processing_charge":"No","external_id":{"isi":["000425601000004"],"arxiv":["1802.07920"]},"publist_id":"7396","author":[{"full_name":"Amaro, Pedro","last_name":"Amaro","first_name":"Pedro"},{"last_name":"Loureiro","full_name":"Loureiro, Ulisses","first_name":"Ulisses"},{"first_name":"Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","full_name":"Safari, Laleh","last_name":"Safari"},{"first_name":"Filippo","full_name":"Fratini, Filippo","last_name":"Fratini"},{"first_name":"Paul","full_name":"Indelicato, Paul","last_name":"Indelicato"},{"first_name":"Thomas","last_name":"Stöhlker","full_name":"Stöhlker, Thomas"},{"last_name":"Santos","full_name":"Santos, José","first_name":"José"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"P. Amaro et al., “Quantum interference in laser spectroscopy of highly charged lithiumlike ions,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 2. American Physical Society, 2018.","short":"P. Amaro, U. Loureiro, L. Safari, F. Fratini, P. Indelicato, T. Stöhlker, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","apa":"Amaro, P., Loureiro, U., Safari, L., Fratini, F., Indelicato, P., Stöhlker, T., & Santos, J. (2018). Quantum interference in laser spectroscopy of highly charged lithiumlike ions. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.022510","ama":"Amaro P, Loureiro U, Safari L, et al. Quantum interference in laser spectroscopy of highly charged lithiumlike ions. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(2). doi:10.1103/PhysRevA.97.022510","mla":"Amaro, Pedro, et al. “Quantum Interference in Laser Spectroscopy of Highly Charged Lithiumlike Ions.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 2, 022510, American Physical Society, 2018, doi:10.1103/PhysRevA.97.022510.","ista":"Amaro P, Loureiro U, Safari L, Fratini F, Indelicato P, Stöhlker T, Santos J. 2018. Quantum interference in laser spectroscopy of highly charged lithiumlike ions. Physical Review A - Atomic, Molecular, and Optical Physics. 97(2), 022510.","chicago":"Amaro, Pedro, Ulisses Loureiro, Laleh Safari, Filippo Fratini, Paul Indelicato, Thomas Stöhlker, and José Santos. “Quantum Interference in Laser Spectroscopy of Highly Charged Lithiumlike Ions.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.022510."},"oa":1,"quality_controlled":"1","publisher":"American Physical Society","acknowledgement":"This work was funded by the Portuguese Fundação para a Ciência e a Tecnologia (FCT/MCTES/PIDDAC) under Grant No. UID/FIS/04559/2013 (LIBPhys). P.A. acknowledges the support of the FCT, under Contract No. SFRH/BPD/92329/2013. L.S. acknowledges financial support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA Grant Agreement No. (291734). Laboratoire Kastler Brossel (LKB) is “Unité Mixte de Recherche de Sorbonne Université, de ENS-PSL Research University, du Collège de France et du CNRS No. 8552.” APPENDIX:\r\n","date_created":"2018-12-11T11:46:25Z","doi":"10.1103/PhysRevA.97.022510","date_published":"2018-02-21T00:00:00Z","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","day":"21","year":"2018","isi":1,"status":"public","article_type":"original","type":"journal_article","_id":"427","department":[{"_id":"MiLe"}],"date_updated":"2023-09-15T12:09:35Z","intvolume":" 97","month":"02","main_file_link":[{"url":"https://arxiv.org/abs/1802.07920","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We investigate the quantum interference induced shifts between energetically close states in highly charged ions, with the energy structure being observed by laser spectroscopy. In this work, we focus on hyperfine states of lithiumlike heavy-Z isotopes and quantify how much quantum interference changes the observed transition frequencies. The process of photon excitation and subsequent photon decay for the transition 2s→2p→2s is implemented with fully relativistic and full-multipole frameworks, which are relevant for such relativistic atomic systems. We consider the isotopes Pb79+207 and Bi80+209 due to experimental interest, as well as other examples of isotopes with lower Z, namely Pr56+141 and Ho64+165. We conclude that quantum interference can induce shifts up to 11% of the linewidth in the measurable resonances of the considered isotopes, if interference between resonances is neglected. The inclusion of relativity decreases the cross section by 35%, mainly due to the complete retardation form of the electric dipole multipole. However, the contribution of the next higher multipoles (e.g., magnetic quadrupole) to the cross section is negligible. This makes the contribution of relativity and higher-order multipoles to the quantum interference induced shifts a minor effect, even for heavy-Z elements."}],"ec_funded":1,"issue":"2","volume":97,"language":[{"iso":"eng"}],"publication_status":"published"},{"day":"01","isi":1,"year":"2018","date_published":"2018-01-01T00:00:00Z","doi":"10.1137/1.9781611975031.20","date_created":"2018-12-11T11:45:45Z","page":"274 - 292","acknowledgement":"∗Research supported in part by the NSF awards CCF-1422311 and CCF-1423615, and the Science Without Borders program. The second author gratefully acknowledges support from Austrian Science Fund (FWF): M2281-N35.","publisher":"ACM","quality_controlled":"1","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Akitaya, Hugo, et al. Recognizing Weak Embeddings of Graphs. ACM, 2018, pp. 274–92, doi:10.1137/1.9781611975031.20.","apa":"Akitaya, H., Fulek, R., & Tóth, C. (2018). Recognizing weak embeddings of graphs (pp. 274–292). Presented at the SODA: Symposium on Discrete Algorithms, New Orleans, LA, USA: ACM. https://doi.org/10.1137/1.9781611975031.20","ama":"Akitaya H, Fulek R, Tóth C. Recognizing weak embeddings of graphs. In: ACM; 2018:274-292. doi:10.1137/1.9781611975031.20","short":"H. Akitaya, R. Fulek, C. Tóth, in:, ACM, 2018, pp. 274–292.","ieee":"H. Akitaya, R. Fulek, and C. Tóth, “Recognizing weak embeddings of graphs,” presented at the SODA: Symposium on Discrete Algorithms, New Orleans, LA, USA, 2018, pp. 274–292.","chicago":"Akitaya, Hugo, Radoslav Fulek, and Csaba Tóth. “Recognizing Weak Embeddings of Graphs,” 274–92. ACM, 2018. https://doi.org/10.1137/1.9781611975031.20.","ista":"Akitaya H, Fulek R, Tóth C. 2018. Recognizing weak embeddings of graphs. SODA: Symposium on Discrete Algorithms, 274–292."},"title":"Recognizing weak embeddings of graphs","author":[{"last_name":"Akitaya","full_name":"Akitaya, Hugo","first_name":"Hugo"},{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","last_name":"Fulek","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774"},{"first_name":"Csaba","last_name":"Tóth","full_name":"Tóth, Csaba"}],"publist_id":"7556","article_processing_charge":"No","external_id":{"isi":["000483921200021"],"arxiv":["1709.09209"]},"project":[{"_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs","grant_number":"M02281"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"id":"6982","status":"public","relation":"later_version"}]},"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We present an efficient algorithm for a problem in the interface between clustering and graph embeddings. An embedding ' : G ! M of a graph G into a 2manifold M maps the vertices in V (G) to distinct points and the edges in E(G) to interior-disjoint Jordan arcs between the corresponding vertices. In applications in clustering, cartography, and visualization, nearby vertices and edges are often bundled to a common node or arc, due to data compression or low resolution. This raises the computational problem of deciding whether a given map ' : G ! M comes from an embedding. A map ' : G ! M is a weak embedding if it can be perturbed into an embedding ψ: G ! M with k' \"k < \" for every " > 0. A polynomial-time algorithm for recognizing weak embeddings was recently found by Fulek and Kyncl [14], which reduces to solving a system of linear equations over Z2. It runs in O(n2!) O(n4:75) time, where 2:373 is the matrix multiplication exponent and n is the number of vertices and edges of G. We improve the running time to O(n log n). Our algorithm is also conceptually simpler than [14]: We perform a sequence of local operations that gradually "untangles" the image '(G) into an embedding (G), or reports that ' is not a weak embedding. It generalizes a recent technique developed for the case that G is a cycle and the embedding is a simple polygon [1], and combines local constraints on the orientation of subgraphs directly, thereby eliminating the need for solving large systems of linear equations."}],"month":"01","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1709.09209","open_access":"1"}],"date_updated":"2023-09-15T12:19:32Z","department":[{"_id":"UlWa"}],"_id":"309","status":"public","type":"conference","conference":{"start_date":"2018-01-07","end_date":"2018-01-10","location":"New Orleans, LA, USA","name":"SODA: Symposium on Discrete Algorithms"}},{"author":[{"full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874","last_name":"Yakaboylu","first_name":"Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shkolnikov, Mikhail","orcid":"0000-0002-4310-178X","last_name":"Shkolnikov","first_name":"Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"}],"article_processing_charge":"No","external_id":{"arxiv":["1809.00222"],"isi":["000454178600009"]},"title":"Quantum groups as hidden symmetries of quantum impurities","citation":{"ista":"Yakaboylu E, Shkolnikov M, Lemeshko M. 2018. Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. 121(25), 255302.","chicago":"Yakaboylu, Enderalp, Mikhail Shkolnikov, and Mikhail Lemeshko. “Quantum Groups as Hidden Symmetries of Quantum Impurities.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.255302.","ama":"Yakaboylu E, Shkolnikov M, Lemeshko M. Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. 2018;121(25). doi:10.1103/PhysRevLett.121.255302","apa":"Yakaboylu, E., Shkolnikov, M., & Lemeshko, M. (2018). Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.255302","ieee":"E. Yakaboylu, M. Shkolnikov, and M. Lemeshko, “Quantum groups as hidden symmetries of quantum impurities,” Physical Review Letters, vol. 121, no. 25. American Physical Society, 2018.","short":"E. Yakaboylu, M. Shkolnikov, M. Lemeshko, Physical Review Letters 121 (2018).","mla":"Yakaboylu, Enderalp, et al. “Quantum Groups as Hidden Symmetries of Quantum Impurities.” Physical Review Letters, vol. 121, no. 25, 255302, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.255302."