[{"ec_funded":1,"publist_id":"7990","publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"TaHa"}],"year":"2018","date_updated":"2023-09-18T08:41:16Z","date_created":"2018-12-11T11:44:26Z","volume":115,"author":[{"full_name":"Kalinin, Nikita","last_name":"Kalinin","first_name":"Nikita"},{"first_name":"Aldo","last_name":"Guzmán Sáenz","full_name":"Guzmán Sáenz, Aldo"},{"full_name":"Prieto, Y","first_name":"Y","last_name":"Prieto"},{"full_name":"Shkolnikov, Mikhail","last_name":"Shkolnikov","first_name":"Mikhail","orcid":"0000-0002-4310-178X","id":"35084A62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kalinina, V","first_name":"V","last_name":"Kalinina"},{"full_name":"Lupercio, Ernesto","last_name":"Lupercio","first_name":"Ernesto"}],"month":"08","publication_identifier":{"issn":["00278424"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"external_id":{"isi":["000442861600009"],"arxiv":["1806.09153"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1806.09153","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1805847115","type":"journal_article","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."}],"issue":"35","status":"public","title":"Self-organized criticality and pattern emergence through the lens of tropical geometry","intvolume":" 115","_id":"64","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","scopus_import":"1","day":"28","article_processing_charge":"No","article_type":"original","page":"E8135 - E8142","publication":"PNAS: Proceedings of the National Academy of Sciences of the United States of America","citation":{"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.","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.","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","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.","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.","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."},"date_published":"2018-08-28T00:00:00Z"},{"type":"research_data_reference","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"}],"year":"2018","_id":"9838","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"AnKi"}],"publisher":"Dryad","status":"public","title":"Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","related_material":{"record":[{"id":"162","relation":"used_in_publication","status":"public"}]},"author":[{"first_name":"Marketa","last_name":"Kaucka","full_name":"Kaucka, Marketa"},{"first_name":"Julian","last_name":"Petersen","full_name":"Petersen, Julian"},{"full_name":"Tesarova, Marketa","first_name":"Marketa","last_name":"Tesarova"},{"first_name":"Bara","last_name":"Szarowska","full_name":"Szarowska, Bara"},{"full_name":"Kastriti, Maria Eleni","first_name":"Maria Eleni","last_name":"Kastriti"},{"full_name":"Xie, Meng","last_name":"Xie","first_name":"Meng"},{"full_name":"Kicheva, Anna","first_name":"Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998"},{"last_name":"Annusver","first_name":"Karl","full_name":"Annusver, Karl"},{"full_name":"Kasper, Maria","first_name":"Maria","last_name":"Kasper"},{"first_name":"Orsolya","last_name":"Symmons","full_name":"Symmons, Orsolya"},{"last_name":"Pan","first_name":"Leslie","full_name":"Pan, Leslie"},{"full_name":"Spitz, Francois","first_name":"Francois","last_name":"Spitz"},{"first_name":"Jozef","last_name":"Kaiser","full_name":"Kaiser, Jozef"},{"last_name":"Hovorakova","first_name":"Maria","full_name":"Hovorakova, Maria"},{"full_name":"Zikmund, Tomas","last_name":"Zikmund","first_name":"Tomas"},{"full_name":"Sunadome, Kazunori","first_name":"Kazunori","last_name":"Sunadome"},{"full_name":"Matise, Michael P","last_name":"Matise","first_name":"Michael P"},{"first_name":"Hui","last_name":"Wang","full_name":"Wang, Hui"},{"full_name":"Marklund, Ulrika","first_name":"Ulrika","last_name":"Marklund"},{"full_name":"Abdo, Hind","last_name":"Abdo","first_name":"Hind"},{"full_name":"Ernfors, Patrik","last_name":"Ernfors","first_name":"Patrik"},{"full_name":"Maire, Pascal","first_name":"Pascal","last_name":"Maire"},{"last_name":"Wurmser","first_name":"Maud","full_name":"Wurmser, Maud"},{"last_name":"Chagin","first_name":"Andrei S","full_name":"Chagin, Andrei S"},{"last_name":"Fried","first_name":"Kaj","full_name":"Fried, Kaj"},{"full_name":"Adameyko, Igor","first_name":"Igor","last_name":"Adameyko"}],"oa_version":"Published Version","date_updated":"2023-09-18T09:29:07Z","date_created":"2021-08-09T12:54:35Z","article_processing_charge":"No","day":"14","month":"06","citation":{"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).","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.","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.","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","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","ieee":"M. Kaucka et al., “Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage.” Dryad, 2018.","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."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.f1s76f2","open_access":"1"}],"oa":1,"doi":"10.5061/dryad.f1s76f2","date_published":"2018-06-14T00:00:00Z"},{"type":"journal_article","abstract":[{"lang":"eng","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."}],"_id":"41","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"status":"public","title":"Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells","intvolume":" 12","file":[{"file_size":6834251,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"fncel-12-00311.pdf","checksum":"0bcaec8d596162af0b7fe3f31325d480","date_created":"2018-12-17T08:49:03Z","date_updated":"2020-07-14T12:46:23Z","relation":"main_file","file_id":"5684"}],"oa_version":"Published Version","scopus_import":"1","day":"19","article_processing_charge":"No","has_accepted_license":"1","publication":"Frontiers in Cellular Neuroscience","citation":{"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.","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","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.","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","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.","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).","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."},"article_type":"original","date_published":"2018-09-19T00:00:00Z","article_number":"311","file_date_updated":"2020-07-14T12:46:23Z","publist_id":"8013","ec_funded":1,"license":"https://creativecommons.org/licenses/by/4.0/","year":"2018","publication_status":"published","department":[{"_id":"RySh"}],"publisher":"Frontiers Media","author":[{"first_name":"Rafæl","last_name":"Luján","full_name":"Luján, Rafæl"},{"last_name":"Aguado","first_name":"Carolina","full_name":"Aguado, Carolina"},{"last_name":"Ciruela","first_name":"Francisco","full_name":"Ciruela, Francisco"},{"first_name":"Xavier","last_name":"Arus","full_name":"Arus, Xavier"},{"full_name":"Martín Belmonte, Alejandro","first_name":"Alejandro","last_name":"Martín Belmonte"},{"last_name":"Alfaro Ruiz","first_name":"Rocío","full_name":"Alfaro Ruiz, Rocío"},{"full_name":"Martinez Gomez, Jesus","last_name":"Martinez Gomez","first_name":"Jesus"},{"full_name":"De La Ossa, Luis","first_name":"Luis","last_name":"De La Ossa"},{"full_name":"Watanabe, Masahiko","first_name":"Masahiko","last_name":"Watanabe"},{"first_name":"John","last_name":"Adelman","full_name":"Adelman, John"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"},{"last_name":"Fukazawa","first_name":"Yugo","full_name":"Fukazawa, Yugo"}],"date_updated":"2023-09-18T09:31:18Z","date_created":"2018-12-11T11:44:19Z","volume":12,"month":"09","publication_identifier":{"issn":["16625102"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000445090100002"]},"quality_controlled":"1","isi":1,"project":[{"name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","call_identifier":"H2020","grant_number":"720270","_id":"25CBA828-B435-11E9-9278-68D0E5697425"}],"doi":"10.3389/fncel.2018.00311","language":[{"iso":"eng"}]},{"day":"25","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-10-25T00:00:00Z","page":"7141 - 7145","publication":"Nano Letters","citation":{"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","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.","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.","short":"L. Vukušić, J. Kukucka, H. Watzinger, J.M. Milem, F. Schäffler, G. Katsaros, Nano Letters 18 (2018) 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.","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."},"abstract":[{"lang":"eng","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."