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"255302","doi":"10.1103/PhysRevLett.121.255302","date_published":"2018-12-17T00:00:00Z","date_created":"2019-01-06T22:59:12Z","isi":1,"year":"2018","day":"17","publication":"Physical Review Letters","publisher":"American Physical Society","quality_controlled":"1","oa":1,"department":[{"_id":"MiLe"}],"date_updated":"2023-09-15T12:09:06Z","type":"journal_article","article_type":"original","status":"public","_id":"5794","volume":121,"issue":"25","ec_funded":1,"publication_identifier":{"issn":["00319007"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1809.00222","open_access":"1"}],"month":"12","intvolume":" 121","abstract":[{"text":"We present an approach to interacting quantum many-body systems based on the notion of quantum groups, also known as q-deformed Lie algebras. In particular, we show that, if the symmetry of a free quantum particle corresponds to a Lie group G, in the presence of a many-body environment this particle can be described by a deformed group, Gq. Crucially, the single deformation parameter, q, contains all the information about the many-particle interactions in the system. We exemplify our approach by considering a quantum rotor interacting with a bath of bosons, and demonstrate that extracting the value of q from closed-form solutions in the perturbative regime allows one to predict the behavior of the system for arbitrary values of the impurity-bath coupling strength, in good agreement with nonperturbative calculations. Furthermore, the value of the deformation parameter allows one to predict at which coupling strengths rotor-bath interactions result in a formation of a stable quasiparticle. The approach based on quantum groups does not only allow for a drastic simplification of impurity problems, but also provides valuable insights into hidden symmetries of interacting many-particle systems.","lang":"eng"}],"oa_version":"Preprint"},{"related_material":{"record":[{"relation":"dissertation_contains","id":"6287","status":"public"}]},"issue":"5","volume":28,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.02870"}],"scopus_import":"1","intvolume":" 28","month":"10","abstract":[{"text":"Using the geodesic distance on the n-dimensional sphere, we study the expected radius function of the Delaunay mosaic of a random set of points. Specifically, we consider the partition of the mosaic into intervals of the radius function and determine the expected number of intervals whose radii are less than or equal to a given threshold. We find that the expectations are essentially the same as for the Poisson–Delaunay mosaic in n-dimensional Euclidean space. Assuming the points are not contained in a hemisphere, the Delaunay mosaic is isomorphic to the boundary complex of the convex hull in Rn+1, so we also get the expected number of faces of a random inscribed polytope. As proved in Antonelli et al. [Adv. in Appl. Probab. 9–12 (1977–1980)], an orthant section of the n-sphere is isometric to the standard n-simplex equipped with the Fisher information metric. It follows that the latter space has similar stochastic properties as the n-dimensional Euclidean space. Our results are therefore relevant in information geometry and in population genetics.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"HeEd"}],"date_updated":"2023-09-15T12:10:35Z","article_type":"original","type":"journal_article","status":"public","_id":"87","page":"3215 - 3238","date_created":"2018-12-11T11:44:33Z","date_published":"2018-10-01T00:00:00Z","doi":"10.1214/18-AAP1389","year":"2018","isi":1,"publication":"Annals of Applied Probability","day":"01","oa":1,"publisher":"Institute of Mathematical Statistics","quality_controlled":"1","article_processing_charge":"No","external_id":{"isi":["000442893500018"],"arxiv":["1705.02870"]},"publist_id":"7967","author":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"first_name":"Anton","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","last_name":"Nikitenko","full_name":"Nikitenko, Anton","orcid":"0000-0002-0659-3201"}],"title":"Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics","citation":{"short":"H. Edelsbrunner, A. Nikitenko, Annals of Applied Probability 28 (2018) 3215–3238.","ieee":"H. Edelsbrunner and A. Nikitenko, “Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics,” Annals of Applied Probability, vol. 28, no. 5. Institute of Mathematical Statistics, pp. 3215–3238, 2018.","ama":"Edelsbrunner H, Nikitenko A. Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 2018;28(5):3215-3238. doi:10.1214/18-AAP1389","apa":"Edelsbrunner, H., & Nikitenko, A. (2018). Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AAP1389","mla":"Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” Annals of Applied Probability, vol. 28, no. 5, Institute of Mathematical Statistics, 2018, pp. 3215–38, doi:10.1214/18-AAP1389.","ista":"Edelsbrunner H, Nikitenko A. 2018. Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 28(5), 3215–3238.","chicago":"Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” Annals of Applied Probability. Institute of Mathematical Statistics, 2018. https://doi.org/10.1214/18-AAP1389."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}]},{"title":"Rapid and reversible root growth inhibition by TIR1 auxin signalling","publist_id":"7728","author":[{"full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","last_name":"Fendrych","first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maria","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","last_name":"Akhmanova","full_name":"Akhmanova, Maria","orcid":"0000-0003-1522-3162"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack"},{"full_name":"Glanc, Matous","last_name":"Glanc","first_name":"Matous"},{"full_name":"Hagihara, Shinya","last_name":"Hagihara","first_name":"Shinya"},{"last_name":"Takahashi","full_name":"Takahashi, Koji","first_name":"Koji"},{"full_name":"Uchida, Naoyuki","last_name":"Uchida","first_name":"Naoyuki"},{"full_name":"Torii, Keiko U","last_name":"Torii","first_name":"Keiko U"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"article_processing_charge":"No","external_id":{"pmid":["29942048"],"isi":["000443221200017"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Fendrych, Matyas, Maria Akhmanova, Jack Merrin, Matous Glanc, Shinya Hagihara, Koji Takahashi, Naoyuki Uchida, Keiko U Torii, and Jiří Friml. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” Nature Plants. Springer Nature, 2018. https://doi.org/10.1038/s41477-018-0190-1.","ista":"Fendrych M, Akhmanova M, Merrin J, Glanc M, Hagihara S, Takahashi K, Uchida N, Torii KU, Friml J. 2018. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 4(7), 453–459.","mla":"Fendrych, Matyas, et al. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” Nature Plants, vol. 4, no. 7, Springer Nature, 2018, pp. 453–59, doi:10.1038/s41477-018-0190-1.","apa":"Fendrych, M., Akhmanova, M., Merrin, J., Glanc, M., Hagihara, S., Takahashi, K., … Friml, J. (2018). Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-018-0190-1","ama":"Fendrych M, Akhmanova M, Merrin J, et al. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 2018;4(7):453-459. doi:10.1038/s41477-018-0190-1","ieee":"M. Fendrych et al., “Rapid and reversible root growth inhibition by TIR1 auxin signalling,” Nature Plants, vol. 4, no. 7. Springer Nature, pp. 453–459, 2018.","short":"M. Fendrych, M. Akhmanova, J. Merrin, M. Glanc, S. Hagihara, K. Takahashi, N. Uchida, K.U. Torii, J. Friml, Nature Plants 4 (2018) 453–459."},"doi":"10.1038/s41477-018-0190-1","date_published":"2018-06-25T00:00:00Z","date_created":"2018-12-11T11:45:07Z","page":"453 - 459","day":"25","publication":"Nature Plants","isi":1,"year":"2018","publisher":"Springer Nature","quality_controlled":"1","oa":1,"department":[{"_id":"JiFr"},{"_id":"DaSi"},{"_id":"NanoFab"}],"date_updated":"2023-09-15T12:11:03Z","status":"public","article_type":"original","type":"journal_article","_id":"192","issue":"7","volume":4,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-mechanism-for-the-plant-hormone-auxin-discovered/","relation":"press_release"}]},"language":[{"iso":"eng"}],"publication_status":"published","month":"06","intvolume":" 4","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29942048"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"The phytohormone auxin is the information carrier in a plethora of developmental and physiological processes in plants(1). It has been firmly established that canonical, nuclear auxin signalling acts through regulation of gene transcription(2). Here, we combined microfluidics, live imaging, genetic engineering and computational modelling to reanalyse the classical case of root growth inhibition(3) by auxin. We show that Arabidopsis roots react to addition and removal of auxin by extremely rapid adaptation of growth rate. This process requires intracellular auxin perception but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA co-receptor complex is required for the growth regulation, hinting to a novel, non-transcriptional branch of this signalling pathway. Our results challenge the current understanding of root growth regulation by auxin and suggest another, presumably non-transcriptional, signalling output of the canonical auxin pathway."}]},{"file_date_updated":"2020-07-14T12:44:50Z","department":[{"_id":"DaSi"},{"_id":"JiFr"}],"ddc":["580"],"date_updated":"2023-09-18T08:09:32Z","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","article_type":"original","_id":"14","ec_funded":1,"issue":"11","volume":19,"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-17T16:04:11Z","file_name":"2018_IJMS_Hille.pdf","creator":"dernst","date_updated":"2020-07-14T12:44:50Z","file_size":2200593,"checksum":"e4b59c2599b0ca26ebf5b8434bcde94a","file_id":"5719","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1422-0067"]},"intvolume":" 19","month":"11","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The intercellular transport of auxin is driven by PIN-formed (PIN) auxin efflux carriers. PINs are localized at the plasma membrane (PM) and on constitutively recycling endomembrane vesicles. Therefore, PINs can mediate auxin transport either by direct translocation across the PM or by pumping auxin into secretory vesicles (SVs), leading to its secretory release upon fusion with the PM. Which of these two mechanisms dominates is a matter of debate. Here, we addressed the issue with a mathematical modeling approach. We demonstrate that the efficiency of secretory transport depends on SV size, half-life of PINs on the PM, pH, exocytosis frequency and PIN density. 