}],"issue":"11","type":"journal_article","oa_version":"Published Version","file":[{"checksum":"3e6034a94c6b5335e939145d88bdb371","date_updated":"2020-07-14T12:45:37Z","date_created":"2018-12-12T10:16:08Z","relation":"main_file","file_id":"5194","content_type":"application/pdf","file_size":1361441,"creator":"system","access_level":"open_access","file_name":"IST-2018-1065-v1+1_ACS_nanoletters_8b03217.pdf"}],"pubrep_id":"1065","ddc":["530"],"status":"public","title":"Single-shot readout of hole spins in Ge","intvolume":" 18","_id":"23","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"10","publication_identifier":{"issn":["15306984"]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"doi":"10.1021/acs.nanolett.8b03217","quality_controlled":"1","isi":1,"project":[{"_id":"25517E86-B435-11E9-9278-68D0E5697425","grant_number":"335497","call_identifier":"FP7","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["30359041"],"isi":["000451102100064"]},"oa":1,"file_date_updated":"2020-07-14T12:45:37Z","publist_id":"8032","ec_funded":1,"date_created":"2018-12-11T11:44:13Z","date_updated":"2023-09-18T09:30:37Z","volume":18,"author":[{"full_name":"Vukušić, Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2424-8636","first_name":"Lada","last_name":"Vukušić"},{"last_name":"Kukucka","first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip"},{"full_name":"Watzinger, Hannes","first_name":"Hannes","last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Milem, Joshua M","id":"4CDE0A96-F248-11E8-B48F-1D18A9856A87","last_name":"Milem","first_name":"Joshua M"},{"full_name":"Schäffler, Friedrich","last_name":"Schäffler","first_name":"Friedrich"},{"full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros"}],"related_material":{"record":[{"id":"7977","relation":"popular_science"},{"relation":"dissertation_contains","status":"public","id":"69"},{"id":"7996","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","department":[{"_id":"GeKa"}],"publisher":"American Chemical Society","year":"2018","pmid":1},{"language":[{"iso":"eng"}],"conference":{"start_date":"2018-08-27","location":"Turin, Italy","end_date":"2018-08-31","name":"Euro-Par: European Conference on Parallel Processing"},"doi":"10.1007/978-3-319-96983-1_33","quality_controlled":"1","isi":1,"project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000851042300031"]},"oa":1,"month":"08","publication_identifier":{"issn":["03029743"]},"date_updated":"2023-09-18T09:32:36Z","date_created":"2018-12-11T11:44:33Z","volume":11014,"author":[{"full_name":"Gilad, Eran","last_name":"Gilad","first_name":"Eran"},{"full_name":"Brown, Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","first_name":"Trevor A","last_name":"Brown"},{"full_name":"Oskin, Mark","first_name":"Mark","last_name":"Oskin"},{"full_name":"Etsion, Yoav","last_name":"Etsion","first_name":"Yoav"}],"publication_status":"published","publisher":"Springer","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.","year":"2018","file_date_updated":"2020-07-14T12:48:14Z","publist_id":"7969","date_published":"2018-08-01T00:00:00Z","page":"465 - 479","citation":{"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","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.","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.","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","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.","short":"E. Gilad, T.A. Brown, M. Oskin, Y. Etsion, in:, Springer, 2018, pp. 465–479.","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."},"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Preprint","file":[{"creator":"dernst","file_size":665372,"content_type":"application/pdf","file_name":"2018_Brown.pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:14Z","date_created":"2019-02-12T07:40:40Z","checksum":"13a3f250be8878405e791b53c19722ad","file_id":"5954","relation":"main_file"}],"ddc":["000"],"title":"Snapshot based synchronization: A fast replacement for Hand-over-Hand locking","status":"public","intvolume":" 11014","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"85","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."}],"alternative_title":["LNCS"],"type":"conference"},{"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.97.104307","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.05026"}],"oa":1,"external_id":{"isi":["000427798800005"]},"month":"03","date_updated":"2023-09-18T09:31:46Z","date_created":"2018-12-11T11:45:50Z","volume":97,"author":[{"first_name":"Alexios","last_name":"Michailidis","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios"},{"last_name":"Žnidarič","first_name":"Marko","full_name":"Žnidarič, Marko"},{"last_name":"Medvedyeva","first_name":"Mariya","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"}],"publication_status":"published","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","year":"2018","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.).","publist_id":"7538","article_number":"104307","date_published":"2018-03-19T00:00:00Z","publication":"Physical Review B","citation":{"short":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, Z. Papić, Physical Review B 97 (2018).","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.","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.","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","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","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.","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."},"day":"19","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","status":"public","title":"Slow dynamics in translation-invariant quantum lattice models","intvolume":" 97","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"327","abstract":[{"lang":"eng","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."}],"issue":"10","type":"journal_article"},{"type":"journal_article","abstract":[{"text":"Social insects have evolved enormous capacities to collectively build nests and defend their colonies against both predators and pathogens. The latter is achieved by a combination of individual immune responses and sophisticated collective behavioral and organizational disease defenses, that is, social immunity. We investigated how the presence or absence of these social defense lines affects individual-level immunity in ant queens after bacterial infection. To this end, we injected queens of the ant Linepithema humile with a mix of gram+ and gram− bacteria or a control solution, reared them either with workers or alone and analyzed their gene expression patterns at 2, 4, 8, and 12 hr post-injection, using RNA-seq. This allowed us to test for the effect of bacterial infection, social context, as well as the interaction between the two over the course of infection and raising of an immune response. We found that social isolation per se affected queen gene expression for metabolism genes, but not for immune genes. When infected, queens reared with and without workers up-regulated similar numbers of innate immune genes revealing activation of Toll and Imd signaling pathways and melanization. Interestingly, however, they mostly regulated different genes along the pathways and showed a different pattern of overall gene up-regulation or down-regulation. Hence, we can conclude that the absence of workers does not compromise the onset of an individual immune response by the queens, but that the social environment impacts the route of the individual innate immune responses.","lang":"eng"}],"issue":"22","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"29","status":"public","title":"Social environment affects the transcriptomic response to bacteria in ant queens","ddc":["576","591"],"intvolume":" 8","file":[{"access_level":"open_access","file_name":"Viljakainen_et_al-2018-Ecology_and_Evolution.pdf","file_size":1272096,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"5682","checksum":"0d1355c78627ca7210aadd9a17a01915","date_updated":"2020-07-14T12:45:52Z","date_created":"2018-12-17T08:27:04Z"}],"oa_version":"Published Version","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication":"Ecology and Evolution","citation":{"chicago":"Viljakainen, Lumi, Jaana Jurvansuu, Ida Holmberg, Tobias Pamminger, Silvio Erler, and Sylvia Cremer. “Social Environment Affects the Transcriptomic Response to Bacteria in Ant Queens.” Ecology and Evolution. Wiley, 2018. https://doi.org/10.1002/ece3.4573.","short":"L. Viljakainen, J. Jurvansuu, I. Holmberg, T. Pamminger, S. Erler, S. Cremer, Ecology and Evolution 8 (2018) 11031–11070.","mla":"Viljakainen, Lumi, et al. “Social Environment Affects the Transcriptomic Response to Bacteria in Ant Queens.” Ecology and Evolution, vol. 8, no. 22, Wiley, 2018, pp. 11031–70, doi:10.1002/ece3.4573.","ieee":"L. Viljakainen, J. Jurvansuu, I. Holmberg, T. Pamminger, S. Erler, and S. Cremer, “Social environment affects the transcriptomic response to bacteria in ant queens,” Ecology and Evolution, vol. 8, no. 22. Wiley, pp. 11031–11070, 2018.","apa":"Viljakainen, L., Jurvansuu, J., Holmberg, I., Pamminger, T., Erler, S., & Cremer, S. (2018). Social environment affects the transcriptomic response to bacteria in ant queens. Ecology and Evolution. Wiley. https://doi.org/10.1002/ece3.4573","ista":"Viljakainen L, Jurvansuu J, Holmberg I, Pamminger T, Erler S, Cremer S. 2018. Social environment affects the transcriptomic response to bacteria in ant queens. Ecology and Evolution. 8(22), 11031–11070.","ama":"Viljakainen L, Jurvansuu J, Holmberg I, Pamminger T, Erler S, Cremer S. Social environment affects the transcriptomic response to bacteria in ant queens. Ecology and Evolution. 2018;8(22):11031-11070. doi:10.1002/ece3.4573"},"page":"11031-11070","date_published":"2018-11-01T00:00:00Z","file_date_updated":"2020-07-14T12:45:52Z","publist_id":"8026","year":"2018","publication_status":"published","publisher":"Wiley","department":[{"_id":"SyCr"}],"author":[{"first_name":"Lumi","last_name":"Viljakainen","full_name":"Viljakainen, Lumi"},{"full_name":"Jurvansuu, Jaana","last_name":"Jurvansuu","first_name":"Jaana"},{"full_name":"Holmberg, Ida","first_name":"Ida","last_name":"Holmberg"},{"full_name":"Pamminger, Tobias","first_name":"Tobias","last_name":"Pamminger"},{"last_name":"Erler","first_name":"Silvio","full_name":"Erler, Silvio"},{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer"}],"date_updated":"2023-09-19T09:29:12Z","date_created":"2018-12-11T11:44:15Z","volume":8,"month":"11","publication_identifier":{"issn":["20457758"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000451611000032"]},"isi":1,"quality_controlled":"1","doi":"10.1002/ece3.4573","language":[{"iso":"eng"}]},{"conference":{"end_date":"2018-07-17","start_date":"2018-07-14","location":"Oxford, United Kingdom","name":"CAV: Computer Aided Verification"},"doi":"10.1007/978-3-319-96145-3_25","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000491481600025"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF","name":"Moderne Concurrency Paradigms"}],"month":"07","publication_identifier":{"issn":["03029743"]},"author":[{"first_name":"Goran","last_name":"Frehse","full_name":"Frehse, Goran"},{"full_name":"Giacobbe, Mirco","first_name":"Mirco","last_name":"Giacobbe","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8180-0904"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6894"}]},"date_updated":"2023-09-19T09:30:43Z","date_created":"2018-12-11T11:44:50Z","volume":10981,"year":"2018","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer","file_date_updated":"2020-07-14T12:44:50Z","publist_id":"7783","date_published":"2018-07-18T00:00:00Z","citation":{"mla":"Frehse, Goran, et al. Space-Time Interpolants. Vol. 10981, Springer, 2018, pp. 468–86, doi:10.1007/978-3-319-96145-3_25.","short":"G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2018, pp. 468–486.","chicago":"Frehse, Goran, Mirco Giacobbe, and Thomas A Henzinger. “Space-Time Interpolants,” 10981:468–86. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_25.","ama":"Frehse G, Giacobbe M, Henzinger TA. Space-time interpolants. In: Vol 10981. Springer; 2018:468-486. doi:10.1007/978-3-319-96145-3_25","ista":"Frehse G, Giacobbe M, Henzinger TA. 2018. Space-time interpolants. CAV: Computer Aided Verification, LNCS, vol. 10981, 468–486.","apa":"Frehse, G., Giacobbe, M., & Henzinger, T. A. (2018). Space-time interpolants (Vol. 10981, pp. 468–486). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96145-3_25","ieee":"G. Frehse, M. Giacobbe, and T. A. Henzinger, “Space-time interpolants,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 468–486."},"page":"468 - 486","day":"18","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","pubrep_id":"1010","file":[{"relation":"main_file","file_id":"5310","checksum":"6dca832f575d6b3f0ea9dff56f579142","date_created":"2018-12-12T10:17:53Z","date_updated":"2020-07-14T12:44:50Z","access_level":"open_access","file_name":"IST-2018-1010-v1+1_space-time_interpolants.pdf","content_type":"application/pdf","file_size":563710,"creator":"system"}],"oa_version":"Published Version","_id":"140","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Space-time interpolants","status":"public","ddc":["005"],"intvolume":" 10981","abstract":[{"text":"Reachability analysis is difficult for hybrid automata with affine differential equations, because the reach set needs to be approximated. Promising abstraction techniques usually employ interval methods or template polyhedra. Interval methods account for dense time and guarantee soundness, and there are interval-based tools that overapproximate affine flowpipes. But interval methods impose bounded and rigid shapes, which make refinement expensive and fixpoint detection difficult. Template polyhedra, on the other hand, can be adapted flexibly and can be unbounded, but sound template refinement for unbounded reachability analysis has been implemented only for systems with piecewise constant dynamics. We capitalize on the advantages of both techniques, combining interval arithmetic and template polyhedra, using the former to abstract time and the latter to abstract space. During a CEGAR loop, whenever a spurious error trajectory is found, we compute additional space constraints and split time intervals, and use these space-time interpolants to eliminate the counterexample. Space-time interpolation offers a lazy, flexible framework for increasing precision while guaranteeing soundness, both for error avoidance and fixpoint detection. To the best of out knowledge, this is the first abstraction refinement scheme for the reachability analysis over unbounded and dense time of affine hybrid systems, which is both sound and automatic. We demonstrate the effectiveness of our algorithm with several benchmark examples, which cannot be handled by other tools.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"]},{"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication":"Mathematical Physics Analysis and Geometry","citation":{"mla":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” Mathematical Physics Analysis and Geometry, vol. 21, no. 3, 19, Springer, 2018, doi:10.1007/s11040-018-9275-3.","short":"T. Moser, R. Seiringer, Mathematical Physics Analysis and Geometry 21 (2018).","chicago":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” Mathematical Physics Analysis and Geometry. Springer, 2018. https://doi.org/10.1007/s11040-018-9275-3.","ama":"Moser T, Seiringer R. Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. 2018;21(3). doi:10.1007/s11040-018-9275-3","ista":"Moser T, Seiringer R. 2018. Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. 21(3), 19.","ieee":"T. Moser and R. Seiringer, “Stability of the 2+2 fermionic system with point interactions,” Mathematical Physics Analysis and Geometry, vol. 21, no. 3. Springer, 2018.","apa":"Moser, T., & Seiringer, R. (2018). Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-018-9275-3"},"article_type":"original","date_published":"2018-09-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We give a lower bound on the ground state energy of a system of two fermions of one species interacting with two fermions of another species via point interactions. We show that there is a critical mass ratio m2 ≈ 0.58 such that the system is stable, i.e., the energy is bounded from below, for m∈[m2,m2−1]. So far it was not known whether this 2 + 2 system exhibits a stable region at all or whether the formation of four-body bound states causes an unbounded spectrum for all mass ratios, similar to the Thomas effect. Our result gives further evidence for the stability of the more general N + M system."}],"issue":"3","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"154","ddc":["530"],"status":"public","title":"Stability of the 2+2 fermionic system with point interactions","intvolume":" 21","file":[{"file_size":496973,"content_type":"application/pdf","creator":"dernst","file_name":"2018_MathPhysics_Moser.pdf","access_level":"open_access","date_created":"2018-12-17T16:49:02Z","date_updated":"2020-07-14T12:45:01Z","checksum":"411c4db5700d7297c9cd8ebc5dd29091","relation":"main_file","file_id":"5729"}],"oa_version":"Published Version","month":"09","publication_identifier":{"issn":["13850172"],"eissn":["15729656"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000439639700001"]},"quality_controlled":"1","isi":1,"project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"},{"grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF","name":"FWF Open Access Fund"}],"doi":"10.1007/s11040-018-9275-3","language":[{"iso":"eng"}],"article_number":"19","file_date_updated":"2020-07-14T12:45:01Z","ec_funded":1,"publist_id":"7767","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF).","year":"2018","publication_status":"published","publisher":"Springer","department":[{"_id":"RoSe"}],"author":[{"id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Moser","full_name":"Moser, Thomas"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"related_material":{"record":[{"id":"52","relation":"dissertation_contains","status":"public"}]},"date_created":"2018-12-11T11:44:55Z","date_updated":"2023-09-19T09:31:15Z","volume":21},{"intvolume":" 60","title":"Statistical theory of branching morphogenesis","status":"public","ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5787","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2018_DevGrowh_Hannezo.pdf","creator":"dernst","file_size":1313606,"content_type":"application/pdf","file_id":"5933","relation":"main_file","checksum":"a6d30b0785db902c734a84fecb2eadd9","date_updated":"2020-07-14T12:47:11Z","date_created":"2019-02-06T10:40:46Z"}],"type":"journal_article","issue":"9","abstract":[{"text":"Branching morphogenesis remains a subject of abiding interest. Although much is \r\nknown about the gene regulatory programs and signaling pathways that operate at \r\nthe cellular scale, it has remained unclear how the macroscopic features of branched \r\norgans, including their size, network topology and spatial patterning, are encoded. \r\nLately, it has been proposed that, these features can be explained quantitatively in \r\nseveral organs within a single unifying framework. Based on large-\r\nscale organ recon\r\n-\r\nstructions and cell lineage tracing, it has been argued that morphogenesis follows \r\nfrom the collective dynamics of sublineage- \r\nrestricted self- \r\nrenewing progenitor cells, \r\nlocalized at ductal tips, that act cooperatively to drive a serial process of ductal elon\r\n-\r\ngation and stochastic tip bifurcation. By correlating differentiation or cell cycle exit \r\nwith proximity to maturing ducts, this dynamic results in the specification of a com-\r\nplex network of defined density and statistical organization. These results suggest \r\nthat, for several mammalian tissues, branched epithelial structures develop as a self- \r\norganized process, reliant upon a strikingly simple, but generic, set of local rules, \r\nwithout recourse to a rigid and deterministic sequence of genetically programmed \r\nevents. Here, we review the basis of these findings and discuss their implications.","lang":"eng"}],"page":"512-521","citation":{"ista":"Hannezo EB, Simons BD. 2018. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 60(9), 512–521.","ieee":"E. B. Hannezo and B. D. Simons, “Statistical theory of branching morphogenesis,” Development Growth and Differentiation, vol. 60, no. 9. Wiley, pp. 512–521, 2018.","apa":"Hannezo, E. B., & Simons, B. D. (2018). Statistical theory of branching morphogenesis. Development Growth and Differentiation. Wiley. https://doi.org/10.1111/dgd.12570","ama":"Hannezo EB, Simons BD. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 2018;60(9):512-521. doi:10.1111/dgd.12570","chicago":"Hannezo, Edouard B, and Benjamin D. Simons. “Statistical Theory of Branching Morphogenesis.” Development Growth and Differentiation. Wiley, 2018. https://doi.org/10.1111/dgd.12570.","mla":"Hannezo, Edouard B., and Benjamin D. Simons. “Statistical Theory of Branching Morphogenesis.” Development Growth and Differentiation, vol. 60, no. 9, Wiley, 2018, pp. 512–21, doi:10.1111/dgd.12570.","short":"E.B. Hannezo, B.D. Simons, Development Growth and Differentiation 60 (2018) 512–521."},"publication":"Development Growth and Differentiation","date_published":"2018-12-09T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"09","department":[{"_id":"EdHa"}],"publisher":"Wiley","year":"2018","volume":60,"date_created":"2018-12-30T22:59:14Z","date_updated":"2023-09-19T09:32:49Z","author":[{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"first_name":"Benjamin D.","last_name":"Simons","full_name":"Simons, Benjamin D."}],"file_date_updated":"2020-07-14T12:47:11Z","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000453555100002"]},"language":[{"iso":"eng"}],"doi":"10.1111/dgd.12570","publication_identifier":{"issn":["00121592"]},"month":"12"},{"abstract":[{"text":"Graph games played by two players over finite-state graphs are central in many problems in computer science. In particular, graph games with ω -regular winning conditions, specified as parity objectives, which can express properties such as safety, liveness, fairness, are the basic framework for verification and synthesis of reactive systems. The decisions for a player at various states of the graph game are represented as strategies. While the algorithmic problem for solving graph games with parity objectives has been widely studied, the most prominent data-structure for strategy representation in graph games has been binary decision diagrams (BDDs). However, due to the bit-level representation, BDDs do not retain the inherent flavor of the decisions of strategies, and are notoriously hard to minimize to obtain succinct representation. In this work we propose decision trees for strategy representation in graph games. Decision trees retain the flavor of decisions of strategies and allow entropy-based minimization to obtain succinct trees. However, decision trees work in settings (e.g., probabilistic models) where errors are allowed, and overfitting of data is typically avoided. In contrast, for strategies in graph games no error is allowed, and the decision tree must represent the entire strategy. We develop new techniques to extend decision trees to overcome the above obstacles, while retaining the entropy-based techniques to obtain succinct trees. We have implemented our techniques to extend the existing decision tree solvers. We present experimental results for problems in reactive synthesis to show that decision trees provide a much more efficient data-structure for strategy representation as compared to BDDs.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Published Version","file":[{"file_id":"5723","relation":"main_file","checksum":"b13874ffb114932ad9cc2586b7469db4","date_updated":"2020-07-14T12:45:57Z","date_created":"2018-12-17T16:29:08Z","access_level":"open_access","file_name":"2018_LNCS_Brazdil.pdf","creator":"dernst","file_size":1829940,"content_type":"application/pdf"}],"intvolume":" 10805","title":"Strategy representation by decision trees in reactive synthesis","status":"public","ddc":["000"],"_id":"297","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","article_processing_charge":"No","day":"12","scopus_import":"1","date_published":"2018-04-12T00:00:00Z","page":"385 - 407","citation":{"ama":"Brázdil T, Chatterjee K, Kretinsky J, Toman V. Strategy representation by decision trees in reactive synthesis. In: Vol 10805. Springer; 2018:385-407. doi:10.1007/978-3-319-89960-2_21","ista":"Brázdil T, Chatterjee K, Kretinsky J, Toman V. 2018. Strategy representation by decision trees in reactive synthesis. TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10805, 385–407.","ieee":"T. Brázdil, K. Chatterjee, J. Kretinsky, and V. Toman, “Strategy representation by decision trees in reactive synthesis,” presented at the TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece, 2018, vol. 10805, pp. 385–407.","apa":"Brázdil, T., Chatterjee, K., Kretinsky, J., & Toman, V. (2018). Strategy representation by decision trees in reactive synthesis (Vol. 10805, pp. 385–407). Presented at the TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece: Springer. https://doi.org/10.1007/978-3-319-89960-2_21","mla":"Brázdil, Tomáš, et al. Strategy Representation by Decision Trees in Reactive Synthesis. Vol. 10805, Springer, 2018, pp. 385–407, doi:10.1007/978-3-319-89960-2_21.","short":"T. Brázdil, K. Chatterjee, J. Kretinsky, V. Toman, in:, Springer, 2018, pp. 385–407.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Jan Kretinsky, and Viktor Toman. “Strategy Representation by Decision Trees in Reactive Synthesis,” 10805:385–407. Springer, 2018. https://doi.org/10.1007/978-3-319-89960-2_21."},"publist_id":"7584","ec_funded":1,"file_date_updated":"2020-07-14T12:45:57Z","volume":10805,"date_updated":"2023-09-19T09:57:08Z","date_created":"2018-12-11T11:45:41Z","author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Kretinsky, Jan","first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881"},{"orcid":"0000-0001-9036-063X","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","last_name":"Toman","first_name":"Viktor","full_name":"Toman, Viktor"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","year":"2018","month":"04","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-89960-2_21","conference":{"end_date":"2018-04-20","location":"Thessaloniki, Greece","start_date":"2018-04-14","name":"TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems"},"project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000546326300021"]}},{"publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2018","acknowledgement":"Acknowledgements. K. C. and M. H. are partially supported by the Vienna Science and Technology Fund (WWTF) grant ICT15-003. K. C. is partially supported by the Austrian Science Fund (FWF): S11407-N23 (RiSE/SHiNE), and an ERC Start Grant (279307: Graph Games). V. T. is partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie Grant Agreement No. 665385.","volume":10982,"date_updated":"2023-09-19T09:59:55Z","date_created":"2018-12-11T11:44:51Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10199"}]},"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H"},{"first_name":"Veronika","last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika"},{"full_name":"Oraee, Simin","last_name":"Oraee","first_name":"Simin"},{"full_name":"Toman, Viktor","last_name":"Toman","first_name":"Viktor","orcid":"0000-0001-9036-063X","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7782","ec_funded":1,"file_date_updated":"2020-07-14T12:44:53Z","project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000491469700013"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-96142-2_13","conference":{"location":"Oxford, United Kingdom","start_date":"2018-07-14","end_date":"2018-07-17","name":"CAV: Computer Aided Verification"},"month":"07","intvolume":" 10982","ddc":["000"],"title":"Symbolic algorithms for graphs and Markov decision processes with fairness objectives","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"141","file":[{"file_name":"2018_LNCS_Chatterjee.pdf","access_level":"open_access","content_type":"application/pdf","file_size":675606,"creator":"dernst","relation":"main_file","file_id":"5737","date_created":"2018-12-18T08:52:38Z","date_updated":"2020-07-14T12:44:53Z","checksum":"1a6ffa4febe8bb8ac28be3adb3eafebc"}],"oa_version":"Published Version","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Given a model and a specification, the fundamental model-checking problem asks for algorithmic verification of whether the model satisfies the specification. We consider graphs and Markov decision processes (MDPs), which are fundamental models for reactive systems. One of the very basic specifications that arise in verification of reactive systems is the strong fairness (aka Streett) objective. Given different types of requests and corresponding grants, the objective requires that for each type, if the request event happens infinitely often, then the corresponding grant event must also happen infinitely often. All ω -regular objectives can be expressed as Streett objectives and hence they are canonical in verification. To handle the state-space explosion, symbolic algorithms are required that operate on a succinct implicit representation of the system rather than explicitly accessing the system. While explicit algorithms for graphs and MDPs with Streett objectives have been widely studied, there has been no improvement of the basic symbolic algorithms. The worst-case numbers of symbolic steps required for the basic symbolic algorithms are as follows: quadratic for graphs and cubic for MDPs. In this work we present the first sub-quadratic symbolic algorithm for graphs with Streett objectives, and our algorithm is sub-quadratic even for MDPs. Based on our algorithmic insights we present an implementation of the new symbolic approach and show that it improves the existing approach on several academic benchmark examples.","lang":"eng"}],"page":"178-197","citation":{"mla":"Chatterjee, Krishnendu, et al. Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives. Vol. 10982, Springer, 2018, pp. 178–97, doi:10.1007/978-3-319-96142-2_13.","short":"K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, S. Oraee, V. Toman, in:, Springer, 2018, pp. 178–197.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Veronika Loitzenbauer, Simin Oraee, and Viktor Toman. “Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives,” 10982:178–97. Springer, 2018. https://doi.org/10.1007/978-3-319-96142-2_13.","ama":"Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. In: Vol 10982. Springer; 2018:178-197. doi:10.1007/978-3-319-96142-2_13","ista":"Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. 2018. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. CAV: Computer Aided Verification, LNCS, vol. 10982, 178–197.","ieee":"K. Chatterjee, M. H. Henzinger, V. Loitzenbauer, S. Oraee, and V. Toman, “Symbolic algorithms for graphs and Markov decision processes with fairness objectives,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10982, pp. 178–197.","apa":"Chatterjee, K., Henzinger, M. H., Loitzenbauer, V., Oraee, S., & Toman, V. (2018). Symbolic algorithms for graphs and Markov decision processes with fairness objectives (Vol. 10982, pp. 178–197). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96142-2_13"},"date_published":"2018-07-18T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"18"},{"day":"31","article_processing_charge":"No","scopus_import":"1","date_published":"2018-03-31T00:00:00Z","citation":{"ama":"Alwen JF, Blocki J, Pietrzak KZ. Sustained space complexity. In: Vol 10821. Springer; 2018:99-130. doi:10.1007/978-3-319-78375-8_4","ieee":"J. F. Alwen, J. Blocki, and K. Z. Pietrzak, “Sustained space complexity,” presented at the Eurocrypt 2018: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10821, pp. 99–130.","apa":"Alwen, J. F., Blocki, J., & Pietrzak, K. Z. (2018). Sustained space complexity (Vol. 10821, pp. 99–130). Presented at the Eurocrypt 2018: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78375-8_4","ista":"Alwen JF, Blocki J, Pietrzak KZ. 2018. Sustained space complexity. Eurocrypt 2018: Advances in Cryptology, LNCS, vol. 10821, 99–130.","short":"J.F. Alwen, J. Blocki, K.Z. Pietrzak, in:, Springer, 2018, pp. 99–130.","mla":"Alwen, Joel F., et al. Sustained Space Complexity. Vol. 10821, Springer, 2018, pp. 99–130, doi:10.1007/978-3-319-78375-8_4.","chicago":"Alwen, Joel F, Jeremiah Blocki, and Krzysztof Z Pietrzak. “Sustained Space Complexity,” 10821:99–130. Springer, 2018. https://doi.org/10.1007/978-3-319-78375-8_4."},"page":"99 - 130","abstract":[{"lang":"eng","text":"Memory-hard functions (MHF) are functions whose evaluation cost is dominated by memory cost. MHFs are egalitarian, in the sense that evaluating them on dedicated hardware (like FPGAs or ASICs) is not much cheaper than on off-the-shelf hardware (like x86 CPUs). MHFs have interesting cryptographic applications, most notably to password hashing and securing blockchains.\r\n\r\nAlwen and Serbinenko [STOC’15] define the cumulative memory complexity (cmc) of a function as the sum (over all time-steps) of the amount of memory required to compute the function. They advocate that a good MHF must have high cmc. Unlike previous notions, cmc takes into account that dedicated hardware might exploit amortization and parallelism. Still, cmc has been critizised as insufficient, as it fails to capture possible time-memory trade-offs; as memory cost doesn’t scale linearly, functions with the same cmc could still have very different actual hardware cost.\r\n\r\nIn this work we address this problem, and introduce the notion of sustained-memory complexity, which requires that any algorithm evaluating the function must use a large amount of memory for many steps. We construct functions (in the parallel random oracle model) whose sustained-memory complexity is almost optimal: our function can be evaluated using n steps and O(n/log(n)) memory, in each step making one query to the (fixed-input length) random oracle, while any algorithm that can make arbitrary many parallel queries to the random oracle, still needs Ω(n/log(n)) memory for Ω(n) steps.\r\n\r\nAs has been done for various notions (including cmc) before, we reduce the task of constructing an MHFs with high sustained-memory complexity to proving pebbling lower bounds on DAGs. Our main technical contribution is the construction is a family of DAGs on n nodes with constant indegree with high “sustained-space complexity”, meaning that any parallel black-pebbling strategy requires Ω(n/log(n)) pebbles for at least Ω(n) steps.\r\n\r\nAlong the way we construct a family of maximally “depth-robust” DAGs with maximum indegree O(logn) , improving upon the construction of Mahmoody et al. [ITCS’13] which had maximum indegree O(log2n⋅"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","_id":"298","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Sustained space complexity","intvolume":" 10821","month":"03","conference":{"start_date":"2018-04-29","location":"Tel Aviv, Israel","end_date":"2018-05-03","name":"Eurocrypt 2018: Advances in Cryptology"},"doi":"10.1007/978-3-319-78375-8_4","language":[{"iso":"eng"}],"external_id":{"isi":["000517098700004"],"arxiv":["1705.05313"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.05313"}],"oa":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"ec_funded":1,"publist_id":"7583","author":[{"full_name":"Alwen, Joel F","first_name":"Joel F","last_name":"Alwen","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Blocki, Jeremiah","last_name":"Blocki","first_name":"Jeremiah"},{"last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"}],"date_updated":"2023-09-19T09:59:30Z","date_created":"2018-12-11T11:45:41Z","volume":10821,"year":"2018","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer"},{"day":"31","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-08-31T00:00:00Z","publication":"Journal of Experimental Botany","citation":{"ama":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 2018;69(19):4609-4624. doi:10.1093/jxb/ery204","ieee":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, and I. De Smet, “Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms,” Journal of Experimental Botany, vol. 69, no. 19. Oxford University Press, pp. 4609–4624, 2018.","apa":"Vu, L., Zhu, T., Verstraeten, I., Van De Cotte, B., Gevaert, K., & De Smet, I. (2018). Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery204","ista":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. 2018. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 69(19), 4609–4624.","short":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, I. De Smet, Journal of Experimental Botany 69 (2018) 4609–4624.","mla":"Vu, Lam, et al. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany, vol. 69, no. 19, Oxford University Press, 2018, pp. 4609–24, doi:10.1093/jxb/ery204.","chicago":"Vu, Lam, Tingting Zhu, Inge Verstraeten, Brigitte Van De Cotte, Kris Gevaert, and Ive De Smet. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery204."},"page":"4609 - 4624","abstract":[{"lang":"eng","text":"Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity."}],"issue":"19","type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5741","date_created":"2018-12-18T09:47:51Z","date_updated":"2020-07-14T12:46:13Z","checksum":"34cb0a1611588b75bd6f4913fb4e30f1","file_name":"2018_JournalExperimBotany_Vu.