3D structured illumination microscopy (SIM) was used to determine PIN density on the PM. Combining this data with published values of the other parameters, we show that the transport activity of PINs in SVs would have to be at least 1000× greater than on the PM in order to produce a comparable macroscopic auxin transport. If both transport mechanisms operated simultaneously and PINs were equally active on SVs and PM, the contribution of secretion to the total auxin flux would be negligible. In conclusion, while secretory vesicle-mediated transport of auxin is an intriguing and theoretically possible model, it is unlikely to be a major mechanism of auxin transport inplanta."}],"title":"Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation","article_processing_charge":"No","external_id":{"isi":["000451528500282"]},"author":[{"first_name":"Sander","last_name":"Hille","full_name":"Hille, Sander"},{"last_name":"Akhmanova","full_name":"Akhmanova, Maria","orcid":"0000-0003-1522-3162","first_name":"Maria","id":"3425EC26-F248-11E8-B48F-1D18A9856A87"},{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","last_name":"Glanc","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783"},{"full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"publist_id":"8042","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Hille, Sander, et al. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” International Journal of Molecular Sciences, vol. 19, no. 11, MDPI, 2018, doi:10.3390/ijms19113566.","ama":"Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. 2018;19(11). doi:10.3390/ijms19113566","apa":"Hille, S., Akhmanova, M., Glanc, M., Johnson, A. J., & Friml, J. (2018). Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms19113566","short":"S. Hille, M. Akhmanova, M. Glanc, A.J. Johnson, J. Friml, International Journal of Molecular Sciences 19 (2018).","ieee":"S. Hille, M. Akhmanova, M. Glanc, A. J. Johnson, and J. Friml, “Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation,” International Journal of Molecular Sciences, vol. 19, no. 11. MDPI, 2018.","chicago":"Hille, Sander, Maria Akhmanova, Matous Glanc, Alexander J Johnson, and Jiří Friml. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” International Journal of Molecular Sciences. MDPI, 2018. https://doi.org/10.3390/ijms19113566.","ista":"Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. 2018. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. 19(11)."},"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}],"date_created":"2018-12-11T11:44:09Z","date_published":"2018-11-12T00:00:00Z","doi":"10.3390/ijms19113566","publication":"International Journal of Molecular Sciences","day":"12","year":"2018","has_accepted_license":"1","isi":1,"oa":1,"publisher":"MDPI","quality_controlled":"1","acknowledgement":"European Research Council (ERC): 742985 to Jiri Friml; M.A. was supported by the Austrian Science Fund (FWF) (M2379-B28); AJ was supported by the Austria Science Fund (FWF): I03630 to Jiri Friml."},{"quality_controlled":"1","publisher":"Genetics Society of America","oa":1,"isi":1,"year":"2018","day":"04","publication":"Genetics","page":"1411-1427","doi":"10.1534/genetics.118.301429","date_published":"2018-12-04T00:00:00Z","date_created":"2018-12-11T11:44:18Z","citation":{"ama":"Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic selection. Genetics. 2018;210(4):1411-1427. doi:10.1534/genetics.118.301429","apa":"Sachdeva, H., & Barton, N. H. (2018). Replicability of introgression under linked, polygenic selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301429","short":"H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427.","ieee":"H. Sachdeva and N. H. Barton, “Replicability of introgression under linked, polygenic selection,” Genetics, vol. 210, no. 4. Genetics Society of America, pp. 1411–1427, 2018.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics, vol. 210, no. 4, Genetics Society of America, 2018, pp. 1411–27, doi:10.1534/genetics.118.301429.","ista":"Sachdeva H, Barton NH. 2018. Replicability of introgression under linked, polygenic selection. Genetics. 210(4), 1411–1427.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301429."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"},{"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":["000452315900021"]},"title":"Replicability of introgression under linked, polygenic selection","abstract":[{"lang":"eng","text":"We study how a block of genome with a large number of weakly selected loci introgresses under directional selection into a genetically homogeneous population. We derive exact expressions for the expected rate of growth of any fragment of the introduced block during the initial phase of introgression, and show that the growth rate of a single-locus variant is largely insensitive to its own additive effect, but depends instead on the combined effect of all loci within a characteristic linkage scale. The expected growth rate of a fragment is highly correlated with its long-term introgression probability in populations of moderate size, and can hence identify variants that are likely to introgress across replicate populations. We clarify how the introgression probability of an individual variant is determined by the interplay between hitchhiking with relatively large fragments during the early phase of introgression and selection on fine-scale variation within these, which at longer times results in differential introgression probabilities for beneficial and deleterious loci within successful fragments. By simulating individuals, we also investigate how introgression probabilities at individual loci depend on the variance of fitness effects, the net fitness of the introduced block, and the size of the recipient population, and how this shapes the net advance under selection. Our work suggests that even highly replicable substitutions may be associated with a range of selective effects, which makes it challenging to fine map the causal loci that underlie polygenic adaptation."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/379578v1","open_access":"1"}],"month":"12","intvolume":" 210","publication_identifier":{"issn":["00166731"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"4","volume":210,"_id":"39","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-09-18T08:10:29Z","department":[{"_id":"NiBa"}]},{"publication_status":"published","language":[{"iso":"eng"}],"volume":32,"issue":"17","abstract":[{"lang":"eng","text":"We analyze the theoretical derivation of the beyond-mean-field equation of state for two-dimensional gas of dilute, ultracold alkali-metal atoms in the Bardeen–Cooper–Schrieffer (BCS) to Bose–Einstein condensate (BEC) crossover. We show that at zero temperature our theory — considering Gaussian fluctuations on top of the mean-field equation of state — is in very good agreement with experimental data. Subsequently, we investigate the superfluid density at finite temperature and its renormalization due to the proliferation of vortex–antivortex pairs. By doing so, we determine the Berezinskii–Kosterlitz–Thouless (BKT) critical temperature — at which the renormalized superfluid density jumps to zero — as a function of the inter-atomic potential strength. We find that the Nelson–Kosterlitz criterion overestimates the BKT temperature with respect to the renormalization group equations, this effect being particularly relevant in the intermediate regime of the crossover."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.11171"}],"month":"07","intvolume":" 32","date_updated":"2023-09-18T08:09:59Z","department":[{"_id":"MiLe"}],"_id":"420","type":"journal_article","status":"public","isi":1,"year":"2018","day":"10","publication":"International Journal of Modern Physics B","page":"1840022","date_published":"2018-07-10T00:00:00Z","doi":"10.1142/S0217979218400222","date_created":"2018-12-11T11:46:22Z","quality_controlled":"1","publisher":"World Scientific Publishing","oa":1,"citation":{"ista":"Bighin G, Salasnich L. 2018. Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. 32(17), 1840022.","chicago":"Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density in the Two-Dimensional BCS-BEC Crossover.” International Journal of Modern Physics B. World Scientific Publishing, 2018. https://doi.org/10.1142/S0217979218400222.","apa":"Bighin, G., & Salasnich, L. (2018). Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. World Scientific Publishing. https://doi.org/10.1142/S0217979218400222","ama":"Bighin G, Salasnich L. Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. 2018;32(17):1840022. doi:10.1142/S0217979218400222","short":"G. Bighin, L. Salasnich, International Journal of Modern Physics B 32 (2018) 1840022.","ieee":"G. Bighin and L. Salasnich, “Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover,” International Journal of Modern Physics B, vol. 32, no. 17. World Scientific Publishing, p. 1840022, 2018.","mla":"Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density in the Two-Dimensional BCS-BEC Crossover.” International Journal of Modern Physics B, vol. 32, no. 17, World Scientific Publishing, 2018, p. 1840022, doi:10.1142/S0217979218400222."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7402","author":[{"orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo","last_name":"Bighin","first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Salasnich, Luca","last_name":"Salasnich","first_name":"Luca"}],"article_processing_charge":"No","external_id":{"isi":["000438217300007"]},"title":"Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover"},{"page":"11006 - 11011","doi":"10.1073/pnas.1801832115","date_published":"2018-10-23T00:00:00Z","date_created":"2018-12-11T11:44:18Z","has_accepted_license":"1","isi":1,"year":"2018","day":"23","publication":"PNAS","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"acknowledgement":" ERC Grant 201252 (to N.H.B.)","publist_id":"8017","author":[{"full_name":"Tavares, Hugo","last_name":"Tavares","first_name":"Hugo"},{"full_name":"Whitley, Annabel","last_name":"Whitley","first_name":"Annabel"},{"last_name":"Field","orcid":"0000-0002-4014-8478","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"first_name":"Desmond","full_name":"Bradley, Desmond","last_name":"Bradley"},{"first_name":"Matthew","last_name":"Couchman","full_name":"Couchman, Matthew"},{"first_name":"Lucy","last_name":"Copsey","full_name":"Copsey, Lucy"},{"first_name":"Joane","last_name":"Elleouet","full_name":"Elleouet, Joane"},{"first_name":"Monique","last_name":"Burrus","full_name":"Burrus, Monique"},{"last_name":"Andalo","full_name":"Andalo, Christophe","first_name":"Christophe"},{"full_name":"Li, Miaomiao","last_name":"Li","first_name":"Miaomiao"},{"last_name":"Li","full_name":"Li, Qun","first_name":"Qun"},{"first_name":"Yongbiao","last_name":"Xue","full_name":"Xue, Yongbiao"},{"first_name":"Alexandra B","last_name":"Rebocho","full_name":"Rebocho, Alexandra B"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Enrico","last_name":"Coen","full_name":"Coen, Enrico"}],"external_id":{"isi":["000448040500065"],"pmid":["30297406"]},"article_processing_charge":"No","title":"Selection and gene flow shape genomic islands that control floral guides","citation":{"mla":"Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS, vol. 115, no. 43, National Academy of Sciences, 2018, pp. 11006–11, doi:10.1073/pnas.1801832115.","short":"H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J. Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton, E. Coen, PNAS 115 (2018) 11006–11011.","ieee":"H. Tavares et al., “Selection and gene flow shape genomic islands that control floral guides,” PNAS, vol. 115, no. 43. National Academy of Sciences, pp. 11006–11011, 2018.","ama":"Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic islands that control floral guides. PNAS. 2018;115(43):11006-11011. doi:10.1073/pnas.1801832115","apa":"Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L., … Coen, E. (2018). Selection and gene flow shape genomic islands that control floral guides. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1801832115","chicago":"Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman, Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1801832115.","ista":"Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J, Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection and gene flow shape genomic islands that control floral guides. PNAS. 115(43), 11006–11011."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"43","volume":115,"publication_identifier":{"issn":["00278424"]},"publication_status":"published","file":[{"date_created":"2018-12-17T08:44:03Z","file_name":"11006.full.pdf","creator":"dernst","date_updated":"2020-07-14T12:46:16Z","file_size":1911302,"file_id":"5683","checksum":"d2305d0cc81dbbe4c1c677d64ad6f6d1","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"10","intvolume":" 115","abstract":[{"lang":"eng","text":"Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightlylinked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding \"sea,\" making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation."}],"pmid":1,"oa_version":"Published Version","file_date_updated":"2020-07-14T12:46:16Z","department":[{"_id":"NiBa"}],"date_updated":"2023-09-18T08:36:49Z","ddc":["570"],"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":"38"},{"author":[{"last_name":"Xuereb","full_name":"Xuereb, André","first_name":"André"},{"first_name":"Matteo","full_name":"Aquilina, Matteo","last_name":"Aquilina"},{"last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir"}],"publist_id":"7766","external_id":{"isi":["000453298500019"],"arxiv":["1806.01000"]},"article_processing_charge":"No","title":"Routing thermal noise through quantum networks","editor":[{"full_name":"Andrews, D L","last_name":"Andrews","first_name":"D L"},{"full_name":"Ostendorf, A","last_name":"Ostendorf","first_name":"A"},{"last_name":"Bain","full_name":"Bain, A J","first_name":"A J"},{"full_name":"Nunzi, J M","last_name":"Nunzi","first_name":"J M"}],"citation":{"mla":"Xuereb, André, et al. Routing Thermal Noise through Quantum Networks. Edited by D L Andrews et al., vol. 10672, 106721N, SPIE, 2018, doi:10.1117/12.2309928.","short":"A. Xuereb, M. Aquilina, S. Barzanjeh, in:, D.L. Andrews, A. Ostendorf, A.J. Bain, J.M. Nunzi (Eds.), SPIE, 2018.","ieee":"A. Xuereb, M. Aquilina, and S. Barzanjeh, “Routing thermal noise through quantum networks,” presented at the SPIE: The international society for optical engineering, Strasbourg, France, 2018, vol. 10672.","apa":"Xuereb, A., Aquilina, M., & Barzanjeh, S. (2018). Routing thermal noise through quantum networks. In D. L. Andrews, A. Ostendorf, A. J. Bain, & J. M. Nunzi (Eds.) (Vol. 10672). Presented at the SPIE: The international society for optical engineering, Strasbourg, France: SPIE. https://doi.org/10.1117/12.2309928","ama":"Xuereb A, Aquilina M, Barzanjeh S. Routing thermal noise through quantum networks. In: Andrews DL, Ostendorf A, Bain AJ, Nunzi JM, eds. Vol 10672. SPIE; 2018. doi:10.1117/12.2309928","chicago":"Xuereb, André, Matteo Aquilina, and Shabir Barzanjeh. “Routing Thermal Noise through Quantum Networks.” edited by D L Andrews, A Ostendorf, A J Bain, and J M Nunzi, Vol. 10672. SPIE, 2018. https://doi.org/10.1117/12.2309928.","ista":"Xuereb A, Aquilina M, Barzanjeh S. 2018. Routing thermal noise through quantum networks. SPIE: The international society for optical engineering, Proceedings of SPIE, vol. 10672, 106721N."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"106721N","doi":"10.1117/12.2309928","date_published":"2018-05-04T00:00:00Z","date_created":"2018-12-11T11:44:55Z","isi":1,"year":"2018","day":"04","quality_controlled":"1","publisher":"SPIE","oa":1,"department":[{"_id":"JoFi"}],"date_updated":"2023-09-18T08:12:24Z","type":"conference","conference":{"name":"SPIE: The international society for optical engineering","start_date":"2018-04-22","location":"Strasbourg, France","end_date":"2018-04-26"},"status":"public","_id":"155","volume":10672,"publication_status":"published","language":[{"iso":"eng"}],"alternative_title":["Proceedings of SPIE"],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1806.01000","open_access":"1"}],"month":"05","intvolume":" 10672","abstract":[{"lang":"eng","text":"There is currently significant interest in operating devices in the quantum regime, where their behaviour cannot be explained through classical mechanics. Quantum states, including entangled states, are fragile and easily disturbed by excessive thermal noise. Here we address the question of whether it is possible to create non-reciprocal devices that encourage the flow of thermal noise towards or away from a particular quantum device in a network. Our work makes use of the cascaded systems formalism to answer this question in the affirmative, showing how a three-port device can be used as an effective thermal transistor, and illustrates how this formalism maps onto an experimentally-realisable optomechanical system. Our results pave the way to more resilient quantum devices and to the use of thermal noise as a resource."}],"oa_version":"Preprint"},{"publisher":"American Association for the Advancement of Science","quality_controlled":"1","oa":1,"acknowledgement":" M.S. was supported by the Gordon and Betty Moore Foundation s EPiQS Initiative through grant GBMF4307","page":"1271-1275","date_published":"2018-12-14T00:00:00Z","doi":"10.1126/science.aao0980","date_created":"2018-12-19T14:53:50Z","isi":1,"year":"2018","day":"14","publication":"Science","author":[{"last_name":"Gotlieb","full_name":"Gotlieb, Kenneth","first_name":"Kenneth"},{"first_name":"Chiu-Yun","last_name":"Lin","full_name":"Lin, Chiu-Yun"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn"},{"last_name":"Zhang","full_name":"Zhang, Wentao","first_name":"Wentao"},{"first_name":"Christopher L.","last_name":"Smallwood","full_name":"Smallwood, Christopher L."},{"first_name":"Christopher","full_name":"Jozwiak, Christopher","last_name":"Jozwiak"},{"full_name":"Eisaki, Hiroshi","last_name":"Eisaki","first_name":"Hiroshi"},{"first_name":"Zahid","last_name":"Hussain","full_name":"Hussain, Zahid"},{"first_name":"Ashvin","full_name":"Vishwanath, Ashvin","last_name":"Vishwanath"},{"first_name":"Alessandra","last_name":"Lanzara","full_name":"Lanzara, Alessandra"}],"article_processing_charge":"No","external_id":{"isi":["000452994400048"]},"title":"Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor","citation":{"chicago":"Gotlieb, Kenneth, Chiu-Yun Lin, Maksym Serbyn, Wentao Zhang, Christopher L. Smallwood, Christopher Jozwiak, Hiroshi Eisaki, Zahid Hussain, Ashvin Vishwanath, and Alessandra Lanzara. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” Science. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aao0980.","ista":"Gotlieb K, Lin C-Y, Serbyn M, Zhang W, Smallwood CL, Jozwiak C, Eisaki H, Hussain Z, Vishwanath A, Lanzara A. 2018. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. 362(6420), 1271–1275.","mla":"Gotlieb, Kenneth, et al. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” Science, vol. 362, no. 6420, American Association for the Advancement of Science, 2018, pp. 1271–75, doi:10.1126/science.aao0980.","apa":"Gotlieb, K., Lin, C.-Y., Serbyn, M., Zhang, W., Smallwood, C. L., Jozwiak, C., … Lanzara, A. (2018). Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aao0980","ama":"Gotlieb K, Lin C-Y, Serbyn M, et al. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. 2018;362(6420):1271-1275. doi:10.1126/science.aao0980","short":"K. Gotlieb, C.-Y. Lin, M. Serbyn, W. Zhang, C.L. Smallwood, C. Jozwiak, H. Eisaki, Z. Hussain, A. Vishwanath, A. Lanzara, Science 362 (2018) 1271–1275.","ieee":"K. Gotlieb et al., “Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor,” Science, vol. 362, no. 6420. American Association for the Advancement of Science, pp. 1271–1275, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1126/science.aao0980","open_access":"1"}],"month":"12","intvolume":" 362","abstract":[{"lang":"eng","text":"Cuprate superconductors have long been thought of as having strong electronic correlations but negligible spin-orbit coupling. Using spin- and angle-resolved photoemission spectroscopy, we discovered that one of the most studied cuprate superconductors, Bi2212, has a nontrivial spin texture with a spin-momentum locking that circles the Brillouin zone center and a spin-layer locking that allows states of opposite spin to be localized in different parts of the unit cell. Our findings pose challenges for the vast majority of models of cuprates, such as the Hubbard model and its variants, where spin-orbit interaction has been mostly neglected, and open the intriguing question of how the high-temperature superconducting state emerges in the presence of this nontrivial spin texture. "}],"oa_version":"Published Version","issue":"6420","volume":362,"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"5767","department":[{"_id":"MaSe"}],"date_updated":"2023-09-18T08:11:56Z"},{"citation":{"ista":"Jiang Y, Liu H, Song H, Kong H, Wang R, Guan Y, Sha L. 2018. Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. 19(10), 3320–3333.","chicago":"Jiang, Yu, Han Liu, Huobing Song, Hui Kong, Rui Wang, Yong Guan, and Lui Sha. “Safety-Assured Model-Driven Design of the Multifunction Vehicle Bus Controller.” IEEE Transactions on Intelligent Transportation Systems. IEEE, 2018. https://doi.org/10.1109/TITS.2017.2778077.","short":"Y. Jiang, H. Liu, H. Song, H. Kong, R. Wang, Y. Guan, L. Sha, IEEE Transactions on Intelligent Transportation Systems 19 (2018) 3320–3333.","ieee":"Y. Jiang et al., “Safety-assured model-driven design of the multifunction vehicle bus controller,” IEEE Transactions on Intelligent Transportation Systems, vol. 19, no. 10. IEEE, pp. 3320–3333, 2018.","apa":"Jiang, Y., Liu, H., Song, H., Kong, H., Wang, R., Guan, Y., & Sha, L. (2018). Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. IEEE. https://doi.org/10.1109/TITS.2017.2778077","ama":"Jiang Y, Liu H, Song H, et al. Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. 2018;19(10):3320-3333. doi:10.1109/TITS.2017.2778077","mla":"Jiang, Yu, et al. “Safety-Assured Model-Driven Design of the Multifunction Vehicle Bus Controller.” IEEE Transactions on Intelligent Transportation Systems, vol. 19, no. 10, IEEE, 2018, pp. 3320–33, doi:10.1109/TITS.2017.2778077."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Jiang, Yu","last_name":"Jiang","first_name":"Yu"},{"last_name":"Liu","full_name":"Liu, Han","first_name":"Han"},{"last_name":"Song","full_name":"Song, Huobing","first_name":"Huobing"},{"id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","first_name":"Hui","last_name":"Kong","full_name":"Kong, Hui","orcid":"0000-0002-3066-6941"},{"first_name":"Rui","full_name":"Wang, Rui","last_name":"Wang"},{"first_name":"Yong","full_name":"Guan, Yong","last_name":"Guan"},{"first_name":"Lui","full_name":"Sha, Lui","last_name":"Sha"}],"publist_id":"7389","article_processing_charge":"No","external_id":{"isi":["000446651100020"]},"title":"Safety-assured model-driven design of the multifunction vehicle bus controller","quality_controlled":"1","publisher":"IEEE","isi":1,"year":"2018","day":"01","publication":"IEEE Transactions on Intelligent Transportation Systems","page":"3320 - 3333","date_published":"2018-01-01T00:00:00Z","doi":"10.1109/TITS.2017.2778077","date_created":"2018-12-11T11:46:27Z","_id":"434","type":"journal_article","status":"public","date_updated":"2023-09-18T08:12:49Z","department":[{"_id":"ToHe"}],"abstract":[{"text":"In this paper, we present a formal model-driven design approach to establish a safety-assured implementation of multifunction vehicle bus controller (MVBC), which controls the data transmission among the devices of the vehicle. First, the generic models and safety requirements described in International Electrotechnical Commission Standard 61375 are formalized as time automata and timed computation tree logic formulas, respectively. With model checking tool Uppaal, we verify whether or not the constructed timed automata satisfy the formulas and several logic inconsistencies in the original standard are detected and corrected. Then, we apply the code generation tool Times to generate C code from the verified model, which is later synthesized into a real MVBC chip, with some handwriting glue code. Furthermore, the runtime verification tool RMOR is applied on the integrated code, to verify some safety requirements that cannot be formalized on the timed automata. For evaluation, we compare the proposed approach with existing MVBC design methods, such as BeagleBone, Galsblock, and Simulink. Experiments show that more ambiguousness or bugs in the standard are detected during Uppaal verification, and the generated code of Times outperforms the C code generated by others in terms of the synthesized binary code size. The errors in the standard have been confirmed and the resulting MVBC has been deployed in the real train communication network.","lang":"eng"}],"oa_version":"None","scopus_import":"1","month":"01","intvolume":" 19","publication_status":"published","language":[{"iso":"eng"}],"volume":19,"related_material":{"record":[{"status":"public","id":"1205","relation":"earlier_version"}]},"issue":"10"},{"oa_version":"Published Version","abstract":[{"text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here, we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts.","lang":"eng"}],"month":"06","intvolume":" 7","scopus_import":"1","file":[{"creator":"dernst","date_updated":"2020-07-14T12:45:07Z","file_size":9816484,"date_created":"2018-12-17T16:41:58Z","file_name":"2018_eLife_Kaucka.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"da2378cdcf6b5461dcde194e4d608343","file_id":"5727"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":7,"related_material":{"record":[{"relation":"research_data","id":"9838","status":"public"}]},"ec_funded":1,"_id":"162","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":["571"],"date_updated":"2023-09-18T09:29:07Z","department":[{"_id":"AnKi"}],"file_date_updated":"2020-07-14T12:45:07Z","quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"day":"13","publication":"eLife","isi":1,"has_accepted_license":"1","year":"2018","doi":"10.7554/eLife.34465","date_published":"2018-06-13T00:00:00Z","date_created":"2018-12-11T11:44:57Z","article_number":"e34465","project":[{"grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Kaucka, Marketa, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” ELife, vol. 7, e34465, eLife Sciences Publications, 2018, doi:10.7554/eLife.34465.","ama":"Kaucka M, Petersen J, Tesarova M, et al. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 2018;7. doi:10.7554/eLife.34465","apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M., Xie, M., … Adameyko, I. (2018). Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.34465","ieee":"M. Kaucka et al., “Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage,” eLife, vol. 7. eLife Sciences Publications, 2018.","short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, ELife 7 (2018).","chicago":"Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Kastriti, Meng Xie, Anna Kicheva, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.34465.","ista":"Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti M, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 7, e34465."},"title":"Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","publist_id":"7759","author":[{"first_name":"Marketa","full_name":"Kaucka, Marketa","last_name":"Kaucka"},{"full_name":"Petersen, Julian","last_name":"Petersen","first_name":"Julian"},{"last_name":"Tesarova","full_name":"Tesarova, Marketa","first_name":"Marketa"},{"last_name":"Szarowska","full_name":"Szarowska, Bara","first_name":"Bara"},{"full_name":"Kastriti, Maria","last_name":"Kastriti","first_name":"Maria"},{"last_name":"Xie","full_name":"Xie, Meng","first_name":"Meng"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998"},{"full_name":"Annusver, Karl","last_name":"Annusver","first_name":"Karl"},{"full_name":"Kasper, Maria","last_name":"Kasper","first_name":"Maria"},{"first_name":"Orsolya","full_name":"Symmons, Orsolya","last_name":"Symmons"},{"first_name":"Leslie","last_name":"Pan","full_name":"Pan, Leslie"},{"last_name":"Spitz","full_name":"Spitz, Francois","first_name":"Francois"},{"last_name":"Kaiser","full_name":"Kaiser, Jozef","first_name":"Jozef"},{"first_name":"Maria","last_name":"Hovorakova","full_name":"Hovorakova, Maria"},{"full_name":"Zikmund, Tomas","last_name":"Zikmund","first_name":"Tomas"},{"first_name":"Kazunori","last_name":"Sunadome","full_name":"Sunadome, Kazunori"},{"full_name":"Matise, Michael P","last_name":"Matise","first_name":"Michael P"},{"first_name":"Hui","full_name":"Wang, Hui","last_name":"Wang"},{"full_name":"Marklund, Ulrika","last_name":"Marklund","first_name":"Ulrika"},{"full_name":"Abdo, Hind","last_name":"Abdo","first_name":"Hind"},{"first_name":"Patrik","last_name":"Ernfors","full_name":"Ernfors, Patrik"},{"last_name":"Maire","full_name":"Maire, Pascal","first_name":"Pascal"},{"last_name":"Wurmser","full_name":"Wurmser, Maud","first_name":"Maud"},{"first_name":"Andrei S","full_name":"Chagin, Andrei S","last_name":"Chagin"},{"first_name":"Kaj","last_name":"Fried","full_name":"Fried, Kaj"},{"first_name":"Igor","last_name":"Adameyko","full_name":"Adameyko, Igor"}],"external_id":{"isi":["000436227500001"]},"article_processing_charge":"No"},{"quality_controlled":"1","publisher":"Springer","oa":1,"page":"451 - 467","doi":"10.1007/978-3-319-78375-8_15","date_published":"2018-05-29T00:00:00Z","date_created":"2018-12-11T11:45:42Z","isi":1,"year":"2018","day":"29","project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publist_id":"7579","author":[{"last_name":"Cohen","full_name":"Cohen, Bram","first_name":"Bram"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak"}],"external_id":{"isi":["000517098700015"]},"article_processing_charge":"No","title":"Simple proofs of sequential work","citation":{"chicago":"Cohen, Bram, and Krzysztof Z Pietrzak. “Simple Proofs of Sequential Work,” 10821:451–67. Springer, 2018. https://doi.org/10.1007/978-3-319-78375-8_15.","ista":"Cohen B, Pietrzak KZ. 2018. Simple proofs of sequential work. Eurocrypt: Advances in Cryptology, LNCS, vol. 10821, 451–467.","mla":"Cohen, Bram, and Krzysztof Z. Pietrzak. Simple Proofs of Sequential Work. Vol. 10821, Springer, 2018, pp. 451–67, doi:10.1007/978-3-319-78375-8_15.","apa":"Cohen, B., & Pietrzak, K. Z. (2018). Simple proofs of sequential work (Vol. 10821, pp. 451–467). Presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78375-8_15","ama":"Cohen B, Pietrzak KZ. Simple proofs of sequential work. In: Vol 10821. Springer; 2018:451-467. doi:10.1007/978-3-319-78375-8_15","short":"B. Cohen, K.Z. Pietrzak, in:, Springer, 2018, pp. 451–467.","ieee":"B. Cohen and K. Z. Pietrzak, “Simple proofs of sequential work,” presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10821, pp. 451–467."