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3359316,"creator":"dernst"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"36","title":"Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms","status":"public","ddc":["581"],"intvolume":" 69","month":"08","doi":"10.1093/jxb/ery204","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000443568700010"]},"oa":1,"isi":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:46:13Z","publist_id":"8019","author":[{"first_name":"Lam","last_name":"Vu","full_name":"Vu, Lam"},{"full_name":"Zhu, Tingting","first_name":"Tingting","last_name":"Zhu"},{"full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","first_name":"Inge"},{"full_name":"Van De Cotte, Brigitte","last_name":"Van De Cotte","first_name":"Brigitte"},{"last_name":"Gevaert","first_name":"Kris","full_name":"Gevaert, Kris"},{"full_name":"De Smet, Ive","last_name":"De Smet","first_name":"Ive"}],"date_created":"2018-12-11T11:44:17Z","date_updated":"2023-09-19T10:00:46Z","volume":69,"year":"2018","acknowledgement":"TZ is supported by a grant from the Chinese Scholarship Council.","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Oxford University Press"},{"month":"03","acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"doi":"10.1111/ejn.13901","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"external_id":{"isi":["000431496400001"]},"license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2020-07-14T12:46:06Z","publist_id":"7539","date_updated":"2023-09-19T09:58:40Z","date_created":"2018-12-11T11:45:50Z","volume":47,"author":[{"full_name":"Sawada, Kazuaki","first_name":"Kazuaki","last_name":"Sawada"},{"last_name":"Kawakami","first_name":"Ryosuke","full_name":"Kawakami, Ryosuke"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"},{"full_name":"Nemoto, Tomomi","last_name":"Nemoto","first_name":"Tomomi"}],"publication_status":"published","department":[{"_id":"RySh"}],"publisher":"Wiley","year":"2018","day":"07","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-03-07T00:00:00Z","page":"1033 - 1042","publication":"European Journal of Neuroscience","citation":{"mla":"Sawada, Kazuaki, et al. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” European Journal of Neuroscience, vol. 47, no. 9, Wiley, 2018, pp. 1033–42, doi:10.1111/ejn.13901.","short":"K. Sawada, R. Kawakami, R. Shigemoto, T. Nemoto, European Journal of Neuroscience 47 (2018) 1033–1042.","chicago":"Sawada, Kazuaki, Ryosuke Kawakami, Ryuichi Shigemoto, and Tomomi Nemoto. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” European Journal of Neuroscience. Wiley, 2018. https://doi.org/10.1111/ejn.13901.","ama":"Sawada K, Kawakami R, Shigemoto R, Nemoto T. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. 2018;47(9):1033-1042. doi:10.1111/ejn.13901","ista":"Sawada K, Kawakami R, Shigemoto R, Nemoto T. 2018. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. 47(9), 1033–1042.","apa":"Sawada, K., Kawakami, R., Shigemoto, R., & Nemoto, T. (2018). Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. Wiley. https://doi.org/10.1111/ejn.13901","ieee":"K. Sawada, R. Kawakami, R. Shigemoto, and T. Nemoto, “Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices,” European Journal of Neuroscience, vol. 47, no. 9. Wiley, pp. 1033–1042, 2018."},"abstract":[{"text":"Three-dimensional (3D) super-resolution microscopy technique structured illumination microscopy (SIM) imaging of dendritic spines along the dendrite has not been previously performed in fixed tissues, mainly due to deterioration of the stripe pattern of the excitation laser induced by light scattering and optical aberrations. To address this issue and solve these optical problems, we applied a novel clearing reagent, LUCID, to fixed brains. In SIM imaging, the penetration depth and the spatial resolution were improved in LUCID-treated slices, and 160-nm spatial resolution was obtained in a large portion of the imaging volume on a single apical dendrite. Furthermore, in a morphological analysis of spine heads of layer V pyramidal neurons (L5PNs) in the medial prefrontal cortex (mPFC) of chronic dexamethasone (Dex)-treated mice, SIM imaging revealed an altered distribution of spine forms that could not be detected by high-NA confocal imaging. Thus, super-resolution SIM imaging represents a promising high-throughput method for revealing spine morphologies in single dendrites.","lang":"eng"}],"issue":"9","type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:46:06Z","date_created":"2018-12-17T16:16:50Z","checksum":"98e901d8229e44aa8f3b51d248dedd09","file_id":"5721","relation":"main_file","creator":"dernst","file_size":4850261,"content_type":"application/pdf","file_name":"2018_EJN_Sawada.pdf","access_level":"open_access"}],"status":"public","title":"Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices","ddc":["570"],"intvolume":" 47","_id":"326","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"doi":"10.1073/pnas.1811580115","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30478053"}],"oa":1,"external_id":{"pmid":["30478053"],"isi":["000452866000022"]},"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["00278424"]},"month":"12","author":[{"first_name":"Kun","last_name":"Qu","full_name":"Qu, Kun"},{"full_name":"Glass, Bärbel","first_name":"Bärbel","last_name":"Glass"},{"full_name":"Doležal, Michal","first_name":"Michal","last_name":"Doležal"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian","full_name":"Schur, Florian"},{"full_name":"Murciano, Brice","first_name":"Brice","last_name":"Murciano"},{"full_name":"Rein, Alan","first_name":"Alan","last_name":"Rein"},{"full_name":"Rumlová, Michaela","first_name":"Michaela","last_name":"Rumlová"},{"first_name":"Tomáš","last_name":"Ruml","full_name":"Ruml, Tomáš"},{"first_name":"Hans-Georg","last_name":"Kräusslich","full_name":"Kräusslich, Hans-Georg"},{"full_name":"Briggs, John A. G.","first_name":"John A. G.","last_name":"Briggs"}],"volume":115,"date_created":"2018-12-20T21:09:37Z","date_updated":"2023-09-19T09:57:45Z","pmid":1,"year":"2018","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"FlSc"}],"publication_status":"published","date_published":"2018-12-11T00:00:00Z","citation":{"mla":"Qu, Kun, et al. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” Proceedings of the National Academy of Sciences, vol. 115, no. 50, Proceedings of the National Academy of Sciences, 2018, pp. E11751–60, doi:10.1073/pnas.1811580115.","short":"K. Qu, B. Glass, M. Doležal, F.K. Schur, B. Murciano, A. Rein, M. Rumlová, T. Ruml, H.-G. Kräusslich, J.A.G. Briggs, Proceedings of the National Academy of Sciences 115 (2018) E11751–E11760.","chicago":"Qu, Kun, Bärbel Glass, Michal Doležal, Florian KM Schur, Brice Murciano, Alan Rein, Michaela Rumlová, Tomáš Ruml, Hans-Georg Kräusslich, and John A. G. Briggs. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1811580115.","ama":"Qu K, Glass B, Doležal M, et al. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. 2018;115(50):E11751-E11760. doi:10.1073/pnas.1811580115","ista":"Qu K, Glass B, Doležal M, Schur FK, Murciano B, Rein A, Rumlová M, Ruml T, Kräusslich H-G, Briggs JAG. 2018. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. 115(50), E11751–E11760.","apa":"Qu, K., Glass, B., Doležal, M., Schur, F. K., Murciano, B., Rein, A., … Briggs, J. A. G. (2018). Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1811580115","ieee":"K. Qu et al., “Structure and architecture of immature and mature murine leukemia virus capsids,” Proceedings of the National Academy of Sciences, vol. 115, no. 50. Proceedings of the National Academy of Sciences, pp. E11751–E11760, 2018."},"publication":"Proceedings of the National Academy of Sciences","page":"E11751-E11760","article_processing_charge":"No","day":"11","scopus_import":"1","oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5770","intvolume":" 115","title":"Structure and architecture of immature and mature murine leukemia virus capsids","status":"public","issue":"50","abstract":[{"text":"Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA subsequently assembles into the mature core, whose architecture varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γ-retrovirus and serves as the basis of retroviral vectors, but the structure of the MLV CA layer is unknown. Here we have combined X-ray crystallography with cryoelectron tomography to determine the structures of immature and mature MLV CA layers within authentic viral particles. This reveals the structural changes associated with maturation, and, by comparison with HIV-1, uncovers conserved and variable features. In contrast to HIV-1, most MLV CA is used for assembly of the mature core, which adopts variable, multilayered morphologies and does not form a closed structure. Unlike in HIV-1, there is similarity between protein–protein interfaces in the immature MLV CA layer and those in the mature CA layer, and structural maturation of MLV could be achieved through domain rotations that largely maintain hexameric interactions. Nevertheless, the dramatic architectural change on maturation indicates that extensive disassembly and reassembly are required for mature core growth. The core morphology suggests that wrapping of the genome in CA sheets may be sufficient to protect the MLV ribonucleoprotein during cell entry.","lang":"eng"}],"type":"journal_article"},{"page":"50 - 72","article_type":"original","citation":{"chicago":"Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” Theoretical Computer Science. Elsevier, 2018. https://doi.org/10.1016/j.tcs.2017.11.001.","mla":"Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” Theoretical Computer Science, vol. 712, Elsevier, 2018, pp. 50–72, doi:10.1016/j.tcs.2017.11.001.","short":"G. Avni, O. Kupferman, Theoretical Computer Science 712 (2018) 50–72.","ista":"Avni G, Kupferman O. 2018. Synthesis from component libraries with costs. Theoretical Computer Science. 712, 50–72.","apa":"Avni, G., & Kupferman, O. (2018). Synthesis from component libraries with costs. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2017.11.001","ieee":"G. Avni and O. Kupferman, “Synthesis from component libraries with costs,” Theoretical Computer Science, vol. 712. Elsevier, pp. 50–72, 2018.","ama":"Avni G, Kupferman O. Synthesis from component libraries with costs. Theoretical Computer Science. 2018;712:50-72. doi:10.1016/j.tcs.2017.11.001"},"publication":"Theoretical Computer Science","date_published":"2018-02-15T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"15","intvolume":" 712","status":"public","title":"Synthesis from component libraries with costs","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"608","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Synthesis is the automated construction of a system from its specification. In real life, hardware and software systems are rarely constructed from scratch. Rather, a system is typically constructed from a library of components. Lustig and Vardi formalized this intuition and studied LTL synthesis from component libraries. In real life, designers seek optimal systems. In this paper we add optimality considerations to the setting. We distinguish between quality considerations (for example, size - the smaller a system is, the better it is), and pricing (for example, the payment to the company who manufactured the component). We study the problem of designing systems with minimal quality-cost and price. A key point is that while the quality cost is individual - the choices of a designer are independent of choices made by other designers that use the same library, pricing gives rise to a resource-allocation game - designers that use the same component share its price, with the share being proportional to the number of uses (a component can be used several times in a design). We study both closed and open settings, and in both we solve the problem of finding an optimal design. In a setting with multiple designers, we also study the game-theoretic problems of the induced resource-allocation game.","lang":"eng"}],"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.636.4529","open_access":"1"}],"external_id":{"isi":["000424959200003"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.tcs.2017.11.001","month":"02","publisher":"Elsevier","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2018","volume":712,"date_created":"2018-12-11T11:47:28Z","date_updated":"2023-09-19T10:00:21Z","author":[{"full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","first_name":"Guy","last_name":"Avni"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"}],"publist_id":"7197","ec_funded":1},{"year":"2018","acknowledgement":"In-Data-Review","pmid":1,"publication_status":"published","publisher":"Cell Press","department":[{"_id":"JiFr"}],"author":[{"last_name":"Nishiyama","first_name":"Tomoaki","full_name":"Nishiyama, Tomoaki"},{"last_name":"Sakayama","first_name":"Hidetoshi","full_name":"Sakayama, Hidetoshi"},{"last_name":"De Vries","first_name":"Jan","full_name":"De Vries, Jan"},{"full_name":"Buschmann, Henrik","first_name":"Henrik","last_name":"Buschmann"},{"full_name":"Saint Marcoux, Denis","first_name":"Denis","last_name":"Saint Marcoux"},{"full_name":"Ullrich, Kristian","first_name":"Kristian","last_name":"Ullrich"},{"full_name":"Haas, Fabian","first_name":"Fabian","last_name":"Haas"},{"last_name":"Vanderstraeten","first_name":"Lisa","full_name":"Vanderstraeten, Lisa"},{"full_name":"Becker, Dirk","first_name":"Dirk","last_name":"Becker"},{"first_name":"Daniel","last_name":"Lang","full_name":"Lang, Daniel"},{"first_name":"Stanislav","last_name":"Vosolsobě","full_name":"Vosolsobě, Stanislav"},{"full_name":"Rombauts, Stephane","first_name":"Stephane","last_name":"Rombauts"},{"full_name":"Wilhelmsson, Per","last_name":"Wilhelmsson","first_name":"Per"},{"first_name":"Philipp","last_name":"Janitza","full_name":"Janitza, Philipp"},{"full_name":"Kern, Ramona","last_name":"Kern","first_name":"Ramona"},{"full_name":"Heyl, Alexander","first_name":"Alexander","last_name":"Heyl"},{"first_name":"Florian","last_name":"Rümpler","full_name":"Rümpler, Florian"},{"last_name":"Calderón Villalobos","first_name":"Luz","full_name":"Calderón Villalobos, Luz"},{"full_name":"Clay, John","last_name":"Clay","first_name":"John"},{"first_name":"Roman","last_name":"Skokan","full_name":"Skokan, Roman"},{"first_name":"Atsushi","last_name":"Toyoda","full_name":"Toyoda, Atsushi"},{"full_name":"Suzuki, Yutaka","last_name":"Suzuki","first_name":"Yutaka"},{"full_name":"Kagoshima, Hiroshi","first_name":"Hiroshi","last_name":"Kagoshima"},{"last_name":"Schijlen","first_name":"Elio","full_name":"Schijlen, Elio"},{"last_name":"Tajeshwar","first_name":"Navindra","full_name":"Tajeshwar, Navindra"},{"first_name":"Bruno","last_name":"Catarino","full_name":"Catarino, Bruno"},{"full_name":"Hetherington, Alexander","first_name":"Alexander","last_name":"Hetherington"},{"last_name":"Saltykova","first_name":"Assia","full_name":"Saltykova, Assia"},{"first_name":"Clemence","last_name":"Bonnot","full_name":"Bonnot, Clemence"},{"first_name":"Holger","last_name":"Breuninger","full_name":"Breuninger, Holger"},{"first_name":"Aikaterini","last_name":"Symeonidi","full_name":"Symeonidi, Aikaterini"},{"first_name":"Guru","last_name":"Radhakrishnan","full_name":"Radhakrishnan, Guru"},{"full_name":"Van Nieuwerburgh, Filip","last_name":"Van Nieuwerburgh","first_name":"Filip"},{"last_name":"Deforce","first_name":"Dieter","full_name":"Deforce, Dieter"},{"first_name":"Caren","last_name":"Chang","full_name":"Chang, Caren"},{"first_name":"Kenneth","last_name":"Karol","full_name":"Karol, Kenneth"},{"first_name":"Rainer","last_name":"Hedrich","full_name":"Hedrich, Rainer"},{"full_name":"Ulvskov, Peter","last_name":"Ulvskov","first_name":"Peter"},{"last_name":"Glöckner","first_name":"Gernot","full_name":"Glöckner, Gernot"},{"first_name":"Charles","last_name":"Delwiche","full_name":"Delwiche, Charles"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"full_name":"Van De Peer, Yves","last_name":"Van De Peer","first_name":"Yves"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"first_name":"Mary","last_name":"Beilby","full_name":"Beilby, Mary"},{"full_name":"Dolan, Liam","last_name":"Dolan","first_name":"Liam"},{"full_name":"Kohara, Yuji","first_name":"Yuji","last_name":"Kohara"},{"last_name":"Sugano","first_name":"Sumio","full_name":"Sugano, Sumio"},{"full_name":"Fujiyama, Asao","first_name":"Asao","last_name":"Fujiyama"},{"full_name":"Delaux, Pierre Marc","first_name":"Pierre Marc","last_name":"Delaux"},{"last_name":"Quint","first_name":"Marcel","full_name":"Quint, Marcel"},{"last_name":"Theissen","first_name":"Gunter","full_name":"Theissen, Gunter"},{"last_name":"Hagemann","first_name":"Martin","full_name":"Hagemann, Martin"},{"full_name":"Harholt, Jesper","last_name":"Harholt","first_name":"Jesper"},{"last_name":"Dunand","first_name":"Christophe","full_name":"Dunand, Christophe"},{"full_name":"Zachgo, Sabine","last_name":"Zachgo","first_name":"Sabine"},{"full_name":"Langdale, Jane","first_name":"Jane","last_name":"Langdale"},{"last_name":"Maumus","first_name":"Florian","full_name":"Maumus, Florian"},{"full_name":"Van Der Straeten, Dominique","last_name":"Van Der Straeten","first_name":"Dominique"},{"full_name":"Gould, Sven B","first_name":"Sven B","last_name":"Gould"},{"full_name":"Rensing, Stefan","first_name":"Stefan","last_name":"Rensing"}],"date_updated":"2023-09-19T10:02:47Z","date_created":"2018-12-11T11:44:53Z","volume":174,"ec_funded":1,"publist_id":"7774","oa":1,"external_id":{"pmid":["30007417"],"isi":["000438482800019"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30007417"}],"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"doi":"10.1016/j.cell.2018.06.033","language":[{"iso":"eng"}],"month":"07","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"148","title":"The Chara genome: Secondary complexity and implications for plant terrestrialization","status":"public","intvolume":" 174","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote.","lang":"eng"}],"issue":"2","publication":"Cell","citation":{"mla":"Nishiyama, Tomoaki, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” Cell, vol. 174, no. 2, Cell Press, 2018, p. 448–464.e24, doi:10.1016/j.cell.2018.06.033.","short":"T. Nishiyama, H. Sakayama, J. De Vries, H. Buschmann, D. Saint Marcoux, K. Ullrich, F. Haas, L. Vanderstraeten, D. Becker, D. Lang, S. Vosolsobě, S. Rombauts, P. Wilhelmsson, P. Janitza, R. Kern, A. Heyl, F. Rümpler, L. Calderón Villalobos, J. Clay, R. Skokan, A. Toyoda, Y. Suzuki, H. Kagoshima, E. Schijlen, N. Tajeshwar, B. Catarino, A. Hetherington, A. Saltykova, C. Bonnot, H. Breuninger, A. Symeonidi, G. Radhakrishnan, F. Van Nieuwerburgh, D. Deforce, C. Chang, K. Karol, R. Hedrich, P. Ulvskov, G. Glöckner, C. Delwiche, J. Petrášek, Y. Van De Peer, J. Friml, M. Beilby, L. Dolan, Y. Kohara, S. Sugano, A. Fujiyama, P.M. Delaux, M. Quint, G. Theissen, M. Hagemann, J. Harholt, C. Dunand, S. Zachgo, J. Langdale, F. Maumus, D. Van Der Straeten, S.B. Gould, S. Rensing, Cell 174 (2018) 448–464.e24.","chicago":"Nishiyama, Tomoaki, Hidetoshi Sakayama, Jan De Vries, Henrik Buschmann, Denis Saint Marcoux, Kristian Ullrich, Fabian Haas, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” Cell. Cell Press, 2018. https://doi.org/10.1016/j.cell.2018.06.033.","ama":"Nishiyama T, Sakayama H, De Vries J, et al. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 2018;174(2):448-464.e24. doi:10.1016/j.cell.2018.06.033","ista":"Nishiyama T, Sakayama H, De Vries J, Buschmann H, Saint Marcoux D, Ullrich K, Haas F, Vanderstraeten L, Becker D, Lang D, Vosolsobě S, Rombauts S, Wilhelmsson P, Janitza P, Kern R, Heyl A, Rümpler F, Calderón Villalobos L, Clay J, Skokan R, Toyoda A, Suzuki Y, Kagoshima H, Schijlen E, Tajeshwar N, Catarino B, Hetherington A, Saltykova A, Bonnot C, Breuninger H, Symeonidi A, Radhakrishnan G, Van Nieuwerburgh F, Deforce D, Chang C, Karol K, Hedrich R, Ulvskov P, Glöckner G, Delwiche C, Petrášek J, Van De Peer Y, Friml J, Beilby M, Dolan L, Kohara Y, Sugano S, Fujiyama A, Delaux PM, Quint M, Theissen G, Hagemann M, Harholt J, Dunand C, Zachgo S, Langdale J, Maumus F, Van Der Straeten D, Gould SB, Rensing S. 2018. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 174(2), 448–464.e24.","ieee":"T. Nishiyama et al., “The Chara genome: Secondary complexity and implications for plant terrestrialization,” Cell, vol. 174, no. 2. Cell Press, p. 448–464.e24, 2018.","apa":"Nishiyama, T., Sakayama, H., De Vries, J., Buschmann, H., Saint Marcoux, D., Ullrich, K., … Rensing, S. (2018). The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. Cell Press. https://doi.org/10.1016/j.cell.2018.06.033"},"page":"448 - 464.e24","date_published":"2018-07-12T00:00:00Z","scopus_import":"1","day":"12","article_processing_charge":"No"},{"date_published":"2018-06-01T00:00:00Z","page":"1010 - 1022","publication":"The Plant Journal","citation":{"apa":"Cavallari, N., Nibau, C., Fuchs, A., Dadarou, D., Barta, A., & Doonan, J. (2018). The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. Wiley. https://doi.org/10.1111/tpj.13914","ieee":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, and J. Doonan, “The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A,” The Plant Journal, vol. 94, no. 6. Wiley, pp. 1010–1022, 2018.","ista":"Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. 2018. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 94(6), 1010–1022.","ama":"Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 2018;94(6):1010-1022. doi:10.1111/tpj.13914","chicago":"Cavallari, Nicola, Candida Nibau, Armin Fuchs, Despoina Dadarou, Andrea Barta, and John Doonan. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” The Plant Journal. Wiley, 2018. https://doi.org/10.1111/tpj.13914.","short":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, J. Doonan, The Plant Journal 94 (2018) 1010–1022.","mla":"Cavallari, Nicola, et al. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” The Plant Journal, vol. 94, no. 6, Wiley, 2018, pp. 1010–22, doi:10.1111/tpj.13914."},"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"creator":"dernst","file_size":1543354,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_PlantJourn_Cavallari.pdf","checksum":"d9d3ad3215ac0e581731443fca312266","date_updated":"2020-07-14T12:46:22Z","date_created":"2019-02-06T11:40:54Z","file_id":"5934","relation":"main_file"}],"status":"public","title":"The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A","ddc":["580"],"intvolume":" 94","_id":"403","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"The ability to adapt growth and development to temperature variations is crucial to generate plant varieties resilient to predicted temperature changes. However, the mechanisms underlying plant response to progressive increases in temperature have just started to be elucidated. Here, we report that the Cyclin-dependent Kinase G1 (CDKG1) is a central element in a thermo-sensitive mRNA splicing cascade that transduces changes in ambient temperature into differential expression of the fundamental spliceosome component, ATU2AF65A. CDKG1 is alternatively spliced in a temperature-dependent manner. We found that this process is partly dependent on both the Cyclin-dependent Kinase G2 (CDKG2) and the interacting co-factor CYCLIN L1 resulting in two distinct messenger RNAs. Relative abundance of both CDKG1 transcripts correlates with ambient temperature and possibly with different expression levels of the associated protein isoforms. Both CDKG1 alternative transcripts are necessary to fully complement the expression of ATU2AF65A across the temperature range. Our data support a previously unidentified temperature-dependent mechanism based on the alternative splicing of CDKG1 and regulated by CDKG2 and CYCLIN L1. We propose that changes in ambient temperature affect the relative abundance of CDKG1 transcripts and this in turn translates into differential CDKG1 protein expression coordinating the alternative splicing of ATU2AF65A. This article is protected by copyright. All rights reserved.","lang":"eng"}],"issue":"6","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1111/tpj.13914","quality_controlled":"1","isi":1,"external_id":{"isi":["000434365500008"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"06","date_created":"2018-12-11T11:46:17Z","date_updated":"2023-09-19T10:07:08Z","volume":94,"author":[{"id":"457160E6-F248-11E8-B48F-1D18A9856A87","last_name":"Cavallari","first_name":"Nicola","full_name":"Cavallari, Nicola"},{"full_name":"Nibau, Candida","last_name":"Nibau","first_name":"Candida"},{"full_name":"Fuchs, Armin","first_name":"Armin","last_name":"Fuchs"},{"full_name":"Dadarou, Despoina","first_name":"Despoina","last_name":"Dadarou"},{"full_name":"Barta, Andrea","first_name":"Andrea","last_name":"Barta"},{"full_name":"Doonan, John","last_name":"Doonan","first_name":"John"}],"publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"Wiley","year":"2018","acknowledgement":"CN, DD and JHD were funded by the BBSRC (grant number BB/M009459/1). NC was funded by the VIPS Program of the Austrian Federal Ministry of Science and Research and the City of Vienna. AB and AF were supported by the Austrian Science Fund (FWF) [DK W1207; SFB RNAreg F43-P10]","file_date_updated":"2020-07-14T12:46:22Z","publist_id":"7426"},{"year":"2018","publication_status":"published","publisher":"Springer","department":[{"_id":"ToHe"}],"author":[{"full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","first_name":"Thomas"}],"date_updated":"2023-09-19T10:05:37Z","date_created":"2018-12-11T11:44:55Z","volume":10951,"file_date_updated":"2020-10-09T06:22:41Z","publist_id":"7765","oa":1,"external_id":{"isi":["000489765800009"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"conference":{"name":"FM: International Symposium on Formal Methods","location":"Oxford, UK","start_date":"2018-07-15","end_date":"2018-07-17"},"doi":"10.1007/978-3-319-95582-7_9","language":[{"iso":"eng"}],"month":"07","_id":"156","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"The compound interest in relaxing punctuality","ddc":["000"],"status":"public","intvolume":" 10951","file":[{"file_name":"2018_LNCS_Ferrere.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":485576,"file_id":"8637","relation":"main_file","date_updated":"2020-10-09T06:22:41Z","date_created":"2020-10-09T06:22:41Z","success":1,"checksum":"a045c213c42c445f1889326f8db82a0a"}],"oa_version":"Submitted Version","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Imprecision in timing can sometimes be beneficial: Metric interval temporal logic (MITL), disabling the expression of punctuality constraints, was shown to translate to timed automata, yielding an elementary decision procedure. We show how this principle extends to other forms of dense-time specification using regular expressions. By providing a clean, automaton-based formal framework for non-punctual languages, we are able to recover and extend several results in timed systems. Metric interval regular expressions (MIRE) are introduced, providing regular expressions with non-singular duration constraints. We obtain that MIRE are expressively complete relative to a class of one-clock timed automata, which can be determinized using additional clocks. Metric interval dynamic logic (MIDL) is then defined using MIRE as temporal modalities. We show that MIDL generalizes known extensions of MITL, while translating to timed automata at comparable cost."}],"citation":{"ama":"Ferrere T. The compound interest in relaxing punctuality. In: Vol 10951. Springer; 2018:147-164. doi:10.1007/978-3-319-95582-7_9","ista":"Ferrere T. 2018. The compound interest in relaxing punctuality. FM: International Symposium on Formal Methods, LNCS, vol. 10951, 147–164.","ieee":"T. Ferrere, “The compound interest in relaxing punctuality,” presented at the FM: International Symposium on Formal Methods, Oxford, UK, 2018, vol. 10951, pp. 147–164.","apa":"Ferrere, T. (2018). The compound interest in relaxing punctuality (Vol. 10951, pp. 147–164). Presented at the FM: International Symposium on Formal Methods, Oxford, UK: Springer. https://doi.org/10.1007/978-3-319-95582-7_9","mla":"Ferrere, Thomas. The Compound Interest in Relaxing Punctuality. Vol. 10951, Springer, 2018, pp. 147–64, doi:10.1007/978-3-319-95582-7_9.","short":"T. Ferrere, in:, Springer, 2018, pp. 147–164.","chicago":"Ferrere, Thomas. “The Compound Interest in Relaxing Punctuality,” 10951:147–64. Springer, 2018. https://doi.org/10.1007/978-3-319-95582-7_9."},"page":"147 - 164","date_published":"2018-07-12T00:00:00Z","scopus_import":"1","day":"12","has_accepted_license":"1","article_processing_charge":"No"}]