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"url":"https://eprint.iacr.org/2018/183.pdf","open_access":"1"}],"month":"05","intvolume":" 10821","abstract":[{"lang":"eng","text":"At ITCS 2013, Mahmoody, Moran and Vadhan [MMV13] introduce and construct publicly verifiable proofs of sequential work, which is a protocol for proving that one spent sequential computational work related to some statement. The original motivation for such proofs included non-interactive time-stamping and universally verifiable CPU benchmarks. A more recent application, and our main motivation, are blockchain designs, where proofs of sequential work can be used – in combination with proofs of space – as a more ecological and economical substitute for proofs of work which are currently used to secure Bitcoin and other cryptocurrencies. The construction proposed by [MMV13] is based on a hash function and can be proven secure in the random oracle model, or assuming inherently sequential hash-functions, which is a new standard model assumption introduced in their work. In a proof of sequential work, a prover gets a “statement” χ, a time parameter N and access to a hash-function H, which for the security proof is modelled as a random oracle. Correctness requires that an honest prover can make a verifier accept making only N queries to H, while soundness requires that any prover who makes the verifier accept must have made (almost) N sequential queries to H. Thus a solution constitutes a proof that N time passed since χ was received. Solutions must be publicly verifiable in time at most polylogarithmic in N. The construction of [MMV13] is based on “depth-robust” graphs, and as a consequence has rather poor concrete parameters. But the major drawback is that the prover needs not just N time, but also N space to compute a proof. In this work we propose a proof of sequential work which is much simpler, more efficient and achieves much better concrete bounds. Most importantly, the space required can be as small as log (N) (but we get better soundness using slightly more memory than that). An open problem stated by [MMV13] that our construction does not solve either is achieving a “unique” proof, where even a cheating prover can only generate a single accepting proof. This property would be extremely useful for applications to blockchains."}],"oa_version":"Submitted Version","volume":10821,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"type":"conference","conference":{"name":"Eurocrypt: Advances in Cryptology","location":"Tel Aviv, Israel","end_date":"2018-05-03","start_date":"2018-04-29"},"status":"public","_id":"302","department":[{"_id":"KrPi"}],"date_updated":"2023-09-18T09:29:33Z"},{"year":"2018","isi":1,"publication":"Physical Review E","day":"17","date_created":"2018-12-11T11:44:15Z","doi":"10.1103/PhysRevE.98.042410","date_published":"2018-10-17T00:00:00Z","acknowledgement":"This work was supported by ANR Trajectory, the French State program Investissements d’Avenir managed by the Agence Nationale de la Recherche (LIFESENSES; ANR-10-LABX-65), EC Grant No. H2020-785907 from the Human Brain Project, NIH Grant No. U01NS090501, and an AVIESAN-UNADEV grant to O.M. M.C. was supported by the Agence Nationale de la Recherche Jeune Chercheur/Jeune Chercheuse grant (ANR-17-CE37-0013).","oa":1,"quality_controlled":"1","publisher":"American Physical Society","citation":{"mla":"Ferrari, Ulisse, et al. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E, vol. 98, no. 4, 042410, American Physical Society, 2018, doi:10.1103/PhysRevE.98.042410.","ieee":"U. Ferrari, S. Deny, M. J. Chalk, G. Tkačik, O. Marre, and T. Mora, “Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons,” Physical Review E, vol. 98, no. 4. American Physical Society, 2018.","short":"U. Ferrari, S. Deny, M.J. Chalk, G. Tkačik, O. Marre, T. Mora, Physical Review E 98 (2018).","ama":"Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 2018;98(4). doi:10.1103/PhysRevE.98.042410","apa":"Ferrari, U., Deny, S., Chalk, M. J., Tkačik, G., Marre, O., & Mora, T. (2018). Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.98.042410","chicago":"Ferrari, Ulisse, Stephane Deny, Matthew J Chalk, Gašper Tkačik, Olivier Marre, and Thierry Mora. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E. American Physical Society, 2018. https://doi.org/10.1103/PhysRevE.98.042410.","ista":"Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. 2018. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 98(4), 042410."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000447486100004"]},"article_processing_charge":"No","author":[{"first_name":"Ulisse","full_name":"Ferrari, Ulisse","last_name":"Ferrari"},{"full_name":"Deny, Stephane","last_name":"Deny","first_name":"Stephane"},{"first_name":"Matthew J","last_name":"Chalk","full_name":"Chalk, Matthew J"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik"},{"last_name":"Marre","full_name":"Marre, Olivier","first_name":"Olivier"},{"full_name":"Mora, Thierry","last_name":"Mora","first_name":"Thierry"}],"publist_id":"8024","title":"Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons","article_number":"042410","project":[{"call_identifier":"H2020","_id":"26436750-B435-11E9-9278-68D0E5697425","name":"Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)","grant_number":"785907"}],"publication_status":"published","publication_identifier":{"issn":["24700045"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":98,"issue":"4","abstract":[{"text":"Correlations in sensory neural networks have both extrinsic and intrinsic origins. Extrinsic or stimulus correlations arise from shared inputs to the network and, thus, depend strongly on the stimulus ensemble. Intrinsic or noise correlations reflect biophysical mechanisms of interactions between neurons, which are expected to be robust to changes in the stimulus ensemble. Despite the importance of this distinction for understanding how sensory networks encode information collectively, no method exists to reliably separate intrinsic interactions from extrinsic correlations in neural activity data, limiting our ability to build predictive models of the network response. In this paper we introduce a general strategy to infer population models of interacting neurons that collectively encode stimulus information. The key to disentangling intrinsic from extrinsic correlations is to infer the couplings between neurons separately from the encoding model and to combine the two using corrections calculated in a mean-field approximation. We demonstrate the effectiveness of this approach in retinal recordings. The same coupling network is inferred from responses to radically different stimulus ensembles, showing that these couplings indeed reflect stimulus-independent interactions between neurons. The inferred model predicts accurately the collective response of retinal ganglion cell populations as a function of the stimulus.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/243816v2.full","open_access":"1"}],"scopus_import":"1","intvolume":" 98","month":"10","date_updated":"2023-09-18T09:18:44Z","department":[{"_id":"GaTk"}],"_id":"31","article_type":"original","type":"journal_article","status":"public"},{"ec_funded":1,"volume":115,"issue":"35","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00278424"]},"intvolume":" 115","month":"08","main_file_link":[{"url":"https://arxiv.org/abs/1806.09153","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Tropical geometry, an established field in pure mathematics, is a place where string theory, mirror symmetry, computational algebra, auction theory, and so forth meet and influence one another. In this paper, we report on our discovery of a tropical model with self-organized criticality (SOC) behavior. Our model is continuous, in contrast to all known models of SOC, and is a certain scaling limit of the sandpile model, the first and archetypical model of SOC. We describe how our model is related to pattern formation and proportional growth phenomena and discuss the dichotomy between continuous and discrete models in several contexts. Our aim in this context is to present an idealized tropical toy model (cf. Turing reaction-diffusion model), requiring further investigation."}],"department":[{"_id":"TaHa"}],"date_updated":"2023-09-18T08:41:16Z","status":"public","type":"journal_article","article_type":"original","_id":"64","date_created":"2018-12-11T11:44:26Z","doi":"10.1073/pnas.1805847115","date_published":"2018-08-28T00:00:00Z","page":"E8135 - E8142","publication":"PNAS: Proceedings of the National Academy of Sciences of the United States of America","day":"28","year":"2018","isi":1,"oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","title":"Self-organized criticality and pattern emergence through the lens of tropical geometry","external_id":{"arxiv":["1806.09153"],"isi":["000442861600009"]},"article_processing_charge":"No","author":[{"full_name":"Kalinin, Nikita","last_name":"Kalinin","first_name":"Nikita"},{"last_name":"Guzmán Sáenz","full_name":"Guzmán Sáenz, Aldo","first_name":"Aldo"},{"full_name":"Prieto, Y","last_name":"Prieto","first_name":"Y"},{"last_name":"Shkolnikov","full_name":"Shkolnikov, Mikhail","orcid":"0000-0002-4310-178X","id":"35084A62-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"},{"full_name":"Kalinina, V","last_name":"Kalinina","first_name":"V"},{"full_name":"Lupercio, Ernesto","last_name":"Lupercio","first_name":"Ernesto"}],"publist_id":"7990","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Kalinin, Nikita, Aldo Guzmán Sáenz, Y Prieto, Mikhail Shkolnikov, V Kalinina, and Ernesto Lupercio. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” PNAS: Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1805847115.","ista":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. 2018. Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. 115(35), E8135–E8142.","mla":"Kalinin, Nikita, et al. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” PNAS: Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 35, National Academy of Sciences, 2018, pp. E8135–42, doi:10.1073/pnas.1805847115.","ama":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. 2018;115(35):E8135-E8142. doi:10.1073/pnas.1805847115","apa":"Kalinin, N., Guzmán Sáenz, A., Prieto, Y., Shkolnikov, M., Kalinina, V., & Lupercio, E. (2018). Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1805847115","ieee":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, and E. Lupercio, “Self-organized criticality and pattern emergence through the lens of tropical geometry,” PNAS: Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 35. National Academy of Sciences, pp. E8135–E8142, 2018.","short":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, E. Lupercio, PNAS: Proceedings of the National Academy of Sciences of the United States of America 115 (2018) E8135–E8142."},"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"date_updated":"2023-09-18T09:29:07Z","citation":{"mla":"Kaucka, Marketa, et al. Data from: Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage. Dryad, 2018, doi:10.5061/dryad.f1s76f2.","apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M. E., Xie, M., … Adameyko, I. (2018). Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. Dryad. https://doi.org/10.5061/dryad.f1s76f2","ama":"Kaucka M, Petersen J, Tesarova M, et al. Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. 2018. doi:10.5061/dryad.f1s76f2","ieee":"M. Kaucka et al., “Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage.” Dryad, 2018.","short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M.E. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, (2018).","chicago":"Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Eleni Kastriti, Meng Xie, Anna Kicheva, et al. “Data from: Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” Dryad, 2018. https://doi.org/10.5061/dryad.f1s76f2.","ista":"Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti ME, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage, Dryad, 10.5061/dryad.f1s76f2."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Kaucka, Marketa","last_name":"Kaucka","first_name":"Marketa"},{"last_name":"Petersen","full_name":"Petersen, Julian","first_name":"Julian"},{"first_name":"Marketa","last_name":"Tesarova","full_name":"Tesarova, Marketa"},{"last_name":"Szarowska","full_name":"Szarowska, Bara","first_name":"Bara"},{"full_name":"Kastriti, Maria Eleni","last_name":"Kastriti","first_name":"Maria Eleni"},{"full_name":"Xie, Meng","last_name":"Xie","first_name":"Meng"},{"full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Karl","last_name":"Annusver","full_name":"Annusver, Karl"},{"first_name":"Maria","last_name":"Kasper","full_name":"Kasper, Maria"},{"first_name":"Orsolya","full_name":"Symmons, Orsolya","last_name":"Symmons"},{"full_name":"Pan, Leslie","last_name":"Pan","first_name":"Leslie"},{"full_name":"Spitz, Francois","last_name":"Spitz","first_name":"Francois"},{"first_name":"Jozef","full_name":"Kaiser, Jozef","last_name":"Kaiser"},{"last_name":"Hovorakova","full_name":"Hovorakova, Maria","first_name":"Maria"},{"last_name":"Zikmund","full_name":"Zikmund, Tomas","first_name":"Tomas"},{"last_name":"Sunadome","full_name":"Sunadome, Kazunori","first_name":"Kazunori"},{"first_name":"Michael P","full_name":"Matise, Michael P","last_name":"Matise"},{"first_name":"Hui","full_name":"Wang, Hui","last_name":"Wang"},{"first_name":"Ulrika","full_name":"Marklund, Ulrika","last_name":"Marklund"},{"full_name":"Abdo, Hind","last_name":"Abdo","first_name":"Hind"},{"last_name":"Ernfors","full_name":"Ernfors, Patrik","first_name":"Patrik"},{"first_name":"Pascal","last_name":"Maire","full_name":"Maire, Pascal"},{"first_name":"Maud","full_name":"Wurmser, Maud","last_name":"Wurmser"},{"first_name":"Andrei S","full_name":"Chagin, Andrei S","last_name":"Chagin"},{"first_name":"Kaj","last_name":"Fried","full_name":"Fried, Kaj"},{"last_name":"Adameyko","full_name":"Adameyko, Igor","first_name":"Igor"}],"article_processing_charge":"No","title":"Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","department":[{"_id":"AnKi"}],"_id":"9838","type":"research_data_reference","status":"public","year":"2018","day":"14","date_published":"2018-06-14T00:00:00Z","doi":"10.5061/dryad.f1s76f2","related_material":{"record":[{"id":"162","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-09T12:54:35Z","abstract":[{"lang":"eng","text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts."}],"oa_version":"Published Version","publisher":"Dryad","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.f1s76f2"}],"month":"06"},{"article_number":"311","project":[{"call_identifier":"H2020","_id":"25CBA828-B435-11E9-9278-68D0E5697425","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","grant_number":"720270"}],"citation":{"mla":"Luján, Rafæl, et al. “Sk2 Channels Associate with MGlu1α Receptors and CaV2.1 Channels in Purkinje Cells.” Frontiers in Cellular Neuroscience, vol. 12, 311, Frontiers Media, 2018, doi:10.3389/fncel.2018.00311.","ama":"Luján R, Aguado C, Ciruela F, et al. Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. 2018;12. doi:10.3389/fncel.2018.00311","apa":"Luján, R., Aguado, C., Ciruela, F., Arus, X., Martín Belmonte, A., Alfaro Ruiz, R., … Fukazawa, Y. (2018). Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. Frontiers Media. https://doi.org/10.3389/fncel.2018.00311","ieee":"R. Luján et al., “Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells,” Frontiers in Cellular Neuroscience, vol. 12. Frontiers Media, 2018.","short":"R. Luján, C. Aguado, F. Ciruela, X. Arus, A. Martín Belmonte, R. Alfaro Ruiz, J. Martinez Gomez, L. De La Ossa, M. Watanabe, J. Adelman, R. Shigemoto, Y. Fukazawa, Frontiers in Cellular Neuroscience 12 (2018).","chicago":"Luján, Rafæl, Carolina Aguado, Francisco Ciruela, Xavier Arus, Alejandro Martín Belmonte, Rocío Alfaro Ruiz, Jesus Martinez Gomez, et al. “Sk2 Channels Associate with MGlu1α Receptors and CaV2.1 Channels in Purkinje Cells.” Frontiers in Cellular Neuroscience. Frontiers Media, 2018. https://doi.org/10.3389/fncel.2018.00311.","ista":"Luján R, Aguado C, Ciruela F, Arus X, Martín Belmonte A, Alfaro Ruiz R, Martinez Gomez J, De La Ossa L, Watanabe M, Adelman J, Shigemoto R, Fukazawa Y. 2018. Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. 12, 311."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000445090100002"]},"article_processing_charge":"No","author":[{"last_name":"Luján","full_name":"Luján, Rafæl","first_name":"Rafæl"},{"full_name":"Aguado, Carolina","last_name":"Aguado","first_name":"Carolina"},{"last_name":"Ciruela","full_name":"Ciruela, Francisco","first_name":"Francisco"},{"first_name":"Xavier","last_name":"Arus","full_name":"Arus, Xavier"},{"first_name":"Alejandro","full_name":"Martín Belmonte, Alejandro","last_name":"Martín Belmonte"},{"last_name":"Alfaro Ruiz","full_name":"Alfaro Ruiz, Rocío","first_name":"Rocío"},{"first_name":"Jesus","last_name":"Martinez Gomez","full_name":"Martinez Gomez, Jesus"},{"full_name":"De La Ossa, Luis","last_name":"De La Ossa","first_name":"Luis"},{"first_name":"Masahiko","last_name":"Watanabe","full_name":"Watanabe, Masahiko"},{"first_name":"John","last_name":"Adelman","full_name":"Adelman, John"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"first_name":"Yugo","last_name":"Fukazawa","full_name":"Fukazawa, Yugo"}],"publist_id":"8013","title":"Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells","oa":1,"quality_controlled":"1","publisher":"Frontiers Media","year":"2018","has_accepted_license":"1","isi":1,"publication":"Frontiers in Cellular Neuroscience","day":"19","date_created":"2018-12-11T11:44:19Z","date_published":"2018-09-19T00:00:00Z","doi":"10.3389/fncel.2018.00311","_id":"41","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-18T09:31:18Z","ddc":["570"],"department":[{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:46:23Z","abstract":[{"text":"The small-conductance, Ca2+-activated K+ (SK) channel subtype SK2 regulates the spike rate and firing frequency, as well as Ca2+ transients in Purkinje cells (PCs). To understand the molecular basis by which SK2 channels mediate these functions, we analyzed the exact location and densities of SK2 channels along the neuronal surface of the mouse cerebellar PCs using SDS-digested freeze-fracture replica labeling (SDS-FRL) of high sensitivity combined with quantitative analyses. Immunogold particles for SK2 were observed on post- and pre-synaptic compartments showing both scattered and clustered distribution patterns. We found an axo-somato-dendritic gradient of the SK2 particle density increasing 12-fold from soma to dendritic spines. Using two different immunogold approaches, we also found that SK2 immunoparticles were frequently adjacent to, but never overlap with, the postsynaptic density of excitatory synapses in PC spines. Co-immunoprecipitation analysis demonstrated that SK2 channels form macromolecular complexes with two types of proteins that mobilize Ca2+: CaV2.1 channels and mGlu1α receptors in the cerebellum. Freeze-fracture replica double-labeling showed significant co-clustering of particles for SK2 with those for CaV2.1 channels and mGlu1α receptors. SK2 channels were also detected at presynaptic sites, mostly at the presynaptic active zone (AZ), where they are close to CaV2.1 channels, though they are not significantly co-clustered. These data demonstrate that SK2 channels located in different neuronal compartments can associate with distinct proteins mobilizing Ca2+, and suggest that the ultrastructural association of SK2 with CaV2.1 and mGlu1α provides the mechanism that ensures voltage (excitability) regulation by distinct intracellular Ca2+ transients in PCs.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 12","month":"09","publication_status":"published","publication_identifier":{"issn":["16625102"]},"language":[{"iso":"eng"}],"file":[{"checksum":"0bcaec8d596162af0b7fe3f31325d480","file_id":"5684","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"fncel-12-00311.pdf","date_created":"2018-12-17T08:49:03Z","file_size":6834251,"date_updated":"2020-07-14T12:46:23Z","creator":"dernst"}],"ec_funded":1,"volume":12},{"has_accepted_license":"1","isi":1,"year":"2018","day":"25","publication":"Nano Letters","page":"7141 - 7145","doi":"10.1021/acs.nanolett.8b03217","date_published":"2018-10-25T00:00:00Z","date_created":"2018-12-11T11:44:13Z","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"citation":{"chicago":"Vukušić, Lada, Josip Kukucka, Hannes Watzinger, Joshua M Milem, Friedrich Schäffler, and Georgios Katsaros. “Single-Shot Readout of Hole Spins in Ge.” Nano Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.8b03217.","ista":"Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. 2018. Single-shot readout of hole spins in Ge. Nano Letters. 18(11), 7141–7145.","mla":"Vukušić, Lada, et al. “Single-Shot Readout of Hole Spins in Ge.” Nano Letters, vol. 18, no. 11, American Chemical Society, 2018, pp. 7141–45, doi:10.1021/acs.nanolett.8b03217.","ama":"Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. Single-shot readout of hole spins in Ge. Nano Letters. 2018;18(11):7141-7145. doi:10.1021/acs.nanolett.8b03217","apa":"Vukušić, L., Kukucka, J., Watzinger, H., Milem, J. M., Schäffler, F., & Katsaros, G. (2018). Single-shot readout of hole spins in Ge. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.8b03217","short":"L. Vukušić, J. Kukucka, H. Watzinger, J.M. Milem, F. Schäffler, G. Katsaros, Nano Letters 18 (2018) 7141–7145.","ieee":"L. Vukušić, J. Kukucka, H. Watzinger, J. M. Milem, F. Schäffler, and G. Katsaros, “Single-shot readout of hole spins in Ge,” Nano Letters, vol. 18, no. 11. American Chemical Society, pp. 7141–7145, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","full_name":"Vukušić, Lada","orcid":"0000-0003-2424-8636","last_name":"Vukušić"},{"last_name":"Kukucka","full_name":"Kukucka, Josip","first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Watzinger, Hannes","last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes"},{"id":"4CDE0A96-F248-11E8-B48F-1D18A9856A87","first_name":"Joshua M","last_name":"Milem","full_name":"Milem, Joshua M"},{"first_name":"Friedrich","last_name":"Schäffler","full_name":"Schäffler, Friedrich"},{"last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"8032","external_id":{"isi":["000451102100064"],"pmid":["30359041"]},"article_processing_charge":"No","title":"Single-shot readout of hole spins in Ge","project":[{"name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","grant_number":"335497","call_identifier":"FP7","_id":"25517E86-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["15306984"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"3e6034a94c6b5335e939145d88bdb371","file_id":"5194","date_updated":"2020-07-14T12:45:37Z","file_size":1361441,"creator":"system","date_created":"2018-12-12T10:16:08Z","file_name":"IST-2018-1065-v1+1_ACS_nanoletters_8b03217.pdf"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"popular_science","id":"7977"},{"id":"69","status":"public","relation":"dissertation_contains"},{"id":"7996","status":"public","relation":"dissertation_contains"}]},"volume":18,"issue":"11","ec_funded":1,"abstract":[{"text":"The strong atomistic spin–orbit coupling of holes makes single-shot spin readout measurements difficult because it reduces the spin lifetimes. By integrating the charge sensor into a high bandwidth radio frequency reflectometry setup, we were able to demonstrate single-shot readout of a germanium quantum dot hole spin and measure the spin lifetime. Hole spin relaxation times of about 90 μs at 500 mT are reported, with a total readout visibility of about 70%. By analyzing separately the spin-to-charge conversion and charge readout fidelities, we have obtained insight into the processes limiting the visibilities of hole spins. The analyses suggest that high hole visibilities are feasible at realistic experimental conditions, underlying the potential of hole spins for the realization of viable qubit devices.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"10","intvolume":" 18","date_updated":"2023-09-18T09:30:37Z","ddc":["530"],"file_date_updated":"2020-07-14T12:45:37Z","department":[{"_id":"GeKa"}],"_id":"23","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":"1065"},{"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Concurrent accesses to shared data structures must be synchronized to avoid data races. Coarse-grained synchronization, which locks the entire data structure, is easy to implement but does not scale. Fine-grained synchronization can scale well, but can be hard to reason about. Hand-over-hand locking, in which operations are pipelined as they traverse the data structure, combines fine-grained synchronization with ease of use. However, the traditional implementation suffers from inherent overheads. This paper introduces snapshot-based synchronization (SBS), a novel hand-over-hand locking mechanism. SBS decouples the synchronization state from the data, significantly improving cache utilization. Further, it relies on guarantees provided by pipelining to minimize synchronization that requires cross-thread communication. Snapshot-based synchronization thus scales much better than traditional hand-over-hand locking, while maintaining the same ease of use."}],"intvolume":" 11014","month":"08","alternative_title":["LNCS"],"scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5954","checksum":"13a3f250be8878405e791b53c19722ad","date_updated":"2020-07-14T12:48:14Z","file_size":665372,"creator":"dernst","date_created":"2019-02-12T07:40:40Z","file_name":"2018_Brown.pdf"}],"publication_status":"published","publication_identifier":{"issn":["03029743"]},"volume":11014,"_id":"85","status":"public","conference":{"name":"Euro-Par: European Conference on Parallel Processing","start_date":"2018-08-27","location":"Turin, Italy","end_date":"2018-08-31"},"type":"conference","ddc":["000"],"date_updated":"2023-09-18T09:32:36Z","file_date_updated":"2020-07-14T12:48:14Z","department":[{"_id":"DaAl"}],"acknowledgement":"Trevor Brown was supported in part by the ISF (grants 2005/17 & 1749/14) and by a NSERC post-doctoral fellowship.","oa":1,"quality_controlled":"1","publisher":"Springer","day":"01","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:44:33Z","doi":"10.1007/978-3-319-96983-1_33","date_published":"2018-08-01T00:00:00Z","page":"465 - 479","project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Gilad, Eran, Trevor A Brown, Mark Oskin, and Yoav Etsion. “Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking,” 11014:465–79. Springer, 2018. https://doi.org/10.1007/978-3-319-96983-1_33.","ista":"Gilad E, Brown TA, Oskin M, Etsion Y. 2018. Snapshot based synchronization: A fast replacement for Hand-over-Hand locking. Euro-Par: European Conference on Parallel Processing, LNCS, vol. 11014, 465–479.","mla":"Gilad, Eran, et al. Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking. Vol. 11014, Springer, 2018, pp. 465–79, doi:10.1007/978-3-319-96983-1_33.","apa":"Gilad, E., Brown, T. A., Oskin, M., & Etsion, Y. (2018). Snapshot based synchronization: A fast replacement for Hand-over-Hand locking (Vol. 11014, pp. 465–479). Presented at the Euro-Par: European Conference on Parallel Processing, Turin, Italy: Springer. https://doi.org/10.1007/978-3-319-96983-1_33","ama":"Gilad E, Brown TA, Oskin M, Etsion Y. Snapshot based synchronization: A fast replacement for Hand-over-Hand locking. In: Vol 11014. Springer; 2018:465-479. doi:10.1007/978-3-319-96983-1_33","ieee":"E. Gilad, T. A. Brown, M. Oskin, and Y. Etsion, “Snapshot based synchronization: A fast replacement for Hand-over-Hand locking,” presented at the Euro-Par: European Conference on Parallel Processing, Turin, Italy, 2018, vol. 11014, pp. 465–479.","short":"E. Gilad, T.A. Brown, M. Oskin, Y. Etsion, in:, Springer, 2018, pp. 465–479."},"title":"Snapshot based synchronization: A fast replacement for Hand-over-Hand locking","article_processing_charge":"No","external_id":{"isi":["000851042300031"]},"publist_id":"7969","author":[{"last_name":"Gilad","full_name":"Gilad, Eran","first_name":"Eran"},{"last_name":"Brown","full_name":"Brown, Trevor A","first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Oskin","full_name":"Oskin, Mark","first_name":"Mark"},{"last_name":"Etsion","full_name":"Etsion, Yoav","first_name":"Yoav"}]},{"article_number":"104307","citation":{"chicago":"Michailidis, Alexios, Marko Žnidarič, Mariya Medvedyeva, Dmitry Abanin, Tomaž Prosen, and Zlatko Papić. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.97.104307.","ista":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. 2018. Slow dynamics in translation-invariant quantum lattice models. Physical Review B. 97(10), 104307.","mla":"Michailidis, Alexios, et al. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” Physical Review B, vol. 97, no. 10, 104307, American Physical Society, 2018, doi:10.1103/PhysRevB.97.104307.","apa":"Michailidis, A., Žnidarič, M., Medvedyeva, M., Abanin, D., Prosen, T., & Papić, Z. (2018). Slow dynamics in translation-invariant quantum lattice models. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.97.104307","ama":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. Slow dynamics in translation-invariant quantum lattice models. Physical Review B. 2018;97(10). doi:10.1103/PhysRevB.97.104307","short":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, Z. Papić, Physical Review B 97 (2018).","ieee":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, and Z. Papić, “Slow dynamics in translation-invariant quantum lattice models,” Physical Review B, vol. 97, no. 10. American Physical Society, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000427798800005"]},"author":[{"first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis","orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios"},{"last_name":"Žnidarič","full_name":"Žnidarič, Marko","first_name":"Marko"},{"first_name":"Mariya","last_name":"Medvedyeva","full_name":"Medvedyeva, Mariya"},{"first_name":"Dmitry","last_name":"Abanin","full_name":"Abanin, Dmitry"},{"full_name":"Prosen, Tomaž","last_name":"Prosen","first_name":"Tomaž"},{"first_name":"Zlatko","last_name":"Papić","full_name":"Papić, Zlatko"}],"publist_id":"7538","title":"Slow dynamics in translation-invariant quantum lattice models","acknowledgement":"We thank F. Huveneers for useful discussions. Z.P. and A.M. acknowledge support by EPSRC Grant No. EP/P009409/1 and and the Royal Society Research Grant No. RG160635. Statement of compliance with EPSRC policy framework on research data: This publication is theoretical work that does not require supporting research data. D.A. acknowledges support by the Swiss National Science Foundation. M.Z., M.M. and T.P. acknowledge Grants J1-7279 (M.Z.) and N1-0025 (M.M. and T.P.) of Slovenian Research Agency, and Advanced Grant of European Research Council, Grant No. 694544 - OMNES (T.P.).","oa":1,"publisher":"American Physical Society","quality_controlled":"1","year":"2018","isi":1,"publication":"Physical Review B","day":"19","date_created":"2018-12-11T11:45:50Z","date_published":"2018-03-19T00:00:00Z","doi":"10.1103/PhysRevB.97.104307","_id":"327","type":"journal_article","status":"public","date_updated":"2023-09-18T09:31:46Z","department":[{"_id":"MaSe"}],"abstract":[{"text":"Many-body quantum systems typically display fast dynamics and ballistic spreading of information. Here we address the open problem of how slow the dynamics can be after a generic breaking of integrability by local interactions. We develop a method based on degenerate perturbation theory that reveals slow dynamical regimes and delocalization processes in general translation invariant models, along with accurate estimates of their delocalization time scales. Our results shed light on the fundamental questions of the robustness of quantum integrable systems and the possibility of many-body localization without disorder. As an example, we construct a large class of one-dimensional lattice models where, despite the absence of asymptotic localization, the transient dynamics is exceptionally slow, i.e., the dynamics is indistinguishable from that of many-body localized systems for the system sizes and time scales accessible in experiments and numerical simulations.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.05026"}],"scopus_import":"1","intvolume":" 97","month":"03","publication_status":"published","language":[{"iso":"eng"}],"issue":"10","volume":97}]